From f010a20a093007468953641fe945d3e84b8ad074 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 11 Dec 2019 21:23:45 +0100
Subject: [PATCH 01/49] Add click to requirements-dev

---
 requirements-dev.txt | 1 +
 1 file changed, 1 insertion(+)

diff --git a/requirements-dev.txt b/requirements-dev.txt
index bd869515..a857e625 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,3 +1,4 @@
+click==7.0
 flake8
 Paver==1.3.4
 pylint

From 4b23e9bf6ebe2ef534eea77237f0597a802b2909 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Thu, 12 Dec 2019 20:52:20 +0100
Subject: [PATCH 02/49] WIP: updat import statements

The new CLI will call commands from outside the package. The import statements
needed to be reworked. Not proud of the solution, but I cannot think of
something better now.
---
 GeoHealthCheck/__init__.py     |  5 ++++-
 GeoHealthCheck/models.py       | 25 ++++++++++++++++++++-----
 GeoHealthCheck/plugin.py       | 10 ++++++++--
 GeoHealthCheck/resourceauth.py | 21 +++++++++++++++++----
 4 files changed, 49 insertions(+), 12 deletions(-)

diff --git a/GeoHealthCheck/__init__.py b/GeoHealthCheck/__init__.py
index e1614da1..7f60751f 100644
--- a/GeoHealthCheck/__init__.py
+++ b/GeoHealthCheck/__init__.py
@@ -27,7 +27,10 @@
 #
 # =================================================================
 
-from util import read
+try:
+    from util import read
+except ImportError:
+    from .util import read
 
 
 def get_package_version(file_):
diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index 1ec7d7e5..137d557e 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -38,11 +38,26 @@
 from sqlalchemy.orm import deferred
 from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
 
-import util
-from enums import RESOURCE_TYPES
-from factory import Factory
-from init import App
-from resourceauth import ResourceAuth
+try:
+    import util
+except ImportError:
+    from GeoHealthCheck import util
+try:
+    from enums import RESOURCE_TYPES
+except ImportError:
+    from GeoHealthCheck.enums import RESOURCE_TYPES
+try:
+    from factory import Factory
+except ImportError:
+    from GeoHealthCheck.factory import Factory
+try:
+    from init import App
+except ImportError:
+    from GeoHealthCheck.init import App
+try:
+    from resourceauth import ResourceAuth
+except ImportError:
+    from GeoHealthCheck.resourceauth import ResourceAuth
 from wtforms.validators import Email, ValidationError
 from owslib.util import bind_url
 
diff --git a/GeoHealthCheck/plugin.py b/GeoHealthCheck/plugin.py
index 3534c4b3..8f38dc21 100644
--- a/GeoHealthCheck/plugin.py
+++ b/GeoHealthCheck/plugin.py
@@ -1,9 +1,15 @@
-from factory import Factory
+try:
+    from factory import Factory
+except ImportError:
+    from GeoHealthCheck.factory import Factory
 import logging
 import inspect
 from collections.abc import Mapping
 import copy
-from init import App
+try:
+    from init import App
+except ImportError:
+    from GeoHealthCheck.init import App
 
 LOGGER = logging.getLogger(__name__)
 
diff --git a/GeoHealthCheck/resourceauth.py b/GeoHealthCheck/resourceauth.py
index ba1982eb..c7446b11 100644
--- a/GeoHealthCheck/resourceauth.py
+++ b/GeoHealthCheck/resourceauth.py
@@ -1,9 +1,22 @@
 import json
 import logging
-from plugin import Plugin
-from factory import Factory
-from util import encode, decode
-from init import App
+try:
+    from plugin import Plugin
+except ImportError:
+    from GeoHealthCheck.plugin import Plugin
+try:
+    from factory import Factory
+except ImportError:
+    from GeoHealthCheck.factory import Factory
+try:
+    from util import encode, decode
+except ImportError:
+    from GeoHealthCheck.util import encode, decode
+try:
+    from init import App
+except ImportError:
+    from GeoHealthCheck.init import App
+
 APP = App.get_app()
 LOGGER = logging.getLogger(__name__)
 

From 284b50b46b8ebcb00a478662019aed1a27522a3e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Thu, 12 Dec 2019 20:53:33 +0100
Subject: [PATCH 03/49] Add first CLI commands

---
 ghc_cli.py | 142 +++++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 142 insertions(+)
 create mode 100644 ghc_cli.py

diff --git a/ghc_cli.py b/ghc_cli.py
new file mode 100644
index 00000000..3c5d068c
--- /dev/null
+++ b/ghc_cli.py
@@ -0,0 +1,142 @@
+# ============================================================================
+#
+# Authors: Rob van Loon <borrob@me.com>
+#
+# Copyright (c) 2019 Rob van Loon
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation
+# files (the "Software"), to deal in the Software without
+# restriction, including without limitation the rights to use,
+# copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following
+# conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# =================================================================
+import click
+import os
+
+from GeoHealthCheck.__init__ import __version__
+
+
+@click.command()
+def cli():
+    """Example thingy"""
+    click.echo('Hello there!')
+
+
+@click.group()
+@click.pass_context
+@click.option('--verbose', '-v', is_flag=True, help='Verbose')
+def cli(ctx, verbose):
+    ctx.ensure_object(dict)
+    ctx.obj['VERBOSE'] = verbose
+
+
+@cli.command()
+@click.pass_context
+def version(ctx):
+    """Show the current version of GHC
+    """
+    verbose_echo(ctx, 'GeoHC: get version')
+    click.echo(__version__)
+
+
+@cli.command()
+@click.pass_context
+def create_instance(ctx):
+    """Create an instance of GeoHealthCheck App
+
+    This command is a copy of `paver setup`
+    """
+    verbose_echo(ctx, 'GeoHC: create instance')
+    # calling paver for the setup
+    # TODO: phase out paver and switch to click
+    os.system('paver setup')
+
+
+@cli.command()
+@click.pass_context
+@click.option('--host', '-h', default='0.0.0.0', help='IP to host the app')
+@click.option('--port', '-p', default=8000, help='port number to host the app')
+def serve(ctx, host, port):
+    """
+    Run the app. Press 'ctrl-c' to exit again.
+
+    This function is a wrapper around `python GeoHealthCheck/app.py`
+    """
+    verbose_echo(ctx, 'GeoHC: serve')
+    click.echo('Press ctrl-c to exit.')
+    os.system(f"python GeoHealthCheck/app.py {host}:{port}")
+
+
+@cli.command()
+@click.pass_context
+def db_create(ctx):
+    """Create the GHC database
+
+    Note: you still need to add a user
+    """
+    verbose_echo(ctx, 'GeoHC: create db')
+    from GeoHealthCheck.init import App
+    DB = App.get_db()
+    DB.create_all()
+    DB.session.remove()
+
+
+@cli.command()
+@click.pass_context
+def db_adduser(ctx):
+    """Add an user to the database
+    """
+    verbose_echo(ctx, 'GeoHC: add user to database')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import User, db_commit
+    DB = App.get_db()
+    user_to_add = User('rob', 'bor', 'rob.v.loon@gmail.com', role='admin')
+    DB.session.add(user_to_add)
+    db_commit()
+    DB.session.remove()
+
+
+@cli.command()
+@click.pass_context
+def db_drop(ctx):
+    verbose_echo(ctx, 'GeoHC: drop db')
+    #drop_db()
+
+@cli.command()
+@click.pass_context
+def db_init(ctx):
+    verbose_echo(ctx, 'GeoHC: init db')
+
+@cli.command()
+@click.pass_context
+def db_upgrade(ctx):
+    verbose_echo(ctx, 'GeoHC: upgrade db')
+
+@cli.command()
+@click.pass_context
+def db_export(ctx):
+    pass
+
+def verbose_echo(ctx, verbose_text):
+    if ctx.obj['VERBOSE']:
+        click.echo(verbose_text)
+
+
+if __name__ == '__main__':
+    cli()

From 84112f4919fba5d80c772856ae790b1c10c5e097 Mon Sep 17 00:00:00 2001
From: Rob van Loon <rob.van.loon@ordina.nl>
Date: Fri, 13 Dec 2019 07:45:18 +0100
Subject: [PATCH 04/49] Add setup.py

With the setup file we can install the cli command `geohc` and build eggs and
wheels.
---
 setup.py | 31 +++++++++++++++++++++++++++++++
 1 file changed, 31 insertions(+)
 create mode 100644 setup.py

diff --git a/setup.py b/setup.py
new file mode 100644
index 00000000..3632e936
--- /dev/null
+++ b/setup.py
@@ -0,0 +1,31 @@
+import io
+import os
+from setuptools import find_packages, setup
+
+def read(filename, encoding='utf-8'):
+    """read file contents"""
+    full_path = os.path.join(os.path.dirname(__file__), filename)
+    with io.open(full_path, encoding=encoding) as fh:
+        contents = fh.read().strip()
+    return contents
+
+def get_package_version():
+    """get version from top-level package init"""
+    version_file = read('VERSION')
+    if version_file:
+        return version_file
+    raise RuntimeError("Unable to find version string.")
+
+setup(
+    name='geohealthcheck',
+    version=get_package_version(),
+    license='MIT',
+    install_requires=read('requirements.txt').splitlines(),
+    packages=find_packages(exclude=['tests']),
+    include_package_data=True,
+    entry_points={
+        'console_scripts': [
+            'geohc=ghc_cli:cli',
+        ]
+    }
+)

From b648a31dbee1b66050cb9af689c7607013a0a62c Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 09:47:21 +0100
Subject: [PATCH 05/49] CLI commands for models.py

Move all the models.py ... commands to the geohc cli and add deprecation
warnings.
---
 GeoHealthCheck/models.py | 16 ++++++-
 ghc_cli.py               | 96 +++++++++++++++++++++++++++++++++-------
 2 files changed, 94 insertions(+), 18 deletions(-)

diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index 137d557e..fa998232 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -30,6 +30,7 @@
 
 import json
 import logging
+import warnings
 from flask_babel import gettext as _
 from datetime import datetime, timedelta
 from itsdangerous import TimedJSONWebSignatureSerializer as Serializer
@@ -908,6 +909,8 @@ def db_commit():
 
     if len(sys.argv) > 1:
         if sys.argv[1] == 'create':
+            warnings.warn('models.py create is deprecated since 0.8.0. Please use cli: '
+                          '`geohc db-create` and `geohc db-adduser`', DeprecationWarning)
             print('Creating database objects')
             DB.create_all()
 
@@ -930,11 +933,17 @@ def db_commit():
             user_to_add = User(username, password1, email1, role='admin')
             DB.session.add(user_to_add)
             db_commit()
+
         elif sys.argv[1] == 'drop':
+            warnings.warn('models.py drop is deprecated since 0.8.0. Please use cli: '
+                          '`geohc db-drop`', DeprecationWarning)
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
+            
         elif sys.argv[1] == 'load':
+            warnings.warn('models.py load is deprecated since 0.8.0. Please use cli: '
+                          '`geohc db-load`', DeprecationWarning)
             print('Load database from JSON file (e.g. tests/fixtures.json)')
             if len(sys.argv) > 2:
                 file_path = sys.argv[2]
@@ -958,9 +967,12 @@ def db_commit():
                 print('Provide path to JSON file, e.g. tests/fixtures.json')
 
         elif sys.argv[1] == 'run':
-            print('NOTICE: models.py no longer here.')
-            print('Use: python healthcheck.py or upcoming cli.py')
+            warnings.warn('models.py run is deprecated. Please use `python healthcheck.py`',
+                          DeprecationWarning)
+
         elif sys.argv[1] == 'flush':
+            warnings.warn('models.py flush is deprecated since 0.8.0. Please use cli: '
+                          '`geohc db-flush`', DeprecationWarning)
             flush_runs()
 
         DB.session.remove()
diff --git a/ghc_cli.py b/ghc_cli.py
index 3c5d068c..b8b92409 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -27,15 +27,18 @@
 #
 # =================================================================
 import click
-import os
 
 from GeoHealthCheck.__init__ import __version__
 
 
-@click.command()
-def cli():
-    """Example thingy"""
-    click.echo('Hello there!')
+def verbose_echo(ctx, verbose_text):
+    if ctx.obj['VERBOSE']:
+        click.echo(verbose_text)
+
+
+def abort_if_false(ctx, _, value):
+    if not value:
+        ctx.abort()
 
 
 @click.group()
@@ -65,7 +68,9 @@ def create_instance(ctx):
     verbose_echo(ctx, 'GeoHC: create instance')
     # calling paver for the setup
     # TODO: phase out paver and switch to click
-    os.system('paver setup')
+    from os import system
+    system('paver setup')
+    verbose_echo(ctx, 'GeoHC: finished creating the instance.')
 
 
 @cli.command()
@@ -80,7 +85,8 @@ def serve(ctx, host, port):
     """
     verbose_echo(ctx, 'GeoHC: serve')
     click.echo('Press ctrl-c to exit.')
-    os.system(f"python GeoHealthCheck/app.py {host}:{port}")
+    from os import system
+    system(f"python GeoHealthCheck/app.py {host}:{port}")
 
 
 @cli.command()
@@ -92,36 +98,98 @@ def db_create(ctx):
     """
     verbose_echo(ctx, 'GeoHC: create db')
     from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
     DB = App.get_db()
+    verbose_echo(ctx, 'GeoHC: create all tables')
     DB.create_all()
+    db_commit()
     DB.session.remove()
+    click.echo('Database is created. Use `geohc db-adduser` to add users to the database.')
 
 
 @cli.command()
 @click.pass_context
-def db_adduser(ctx):
+@click.option('-u', '--user', type=str, help='username', prompt=True)
+@click.option('-e', '--email', type=str, help='email address', prompt=True)
+@click.option('-p', '--password', type=str, help='password', prompt=True, hide_input=True,
+              confirmation_prompt=True)
+@click.option('-r', '--role', type=click.Choice(['admin', 'user']), prompt=True,
+              help='role for this user')
+def db_adduser(ctx, user, email, password, role):
     """Add an user to the database
     """
     verbose_echo(ctx, 'GeoHC: add user to database')
     from GeoHealthCheck.init import App
     from GeoHealthCheck.models import User, db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
     DB = App.get_db()
-    user_to_add = User('rob', 'bor', 'rob.v.loon@gmail.com', role='admin')
+    verbose_echo(ctx, 'GeoHC: create user')
+    user_to_add = User(user, password, email, role=role)
+    verbose_echo(ctx, 'GeoHC: adding user to database')
     DB.session.add(user_to_add)
     db_commit()
     DB.session.remove()
+    click.echo(f'User {user} is added.')
 
 
 @cli.command()
 @click.pass_context
+@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
+              expose_value=False, help='Confirm dropping tables',
+              prompt='This will drop the tables in the database. Are you sure?')
 def db_drop(ctx):
+    """Drop the current database
+    """
     verbose_echo(ctx, 'GeoHC: drop db')
-    #drop_db()
+    click.confirm("This will drop the tables in the database. Are you sure?", abort=True)
+    verbose_echo(ctx, 'User confirmed dropping tables')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
+    DB = App.get_db()
+    verbose_echo(ctx, 'GeoHC: dropping all tables')
+    DB.drop_all()
+    db_commit()
+    DB.session.remove()
+    click.echo('Database dropped all tables.')
+
 
 @cli.command()
 @click.pass_context
-def db_init(ctx):
-    verbose_echo(ctx, 'GeoHC: init db')
+@click.option('-f', '--file', type=click.Path(), multiple=False, required=True,
+              help='Path to the file to load into the database. MUST be JSON.')
+@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
+              expose_value=False, help='Confirm dropping old content.',
+              prompt='WARNING: all database data will be lost. Proceed?')
+def db_load(ctx, file):
+    """Load JSON into the database
+
+    e.g. test/data/fixtures.json
+    """
+    verbose_echo(ctx, 'GeoHC: load data into db')
+    verbose_echo(ctx, 'User confirmed loading new data and losing old data.')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import load_data
+    DB = App.get_db()
+    if file[-5:].lower() != '.json':
+        click.echo("File must have '.json' file extension. Aborting import.")
+        ctx.exit()
+    verbose_echo(ctx, 'Start loading file.')
+    load_data(file)
+    verbose_echo(ctx, 'Data loaded!')
+    DB.session.remove()
+    click.echo('Finished loading data.')
+
+@cli.command()
+@click.pass_context
+def db_flush(ctx):
+    """Flush runs: remove old data over retention date.
+    """
+    verbose_echo(ctx, 'GeoHC: flush old runs from database.')
+    from GeoHealthCheck.models import flush_runs
+    flush_runs()
+    click.echo('Finished flushing old runs from database.')
 
 @cli.command()
 @click.pass_context
@@ -133,10 +201,6 @@ def db_upgrade(ctx):
 def db_export(ctx):
     pass
 
-def verbose_echo(ctx, verbose_text):
-    if ctx.obj['VERBOSE']:
-        click.echo(verbose_text)
-
 
 if __name__ == '__main__':
     cli()

From 7aff5b17f76125bb55d3549629e911b7723b976c Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 15:54:28 +0100
Subject: [PATCH 06/49] Move all paver commands to click

---
 GeoHealthCheck/models.py |   2 +-
 ghc_cli.py               | 220 ++++++++++++++++++++++++++++++++++++++-
 pavement.py              |  47 ++++++---
 3 files changed, 252 insertions(+), 17 deletions(-)

diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index fa998232..3c44665c 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -940,7 +940,7 @@ def db_commit():
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
-            
+
         elif sys.argv[1] == 'load':
             warnings.warn('models.py load is deprecated since 0.8.0. Please use cli: '
                           '`geohc db-load`', DeprecationWarning)
diff --git a/ghc_cli.py b/ghc_cli.py
index b8b92409..4ff3c865 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -41,6 +41,14 @@ def abort_if_false(ctx, _, value):
         ctx.abort()
 
 
+def sphinx_make():
+    """return what command Sphinx is using for make"""
+    from os import name
+    if name == 'nt':
+        return 'make.bat'
+    return 'make'
+
+
 @click.group()
 @click.pass_context
 @click.option('--verbose', '-v', is_flag=True, help='Verbose')
@@ -85,8 +93,9 @@ def serve(ctx, host, port):
     """
     verbose_echo(ctx, 'GeoHC: serve')
     click.echo('Press ctrl-c to exit.')
-    from os import system
-    system(f"python GeoHealthCheck/app.py {host}:{port}")
+    from os import system, chdir
+    chdir('GeoHealthCheck')
+    system(f"python app.py {host}:{port}")
 
 
 @cli.command()
@@ -181,6 +190,7 @@ def db_load(ctx, file):
     DB.session.remove()
     click.echo('Finished loading data.')
 
+
 @cli.command()
 @click.pass_context
 def db_flush(ctx):
@@ -191,10 +201,216 @@ def db_flush(ctx):
     flush_runs()
     click.echo('Finished flushing old runs from database.')
 
+
+@cli.command()
+@click.pass_context
+def create_secret_key(ctx):
+    """
+    Create a secret key for the application.
+    """
+    from codecs import encode
+    from os import urandom
+    click.echo('Secret key: \'%s\'' % encode(urandom(24), 'hex').decode())
+    click.echo('Copy/paste this key to set the SECRET_KEY value in instance/config_site.py')
+
+
+@cli.command()
+@click.option('-p', '--password', prompt=True, hide_input=True, help='password')
+@click.pass_context
+def create_hash(ctx, password):
+    """Create a password hash
+    """
+    from GeoHealthCheck.util import create_hash
+    token = create_hash(password)
+    click.echo('Copy/paste the entire token below for example to set password')
+    click.echo(token)
+
+
 @cli.command()
 @click.pass_context
 def db_upgrade(ctx):
+    """Upgrade the database
+    """
     verbose_echo(ctx, 'GeoHC: upgrade db')
+    from os import system, chdir
+    chdir('GeoHealthCheck')
+    system('python manage.py db upgrade')
+    click.echo('Upgrade DB finished.')
+
+
+@cli.command()
+@click.pass_context
+def create_wsgi(ctx):
+    """Create an apache wsgi and conf file"""
+    verbose_echo(ctx, 'GeoHC: creating apache wsgi and conf files.')
+    import os
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    instance = '%s%sinstance' % (basedir, os.sep)
+    verbose_echo(ctx, 'GeoHC: Files will be created in: %s' % instance)
+
+    wsgi_script = '%s%sGeoHealthCheck.wsgi' % (instance, os.sep)
+    with open(wsgi_script, 'w') as ff:
+        ff.write('import sys\n')
+        ff.write('sys.path.insert(0, \'%s\')\n' % basedir)
+        ff.write('from GeoHealthCheck.app import APP as application')
+    verbose_echo(ctx, 'GeoHC: finished wsgi script.')
+
+    wsgi_conf = '%s%sGeoHealthCheck.conf' % (instance, os.sep)
+    with open(wsgi_conf, 'w') as ff:
+        ff.write('WSGIScriptAlias / %s%sGeoHealthCheck.wsgi\n' % (instance, os.sep))
+        ff.write('<Directory %s%s>\n' % (basedir, os.sep))
+        ff.write('Order deny,allow\n')
+        ff.write('Allow from all\n')
+        ff.write('</Directory>')
+    verbose_echo(ctx, 'GeoHC: finished conf file.')
+
+
+@cli.command()
+@click.pass_context
+def update_docs(ctx):
+    """Update the spinx build of the documentation."""
+    verbose_echo(ctx, 'GeoHC: start building documentation.')
+
+    import os
+    import shutil
+
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    static_docs = os.path.normpath('%s/GeoHealthCheck/static/docs' % basedir)
+    docs = os.path.normpath('%s/docs' % basedir)
+
+    if os.path.exists(static_docs):
+        verbose_echo(ctx, 'GeoHC: deleting previous doc directory.')
+        shutil.rmtree(static_docs)
+
+    os.chdir(docs)
+    make = sphinx_make()
+    verbose_echo(ctx, 'GeoHC: cleaning old documentation.')
+    os.system('%s clean' % make)
+    verbose_echo(ctx, 'GeoHC: building new documentation.')
+    os.system('%s html' % make)
+    os.chdir(basedir)
+
+    verbose_echo(ctx, 'GeoHC: copying documentation to build folder.')
+    source_html_dir = os.path.normpath('%s/docs/_build/html' % basedir)
+    shutil.copytree(source_html_dir, static_docs)
+    click.echo('GeoHC: finished refreshing documentation.')
+
+
+@cli.command()
+@click.pass_context
+def clean(ctx):
+    """Clean Environment
+    """
+    import os
+    import shutil
+    import tempfile
+
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    static_docs = os.path.normpath('%s/GeoHealthCheck/static/docs' % basedir)
+    static_lib = os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir)
+    tmp = os.path.normpath(tempfile.mkdtemp())
+
+    try:
+        shutil.rmtree(static_lib)
+        verbose_echo(ctx, 'GeoHC: removed %s' % static_lib)
+    except FileNotFoundError:
+        pass
+    try:
+        shutil.rmtree(tmp)
+        verbose_echo(ctx, 'GeoHC: removed temp directory: %s' % tmp)
+    except FileNotFoundError:
+        pass
+    try:
+        shutil.rmtree(static_docs)
+        verbose_echo(ctx, 'GeoHC: removed %s' % static_docs)
+    except FileNotFoundError:
+        pass
+
+    click.echo('GeoHC: finished cleaning environment.')
+
+
+@cli.command()
+@click.pass_context
+def extract_translations(ctx):
+    """extract translations wrapped in _() or gettext()"""
+    verbose_echo(ctx, 'GeoHC: extracting translations')
+    import os
+
+    pot_dir = os.path.normpath('GeoHealthCheck/translations/en/LC_MESSAGES')
+    verbose_echo(ctx, 'GeoHC: Translations directory: %s' % pot_dir)
+    if not os.path.exists(pot_dir):
+        pot_dir.makedirs()
+
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    base_pot = os.path.normpath('%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' % basedir)
+    verbose_echo(ctx, 'GeoHC: starting translation')
+    os.system('pybabel extract -F babel.cfg -o %s GeoHealthCheck' % base_pot)
+    click.echo('GeoHC: finished extracting translations.')
+
+
+@cli.command()
+@click.option('-l', '--lang', required=True, help='2-letter language code')
+@click.pass_context
+def add_language_catalogue(ctx, lang):
+    """adds new language profile"""
+    verbose_echo(ctx, 'GeoHC: Adding language catalogue.')
+    import os
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    base_pot = os.path.normpath(
+        '%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' % basedir)
+    translations = os.path.normpath('%s/GeoHealthCheck/translations' % basedir)
+    verbose_echo(ctx, 'GeoHC: Base translation set: %s' % base_pot)
+    os.system('pybabel init -i %s -d %s -l %s' % (
+        base_pot, translations, lang))
+    click.echo('GeoHC: Finished translating: %s' % lang)
+
+
+@cli.command()
+@click.pass_context
+def compile_translations(ctx):
+    """build language files"""
+    verbose_echo(ctx, 'GeoHC: start building language files.')
+    import os
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    translations = os.path.normpath('%s/GeoHealthCheck/translations' % basedir)
+    os.system('pybabel compile -d %s' % translations)
+    click.echo('GeoHC: Finished building language files.')
+
+
+@cli.command()
+@click.pass_context
+def update_translations(ctx):
+    """update language strings"""
+    verbose_echo(ctx, 'GeoHC: update translations.')
+    extract_translations(ctx)
+
+    import os
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    base_pot = os.path.normpath(
+        '%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' % basedir)
+    translations = os.path.normpath('%s/GeoHealthCheck/translations' % basedir)
+    os.system('pybabel update -i %s -d %s' % (base_pot, translations))
+    click.echo('GeoHC: Finished updating translations.')
+
+
+@cli.command()
+@click.pass_context
+def runner_daemon(ctx):
+    """Run the HealthCheck runner daemon scheduler"""
+    verbose_echo(ctx, 'GeoHC: going to run the scheduler daemon. Press ctrl-c to stop.')
+    import os
+    os.system('python %s' % os.path.normpath('GeoHealthCheck/scheduler.py'))
+
+
+@cli.command()
+@click.pass_context
+def run_healthchecks(ctx):
+    """Run all HealthChecks directly"""
+    verbose_echo(ctx, 'GeoHC: going to run all the healthchecks once.')
+    import os
+    os.system('python %s' % os.path.normpath('GeoHealthCheck/healthcheck.py'))
+    click.echo('GeoHC: Finished running the healthchecks.')
+
 
 @cli.command()
 @click.pass_context
diff --git a/pavement.py b/pavement.py
index daeb802e..9361b3d9 100644
--- a/pavement.py
+++ b/pavement.py
@@ -159,14 +159,6 @@ def setup():
     info('development instance with "python GeoHealthCheck/app.py"')
 
 
-@task
-def create_secret_key():
-    """create secret key for SECRET_KEY in instance/config_site.py"""
-    info('Secret key: \'%s\'' % codecs.encode(os.urandom(24), 'hex').decode())
-    info('Copy/paste this key to set the SECRET_KEY')
-    info('value in instance/config_site.py')
-
-
 @task
 @cmdopts([
     ('email=', 'e', 'email'),
@@ -175,17 +167,28 @@ def create_secret_key():
 ])
 def create(options):
     """create database objects and superuser account"""
-
+    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use cli: '
+         '`geohc db-create` and `geohc db-adduser`')
     args = ''
     username = options.get('username', None)
     password = options.get('password', None)
     email = options.get('email', None)
-
+    info(username)
     if all([username, password, email]):
         args = '%s %s %s' % (username, password, email)
     sh('python %s create %s' % (path('GeoHealthCheck/models.py'), args))
 
 
+@task
+def create_secret_key():
+    """create secret key for SECRET_KEY in instance/config_site.py"""
+    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use cli: '
+         '`geohc create-secret-key`')
+    info('Secret key: \'%s\'' % codecs.encode(os.urandom(24), 'hex').decode())
+    info('Copy/paste this key to set the SECRET_KEY')
+    info('value in instance/config_site.py')
+
+
 @task
 @cmdopts([
     ('password=', 'p', 'password')
@@ -195,7 +198,8 @@ def create_hash(options):
     Create hash, mainly for passwords.
     Usage: paver create_hash -p mypass
     """
-
+    info('Warning!: create_hash is deprecated since 0.8.0. Please use cli: '
+         '`geohc create-hash`')
     import sys
     sys.path.insert(0, BASEDIR + '/GeoHealthCheck')
     from util import create_hash
@@ -207,7 +211,8 @@ def create_hash(options):
 @task
 def upgrade():
     """upgrade database if changed; be sure to backup first!"""
-
+    info('Warning!: upgrade is deprecated since 0.8.0. Please use cli: '
+         '`geohc db-upgrade`')
     info('Upgrading database...')
     with pushd(path('%s/GeoHealthCheck' % BASEDIR)):
         sh('python manage.py db upgrade')
@@ -216,6 +221,8 @@ def upgrade():
 @task
 def create_wsgi():
     """create WSGI wrapper and Apache2 configuration"""
+    info('Warning!: create_wsgi is deprecated since 0.8.0. Please use cli: '
+         '`geohc create-wsgi`')
     wsgi_script = '%s%sGeoHealthCheck.wsgi' % (options.base.instance, os.sep)
     with open(wsgi_script, 'w') as ff:
         ff.write('import sys\n')
@@ -235,6 +242,8 @@ def create_wsgi():
 @task
 def refresh_docs():
     """Build sphinx docs from scratch"""
+    info('Warning!: refresh_docs is deprecated since 0.8.0. Please use cli: '
+         '`geohc refresh-docs`')
 
     make = sphinx_make()
 
@@ -251,6 +260,8 @@ def refresh_docs():
 @task
 def clean():
     """clean environment"""
+    info('Warning!: clean is deprecated since 0.8.0. Please use cli: '
+         '`geohc clean`')
 
     if os.path.exists(options.base.static_lib):
         shutil.rmtree(options.base.static_lib)
@@ -264,6 +275,8 @@ def clean():
 def extract_translations():
     """extract translations wrapped in _() or gettext()"""
 
+    info('Warning!: extract_translations is deprecated since 0.8.0. Please use cli: '
+         '`geohc extract-translations`')
     pot_dir = path('GeoHealthCheck/translations/en/LC_MESSAGES')
     if not os.path.exists(pot_dir):
         pot_dir.makedirs()
@@ -278,6 +291,8 @@ def extract_translations():
 def add_language_catalogue(options):
     """adds new language profile"""
 
+    info('Warning!: add_language_catalogue is deprecated since 0.8.0. Please use cli: '
+         '`geohc add-language-catalogue`')
     lang = options.get('lang', None)
 
     if lang is None:
@@ -290,14 +305,16 @@ def add_language_catalogue(options):
 @task
 def compile_translations():
     """build .mo files"""
-
+    info('Warning!: compile_translations is deprecated since 0.8.0. Please use cli: '
+         '`geohc compile-translations`')
     sh('pybabel compile -d %s' % options.base.translations)
 
 
 @task
 def update_translations():
     """update language strings"""
-
+    info('Warning!: update_translations is deprecated since 0.8.0. Please use cli: '
+         '`geohc update-translations`')
     call_task('extract_translations')
     sh('pybabel update -i %s -d %s' % (
         options.base.pot, options.base.translations))
@@ -306,6 +323,8 @@ def update_translations():
 @task
 def runner_daemon():
     """Run the HealthCheck runner daemon scheduler"""
+    info('Warning!: runner_daemon is deprecated since 0.8.0. Please use cli: '
+         '`geohc runner-daemon`')
     sh('python %s' % path('GeoHealthCheck/scheduler.py'))
 
 

From bfb74ebbc07088433386d5f42eeee52121932154 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 15:58:02 +0100
Subject: [PATCH 07/49] Update command calls

---
 ghc_cli.py  | 10 +++++-----
 pavement.py | 10 ++++++----
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/ghc_cli.py b/ghc_cli.py
index 4ff3c865..f1640c66 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -331,7 +331,7 @@ def clean(ctx):
 
 @cli.command()
 @click.pass_context
-def extract_translations(ctx):
+def lang_extract_translations(ctx):
     """extract translations wrapped in _() or gettext()"""
     verbose_echo(ctx, 'GeoHC: extracting translations')
     import os
@@ -351,7 +351,7 @@ def extract_translations(ctx):
 @cli.command()
 @click.option('-l', '--lang', required=True, help='2-letter language code')
 @click.pass_context
-def add_language_catalogue(ctx, lang):
+def lang_add_language_catalogue(ctx, lang):
     """adds new language profile"""
     verbose_echo(ctx, 'GeoHC: Adding language catalogue.')
     import os
@@ -367,7 +367,7 @@ def add_language_catalogue(ctx, lang):
 
 @cli.command()
 @click.pass_context
-def compile_translations(ctx):
+def lang_compile_translations(ctx):
     """build language files"""
     verbose_echo(ctx, 'GeoHC: start building language files.')
     import os
@@ -379,10 +379,10 @@ def compile_translations(ctx):
 
 @cli.command()
 @click.pass_context
-def update_translations(ctx):
+def lang_update_translations(ctx):
     """update language strings"""
     verbose_echo(ctx, 'GeoHC: update translations.')
-    extract_translations(ctx)
+    lang_extract_translations(ctx)
 
     import os
     basedir = os.path.abspath(os.path.dirname(__file__))
diff --git a/pavement.py b/pavement.py
index 9361b3d9..d3abf2d7 100644
--- a/pavement.py
+++ b/pavement.py
@@ -276,7 +276,7 @@ def extract_translations():
     """extract translations wrapped in _() or gettext()"""
 
     info('Warning!: extract_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc extract-translations`')
+         '`geohc lang-extract-translations`')
     pot_dir = path('GeoHealthCheck/translations/en/LC_MESSAGES')
     if not os.path.exists(pot_dir):
         pot_dir.makedirs()
@@ -292,7 +292,7 @@ def add_language_catalogue(options):
     """adds new language profile"""
 
     info('Warning!: add_language_catalogue is deprecated since 0.8.0. Please use cli: '
-         '`geohc add-language-catalogue`')
+         '`geohc lang-add-language-catalogue`')
     lang = options.get('lang', None)
 
     if lang is None:
@@ -306,7 +306,7 @@ def add_language_catalogue(options):
 def compile_translations():
     """build .mo files"""
     info('Warning!: compile_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc compile-translations`')
+         '`geohc lang-compile-translations`')
     sh('pybabel compile -d %s' % options.base.translations)
 
 
@@ -314,7 +314,7 @@ def compile_translations():
 def update_translations():
     """update language strings"""
     info('Warning!: update_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc update-translations`')
+         '`geohc lang-update-translations`')
     call_task('extract_translations')
     sh('pybabel update -i %s -d %s' % (
         options.base.pot, options.base.translations))
@@ -331,6 +331,8 @@ def runner_daemon():
 @task
 def run_healthchecks():
     """Run all HealthChecks directly"""
+    info('Warning!: run_healthchecks is deprecated since 0.8.0. Please use cli: '
+         '`geohc run-healthchecks`')
     sh('python %s' % path('GeoHealthCheck/healthcheck.py'))
 
 

From dd9d26ba86d4a37b1f94102d43e414acb34f384b Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 16:24:36 +0100
Subject: [PATCH 08/49] Update documentation to add new cli

---
 docs/admin.rst   | 27 +++++++++++++++++++--------
 docs/config.rst  |  6 +++---
 docs/install.rst | 29 ++++++++++++++---------------
 ghc_cli.py       |  9 ++++++++-
 pavement.py      |  2 ++
 5 files changed, 46 insertions(+), 27 deletions(-)

diff --git a/docs/admin.rst b/docs/admin.rst
index 2ee3b142..423b4928 100644
--- a/docs/admin.rst
+++ b/docs/admin.rst
@@ -7,7 +7,18 @@ This chapter describes maintenance tasks for the administrator of a GHC instance
 There is a separate :ref:`userguide` that provides guidance to the end-user to
 configure the actual Resource healthchecks.
 
-Each of the sections below is geared at a specific administrative task area.
+Each of the sections below is geared at a specific administrative task area. We
+assume you have installed GeoHealthCheck with `pip install`, and that you have
+acces to the command line interface `geohc`. You can get help from the cli via ::
+
+    geohc --help
+
+This will list all available commands. To get help with a specific command, run
+`geohc command --help`, e.g. ::
+
+    geohc db-adduser --help
+
+This will show you all the (required) options to add a user to the database.
 
 Database
 --------
@@ -21,7 +32,7 @@ To create the database execute the following:
 
 Open a command line, (if needed activate your virtualenv), and do ::
 
-    python GeoHealthCheck/models.py create
+    geohc db-create
 
 drop db
 .......
@@ -30,7 +41,7 @@ To delete the database execute the following, however you will loose all your in
 
 Open a command line, (if needed activate your virtualenv), and do ::
 
-    python GeoHealthCheck/models.py drop
+    geohc db-drop
 
 Note: you need to create a Database again before you can start GHC again.
 
@@ -39,7 +50,7 @@ load data
 
 To load a JSON data file, do (WARN: deletes existing data!) ::
 
-    python GeoHealthCheck/models.py load <datafile.json> [y/n]
+    geohc db-load --file my_data.json
 
 Hint: see `tests/data` for example JSON data files.
 
@@ -92,10 +103,9 @@ Or more compact within the root dir of your GHC installation: ::
 	>>> create_hash('mynewpassword')
 	'$pbkdf2-sha256$29000$8X4PAUAIAcC4V2rNea9Vqg$XnMx1SfEiBzBAMOQOOC7uxCcyzVuKaHENLj3IfXvfu0'
 
-Or even more compact within the root dir of your GHC installation via Paver: ::
+Or even more compact within the root dir of your GHC installation via the cli: ::
 
-	$ paver create_hash -p mypass
-	---> pavement.create_hash
+	$ geohc create_hash -p mypass
 	Copy/paste the entire token below for example to set password
 	$pbkdf2-sha256$29000$FkJoTYnxPqc0pjQG4HxP6Q$C3SZb8jqtM7zKS1DSLcouc/CL9XMI9cL5xT6DRTOEd4
 
@@ -110,4 +120,5 @@ Build Documentation
 -------------------
 
 Open a command line, (if needed activate your virtualenv) and move into the directory  ``GeoHealthCheck/doc/``.
-In there, type ``make html`` plus ENTER and the documentation should be built locally.
+In there, type ``make html`` plus ENTER and the documentation should be built locally. Or you can
+use the cli: `geohc refresh-docs`.
diff --git a/docs/config.rst b/docs/config.rst
index 14e2c0e7..5716f565 100644
--- a/docs/config.rst
+++ b/docs/config.rst
@@ -46,7 +46,7 @@ The configuration options are:
 Example on overriding the configuration with an environment variable: ::
 
     export GHC_SETTINGS=/tmp/my_GHC_settings.py
-    paver run_tests
+    geohc run-tests
 
 As an example: the `my_GHC_settings.py` file can contain a single line to define a test database: ::
 
@@ -148,7 +148,7 @@ Compiling Language Files
 ........................
 
 At runtime compiled versions, `*.mo` files, of the language-files are used.
-Easiest to compile is via: `paver compile_translations` in the project root dir.
+Easiest to compile is via: `geohc compile-translations` in the project root dir.
 This basically calls ``pybabel compile` with the proper options.
 Now you can e.g. test your new translations by starting GHC.
 
@@ -170,7 +170,7 @@ Missing translations will have `msgstr ""` like in this excerpt: ::
 
 Next all empty `msgstr`s can be filled.
 
-Updating is easiest using the command `paver update_translations` within the root dir of the project.
+Updating is easiest using the command `geohc update-translations` within the root dir of the project.
 This will basically call `pybabel extract` followed by `pybabel update` with the proper parameters.
 
 Customizing the Score Matrix
diff --git a/docs/install.rst b/docs/install.rst
index f93aad90..b94573d1 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -27,9 +27,8 @@ GeoHealthCheck is built on the awesome Flask micro-framework and uses
 
 `APScheduler` is used to run scheduled healthchecks.
 
-These dependencies are automatically installed (see below). ``Paver`` is used
-for installation and management. ``Cron`` was used for scheduling the actual
-healthchecks before v0.5.0.
+These dependencies are automatically installed (see below). A command line interface is provided
+ with `click`. ``Cron`` was used for scheduling the actual healthchecks before v0.5.0.
 
 Starting from version v0.8.0.0 GeoHealthCheck requires **python 3**. Previous
 versions require **python 2**.
@@ -56,13 +55,13 @@ Install
   cd GeoHealthCheck
 
   # install paver dependency for admin tool
-  pip install Paver
+  pip install .
 
   # setup app
-  paver setup
+  geohc create-instance
 
   # create secret key to use for auth
-  paver create_secret_key
+  geohc create-secret-key
 
   # almost there!  Customize config
   vi instance/config_site.py
@@ -83,10 +82,10 @@ Install
   # - GHC_MAP  # or use default settings
 
   # init database
-  python GeoHealthCheck/models.py create
+  geohc db-create
 
   # start web-app
-  python GeoHealthCheck/app.py  # http://localhost:8000/
+  geohc serve
 
   # when you are done, you can exit the virtualenv
   deactivate
@@ -103,7 +102,7 @@ An existing GHC database installation can be upgraded with:
 .. code-block:: bash
 
   # In the top directory (e.g. the topdir cloned from github)
-  paver upgrade
+  geohc db-upgrade
 
   # Notice any output, in particular errors
 
@@ -119,7 +118,7 @@ Notes:
 
 When running with Docker see the
 `Docker Readme <https://github.com/geopython/GeoHealthCheck/blob/master/docker/README.md>`_
-how to run `paver upgrade` within your Docker Container.
+how to run `geohc upgrade` within your Docker Container.
 
 Upgrade notes v0.5.0
 ....................
@@ -144,9 +143,9 @@ Start using Flask's built-in WSGI server:
 
 .. code-block:: bash
 
-  python GeoHealthCheck/app.py  # http://localhost:8000
-  python GeoHealthCheck/app.py 0.0.0.0:8881  # http://localhost:8881
-  python GeoHealthCheck/app.py 192.168.0.105:8957  # http://192.168.0.105:8957
+  geohc serve  # http://localhost:8000
+  geohc serve --port 8881  # http://localhost:8881
+  geohc serve --host 192.168.0.105 --port 8957  # http://192.168.0.105:8957
 
 
 This runs the (Flask) **GHC Webapp**, by default with the **GHC Runner** (scheduled healthchecker) internally.
@@ -157,10 +156,10 @@ From the command-line run both processes, e.g. in background or different termin
 .. code-block:: bash
 
   # run GHC Runner, here in background
-  python GeoHealthCheck/scheduler.py &
+  geohc runner-daemon &
 
   # run GHC Webapp for http://localhost:8000
-  python GeoHealthCheck/app.py
+  geohc serve
 
 
 To enable in Apache, use ``GeoHealthCheck.wsgi`` and configure in Apache
diff --git a/ghc_cli.py b/ghc_cli.py
index f1640c66..ba44c555 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -415,7 +415,14 @@ def run_healthchecks(ctx):
 @cli.command()
 @click.pass_context
 def db_export(ctx):
-    pass
+    click.exho('GeoHC: todo- write export.')
+
+@cli.command()
+@click.pass_context
+def run_tests(ctx):
+    """Run all tests"""
+    import os
+    os.system('python %s' % os.path.normpath('tests/run_tests.py'))
 
 
 if __name__ == '__main__':
diff --git a/pavement.py b/pavement.py
index d3abf2d7..7247ee52 100644
--- a/pavement.py
+++ b/pavement.py
@@ -347,4 +347,6 @@ def sphinx_make():
 @task
 def run_tests():
     """Run all tests"""
+    info('Warning!: run_tests is deprecated since 0.8.0. Please use cli: '
+         '`geohc run-tests`')
     sh('python %s' % path('tests/run_tests.py'))

From adde2aba530d0e96810aeb90f3be20adc6a99f14 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 19:21:30 +0100
Subject: [PATCH 09/49] Update readme on cli

---
 README.md | 35 ++++++++++++++++++++++-------------
 1 file changed, 22 insertions(+), 13 deletions(-)

diff --git a/README.md b/README.md
index 8891d525..6795cd17 100644
--- a/README.md
+++ b/README.md
@@ -13,15 +13,15 @@ Easiest is [to run GHC using Docker](https://github.com/geopython/GeoHealthCheck
 Below a quick overview of a manual install on Unix-based systems like Apple Mac and Linux.
 
 ```bash
-virtualenv GeoHealthCheck && cd $_
+python3 -m venv venv
 . bin/activate
 git clone https://github.com/geopython/GeoHealthCheck.git
 cd GeoHealthCheck
-pip install Paver
+pip install .
 # setup installation
-paver setup
+geohc create-instance
 # generate secret key
-paver create_secret_key
+geohc create-secret-key
 # setup local configuration (overrides GeoHealthCheck/config_main.py)
 vi instance/config_site.py
 # edit at least secret key:
@@ -36,33 +36,42 @@ vi instance/config_site.py
 # - GHC_SITE_TITLE
 # - GHC_MAP (or use default settings)
 
-# setup database and superuser account interactively 
-paver create
+# setup database 
+geohc db-create
+
+# create superuser account interactively
+geohc db-adduser
 
 # start webserver with healthcheck runner daemon inside 
 # (default is 0.0.0.0:8000)
-python GeoHealthCheck/app.py  
+geohc serve  
 # or start webserver on another port
-python GeoHealthCheck/app.py 0.0.0.0:8881
+geohc serve -p 8881
 # or start webserver on another IP
-python GeoHealthCheck/app.py 192.168.0.105:8001
+geohc serve -h 192.168.0.105 -p 8001
 
 # OR start webserver and separate runner daemon (scheduler) process
 vi instance/config_site.py
 # GHC_RUNNER_IN_WEBAPP = False
-python GeoHealthCheck/scheduler.py & 
-python GeoHealthCheck/app.py  
+geohc runner-daemon & 
+geohc serve
 
 # next: use a real webserver or preferably Docker for production
 
 # other commands
 #
 # drop database
-python GeoHealthCheck/models.py drop
+geohc db-drop
 
 # load data in database (WARN: deletes existing data!)
 # See example data .json files in tests/data
-python GeoHealthCheck/models.py load <.json data file> [y/n]
+geohc db-load -f <.json data file> -y
+
+# More help on the `geohc` cli command:
+geohc --help
+
+# More help on a specific command
+geohc db-load --help
 
 ```
 

From 272d21d10ce0a00b8ed9ebc211f5a0cb954501ac Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 19:31:06 +0100
Subject: [PATCH 10/49] Update README - fix sourcing venv

---
 README.md | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6795cd17..ef69c9d0 100644
--- a/README.md
+++ b/README.md
@@ -13,8 +13,8 @@ Easiest is [to run GHC using Docker](https://github.com/geopython/GeoHealthCheck
 Below a quick overview of a manual install on Unix-based systems like Apple Mac and Linux.
 
 ```bash
-python3 -m venv venv
-. bin/activate
+python3 -m venv ghc_venv
+. ghc_venv/bin/activate
 git clone https://github.com/geopython/GeoHealthCheck.git
 cd GeoHealthCheck
 pip install .

From 8df7fd936ab6555e61e1f5ae5d02961e872ba635 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 13 Dec 2019 20:50:52 +0100
Subject: [PATCH 11/49] Update setup.py to complete build egg and wheel

---
 ghc_cli.py           | 10 ++++++++
 requirements-dev.txt |  1 +
 setup.py             | 56 +++++++++++++++++++++++++++++++++++++++++++-
 3 files changed, 66 insertions(+), 1 deletion(-)

diff --git a/ghc_cli.py b/ghc_cli.py
index ba44c555..4aeb38c3 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -425,5 +425,15 @@ def run_tests(ctx):
     os.system('python %s' % os.path.normpath('tests/run_tests.py'))
 
 
+@cli.command()
+@click.pass_context
+def build_wheel(ctx):
+    """Build a python wheel"""
+    verbose_echo(ctx, 'GeoHC: Build a python wheel')
+    from os import system
+    system('python setup.py bdist_wheel')
+    click.echo('GeoHC: Finished building a wheel.')
+
+
 if __name__ == '__main__':
     cli()
diff --git a/requirements-dev.txt b/requirements-dev.txt
index a857e625..095bdec7 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -2,3 +2,4 @@ click==7.0
 flake8
 Paver==1.3.4
 pylint
+wheel==0.33.6
diff --git a/setup.py b/setup.py
index 3632e936..028a8943 100644
--- a/setup.py
+++ b/setup.py
@@ -1,7 +1,37 @@
+# =================================================================
+#
+# Authors: Rob van Loon <borrob@me.com>
+#          Tom Kralidis <tomkralidis@gmail.com>
+#
+# Copyright (c) 2019 Rob van Loon
+#
+# Permission is hereby granted, free of charge, to any person
+# obtaining a copy of this software and associated documentation
+# files (the "Software"), to deal in the Software without
+# restriction, including without limitation the rights to use,
+# copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the
+# Software is furnished to do so, subject to the following
+# conditions:
+#
+# The above copyright notice and this permission notice shall be
+# included in all copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+# OTHER DEALINGS IN THE SOFTWARE.
+#
+# =================================================================
 import io
 import os
 from setuptools import find_packages, setup
 
+
 def read(filename, encoding='utf-8'):
     """read file contents"""
     full_path = os.path.join(os.path.dirname(__file__), filename)
@@ -16,9 +46,21 @@ def get_package_version():
         return version_file
     raise RuntimeError("Unable to find version string.")
 
+LONG_DESCRIPTION = read('README.md')
+
+DESCRIPTION = 'GeoHealthCheck is a Quality of Service Checker for OGC Web Services and web APIs.'
+
 setup(
     name='geohealthcheck',
     version=get_package_version(),
+    description=DESCRIPTION,
+    long_description=LONG_DESCRIPTION,
+    long_description_content_type="text/markdown",
+    author='Tom Kralidis',
+    author_email='tomkralidis@gmail.com',
+    maintainer='Tom Kralidis',
+    maintainer_email='tomkralidis@gmail.com',
+    url='https://geohealthcheck.org',
     license='MIT',
     install_requires=read('requirements.txt').splitlines(),
     packages=find_packages(exclude=['tests']),
@@ -27,5 +69,17 @@ def get_package_version():
         'console_scripts': [
             'geohc=ghc_cli:cli',
         ]
-    }
+    },
+    classifiers=[
+        'Development Status :: 5 - Production/Stable',
+        'Environment :: Console',
+        'Framework :: Flask',
+        'Intended Audience :: Developers',
+        'Intended Audience :: System Administrators',
+        'Intended Audience :: Science/Research',
+        'License :: OSI Approved :: MIT License',
+        'Operating System :: OS Independent',
+        'Programming Language :: Python',
+        'Topic :: Scientific/Engineering :: GIS'
+    ],
 )

From 531162f3c9f58f43915e4291cf1ca4e93fc3fe1e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Sat, 14 Dec 2019 22:13:00 +0100
Subject: [PATCH 12/49] Update travis to cli commands

---
 .travis.yml | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 3b43f7be..6986bcc5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,17 +6,17 @@ python:
 sudo: false
 
 install:
-  - pip install -r requirements.txt
-  - pip install -r requirements-dev.txt
-  - paver setup
+  - pip install .
+  - geohc create-instance
 
 script:
-  - echo -e "admin\ntest\ntest\nyou@example.com\nyou@example.com" | python GeoHealthCheck/models.py create
+  - geohc db-create
+  - geohc db-adduser -u admin -p test -e you@example.com -r admin
   - flake8
-  - python GeoHealthCheck/models.py load tests/data/fixtures.json y
-  - python GeoHealthCheck/healthcheck.py
-  - python tests/run_tests.py
+  - geohc db-load -y tests/data/fixtures.json -y
+  - geohc run-healthchecks
+  - geohc run-tests
   - cd docs && make html
 
 after-script:
-  - python GeoHealthCheck/models.py drop
+  - geohc db-drop

From f3ee207b0b4cc5d3a46e0910f53982542f896ba2 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Sat, 14 Dec 2019 22:19:08 +0100
Subject: [PATCH 13/49] Update docker scripts to cli

---
 docker/scripts/install.sh       | 1 +
 docker/scripts/requirements.txt | 1 -
 docker/scripts/run-runner.sh    | 2 +-
 docker/scripts/run-web.sh       | 2 +-
 4 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/docker/scripts/install.sh b/docker/scripts/install.sh
index 16532c83..5c819ca3 100755
--- a/docker/scripts/install.sh
+++ b/docker/scripts/install.sh
@@ -11,6 +11,7 @@ source /venv/bin/activate
 pip install -I -r /GeoHealthCheck/docker/scripts/requirements.txt
 
 cd /GeoHealthCheck
+pip install .
 
 # Sets up GHC itself
 paver setup
diff --git a/docker/scripts/requirements.txt b/docker/scripts/requirements.txt
index fd68b637..1a716f6f 100644
--- a/docker/scripts/requirements.txt
+++ b/docker/scripts/requirements.txt
@@ -1,4 +1,3 @@
-Paver==1.3.4
 Sphinx==1.8.1
 psycopg2==2.7.5
 eventlet==0.24.1
diff --git a/docker/scripts/run-runner.sh b/docker/scripts/run-runner.sh
index bfcaa8af..6f09a838 100755
--- a/docker/scripts/run-runner.sh
+++ b/docker/scripts/run-runner.sh
@@ -16,6 +16,6 @@ source /venv/bin/activate .
 export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
 cd /GeoHealthCheck
-paver runner_daemon
+geohc runner-daemon
 
 echo "END /run-runner.sh"
diff --git a/docker/scripts/run-web.sh b/docker/scripts/run-web.sh
index 9e25ed23..11df065e 100755
--- a/docker/scripts/run-web.sh
+++ b/docker/scripts/run-web.sh
@@ -16,7 +16,7 @@ export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
 cd /GeoHealthCheck
 
-paver upgrade
+geohc db-upgrade
 
 # SCRIPT_NAME should not have value '/'
 [ "${SCRIPT_NAME}" = '/' ] && export SCRIPT_NAME="" && echo "make SCRIPT_NAME empty from /"

From b4513a8338432f695b02ba421a82309e399975ce Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Sun, 15 Dec 2019 21:37:00 +0100
Subject: [PATCH 14/49] Fix flake8 issues

---
 GeoHealthCheck/models.py | 21 +++++++++++----------
 ghc_cli.py               | 33 +++++++++++++++++++++------------
 pavement.py              | 28 ++++++++++++++--------------
 3 files changed, 46 insertions(+), 36 deletions(-)

diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index 3c44665c..30882353 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -909,8 +909,9 @@ def db_commit():
 
     if len(sys.argv) > 1:
         if sys.argv[1] == 'create':
-            warnings.warn('models.py create is deprecated since 0.8.0. Please use cli: '
-                          '`geohc db-create` and `geohc db-adduser`', DeprecationWarning)
+            warnings.warn('models.py create is deprecated since 0.8.0. Please'
+                          ' use cli: `geohc db-create` and `geohc db-adduser`',
+                          DeprecationWarning)
             print('Creating database objects')
             DB.create_all()
 
@@ -935,15 +936,15 @@ def db_commit():
             db_commit()
 
         elif sys.argv[1] == 'drop':
-            warnings.warn('models.py drop is deprecated since 0.8.0. Please use cli: '
-                          '`geohc db-drop`', DeprecationWarning)
+            warnings.warn('models.py drop is deprecated since 0.8.0. Please '
+                          'use cli: `geohc db-drop`', DeprecationWarning)
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
 
         elif sys.argv[1] == 'load':
-            warnings.warn('models.py load is deprecated since 0.8.0. Please use cli: '
-                          '`geohc db-load`', DeprecationWarning)
+            warnings.warn('models.py load is deprecated since 0.8.0. Please '
+                          'use cli: `geohc db-load`', DeprecationWarning)
             print('Load database from JSON file (e.g. tests/fixtures.json)')
             if len(sys.argv) > 2:
                 file_path = sys.argv[2]
@@ -967,12 +968,12 @@ def db_commit():
                 print('Provide path to JSON file, e.g. tests/fixtures.json')
 
         elif sys.argv[1] == 'run':
-            warnings.warn('models.py run is deprecated. Please use `python healthcheck.py`',
-                          DeprecationWarning)
+            warnings.warn('models.py run is deprecated. Please use `python '
+                          'healthcheck.py`', DeprecationWarning)
 
         elif sys.argv[1] == 'flush':
-            warnings.warn('models.py flush is deprecated since 0.8.0. Please use cli: '
-                          '`geohc db-flush`', DeprecationWarning)
+            warnings.warn('models.py flush is deprecated since 0.8.0. Please '
+                          'use cli: `geohc db-flush`', DeprecationWarning)
             flush_runs()
 
         DB.session.remove()
diff --git a/ghc_cli.py b/ghc_cli.py
index 4aeb38c3..2f0c51c0 100644
--- a/ghc_cli.py
+++ b/ghc_cli.py
@@ -114,17 +114,18 @@ def db_create(ctx):
     DB.create_all()
     db_commit()
     DB.session.remove()
-    click.echo('Database is created. Use `geohc db-adduser` to add users to the database.')
+    click.echo('Database is created. Use `geohc db-adduser` to add users to '
+               'the database.')
 
 
 @cli.command()
 @click.pass_context
 @click.option('-u', '--user', type=str, help='username', prompt=True)
 @click.option('-e', '--email', type=str, help='email address', prompt=True)
-@click.option('-p', '--password', type=str, help='password', prompt=True, hide_input=True,
-              confirmation_prompt=True)
-@click.option('-r', '--role', type=click.Choice(['admin', 'user']), prompt=True,
-              help='role for this user')
+@click.option('-p', '--password', type=str, help='password', prompt=True,
+              hide_input=True, confirmation_prompt=True)
+@click.option('-r', '--role', type=click.Choice(['admin', 'user']),
+              prompt=True, help='role for this user')
 def db_adduser(ctx, user, email, password, role):
     """Add an user to the database
     """
@@ -146,12 +147,14 @@ def db_adduser(ctx, user, email, password, role):
 @click.pass_context
 @click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
               expose_value=False, help='Confirm dropping tables',
-              prompt='This will drop the tables in the database. Are you sure?')
+              prompt='This will drop the tables in the database. Are you '
+                     'sure?')
 def db_drop(ctx):
     """Drop the current database
     """
     verbose_echo(ctx, 'GeoHC: drop db')
-    click.confirm("This will drop the tables in the database. Are you sure?", abort=True)
+    click.confirm("This will drop the tables in the database. Are you sure?",
+                  abort=True)
     verbose_echo(ctx, 'User confirmed dropping tables')
     from GeoHealthCheck.init import App
     from GeoHealthCheck.models import db_commit
@@ -211,11 +214,13 @@ def create_secret_key(ctx):
     from codecs import encode
     from os import urandom
     click.echo('Secret key: \'%s\'' % encode(urandom(24), 'hex').decode())
-    click.echo('Copy/paste this key to set the SECRET_KEY value in instance/config_site.py')
+    click.echo('Copy/paste this key to set the SECRET_KEY value in '
+               'instance/config_site.py')
 
 
 @cli.command()
-@click.option('-p', '--password', prompt=True, hide_input=True, help='password')
+@click.option('-p', '--password', prompt=True, hide_input=True,
+              help='password')
 @click.pass_context
 def create_hash(ctx, password):
     """Create a password hash
@@ -257,7 +262,8 @@ def create_wsgi(ctx):
 
     wsgi_conf = '%s%sGeoHealthCheck.conf' % (instance, os.sep)
     with open(wsgi_conf, 'w') as ff:
-        ff.write('WSGIScriptAlias / %s%sGeoHealthCheck.wsgi\n' % (instance, os.sep))
+        ff.write('WSGIScriptAlias / %s%sGeoHealthCheck.wsgi\n' % (instance,
+                                                                  os.sep))
         ff.write('<Directory %s%s>\n' % (basedir, os.sep))
         ff.write('Order deny,allow\n')
         ff.write('Allow from all\n')
@@ -342,7 +348,8 @@ def lang_extract_translations(ctx):
         pot_dir.makedirs()
 
     basedir = os.path.abspath(os.path.dirname(__file__))
-    base_pot = os.path.normpath('%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' % basedir)
+    base_pot = os.path.normpath('%s/GeoHealthCheck/translations/en/'
+                                'LC_MESSAGES/messages.po' % basedir)
     verbose_echo(ctx, 'GeoHC: starting translation')
     os.system('pybabel extract -F babel.cfg -o %s GeoHealthCheck' % base_pot)
     click.echo('GeoHC: finished extracting translations.')
@@ -397,7 +404,8 @@ def lang_update_translations(ctx):
 @click.pass_context
 def runner_daemon(ctx):
     """Run the HealthCheck runner daemon scheduler"""
-    verbose_echo(ctx, 'GeoHC: going to run the scheduler daemon. Press ctrl-c to stop.')
+    verbose_echo(ctx, 'GeoHC: going to run the scheduler daemon. Press ctrl-c '
+                      'to stop.')
     import os
     os.system('python %s' % os.path.normpath('GeoHealthCheck/scheduler.py'))
 
@@ -417,6 +425,7 @@ def run_healthchecks(ctx):
 def db_export(ctx):
     click.exho('GeoHC: todo- write export.')
 
+
 @cli.command()
 @click.pass_context
 def run_tests(ctx):
diff --git a/pavement.py b/pavement.py
index 7247ee52..ecd35738 100644
--- a/pavement.py
+++ b/pavement.py
@@ -167,8 +167,8 @@ def setup():
 ])
 def create(options):
     """create database objects and superuser account"""
-    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use cli: '
-         '`geohc db-create` and `geohc db-adduser`')
+    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use '
+         'cli: `geohc db-create` and `geohc db-adduser`')
     args = ''
     username = options.get('username', None)
     password = options.get('password', None)
@@ -182,8 +182,8 @@ def create(options):
 @task
 def create_secret_key():
     """create secret key for SECRET_KEY in instance/config_site.py"""
-    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use cli: '
-         '`geohc create-secret-key`')
+    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use '
+         'cli: `geohc create-secret-key`')
     info('Secret key: \'%s\'' % codecs.encode(os.urandom(24), 'hex').decode())
     info('Copy/paste this key to set the SECRET_KEY')
     info('value in instance/config_site.py')
@@ -275,8 +275,8 @@ def clean():
 def extract_translations():
     """extract translations wrapped in _() or gettext()"""
 
-    info('Warning!: extract_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc lang-extract-translations`')
+    info('Warning!: extract_translations is deprecated since 0.8.0. Please use'
+         ' cli: `geohc lang-extract-translations`')
     pot_dir = path('GeoHealthCheck/translations/en/LC_MESSAGES')
     if not os.path.exists(pot_dir):
         pot_dir.makedirs()
@@ -291,8 +291,8 @@ def extract_translations():
 def add_language_catalogue(options):
     """adds new language profile"""
 
-    info('Warning!: add_language_catalogue is deprecated since 0.8.0. Please use cli: '
-         '`geohc lang-add-language-catalogue`')
+    info('Warning!: add_language_catalogue is deprecated since 0.8.0. Please '
+         'use cli: `geohc lang-add-language-catalogue`')
     lang = options.get('lang', None)
 
     if lang is None:
@@ -305,16 +305,16 @@ def add_language_catalogue(options):
 @task
 def compile_translations():
     """build .mo files"""
-    info('Warning!: compile_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc lang-compile-translations`')
+    info('Warning!: compile_translations is deprecated since 0.8.0. Please use'
+         ' cli: `geohc lang-compile-translations`')
     sh('pybabel compile -d %s' % options.base.translations)
 
 
 @task
 def update_translations():
     """update language strings"""
-    info('Warning!: update_translations is deprecated since 0.8.0. Please use cli: '
-         '`geohc lang-update-translations`')
+    info('Warning!: update_translations is deprecated since 0.8.0. Please use '
+         'cli: `geohc lang-update-translations`')
     call_task('extract_translations')
     sh('pybabel update -i %s -d %s' % (
         options.base.pot, options.base.translations))
@@ -331,8 +331,8 @@ def runner_daemon():
 @task
 def run_healthchecks():
     """Run all HealthChecks directly"""
-    info('Warning!: run_healthchecks is deprecated since 0.8.0. Please use cli: '
-         '`geohc run-healthchecks`')
+    info('Warning!: run_healthchecks is deprecated since 0.8.0. Please use '
+         'cli: `geohc run-healthchecks`')
     sh('python %s' % path('GeoHealthCheck/healthcheck.py'))
 
 

From 3c427a50ee6b2cba3f2fcf596e589b5022316453 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 18 Dec 2019 08:00:24 +0100
Subject: [PATCH 15/49] Update docker commands

---
 docker/README.md            | 4 ++--
 docker/scripts/configure.sh | 2 +-
 docker/scripts/install.sh   | 2 +-
 3 files changed, 4 insertions(+), 4 deletions(-)

diff --git a/docker/README.md b/docker/README.md
index a1b0977f..d0d3d4ca 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -235,8 +235,8 @@ docker exec -it docker_geohealthcheck_1 bash
 source /venv/bin/activate .
 cd /GeoHealthCheck/
  
-# next can use Paver commands e.g. DB upgrade
-paver upgrade
+# next can use cli commands e.g. DB upgrade
+geohc db-upgrade
 
 etc
 ```
diff --git a/docker/scripts/configure.sh b/docker/scripts/configure.sh
index 8256ff23..ab0104cc 100755
--- a/docker/scripts/configure.sh
+++ b/docker/scripts/configure.sh
@@ -15,7 +15,7 @@ echo "Using DB_TYPE=${DB_TYPE}"
 # Create DB shorthand
 function create_db() {
 	pushd /GeoHealthCheck/
-	paver create -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL}
+	geohc db-adduser -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL} -r admin
 	popd
 }
 
diff --git a/docker/scripts/install.sh b/docker/scripts/install.sh
index 5c819ca3..363fb03c 100755
--- a/docker/scripts/install.sh
+++ b/docker/scripts/install.sh
@@ -14,7 +14,7 @@ cd /GeoHealthCheck
 pip install .
 
 # Sets up GHC itself
-paver setup
+geohc create-instance
 mv /config_site.py /GeoHealthCheck/instance/config_site.py
 
 # Copy possible Plugins into app tree

From 0741f99a96bd93f14e530539c1434a95ed53258e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 18 Dec 2019 08:07:50 +0100
Subject: [PATCH 16/49] Rename cli script

---
 ghc_cli.py => geohc_cli.py | 0
 setup.py                   | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename ghc_cli.py => geohc_cli.py (100%)

diff --git a/ghc_cli.py b/geohc_cli.py
similarity index 100%
rename from ghc_cli.py
rename to geohc_cli.py
diff --git a/setup.py b/setup.py
index 028a8943..ccc2918a 100644
--- a/setup.py
+++ b/setup.py
@@ -67,7 +67,7 @@ def get_package_version():
     include_package_data=True,
     entry_points={
         'console_scripts': [
-            'geohc=ghc_cli:cli',
+            'geohc=geohc_cli:cli',
         ]
     },
     classifiers=[

From efda72c37d1e45b4a305714826a8f95a4694ef24 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 18 Dec 2019 13:15:26 +0100
Subject: [PATCH 17/49] Final touches

---
 docs/admin.rst   | 32 ++++++++++++++++++++++++++++++--
 docs/install.rst |  3 +++
 setup.py         |  2 ++
 3 files changed, 35 insertions(+), 2 deletions(-)

diff --git a/docs/admin.rst b/docs/admin.rst
index 423b4928..6cf37892 100644
--- a/docs/admin.rst
+++ b/docs/admin.rst
@@ -14,7 +14,7 @@ acces to the command line interface `geohc`. You can get help from the cli via :
     geohc --help
 
 This will list all available commands. To get help with a specific command, run
-`geohc command --help`, e.g. ::
+`geohc <<command>> --help`, e.g. ::
 
     geohc db-adduser --help
 
@@ -23,7 +23,7 @@ This will show you all the (required) options to add a user to the database.
 Database
 --------
 
-For database administration the following commands are available.
+For database administration the following commands are available:
 
 create db
 .........
@@ -34,6 +34,17 @@ Open a command line, (if needed activate your virtualenv), and do ::
 
     geohc db-create
 
+add user
+........
+
+To add a new user to the database:
+
+Open a command line, (if needed activate your virtualenv), and do ::
+
+    geohc db-adduser
+    # or
+    geohc db-adduser -u username -p password -e email@address.com -r admin
+
 drop db
 .......
 
@@ -52,8 +63,25 @@ To load a JSON data file, do (WARN: deletes existing data!) ::
 
     geohc db-load --file my_data.json
 
+You will be asked for confirmation. You can also specify the `-y` or `--yes`
+flag to indicate you are sure and to skip the confirmation question.
 Hint: see `tests/data` for example JSON data files.
 
+
+flush
+.....
+
+To flush the old records from the system, you can flush the records ::
+
+    geohc db-flush
+
+upgrade
+.......
+
+To upgrade the database structure (might be necessary with a new release of GeoHealthCheck) ::
+
+    geohc db-upgrade
+
 export data
 ...........
 
diff --git a/docs/install.rst b/docs/install.rst
index b94573d1..905a15bc 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -84,6 +84,9 @@ Install
   # init database
   geohc db-create
 
+  # create an (admin) user account
+  geohc db-adduser -u my_user_name -p my_pass -e e@mail.com -r admin
+
   # start web-app
   geohc serve
 
diff --git a/setup.py b/setup.py
index ccc2918a..1c9d2e6a 100644
--- a/setup.py
+++ b/setup.py
@@ -39,6 +39,7 @@ def read(filename, encoding='utf-8'):
         contents = fh.read().strip()
     return contents
 
+
 def get_package_version():
     """get version from top-level package init"""
     version_file = read('VERSION')
@@ -46,6 +47,7 @@ def get_package_version():
         return version_file
     raise RuntimeError("Unable to find version string.")
 
+
 LONG_DESCRIPTION = read('README.md')
 
 DESCRIPTION = 'GeoHealthCheck is a Quality of Service Checker for OGC Web Services and web APIs.'

From ce5ced3b7fe5863811389144bb9cb87d25319bc3 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Thu, 19 Dec 2019 21:38:27 +0100
Subject: [PATCH 18/49] Add Pycharm files to gitignore

---
 .gitignore | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/.gitignore b/.gitignore
index a8186829..755229f5 100644
--- a/.gitignore
+++ b/.gitignore
@@ -63,3 +63,6 @@ GeoHealthCheck.conf
 
 # Data
 GeoHealthCheck/data.db
+
+# IDE
+.idea

From b3bbe004cd95b541fefc056a3ffc0078b8a248bc Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Thu, 19 Dec 2019 21:38:44 +0100
Subject: [PATCH 19/49] WIP: fix docker

Need to fix loose ends:
- DB exists, but still needs db-create
- check import statements
- fix env setting for GHC_SETTINGS_CONF
- check non-docker build
- update docs
---
 Dockerfile                                  |  1 +
 GeoHealthCheck/__init__.py                  | 13 +----------
 GeoHealthCheck/app.py                       | 16 ++++++-------
 GeoHealthCheck/check.py                     |  4 ++--
 geohc_cli.py => GeoHealthCheck/geohc_cli.py |  0
 GeoHealthCheck/healthcheck.py               | 12 +++++-----
 GeoHealthCheck/init.py                      |  6 ++++-
 GeoHealthCheck/manage.py                    |  2 +-
 GeoHealthCheck/models.py                    | 25 +++++----------------
 GeoHealthCheck/notifications.py             |  2 +-
 GeoHealthCheck/plugin.py                    |  5 +----
 GeoHealthCheck/probe.py                     |  8 +++----
 GeoHealthCheck/resourceauth.py              | 20 ++++-------------
 GeoHealthCheck/scheduler.py                 |  6 ++---
 GeoHealthCheck/views.py                     | 10 ++++-----
 docker/scripts/configure.sh                 |  2 ++
 docker/scripts/requirements.txt             |  1 +
 docker/scripts/run-web.sh                   |  2 +-
 setup.py                                    |  4 ++--
 19 files changed, 53 insertions(+), 86 deletions(-)
 rename geohc_cli.py => GeoHealthCheck/geohc_cli.py (100%)

diff --git a/Dockerfile b/Dockerfile
index 04ed6203..fb87b079 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,6 +17,7 @@ ENV LC_ALL="en_US.UTF-8" \
     \
 	\
 	# GHC ENV settings\
+	GHC_SETTINGS_FILE='/GeoHealthCheck/instance/config_site.py' \
 	ADMIN_NAME=admin \
 	ADMIN_PWD=admin \
 	ADMIN_EMAIL=admin.istrator@mydomain.com \
diff --git a/GeoHealthCheck/__init__.py b/GeoHealthCheck/__init__.py
index 7f60751f..99e02e83 100644
--- a/GeoHealthCheck/__init__.py
+++ b/GeoHealthCheck/__init__.py
@@ -27,15 +27,4 @@
 #
 # =================================================================
 
-try:
-    from util import read
-except ImportError:
-    from .util import read
-
-
-def get_package_version(file_):
-    """get version from top-level package init"""
-    return read(file_)
-
-
-__version__ = get_package_version('../VERSION')
+__version__ = '0.8.0dev'
diff --git a/GeoHealthCheck/app.py b/GeoHealthCheck/app.py
index f7feba37..f0a14816 100644
--- a/GeoHealthCheck/app.py
+++ b/GeoHealthCheck/app.py
@@ -42,14 +42,14 @@
 from flask_migrate import Migrate
 from itertools import chain
 
-import views
-from __init__ import __version__
-from enums import RESOURCE_TYPES
-from factory import Factory
-from init import App
-from models import Resource, Run, ProbeVars, CheckVars, Tag, User, Recipient
-from resourceauth import ResourceAuth
-from util import send_email, geocode, format_checked_datetime, \
+from GeoHealthCheck import views
+from GeoHealthCheck.__init__ import __version__
+from GeoHealthCheck.enums import RESOURCE_TYPES
+from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.init import App
+from GeoHealthCheck.models import Resource, Run, ProbeVars, CheckVars, Tag, User, Recipient
+from GeoHealthCheck.resourceauth import ResourceAuth
+from GeoHealthCheck.util import send_email, geocode, format_checked_datetime, \
     format_run_status, format_obj_value
 
 # Module globals for convenience
diff --git a/GeoHealthCheck/check.py b/GeoHealthCheck/check.py
index e08770f5..6b9874a8 100644
--- a/GeoHealthCheck/check.py
+++ b/GeoHealthCheck/check.py
@@ -1,5 +1,5 @@
-from plugin import Plugin
-from result import CheckResult
+from GeoHealthCheck.plugin import Plugin
+from GeoHealthCheck.result import CheckResult
 
 
 class Check(Plugin):
diff --git a/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
similarity index 100%
rename from geohc_cli.py
rename to GeoHealthCheck/geohc_cli.py
diff --git a/GeoHealthCheck/healthcheck.py b/GeoHealthCheck/healthcheck.py
index 8897fa56..1b2dac59 100644
--- a/GeoHealthCheck/healthcheck.py
+++ b/GeoHealthCheck/healthcheck.py
@@ -44,12 +44,12 @@
 from owslib.csw import CatalogueServiceWeb
 from owslib.sos import SensorObservationService
 
-from init import App
-from enums import RESOURCE_TYPES
-from models import Resource, Run
-from probe import Probe
-from result import ResourceResult
-from notifications import notify
+from GeoHealthCheck.init import App
+from GeoHealthCheck.enums import RESOURCE_TYPES
+from GeoHealthCheck.models import Resource, Run
+from GeoHealthCheck.probe import Probe
+from GeoHealthCheck.result import ResourceResult
+from GeoHealthCheck.notifications import notify
 
 LOGGER = logging.getLogger(__name__)
 APP = App.get_app()
diff --git a/GeoHealthCheck/init.py b/GeoHealthCheck/init.py
index c46466a5..43003e88 100644
--- a/GeoHealthCheck/init.py
+++ b/GeoHealthCheck/init.py
@@ -67,7 +67,11 @@ def init():
 
         # Read and override configs
         app.config.from_pyfile('config_main.py')
-        app.config.from_pyfile('../instance/config_site.py')
+        try:
+            app.config.from_pyfile('../instance/config_site.py')
+        except FileNotFoundError:
+            # for Docker build
+            app.config.from_pyfile('/GeoHealthCheck/instance/config_site.py')
         app.config.from_envvar('GHC_SETTINGS', silent=True)
 
         # Global Logging config
diff --git a/GeoHealthCheck/manage.py b/GeoHealthCheck/manage.py
index 82c029df..1e14569f 100644
--- a/GeoHealthCheck/manage.py
+++ b/GeoHealthCheck/manage.py
@@ -39,7 +39,7 @@
 
 from flask_script import Manager
 from flask_migrate import Migrate, MigrateCommand
-from init import App
+from GeoHealthCheck.init import App
 
 DB = App.get_db()
 APP = App.get_app()
diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index 30882353..fc029b18 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -39,26 +39,11 @@
 from sqlalchemy.orm import deferred
 from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
 
-try:
-    import util
-except ImportError:
-    from GeoHealthCheck import util
-try:
-    from enums import RESOURCE_TYPES
-except ImportError:
-    from GeoHealthCheck.enums import RESOURCE_TYPES
-try:
-    from factory import Factory
-except ImportError:
-    from GeoHealthCheck.factory import Factory
-try:
-    from init import App
-except ImportError:
-    from GeoHealthCheck.init import App
-try:
-    from resourceauth import ResourceAuth
-except ImportError:
-    from GeoHealthCheck.resourceauth import ResourceAuth
+from GeoHealthCheck import util
+from GeoHealthCheck.enums import RESOURCE_TYPES
+from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.init import App
+from GeoHealthCheck.resourceauth import ResourceAuth
 from wtforms.validators import Email, ValidationError
 from owslib.util import bind_url
 
diff --git a/GeoHealthCheck/notifications.py b/GeoHealthCheck/notifications.py
index 8b22af4a..bf6e4e9f 100644
--- a/GeoHealthCheck/notifications.py
+++ b/GeoHealthCheck/notifications.py
@@ -35,7 +35,7 @@
 
 import requests
 from flask_babel import gettext
-from util import render_template2
+from GeoHealthCheck.util import render_template2
 
 LOGGER = logging.getLogger(__name__)
 
diff --git a/GeoHealthCheck/plugin.py b/GeoHealthCheck/plugin.py
index 8f38dc21..da73529a 100644
--- a/GeoHealthCheck/plugin.py
+++ b/GeoHealthCheck/plugin.py
@@ -1,7 +1,4 @@
-try:
-    from factory import Factory
-except ImportError:
-    from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.factory import Factory
 import logging
 import inspect
 from collections.abc import Mapping
diff --git a/GeoHealthCheck/probe.py b/GeoHealthCheck/probe.py
index 2501b593..eaa53781 100644
--- a/GeoHealthCheck/probe.py
+++ b/GeoHealthCheck/probe.py
@@ -4,10 +4,10 @@
 import datetime
 import requests
 
-from factory import Factory
-from init import App
-from plugin import Plugin
-from result import ProbeResult
+from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.init import App
+from GeoHealthCheck.plugin import Plugin
+from GeoHealthCheck.result import ProbeResult
 
 LOGGER = logging.getLogger(__name__)
 
diff --git a/GeoHealthCheck/resourceauth.py b/GeoHealthCheck/resourceauth.py
index c7446b11..16b07379 100644
--- a/GeoHealthCheck/resourceauth.py
+++ b/GeoHealthCheck/resourceauth.py
@@ -1,21 +1,9 @@
 import json
 import logging
-try:
-    from plugin import Plugin
-except ImportError:
-    from GeoHealthCheck.plugin import Plugin
-try:
-    from factory import Factory
-except ImportError:
-    from GeoHealthCheck.factory import Factory
-try:
-    from util import encode, decode
-except ImportError:
-    from GeoHealthCheck.util import encode, decode
-try:
-    from init import App
-except ImportError:
-    from GeoHealthCheck.init import App
+from GeoHealthCheck.plugin import Plugin
+from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.util import encode, decode
+from GeoHealthCheck.init import App
 
 APP = App.get_app()
 LOGGER = logging.getLogger(__name__)
diff --git a/GeoHealthCheck/scheduler.py b/GeoHealthCheck/scheduler.py
index 62fa9c2c..83846786 100644
--- a/GeoHealthCheck/scheduler.py
+++ b/GeoHealthCheck/scheduler.py
@@ -33,14 +33,14 @@
 import random
 import string
 from datetime import datetime, timedelta
-from models import Resource, ResourceLock, flush_runs
-from healthcheck import run_resource
+from GeoHealthCheck.models import Resource, ResourceLock, flush_runs
+from GeoHealthCheck.healthcheck import run_resource
 from apscheduler.schedulers.background import BackgroundScheduler
 from apscheduler.jobstores.base import JobLookupError
 from apscheduler.events import \
     EVENT_SCHEDULER_STARTED, EVENT_SCHEDULER_SHUTDOWN, \
     EVENT_JOB_MISSED, EVENT_JOB_ERROR
-from init import App
+from GeoHealthCheck.init import App
 
 LOGGER = logging.getLogger(__name__)
 DB = App.get_db()
diff --git a/GeoHealthCheck/views.py b/GeoHealthCheck/views.py
index d5102e7c..0f3db82c 100644
--- a/GeoHealthCheck/views.py
+++ b/GeoHealthCheck/views.py
@@ -28,12 +28,12 @@
 # =================================================================
 
 import logging
-import models
-import util
+from GeoHealthCheck import models
+from GeoHealthCheck import util
 from sqlalchemy import text
-from plugin import Plugin
-from factory import Factory
-from init import App
+from GeoHealthCheck.plugin import Plugin
+from GeoHealthCheck.factory import Factory
+from GeoHealthCheck.init import App
 APP = App.get_app()
 
 LOGGER = logging.getLogger(__name__)
diff --git a/docker/scripts/configure.sh b/docker/scripts/configure.sh
index ab0104cc..c0386b54 100755
--- a/docker/scripts/configure.sh
+++ b/docker/scripts/configure.sh
@@ -15,6 +15,7 @@ echo "Using DB_TYPE=${DB_TYPE}"
 # Create DB shorthand
 function create_db() {
 	pushd /GeoHealthCheck/
+  geohc db-create
 	geohc db-adduser -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL} -r admin
 	popd
 }
@@ -29,6 +30,7 @@ case ${DB_TYPE} in
 			create_db
 		else
 			echo "NOT creating SQLite DB tables..."
+			geohc db-create #hoort hier niet
 		fi
 	    ;;
 
diff --git a/docker/scripts/requirements.txt b/docker/scripts/requirements.txt
index 1a716f6f..fd68b637 100644
--- a/docker/scripts/requirements.txt
+++ b/docker/scripts/requirements.txt
@@ -1,3 +1,4 @@
+Paver==1.3.4
 Sphinx==1.8.1
 psycopg2==2.7.5
 eventlet==0.24.1
diff --git a/docker/scripts/run-web.sh b/docker/scripts/run-web.sh
index 11df065e..b30327e4 100755
--- a/docker/scripts/run-web.sh
+++ b/docker/scripts/run-web.sh
@@ -12,7 +12,7 @@ echo "START /run-web.sh"
 
 source /venv/bin/activate .
 # Make sure PYTHONPATH includes GeoHealthCheck
-export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
+export PYTHONPATH=/GeoHealthCheck:$PYTHONPATH
 
 cd /GeoHealthCheck
 
diff --git a/setup.py b/setup.py
index 1c9d2e6a..3caf46a1 100644
--- a/setup.py
+++ b/setup.py
@@ -35,7 +35,7 @@
 def read(filename, encoding='utf-8'):
     """read file contents"""
     full_path = os.path.join(os.path.dirname(__file__), filename)
-    with io.open(full_path, encoding=encoding) as fh:
+    with io.open(filename, encoding=encoding) as fh:
         contents = fh.read().strip()
     return contents
 
@@ -69,7 +69,7 @@ def get_package_version():
     include_package_data=True,
     entry_points={
         'console_scripts': [
-            'geohc=geohc_cli:cli',
+            'geohc=GeoHealthCheck.geohc_cli:cli',
         ]
     },
     classifiers=[

From ba875b673cf733efbfec8758870dfb9f01b65092 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 20 Dec 2019 08:20:31 +0100
Subject: [PATCH 20/49] Fix import statements app.py

---
 GeoHealthCheck/app.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/GeoHealthCheck/app.py b/GeoHealthCheck/app.py
index f0a14816..37d37764 100644
--- a/GeoHealthCheck/app.py
+++ b/GeoHealthCheck/app.py
@@ -76,7 +76,7 @@
 # Should GHC Runner be run within GHC webapp?
 if CONFIG['GHC_RUNNER_IN_WEBAPP'] is True:
     LOGGER.info('Running GHC Scheduler in WebApp')
-    from scheduler import start_schedule
+    from GeoHealthCheck.scheduler import start_schedule
 
     # Start scheduler
     start_schedule()
@@ -531,7 +531,7 @@ def add():
     url = request.form['url'].strip()
     resources_to_add = []
 
-    from healthcheck import sniff_test_resource, run_test_resource
+    from GeoHealthCheck.healthcheck import sniff_test_resource, run_test_resource
     sniffed_resources = sniff_test_resource(CONFIG, resource_type, url)
 
     if not sniffed_resources:
@@ -734,7 +734,7 @@ def test(resource_identifier):
         flash(gettext('Resource not found'), 'danger')
         return redirect(request.referrer)
 
-    from healthcheck import run_test_resource
+    from GeoHealthCheck.healthcheck import run_test_resource
     result = run_test_resource(
         resource)
 

From 727704404670696a8dbe9f9cd94275d939ffd990 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 20 Dec 2019 08:21:11 +0100
Subject: [PATCH 21/49] Format dockerfile

---
 Dockerfile | 33 ++++++++++++++++-----------------
 1 file changed, 16 insertions(+), 17 deletions(-)

diff --git a/Dockerfile b/Dockerfile
index fb87b079..1ca2f69d 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -17,7 +17,6 @@ ENV LC_ALL="en_US.UTF-8" \
     \
 	\
 	# GHC ENV settings\
-	GHC_SETTINGS_FILE='/GeoHealthCheck/instance/config_site.py' \
 	ADMIN_NAME=admin \
 	ADMIN_PWD=admin \
 	ADMIN_EMAIL=admin.istrator@mydomain.com \
@@ -46,22 +45,22 @@ ENV LC_ALL="en_US.UTF-8" \
 	GHC_SMTP_PASSWORD=None \
 	GHC_METADATA_CACHE_SECS=900 \
     \
-# WSGI server settings, assumed is gunicorn  \
-HOST=0.0.0.0 \
-PORT=80 \
-WSGI_WORKERS=4 \
-WSGI_WORKER_TIMEOUT=6000 \
-WSGI_WORKER_CLASS='eventlet' \
-\
-# GHC Core Plugins modules and/or classes, seldom needed to set:  \
-# if not specified here or in Container environment  \
-# all GHC built-in Plugins will be active.  \
-#ENV GHC_PLUGINS 'GeoHealthCheck.plugins.probe.owsgetcaps,\
-#        GeoHealthCheck.plugins.probe.wms, ...., ...\
-#        GeoHealthCheck.plugins.check.checks' \
-\
-# GHC User Plugins, best be overridden via Container environment \
-GHC_USER_PLUGINS=''
+    # WSGI server settings, assumed is gunicorn  \
+    HOST=0.0.0.0 \
+    PORT=80 \
+    WSGI_WORKERS=4 \
+    WSGI_WORKER_TIMEOUT=6000 \
+    WSGI_WORKER_CLASS='eventlet' \
+    \
+    # GHC Core Plugins modules and/or classes, seldom needed to set:  \
+    # if not specified here or in Container environment  \
+    # all GHC built-in Plugins will be active.  \
+    #ENV GHC_PLUGINS 'GeoHealthCheck.plugins.probe.owsgetcaps,\
+    #        GeoHealthCheck.plugins.probe.wms, ...., ...\
+    #        GeoHealthCheck.plugins.check.checks' \
+    \
+    # GHC User Plugins, best be overridden via Container environment \
+    GHC_USER_PLUGINS=''
 
 RUN apk add --no-cache --virtual .build-deps gcc build-base libxslt-dev libxml2-dev linux-headers postgresql-dev \
     && apk add --no-cache bash postgresql-client libxslt libxml2 tzdata openntpd python3 python3-dev \

From a99bd78c1cb30c74d30e1dd7b04de0f66b145be1 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 20 Dec 2019 16:15:30 +0100
Subject: [PATCH 22/49] Add paver again

---
 docker/scripts/requirements.txt | 3 +--
 requirements.txt                | 1 +
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/docker/scripts/requirements.txt b/docker/scripts/requirements.txt
index fd68b637..e5794fdd 100644
--- a/docker/scripts/requirements.txt
+++ b/docker/scripts/requirements.txt
@@ -1,5 +1,4 @@
-Paver==1.3.4
-Sphinx==1.8.1
+Paver==1.3.4  # Paver is still required for 1 geohc cli command: geohc create-instance
 psycopg2==2.7.5
 eventlet==0.24.1
 gunicorn==19.9.0
diff --git a/requirements.txt b/requirements.txt
index a937e4ce..7736133f 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,3 +15,4 @@ requests>=2.20.0
 WTForms==2.2.1
 APScheduler==3.6.1
 passlib==1.7.1
+paver==1.3.4

From 6f8508d6c32cbe7c6255e586c88d3fa6dbfb7bc5 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 20 Dec 2019 16:16:03 +0100
Subject: [PATCH 23/49] Update tests to new imports

---
 tests/test_plugins.py   | 10 +++++-----
 tests/test_resources.py | 10 +++++-----
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/tests/test_plugins.py b/tests/test_plugins.py
index 1ee3cdcd..864fcc1c 100644
--- a/tests/test_plugins.py
+++ b/tests/test_plugins.py
@@ -30,11 +30,11 @@
 import unittest
 import os
 
-from models import DB, load_data, Resource
-from views import get_probes_avail
-from plugin import Plugin
-from probe import Probe
-from factory import Factory
+from GeoHealthCheck.models import DB, load_data, Resource
+from GeoHealthCheck.views import get_probes_avail
+from GeoHealthCheck.plugin import Plugin
+from GeoHealthCheck.probe import Probe
+from GeoHealthCheck.factory import Factory
 
 TEST_DIR = os.path.dirname(os.path.abspath(__file__))
 
diff --git a/tests/test_resources.py b/tests/test_resources.py
index ab9df17e..ea418165 100644
--- a/tests/test_resources.py
+++ b/tests/test_resources.py
@@ -31,11 +31,11 @@
 import unittest
 import os
 
-from init import App
-from models import (DB, Resource, Run, load_data, Recipient)
-from healthcheck import run_test_resource
-from notifications import _parse_webhook_location
-from resourceauth import ResourceAuth
+from GeoHealthCheck.init import App
+from GeoHealthCheck.models import (DB, Resource, Run, load_data, Recipient)
+from GeoHealthCheck.healthcheck import run_test_resource
+from GeoHealthCheck.notifications import _parse_webhook_location
+from GeoHealthCheck.resourceauth import ResourceAuth
 
 TEST_DIR = os.path.dirname(os.path.abspath(__file__))
 

From 898959008c9737d939621d12e9264dc498d5a601 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 20 Dec 2019 16:16:34 +0100
Subject: [PATCH 24/49] Cleanup and add documentation

---
 docker/README.md             | 3 +++
 docker/scripts/configure.sh  | 1 -
 docker/scripts/run-runner.sh | 1 -
 docker/scripts/run-web.sh    | 2 --
 4 files changed, 3 insertions(+), 4 deletions(-)

diff --git a/docker/README.md b/docker/README.md
index d0d3d4ca..d188cae3 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -97,6 +97,9 @@ docker-compose -f docker-compose.yml up  [-d]
 # go to http://localhost:8083 (port 80 in GHC Container is mapped to 8083 on host)
 
 ```
+This setup maps the sqlite database to a docker volume (`ghc_sqlitedb`) that is stored on the
+machine (outside the docker container). To get more information about the volume, run
+`docker volume inspect ghc_sqlitedb`.
   
 ### Using PostGIS DB
 
diff --git a/docker/scripts/configure.sh b/docker/scripts/configure.sh
index c0386b54..71b2c85d 100755
--- a/docker/scripts/configure.sh
+++ b/docker/scripts/configure.sh
@@ -30,7 +30,6 @@ case ${DB_TYPE} in
 			create_db
 		else
 			echo "NOT creating SQLite DB tables..."
-			geohc db-create #hoort hier niet
 		fi
 	    ;;
 
diff --git a/docker/scripts/run-runner.sh b/docker/scripts/run-runner.sh
index 6f09a838..d8c3e24f 100755
--- a/docker/scripts/run-runner.sh
+++ b/docker/scripts/run-runner.sh
@@ -15,7 +15,6 @@ source /venv/bin/activate .
 # Make sure PYTHONPATH includes GeoHealthCheck
 export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
 
-cd /GeoHealthCheck
 geohc runner-daemon
 
 echo "END /run-runner.sh"
diff --git a/docker/scripts/run-web.sh b/docker/scripts/run-web.sh
index b30327e4..93726305 100755
--- a/docker/scripts/run-web.sh
+++ b/docker/scripts/run-web.sh
@@ -14,8 +14,6 @@ source /venv/bin/activate .
 # Make sure PYTHONPATH includes GeoHealthCheck
 export PYTHONPATH=/GeoHealthCheck:$PYTHONPATH
 
-cd /GeoHealthCheck
-
 geohc db-upgrade
 
 # SCRIPT_NAME should not have value '/'

From 8a25408c4084f2022aecfb86ea0314420667a8ef Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 23 Dec 2019 07:02:57 +0100
Subject: [PATCH 25/49] Update install doc

---
 README.md        | 3 +++
 docs/install.rst | 8 +++++++-
 2 files changed, 10 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ef69c9d0..b670d63e 100644
--- a/README.md
+++ b/README.md
@@ -75,4 +75,7 @@ geohc db-load --help
 
 ```
 
+**Note for developers:** instead of `pip install .`, you might want to install with the *editable*
+option specified: `pip install -e .`
+
 More in the [full GHC documentation](http://docs.geohealthcheck.org/).
\ No newline at end of file
diff --git a/docs/install.rst b/docs/install.rst
index 905a15bc..a034413c 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -54,7 +54,7 @@ Install
   git clone https://github.com/geopython/GeoHealthCheck.git
   cd GeoHealthCheck
 
-  # install paver dependency for admin tool
+  # install
   pip install .
 
   # setup app
@@ -95,6 +95,12 @@ Install
 
 NB GHC supports internal scheduling, no cronjobs required.
 
+Developing
+..........
+If you plan to develop with the GeoHealthCheck code base, you might want to install with the
+*editable* option specified: `pip install -e`. This gives you access to the command line interface,
+and you can still edit and run the code.
+
 .. _upgrade:
 
 Upgrade

From abf71b8e7feda63fd33162123b0522f2b6d2892e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Thu, 26 Dec 2019 21:45:32 +0100
Subject: [PATCH 26/49] WIP: convert setup command

TODO: test the create-instance, double check os.path things
---
 GeoHealthCheck/geohc_cli.py | 102 ++++++++++++++++++++++++++++++++++--
 1 file changed, 98 insertions(+), 4 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 2f0c51c0..68dac310 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -74,10 +74,104 @@ def create_instance(ctx):
     This command is a copy of `paver setup`
     """
     verbose_echo(ctx, 'GeoHC: create instance')
-    # calling paver for the setup
-    # TODO: phase out paver and switch to click
-    from os import system
-    system('paver setup')
+    import glob, os, shutil
+    from io import BytesIO
+    from urllib.request import urlopen
+    import zipfile
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    config_file = os.path.normpath('%s/GeoHealthCheck/config_main.py' % basedir)
+    config_site = os.path.normpath('%s/config_site.py' % basedir)
+
+    # setup dirs
+    if not os.path.exists(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir)):
+        os.mkdir(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
+    if not os.path.exists(os.path.normpath('%s/instance' % basedir)):
+        os.mkdir(os.path.normpath('%s/instance' % basedir))
+        data_dir = os.path.normpath('%s/instance/data' % basedir)
+        os.mkdir(data_dir, mode=0o777)
+        # setup config
+        config_file.copy(config_site)
+
+    skin = 'http://github.com/BlackrockDigital/startbootstrap-sb-admin-2/archive/v3.3.7+1.zip'  # noqa
+
+    skin_dirs = ['dist', 'vendor']
+    need_to_fetch = False
+
+    for skin_dir in skin_dirs:
+        skin_dir_path = os.sep.join(
+            ['startbootstrap-sb-admin-2-3.3.7-1', skin_dir])
+        if not os.path.exists(skin_dir_path):
+            need_to_fetch = True
+
+    if need_to_fetch:
+        zipstr = BytesIO(urlopen(skin).read())
+        zipfile_obj = zipfile.ZipFile(zipstr)
+        zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
+
+        for zf_mem in skin_dirs:
+            src_loc = os.path.normpath('%s/GeoHealthCheck/static/lib' 
+                           'startbootstrap-sb-admin-2-3.3.7-1/%s' %basedir, zf_mem)
+            dest_loc = os.path.normpath('%s/GeoHealthCheck/static/lib%s' %basedir, zf_mem)
+            if not os.path.exists(dest_loc):
+                src_loc.move(dest_loc)
+            else:
+                click.echo('directory already exists.  Skipping')
+
+        shutil.rmtree(os.path.normpath('%s/GeoHealthCheck/static/lib' 
+                           'startbootstrap-sb-admin-2-3.3.7-1' %basedir))
+
+    # install sparklines to static/site/js
+    with open(os.path.normpath('%s/GeoHealthCheck/static/lib' 
+                           'startbootstrap-sb-admin-2-3.3.7-1/jspark.js' %basedir ), 'w') as f:
+        content = urlopen('http://ejohn.org/files/jspark.js').read().decode()
+        content.replace('red', 'green')
+        f.write(content)
+
+    # install bootstrap-tagsinput to static/lib
+    click.echo('Getting select2')
+    select2 = 'https://github.com/select2/select2/archive/4.0.3.zip'
+
+    zipstr = BytesIO(urlopen(select2).read())
+    zipfile_obj = zipfile.ZipFile(zipstr)
+    zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
+    dirname = glob.glob(os.path.normpath('%s/GeoHealthCheck/static/lib/select2-*' % basedir))[0]
+    dstdir = ''.join(dirname.rsplit('-', 1)[:-1])
+    try:
+        os.rename(dirname, dstdir)
+    except OSError:
+        shutil.rmtree(dstdir)
+        os.rename(dirname, dstdir)
+
+    # install leafletjs to static/lib
+    click.echo('Getting leaflet')
+    leafletjs = 'http://cdn.leafletjs.com/downloads/leaflet-0.7.5.zip'
+
+    zipstr = BytesIO(urlopen(leafletjs).read())
+    zipfile_obj = zipfile.ZipFile(zipstr)
+    zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib/leaflet' % basedir))
+
+    # install html5shiv to static/lib
+    with open(os.path.normpath('%s/GeoHealthCheck/static/lib/html5shiv.min.js' % basedir), 'w') as f:
+        url = 'http://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js'
+        content = urlopen(url).read().decode()
+        f.write(content)
+
+    # install respond to static/lib
+    with open(os.path.normpath('%s/GeoHealthCheck/static/lib/respond.min.js' % basedir), 'w') as f:
+        url = 'http://oss.maxcdn.com/respond/1.4.2/respond.min.js'
+        content = urlopen(url).read().decode()
+        f.write(content)
+
+    # build i18n .mo files
+    lang_compile_translations(ctx)
+
+    # build local docs
+    update_docs(ctx)
+
+    # message user
+    click.echo('GeoHealthCheck is now built. Edit settings in %s' % config_site)
+    click.echo('before deploying the application. Alternatively, you can start a')
+    click.echo('development instance with "python GeoHealthCheck/app.py"')
     verbose_echo(ctx, 'GeoHC: finished creating the instance.')
 
 

From 3a3bd773326eb260edd90b44dabdc88df56c12b7 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 1 Jan 2020 22:41:30 +0100
Subject: [PATCH 27/49] Fix path errors and wrap click functions

---
 GeoHealthCheck/geohc_cli.py | 62 +++++++++++++++++++++----------------
 1 file changed, 36 insertions(+), 26 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 68dac310..c2d42aa9 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -76,21 +76,24 @@ def create_instance(ctx):
     verbose_echo(ctx, 'GeoHC: create instance')
     import glob, os, shutil
     from io import BytesIO
+    from pathlib import Path
     from urllib.request import urlopen
     import zipfile
     basedir = os.path.abspath(os.path.dirname(__file__))
-    config_file = os.path.normpath('%s/GeoHealthCheck/config_main.py' % basedir)
-    config_site = os.path.normpath('%s/config_site.py' % basedir)
+    config_file = os.path.normpath('%s/config_main.py' % basedir)
+    config_site = os.path.normpath(str(Path(os.path.normpath('%s' % basedir)).
+                                       parent)
+                                   + '/instance/config_site.py')
 
     # setup dirs
-    if not os.path.exists(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir)):
-        os.mkdir(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
+    if not os.path.exists(os.path.normpath('%s/static/lib' % basedir)):
+        os.mkdir(os.path.normpath('%s/static/lib' % basedir))
     if not os.path.exists(os.path.normpath('%s/instance' % basedir)):
         os.mkdir(os.path.normpath('%s/instance' % basedir))
         data_dir = os.path.normpath('%s/instance/data' % basedir)
         os.mkdir(data_dir, mode=0o777)
         # setup config
-        config_file.copy(config_site)
+        shutil.copy(config_file, config_site)
 
     skin = 'http://github.com/BlackrockDigital/startbootstrap-sb-admin-2/archive/v3.3.7+1.zip'  # noqa
 
@@ -106,23 +109,23 @@ def create_instance(ctx):
     if need_to_fetch:
         zipstr = BytesIO(urlopen(skin).read())
         zipfile_obj = zipfile.ZipFile(zipstr)
-        zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
+        zipfile_obj.extractall(os.path.normpath('%s/static/lib' % basedir))
 
         for zf_mem in skin_dirs:
-            src_loc = os.path.normpath('%s/GeoHealthCheck/static/lib' 
-                           'startbootstrap-sb-admin-2-3.3.7-1/%s' %basedir, zf_mem)
-            dest_loc = os.path.normpath('%s/GeoHealthCheck/static/lib%s' %basedir, zf_mem)
+            src_loc = os.path.normpath('%s/static/lib/'
+                           'startbootstrap-sb-admin-2-3.3.7-1/%s' %(basedir, zf_mem))
+            dest_loc = os.path.normpath('%s/static/lib/%s' %(basedir, zf_mem))
             if not os.path.exists(dest_loc):
-                src_loc.move(dest_loc)
+                shutil.move(src_loc, dest_loc)
             else:
                 click.echo('directory already exists.  Skipping')
 
-        shutil.rmtree(os.path.normpath('%s/GeoHealthCheck/static/lib' 
+        shutil.rmtree(os.path.normpath('%s/static/lib/' 
                            'startbootstrap-sb-admin-2-3.3.7-1' %basedir))
 
     # install sparklines to static/site/js
-    with open(os.path.normpath('%s/GeoHealthCheck/static/lib' 
-                           'startbootstrap-sb-admin-2-3.3.7-1/jspark.js' %basedir ), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/' 
+                           'jspark.js' %basedir ), 'w') as f:
         content = urlopen('http://ejohn.org/files/jspark.js').read().decode()
         content.replace('red', 'green')
         f.write(content)
@@ -133,14 +136,14 @@ def create_instance(ctx):
 
     zipstr = BytesIO(urlopen(select2).read())
     zipfile_obj = zipfile.ZipFile(zipstr)
-    zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib' % basedir))
-    dirname = glob.glob(os.path.normpath('%s/GeoHealthCheck/static/lib/select2-*' % basedir))[0]
+    zipfile_obj.extractall(os.path.normpath('%s/static/lib' % basedir))
+    dirname = glob.glob(os.path.normpath('%s/static/lib/select2-*' % basedir))[0]
     dstdir = ''.join(dirname.rsplit('-', 1)[:-1])
     try:
-        os.rename(dirname, dstdir)
+        shutil.move(dirname, dstdir)
     except OSError:
         shutil.rmtree(dstdir)
-        os.rename(dirname, dstdir)
+        shutil.move(dirname, dstdir)
 
     # install leafletjs to static/lib
     click.echo('Getting leaflet')
@@ -148,25 +151,25 @@ def create_instance(ctx):
 
     zipstr = BytesIO(urlopen(leafletjs).read())
     zipfile_obj = zipfile.ZipFile(zipstr)
-    zipfile_obj.extractall(os.path.normpath('%s/GeoHealthCheck/static/lib/leaflet' % basedir))
+    zipfile_obj.extractall(os.path.normpath('%s/static/lib/leaflet' % basedir))
 
     # install html5shiv to static/lib
-    with open(os.path.normpath('%s/GeoHealthCheck/static/lib/html5shiv.min.js' % basedir), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/html5shiv.min.js' % basedir), 'w') as f:
         url = 'http://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js'
         content = urlopen(url).read().decode()
         f.write(content)
 
     # install respond to static/lib
-    with open(os.path.normpath('%s/GeoHealthCheck/static/lib/respond.min.js' % basedir), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/respond.min.js' % basedir), 'w') as f:
         url = 'http://oss.maxcdn.com/respond/1.4.2/respond.min.js'
         content = urlopen(url).read().decode()
         f.write(content)
 
     # build i18n .mo files
-    lang_compile_translations(ctx)
+    compile_translations(ctx)
 
     # build local docs
-    update_docs(ctx)
+    update_documentation(ctx)
 
     # message user
     click.echo('GeoHealthCheck is now built. Edit settings in %s' % config_site)
@@ -369,12 +372,16 @@ def create_wsgi(ctx):
 @click.pass_context
 def update_docs(ctx):
     """Update the spinx build of the documentation."""
+    update_documentation(ctx)
+
+def update_documentation(ctx):
     verbose_echo(ctx, 'GeoHC: start building documentation.')
 
     import os
     import shutil
+    from pathlib import Path
 
-    basedir = os.path.abspath(os.path.dirname(__file__))
+    basedir = str(Path(os.path.abspath(os.path.dirname(__file__))).parent)
     static_docs = os.path.normpath('%s/GeoHealthCheck/static/docs' % basedir)
     docs = os.path.normpath('%s/docs' % basedir)
 
@@ -458,8 +465,8 @@ def lang_add_language_catalogue(ctx, lang):
     import os
     basedir = os.path.abspath(os.path.dirname(__file__))
     base_pot = os.path.normpath(
-        '%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' % basedir)
-    translations = os.path.normpath('%s/GeoHealthCheck/translations' % basedir)
+        '%s/translations/en/LC_MESSAGES/messages.po' % basedir)
+    translations = os.path.normpath('%s/translations' % basedir)
     verbose_echo(ctx, 'GeoHC: Base translation set: %s' % base_pot)
     os.system('pybabel init -i %s -d %s -l %s' % (
         base_pot, translations, lang))
@@ -469,11 +476,14 @@ def lang_add_language_catalogue(ctx, lang):
 @cli.command()
 @click.pass_context
 def lang_compile_translations(ctx):
+    compile_translations(ctx)
+
+def compile_translations(ctx):
     """build language files"""
     verbose_echo(ctx, 'GeoHC: start building language files.')
     import os
     basedir = os.path.abspath(os.path.dirname(__file__))
-    translations = os.path.normpath('%s/GeoHealthCheck/translations' % basedir)
+    translations = os.path.normpath('%s/translations' % basedir)
     os.system('pybabel compile -d %s' % translations)
     click.echo('GeoHC: Finished building language files.')
 

From 8e5c8bb36287c155ee41638a322369c2e06951cd Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 3 Jan 2020 22:49:54 +0100
Subject: [PATCH 28/49] Update path things in cli

---
 GeoHealthCheck/geohc_cli.py | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index c2d42aa9..990d1ebf 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -80,17 +80,16 @@ def create_instance(ctx):
     from urllib.request import urlopen
     import zipfile
     basedir = os.path.abspath(os.path.dirname(__file__))
+    basedir_parent = os.path.normpath(str(Path(basedir)))
     config_file = os.path.normpath('%s/config_main.py' % basedir)
-    config_site = os.path.normpath(str(Path(os.path.normpath('%s' % basedir)).
-                                       parent)
-                                   + '/instance/config_site.py')
+    config_site = os.path.normpath(basedir_parent + '/instance/config_site.py')
 
     # setup dirs
     if not os.path.exists(os.path.normpath('%s/static/lib' % basedir)):
         os.mkdir(os.path.normpath('%s/static/lib' % basedir))
     if not os.path.exists(os.path.normpath('%s/instance' % basedir)):
-        os.mkdir(os.path.normpath('%s/instance' % basedir))
-        data_dir = os.path.normpath('%s/instance/data' % basedir)
+        os.mkdir(os.path.normpath('%s/instance' % basedir_parent))
+        data_dir = os.path.normpath('%s/instance/data' % basedir_parent)
         os.mkdir(data_dir, mode=0o777)
         # setup config
         shutil.copy(config_file, config_site)

From 1e6129e6f26d23f6e0d25fe9349de1724e816e2a Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 3 Jan 2020 23:14:01 +0100
Subject: [PATCH 29/49] Fix flake8 issues

---
 GeoHealthCheck/app.py       |  6 ++++--
 GeoHealthCheck/geohc_cli.py | 37 ++++++++++++++++++++++++-------------
 2 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/GeoHealthCheck/app.py b/GeoHealthCheck/app.py
index 37d37764..66a5440b 100644
--- a/GeoHealthCheck/app.py
+++ b/GeoHealthCheck/app.py
@@ -47,7 +47,8 @@
 from GeoHealthCheck.enums import RESOURCE_TYPES
 from GeoHealthCheck.factory import Factory
 from GeoHealthCheck.init import App
-from GeoHealthCheck.models import Resource, Run, ProbeVars, CheckVars, Tag, User, Recipient
+from GeoHealthCheck.models import Resource, Run, ProbeVars, CheckVars, Tag, \
+    User, Recipient
 from GeoHealthCheck.resourceauth import ResourceAuth
 from GeoHealthCheck.util import send_email, geocode, format_checked_datetime, \
     format_run_status, format_obj_value
@@ -531,7 +532,8 @@ def add():
     url = request.form['url'].strip()
     resources_to_add = []
 
-    from GeoHealthCheck.healthcheck import sniff_test_resource, run_test_resource
+    from GeoHealthCheck.healthcheck import sniff_test_resource, \
+        run_test_resource
     sniffed_resources = sniff_test_resource(CONFIG, resource_type, url)
 
     if not sniffed_resources:
diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 990d1ebf..717c52eb 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -74,7 +74,9 @@ def create_instance(ctx):
     This command is a copy of `paver setup`
     """
     verbose_echo(ctx, 'GeoHC: create instance')
-    import glob, os, shutil
+    import glob
+    import os
+    import shutil
     from io import BytesIO
     from pathlib import Path
     from urllib.request import urlopen
@@ -112,19 +114,21 @@ def create_instance(ctx):
 
         for zf_mem in skin_dirs:
             src_loc = os.path.normpath('%s/static/lib/'
-                           'startbootstrap-sb-admin-2-3.3.7-1/%s' %(basedir, zf_mem))
-            dest_loc = os.path.normpath('%s/static/lib/%s' %(basedir, zf_mem))
+                                       'startbootstrap-sb-admin-2-3.3.7-1/%s'
+                                       % (basedir, zf_mem))
+            dest_loc = os.path.normpath('%s/static/lib/%s' % (basedir, zf_mem))
             if not os.path.exists(dest_loc):
                 shutil.move(src_loc, dest_loc)
             else:
                 click.echo('directory already exists.  Skipping')
 
-        shutil.rmtree(os.path.normpath('%s/static/lib/' 
-                           'startbootstrap-sb-admin-2-3.3.7-1' %basedir))
+        shutil.rmtree(os.path.normpath('%s/static/lib/'
+                                       'startbootstrap-sb-admin-2-3.3.7-1'
+                                       % basedir))
 
     # install sparklines to static/site/js
-    with open(os.path.normpath('%s/static/lib/' 
-                           'jspark.js' %basedir ), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/'
+                               'jspark.js' % basedir), 'w') as f:
         content = urlopen('http://ejohn.org/files/jspark.js').read().decode()
         content.replace('red', 'green')
         f.write(content)
@@ -136,7 +140,8 @@ def create_instance(ctx):
     zipstr = BytesIO(urlopen(select2).read())
     zipfile_obj = zipfile.ZipFile(zipstr)
     zipfile_obj.extractall(os.path.normpath('%s/static/lib' % basedir))
-    dirname = glob.glob(os.path.normpath('%s/static/lib/select2-*' % basedir))[0]
+    dirname = glob.glob(os.path.normpath('%s/static/lib/select2-*'
+                                         % basedir))[0]
     dstdir = ''.join(dirname.rsplit('-', 1)[:-1])
     try:
         shutil.move(dirname, dstdir)
@@ -153,13 +158,15 @@ def create_instance(ctx):
     zipfile_obj.extractall(os.path.normpath('%s/static/lib/leaflet' % basedir))
 
     # install html5shiv to static/lib
-    with open(os.path.normpath('%s/static/lib/html5shiv.min.js' % basedir), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/html5shiv.min.js' % basedir),
+              'w') as f:
         url = 'http://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js'
         content = urlopen(url).read().decode()
         f.write(content)
 
     # install respond to static/lib
-    with open(os.path.normpath('%s/static/lib/respond.min.js' % basedir), 'w') as f:
+    with open(os.path.normpath('%s/static/lib/respond.min.js' % basedir),
+              'w') as f:
         url = 'http://oss.maxcdn.com/respond/1.4.2/respond.min.js'
         content = urlopen(url).read().decode()
         f.write(content)
@@ -171,9 +178,11 @@ def create_instance(ctx):
     update_documentation(ctx)
 
     # message user
-    click.echo('GeoHealthCheck is now built. Edit settings in %s' % config_site)
-    click.echo('before deploying the application. Alternatively, you can start a')
-    click.echo('development instance with "python GeoHealthCheck/app.py"')
+    click.echo('GeoHealthCheck is now built. Edit settings in %s'
+               % config_site)
+    click.echo('before deploying the application. Alternatively, you can')
+    click.echo('start a development instance with ')
+    click.echo('"python GeoHealthCheck/app.py"')
     verbose_echo(ctx, 'GeoHC: finished creating the instance.')
 
 
@@ -373,6 +382,7 @@ def update_docs(ctx):
     """Update the spinx build of the documentation."""
     update_documentation(ctx)
 
+
 def update_documentation(ctx):
     verbose_echo(ctx, 'GeoHC: start building documentation.')
 
@@ -477,6 +487,7 @@ def lang_add_language_catalogue(ctx, lang):
 def lang_compile_translations(ctx):
     compile_translations(ctx)
 
+
 def compile_translations(ctx):
     """build language files"""
     verbose_echo(ctx, 'GeoHC: start building language files.')

From fce898f90b879ae643199f502f449558e18f3761 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Fri, 3 Jan 2020 23:27:21 +0100
Subject: [PATCH 30/49] Remove paver from docker requirements

---
 docker/scripts/requirements.txt | 1 -
 1 file changed, 1 deletion(-)

diff --git a/docker/scripts/requirements.txt b/docker/scripts/requirements.txt
index e5794fdd..30ed0374 100644
--- a/docker/scripts/requirements.txt
+++ b/docker/scripts/requirements.txt
@@ -1,4 +1,3 @@
-Paver==1.3.4  # Paver is still required for 1 geohc cli command: geohc create-instance
 psycopg2==2.7.5
 eventlet==0.24.1
 gunicorn==19.9.0

From 88675bfa9ecc1925fd862bb985ed8c1691db5c14 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 6 Jan 2020 22:37:26 +0100
Subject: [PATCH 31/49] WIP: fix paths in docker

---
 GeoHealthCheck/geohc_cli.py | 12 +++++++++---
 docker/scripts/install.sh   |  2 +-
 2 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 717c52eb..2e06ba7d 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -68,7 +68,8 @@ def version(ctx):
 
 @cli.command()
 @click.pass_context
-def create_instance(ctx):
+@click.option('--basepath', '-p', type=str, help='path to the directory to install the instance data and help files.')
+def create_instance(ctx, basepath):
     """Create an instance of GeoHealthCheck App
 
     This command is a copy of `paver setup`
@@ -82,6 +83,9 @@ def create_instance(ctx):
     from urllib.request import urlopen
     import zipfile
     basedir = os.path.abspath(os.path.dirname(__file__))
+    if (basepath != None):
+        basedir = os.path.abspath(basepath)
+        verbose_echo(ctx, 'Setting base install directory to %s' %basedir)
     basedir_parent = os.path.normpath(str(Path(basedir)))
     config_file = os.path.normpath('%s/config_main.py' % basedir)
     config_site = os.path.normpath(basedir_parent + '/instance/config_site.py')
@@ -175,7 +179,7 @@ def create_instance(ctx):
     compile_translations(ctx)
 
     # build local docs
-    update_documentation(ctx)
+    update_documentation(ctx, basedir_parent)
 
     # message user
     click.echo('GeoHealthCheck is now built. Edit settings in %s'
@@ -383,7 +387,7 @@ def update_docs(ctx):
     update_documentation(ctx)
 
 
-def update_documentation(ctx):
+def update_documentation(ctx, basepath=None):
     verbose_echo(ctx, 'GeoHC: start building documentation.')
 
     import os
@@ -391,6 +395,8 @@ def update_documentation(ctx):
     from pathlib import Path
 
     basedir = str(Path(os.path.abspath(os.path.dirname(__file__))).parent)
+    if basepath:
+        basedir = os.path.abspath(basepath)
     static_docs = os.path.normpath('%s/GeoHealthCheck/static/docs' % basedir)
     docs = os.path.normpath('%s/docs' % basedir)
 
diff --git a/docker/scripts/install.sh b/docker/scripts/install.sh
index 363fb03c..07c77ec3 100755
--- a/docker/scripts/install.sh
+++ b/docker/scripts/install.sh
@@ -14,7 +14,7 @@ cd /GeoHealthCheck
 pip install .
 
 # Sets up GHC itself
-geohc create-instance
+geohc create-instance --basepath /GeoHealthCheck/GeoHealthCheck
 mv /config_site.py /GeoHealthCheck/instance/config_site.py
 
 # Copy possible Plugins into app tree

From a6a1da067abed11a23886d0ca0b1266518861a4a Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Tue, 7 Jan 2020 22:28:11 +0100
Subject: [PATCH 32/49] Fix docker build

---
 GeoHealthCheck/geohc_cli.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 2e06ba7d..9d8f2507 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -86,7 +86,7 @@ def create_instance(ctx, basepath):
     if (basepath != None):
         basedir = os.path.abspath(basepath)
         verbose_echo(ctx, 'Setting base install directory to %s' %basedir)
-    basedir_parent = os.path.normpath(str(Path(basedir)))
+    basedir_parent = os.path.normpath(str(Path(basedir).parent))
     config_file = os.path.normpath('%s/config_main.py' % basedir)
     config_site = os.path.normpath(basedir_parent + '/instance/config_site.py')
 
@@ -176,10 +176,10 @@ def create_instance(ctx, basepath):
         f.write(content)
 
     # build i18n .mo files
-    compile_translations(ctx)
+    compile_translations(ctx, path=basedir)
 
     # build local docs
-    update_documentation(ctx, basedir_parent)
+    update_documentation(ctx, basepath=basedir_parent)
 
     # message user
     click.echo('GeoHealthCheck is now built. Edit settings in %s'
@@ -494,11 +494,11 @@ def lang_compile_translations(ctx):
     compile_translations(ctx)
 
 
-def compile_translations(ctx):
+def compile_translations(ctx, path=None):
     """build language files"""
     verbose_echo(ctx, 'GeoHC: start building language files.')
     import os
-    basedir = os.path.abspath(os.path.dirname(__file__))
+    basedir = path if path else os.path.abspath(os.path.dirname(__file__))
     translations = os.path.normpath('%s/translations' % basedir)
     os.system('pybabel compile -d %s' % translations)
     click.echo('GeoHC: Finished building language files.')

From 74d14554fae88f152dc31b4b1f2c9a01608a63a7 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 21:31:08 +0100
Subject: [PATCH 33/49] Fix flake8

---
 GeoHealthCheck/geohc_cli.py | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/geohc_cli.py
index 9d8f2507..25523098 100644
--- a/GeoHealthCheck/geohc_cli.py
+++ b/GeoHealthCheck/geohc_cli.py
@@ -68,7 +68,8 @@ def version(ctx):
 
 @cli.command()
 @click.pass_context
-@click.option('--basepath', '-p', type=str, help='path to the directory to install the instance data and help files.')
+@click.option('--basepath', '-p', type=str, help='path to the directory to'
+              'install the instance data and help files.')
 def create_instance(ctx, basepath):
     """Create an instance of GeoHealthCheck App
 
@@ -83,9 +84,9 @@ def create_instance(ctx, basepath):
     from urllib.request import urlopen
     import zipfile
     basedir = os.path.abspath(os.path.dirname(__file__))
-    if (basepath != None):
+    if (basepath is not None):
         basedir = os.path.abspath(basepath)
-        verbose_echo(ctx, 'Setting base install directory to %s' %basedir)
+        verbose_echo(ctx, 'Setting base install directory to %s' % basedir)
     basedir_parent = os.path.normpath(str(Path(basedir).parent))
     config_file = os.path.normpath('%s/config_main.py' % basedir)
     config_site = os.path.normpath(basedir_parent + '/instance/config_site.py')

From 09e87bb5e17603263950394969da0d0ce6e3fa2e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 22:19:11 +0100
Subject: [PATCH 34/49] Fix travis build

---
 .travis.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 6986bcc5..ef1f1f5b 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,7 +7,7 @@ sudo: false
 
 install:
   - pip install .
-  - geohc create-instance
+  - geohc create-instance -p /home/travis/geopython/geohealthcheck
 
 script:
   - geohc db-create

From 25a3cbc71161936c808849b41bf0104bbabf2348 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 22:25:03 +0100
Subject: [PATCH 35/49] Fix travis build -2

---
 .travis.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index ef1f1f5b..76622454 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -6,8 +6,8 @@ python:
 sudo: false
 
 install:
-  - pip install .
-  - geohc create-instance -p /home/travis/geopython/geohealthcheck
+  - pip install -e .
+  - geohc create-instance
 
 script:
   - geohc db-create

From 7e194256693ac05e30ab06e777d1f3943d86f9c7 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 22:28:46 +0100
Subject: [PATCH 36/49] Fix travis build -3

---
 .travis.yml | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/.travis.yml b/.travis.yml
index 76622454..7a3529b5 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -7,13 +7,14 @@ sudo: false
 
 install:
   - pip install -e .
+  - pip install -r requirements-dev.txt
   - geohc create-instance
 
 script:
   - geohc db-create
   - geohc db-adduser -u admin -p test -e you@example.com -r admin
   - flake8
-  - geohc db-load -y tests/data/fixtures.json -y
+  - geohc db-load -f tests/data/fixtures.json -y
   - geohc run-healthchecks
   - geohc run-tests
   - cd docs && make html

From 5b708d5c5bba2f664bc3ec3fdece582f10aae7f5 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 22:34:27 +0100
Subject: [PATCH 37/49] Fix flake8 issues

---
 setup.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/setup.py b/setup.py
index 3caf46a1..ee8501fb 100644
--- a/setup.py
+++ b/setup.py
@@ -34,7 +34,8 @@
 
 def read(filename, encoding='utf-8'):
     """read file contents"""
-    full_path = os.path.join(os.path.dirname(__file__), filename)
+    full_path = os.path.join(os.path.dirname(__file__),
+                             filename)
     with io.open(filename, encoding=encoding) as fh:
         contents = fh.read().strip()
     return contents
@@ -50,7 +51,8 @@ def get_package_version():
 
 LONG_DESCRIPTION = read('README.md')
 
-DESCRIPTION = 'GeoHealthCheck is a Quality of Service Checker for OGC Web Services and web APIs.'
+DESCRIPTION = 'GeoHealthCheck is a Quality of Service Checker for OGC Web' \
+              'Services and web APIs.'
 
 setup(
     name='geohealthcheck',

From 71ea488701659ae232a22efa1f53cab9ce563d04 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 8 Jan 2020 22:37:05 +0100
Subject: [PATCH 38/49] Fix flake8 issues

---
 setup.py | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/setup.py b/setup.py
index ee8501fb..9a21c861 100644
--- a/setup.py
+++ b/setup.py
@@ -28,14 +28,11 @@
 #
 # =================================================================
 import io
-import os
 from setuptools import find_packages, setup
 
 
 def read(filename, encoding='utf-8'):
     """read file contents"""
-    full_path = os.path.join(os.path.dirname(__file__),
-                             filename)
     with io.open(filename, encoding=encoding) as fh:
         contents = fh.read().strip()
     return contents

From 0d2cc5c501696cb2c3fbb56f513a4d6b242909a4 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 06:53:13 +0100
Subject: [PATCH 39/49] Update format versionnumner

---
 GeoHealthCheck/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/GeoHealthCheck/__init__.py b/GeoHealthCheck/__init__.py
index 99e02e83..f8ac92ff 100644
--- a/GeoHealthCheck/__init__.py
+++ b/GeoHealthCheck/__init__.py
@@ -27,4 +27,4 @@
 #
 # =================================================================
 
-__version__ = '0.8.0dev'
+__version__ = '0.8.dev0'

From 4263ffe3c9a185560c3f854eba33af22f01580eb Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 06:54:15 +0100
Subject: [PATCH 40/49] Rename file geohc_cli to cli

---
 GeoHealthCheck/{geohc_cli.py => cli.py} | 0
 setup.py                                | 2 +-
 2 files changed, 1 insertion(+), 1 deletion(-)
 rename GeoHealthCheck/{geohc_cli.py => cli.py} (100%)

diff --git a/GeoHealthCheck/geohc_cli.py b/GeoHealthCheck/cli.py
similarity index 100%
rename from GeoHealthCheck/geohc_cli.py
rename to GeoHealthCheck/cli.py
diff --git a/setup.py b/setup.py
index 9a21c861..db3d1905 100644
--- a/setup.py
+++ b/setup.py
@@ -68,7 +68,7 @@ def get_package_version():
     include_package_data=True,
     entry_points={
         'console_scripts': [
-            'geohc=GeoHealthCheck.geohc_cli:cli',
+            'geohc=GeoHealthCheck.cli:cli',
         ]
     },
     classifiers=[

From b68098dd8a5145dc74ea0ee9649bdabdb1014c2e Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 06:58:09 +0100
Subject: [PATCH 41/49] Use LOGGER.warning instead of warnings module

---
 GeoHealthCheck/models.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index fc029b18..57b5c901 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -30,7 +30,6 @@
 
 import json
 import logging
-import warnings
 from flask_babel import gettext as _
 from datetime import datetime, timedelta
 from itsdangerous import TimedJSONWebSignatureSerializer as Serializer
@@ -894,7 +893,7 @@ def db_commit():
 
     if len(sys.argv) > 1:
         if sys.argv[1] == 'create':
-            warnings.warn('models.py create is deprecated since 0.8.0. Please'
+            LOGGER.warning('models.py create is deprecated since 0.8.0. Please'
                           ' use cli: `geohc db-create` and `geohc db-adduser`',
                           DeprecationWarning)
             print('Creating database objects')
@@ -921,14 +920,14 @@ def db_commit():
             db_commit()
 
         elif sys.argv[1] == 'drop':
-            warnings.warn('models.py drop is deprecated since 0.8.0. Please '
+            LOGGER.warning('models.py drop is deprecated since 0.8.0. Please '
                           'use cli: `geohc db-drop`', DeprecationWarning)
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
 
         elif sys.argv[1] == 'load':
-            warnings.warn('models.py load is deprecated since 0.8.0. Please '
+            LOGGER.warning('models.py load is deprecated since 0.8.0. Please '
                           'use cli: `geohc db-load`', DeprecationWarning)
             print('Load database from JSON file (e.g. tests/fixtures.json)')
             if len(sys.argv) > 2:
@@ -953,11 +952,11 @@ def db_commit():
                 print('Provide path to JSON file, e.g. tests/fixtures.json')
 
         elif sys.argv[1] == 'run':
-            warnings.warn('models.py run is deprecated. Please use `python '
+            LOGGER.warning('models.py run is deprecated. Please use `python '
                           'healthcheck.py`', DeprecationWarning)
 
         elif sys.argv[1] == 'flush':
-            warnings.warn('models.py flush is deprecated since 0.8.0. Please '
+            LOGGER.warning('models.py flush is deprecated since 0.8.0. Please '
                           'use cli: `geohc db-flush`', DeprecationWarning)
             flush_runs()
 

From bb96eb0f11ada1a71b80151a5aa1d7a7e5401d61 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 07:10:07 +0100
Subject: [PATCH 42/49] Fix acquiring version number

---
 VERSION  | 1 -
 setup.py | 9 ++++++---
 2 files changed, 6 insertions(+), 4 deletions(-)
 delete mode 100644 VERSION

diff --git a/VERSION b/VERSION
deleted file mode 100644
index 3128c152..00000000
--- a/VERSION
+++ /dev/null
@@ -1 +0,0 @@
-0.8.dev0
diff --git a/setup.py b/setup.py
index db3d1905..15241dc3 100644
--- a/setup.py
+++ b/setup.py
@@ -28,6 +28,7 @@
 #
 # =================================================================
 import io
+import re
 from setuptools import find_packages, setup
 
 
@@ -40,9 +41,11 @@ def read(filename, encoding='utf-8'):
 
 def get_package_version():
     """get version from top-level package init"""
-    version_file = read('VERSION')
-    if version_file:
-        return version_file
+    version_file = read('GeoHealthCheck/__init__.py')
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        return version_match.group(1)
     raise RuntimeError("Unable to find version string.")
 
 

From f6da999fe568ad61ba1b95f10759de18bf1f1f46 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 15:53:30 +0100
Subject: [PATCH 43/49] Update name to correct use of capitals

---
 setup.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/setup.py b/setup.py
index 15241dc3..85a3effd 100644
--- a/setup.py
+++ b/setup.py
@@ -55,7 +55,7 @@ def get_package_version():
               'Services and web APIs.'
 
 setup(
-    name='geohealthcheck',
+    name='GeoHealthCheck',
     version=get_package_version(),
     description=DESCRIPTION,
     long_description=LONG_DESCRIPTION,

From 040aa0a74c8d810e27144e889ca9732ea669611c Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 21:42:31 +0100
Subject: [PATCH 44/49] Create cli subcommand for database

---
 .travis.yml                 |   8 +-
 GeoHealthCheck/cli.py       | 260 +++++++++++++++++++-----------------
 GeoHealthCheck/models.py    |   8 +-
 README.md                   |  12 +-
 docker/scripts/configure.sh |   4 +-
 docker/scripts/run-web.sh   |   2 +-
 docs/admin.rst              |  16 +--
 7 files changed, 160 insertions(+), 150 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 7a3529b5..c0ee9d76 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -11,13 +11,13 @@ install:
   - geohc create-instance
 
 script:
-  - geohc db-create
-  - geohc db-adduser -u admin -p test -e you@example.com -r admin
+  - geohc db create
+  - geohc db adduser -u admin -p test -e you@example.com -r admin
   - flake8
-  - geohc db-load -f tests/data/fixtures.json -y
+  - geohc db load -f tests/data/fixtures.json -y
   - geohc run-healthchecks
   - geohc run-tests
   - cd docs && make html
 
 after-script:
-  - geohc db-drop
+  - geohc db drop
diff --git a/GeoHealthCheck/cli.py b/GeoHealthCheck/cli.py
index 25523098..35c5070b 100644
--- a/GeoHealthCheck/cli.py
+++ b/GeoHealthCheck/cli.py
@@ -208,113 +208,6 @@ def serve(ctx, host, port):
     system(f"python app.py {host}:{port}")
 
 
-@cli.command()
-@click.pass_context
-def db_create(ctx):
-    """Create the GHC database
-
-    Note: you still need to add a user
-    """
-    verbose_echo(ctx, 'GeoHC: create db')
-    from GeoHealthCheck.init import App
-    from GeoHealthCheck.models import db_commit
-    verbose_echo(ctx, 'GeoHC: get database')
-    DB = App.get_db()
-    verbose_echo(ctx, 'GeoHC: create all tables')
-    DB.create_all()
-    db_commit()
-    DB.session.remove()
-    click.echo('Database is created. Use `geohc db-adduser` to add users to '
-               'the database.')
-
-
-@cli.command()
-@click.pass_context
-@click.option('-u', '--user', type=str, help='username', prompt=True)
-@click.option('-e', '--email', type=str, help='email address', prompt=True)
-@click.option('-p', '--password', type=str, help='password', prompt=True,
-              hide_input=True, confirmation_prompt=True)
-@click.option('-r', '--role', type=click.Choice(['admin', 'user']),
-              prompt=True, help='role for this user')
-def db_adduser(ctx, user, email, password, role):
-    """Add an user to the database
-    """
-    verbose_echo(ctx, 'GeoHC: add user to database')
-    from GeoHealthCheck.init import App
-    from GeoHealthCheck.models import User, db_commit
-    verbose_echo(ctx, 'GeoHC: get database')
-    DB = App.get_db()
-    verbose_echo(ctx, 'GeoHC: create user')
-    user_to_add = User(user, password, email, role=role)
-    verbose_echo(ctx, 'GeoHC: adding user to database')
-    DB.session.add(user_to_add)
-    db_commit()
-    DB.session.remove()
-    click.echo(f'User {user} is added.')
-
-
-@cli.command()
-@click.pass_context
-@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
-              expose_value=False, help='Confirm dropping tables',
-              prompt='This will drop the tables in the database. Are you '
-                     'sure?')
-def db_drop(ctx):
-    """Drop the current database
-    """
-    verbose_echo(ctx, 'GeoHC: drop db')
-    click.confirm("This will drop the tables in the database. Are you sure?",
-                  abort=True)
-    verbose_echo(ctx, 'User confirmed dropping tables')
-    from GeoHealthCheck.init import App
-    from GeoHealthCheck.models import db_commit
-    verbose_echo(ctx, 'GeoHC: get database')
-    DB = App.get_db()
-    verbose_echo(ctx, 'GeoHC: dropping all tables')
-    DB.drop_all()
-    db_commit()
-    DB.session.remove()
-    click.echo('Database dropped all tables.')
-
-
-@cli.command()
-@click.pass_context
-@click.option('-f', '--file', type=click.Path(), multiple=False, required=True,
-              help='Path to the file to load into the database. MUST be JSON.')
-@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
-              expose_value=False, help='Confirm dropping old content.',
-              prompt='WARNING: all database data will be lost. Proceed?')
-def db_load(ctx, file):
-    """Load JSON into the database
-
-    e.g. test/data/fixtures.json
-    """
-    verbose_echo(ctx, 'GeoHC: load data into db')
-    verbose_echo(ctx, 'User confirmed loading new data and losing old data.')
-    from GeoHealthCheck.init import App
-    from GeoHealthCheck.models import load_data
-    DB = App.get_db()
-    if file[-5:].lower() != '.json':
-        click.echo("File must have '.json' file extension. Aborting import.")
-        ctx.exit()
-    verbose_echo(ctx, 'Start loading file.')
-    load_data(file)
-    verbose_echo(ctx, 'Data loaded!')
-    DB.session.remove()
-    click.echo('Finished loading data.')
-
-
-@cli.command()
-@click.pass_context
-def db_flush(ctx):
-    """Flush runs: remove old data over retention date.
-    """
-    verbose_echo(ctx, 'GeoHC: flush old runs from database.')
-    from GeoHealthCheck.models import flush_runs
-    flush_runs()
-    click.echo('Finished flushing old runs from database.')
-
-
 @cli.command()
 @click.pass_context
 def create_secret_key(ctx):
@@ -341,18 +234,6 @@ def create_hash(ctx, password):
     click.echo(token)
 
 
-@cli.command()
-@click.pass_context
-def db_upgrade(ctx):
-    """Upgrade the database
-    """
-    verbose_echo(ctx, 'GeoHC: upgrade db')
-    from os import system, chdir
-    chdir('GeoHealthCheck')
-    system('python manage.py db upgrade')
-    click.echo('Upgrade DB finished.')
-
-
 @cli.command()
 @click.pass_context
 def create_wsgi(ctx):
@@ -541,12 +422,6 @@ def run_healthchecks(ctx):
     click.echo('GeoHC: Finished running the healthchecks.')
 
 
-@cli.command()
-@click.pass_context
-def db_export(ctx):
-    click.exho('GeoHC: todo- write export.')
-
-
 @cli.command()
 @click.pass_context
 def run_tests(ctx):
@@ -565,5 +440,140 @@ def build_wheel(ctx):
     click.echo('GeoHC: Finished building a wheel.')
 
 
+# Database sub commands
+@cli.group()
+@click.pass_context
+@click.option('--verbose', '-v', is_flag=True, help='Verbose')
+def db(ctx, verbose):
+    """Database subcommands"""
+    ctx.ensure_object(dict)
+    ctx.obj['VERBOSE'] = verbose
+
+
+@db.command()
+@click.pass_context
+def create(ctx):
+    """Create the GHC database
+
+    Note: you still need to add a user
+    """
+    verbose_echo(ctx, 'GeoHC: create db')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
+    DB = App.get_db()
+    verbose_echo(ctx, 'GeoHC: create all tables')
+    DB.create_all()
+    db_commit()
+    DB.session.remove()
+    click.echo('Database is created. Use `geohc db-adduser` to add users to '
+               'the database.')
+
+
+@db.command()
+@click.pass_context
+@click.option('-u', '--user', type=str, help='username', prompt=True)
+@click.option('-e', '--email', type=str, help='email address', prompt=True)
+@click.option('-p', '--password', type=str, help='password', prompt=True,
+              hide_input=True, confirmation_prompt=True)
+@click.option('-r', '--role', type=click.Choice(['admin', 'user']),
+              prompt=True, help='role for this user')
+def adduser(ctx, user, email, password, role):
+    """Add an user to the database
+    """
+    verbose_echo(ctx, 'GeoHC: add user to database')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import User, db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
+    DB = App.get_db()
+    verbose_echo(ctx, 'GeoHC: create user')
+    user_to_add = User(user, password, email, role=role)
+    verbose_echo(ctx, 'GeoHC: adding user to database')
+    DB.session.add(user_to_add)
+    db_commit()
+    DB.session.remove()
+    click.echo(f'User {user} is added.')
+
+
+@db.command()
+@click.pass_context
+@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
+              expose_value=False, help='Confirm dropping tables',
+              prompt='This will drop the tables in the database. Are you '
+                     'sure?')
+def drop(ctx):
+    """Drop the current database
+    """
+    verbose_echo(ctx, 'GeoHC: drop db')
+    click.confirm("This will drop the tables in the database. Are you sure?",
+                  abort=True)
+    verbose_echo(ctx, 'User confirmed dropping tables')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import db_commit
+    verbose_echo(ctx, 'GeoHC: get database')
+    DB = App.get_db()
+    verbose_echo(ctx, 'GeoHC: dropping all tables')
+    DB.drop_all()
+    db_commit()
+    DB.session.remove()
+    click.echo('Database dropped all tables.')
+
+
+@db.command()
+@click.pass_context
+@click.option('-f', '--file', type=click.Path(), multiple=False, required=True,
+              help='Path to the file to load into the database. MUST be JSON.')
+@click.option('-y', '--yes', is_flag=True, callback=abort_if_false,
+              expose_value=False, help='Confirm dropping old content.',
+              prompt='WARNING: all database data will be lost. Proceed?')
+def load(ctx, file):
+    """Load JSON into the database
+
+    e.g. test/data/fixtures.json
+    """
+    verbose_echo(ctx, 'GeoHC: load data into db')
+    verbose_echo(ctx, 'User confirmed loading new data and losing old data.')
+    from GeoHealthCheck.init import App
+    from GeoHealthCheck.models import load_data
+    DB = App.get_db()
+    if file[-5:].lower() != '.json':
+        click.echo("File must have '.json' file extension. Aborting import.")
+        ctx.exit()
+    verbose_echo(ctx, 'Start loading file.')
+    load_data(file)
+    verbose_echo(ctx, 'Data loaded!')
+    DB.session.remove()
+    click.echo('Finished loading data.')
+
+
+@db.command()
+@click.pass_context
+def flush(ctx):
+    """Flush runs: remove old data over retention date.
+    """
+    verbose_echo(ctx, 'GeoHC: flush old runs from database.')
+    from GeoHealthCheck.models import flush_runs
+    flush_runs()
+    click.echo('Finished flushing old runs from database.')
+
+
+@db.command()
+@click.pass_context
+def upgrade(ctx):
+    """Upgrade the database
+    """
+    verbose_echo(ctx, 'GeoHC: upgrade db')
+    from os import system, chdir
+    chdir('GeoHealthCheck')
+    system('python manage.py db upgrade')
+    click.echo('Upgrade DB finished.')
+
+
+@db.command()
+@click.pass_context
+def export(ctx):
+    click.exho('GeoHC: todo- write export.')
+
+
 if __name__ == '__main__':
     cli()
diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index 57b5c901..b1289e69 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -894,7 +894,7 @@ def db_commit():
     if len(sys.argv) > 1:
         if sys.argv[1] == 'create':
             LOGGER.warning('models.py create is deprecated since 0.8.0. Please'
-                          ' use cli: `geohc db-create` and `geohc db-adduser`',
+                          ' use cli: `geohc db create` and `geohc db adduser`',
                           DeprecationWarning)
             print('Creating database objects')
             DB.create_all()
@@ -921,14 +921,14 @@ def db_commit():
 
         elif sys.argv[1] == 'drop':
             LOGGER.warning('models.py drop is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db-drop`', DeprecationWarning)
+                          'use cli: `geohc db drop`', DeprecationWarning)
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
 
         elif sys.argv[1] == 'load':
             LOGGER.warning('models.py load is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db-load`', DeprecationWarning)
+                          'use cli: `geohc db load`', DeprecationWarning)
             print('Load database from JSON file (e.g. tests/fixtures.json)')
             if len(sys.argv) > 2:
                 file_path = sys.argv[2]
@@ -957,7 +957,7 @@ def db_commit():
 
         elif sys.argv[1] == 'flush':
             LOGGER.warning('models.py flush is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db-flush`', DeprecationWarning)
+                          'use cli: `geohc db flush`', DeprecationWarning)
             flush_runs()
 
         DB.session.remove()
diff --git a/README.md b/README.md
index b670d63e..22ed6048 100644
--- a/README.md
+++ b/README.md
@@ -37,10 +37,10 @@ vi instance/config_site.py
 # - GHC_MAP (or use default settings)
 
 # setup database 
-geohc db-create
+geohc db create
 
 # create superuser account interactively
-geohc db-adduser
+geohc db adduser
 
 # start webserver with healthcheck runner daemon inside 
 # (default is 0.0.0.0:8000)
@@ -61,21 +61,21 @@ geohc serve
 # other commands
 #
 # drop database
-geohc db-drop
+geohc db drop
 
 # load data in database (WARN: deletes existing data!)
 # See example data .json files in tests/data
-geohc db-load -f <.json data file> -y
+geohc db load -f <.json data file> -y
 
 # More help on the `geohc` cli command:
 geohc --help
 
 # More help on a specific command
-geohc db-load --help
+geohc db load --help
 
 ```
 
 **Note for developers:** instead of `pip install .`, you might want to install with the *editable*
 option specified: `pip install -e .`
 
-More in the [full GHC documentation](http://docs.geohealthcheck.org/).
\ No newline at end of file
+More in the [full GHC documentation](http://docs.geohealthcheck.org/).
diff --git a/docker/scripts/configure.sh b/docker/scripts/configure.sh
index 71b2c85d..54d33c02 100755
--- a/docker/scripts/configure.sh
+++ b/docker/scripts/configure.sh
@@ -15,8 +15,8 @@ echo "Using DB_TYPE=${DB_TYPE}"
 # Create DB shorthand
 function create_db() {
 	pushd /GeoHealthCheck/
-  geohc db-create
-	geohc db-adduser -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL} -r admin
+  geohc db create
+	geohc db adduser -u ${ADMIN_NAME} -p ${ADMIN_PWD} -e ${ADMIN_EMAIL} -r admin
 	popd
 }
 
diff --git a/docker/scripts/run-web.sh b/docker/scripts/run-web.sh
index 93726305..ca83f70e 100755
--- a/docker/scripts/run-web.sh
+++ b/docker/scripts/run-web.sh
@@ -14,7 +14,7 @@ source /venv/bin/activate .
 # Make sure PYTHONPATH includes GeoHealthCheck
 export PYTHONPATH=/GeoHealthCheck:$PYTHONPATH
 
-geohc db-upgrade
+geohc db upgrade
 
 # SCRIPT_NAME should not have value '/'
 [ "${SCRIPT_NAME}" = '/' ] && export SCRIPT_NAME="" && echo "make SCRIPT_NAME empty from /"
diff --git a/docs/admin.rst b/docs/admin.rst
index 6cf37892..d53ddac3 100644
--- a/docs/admin.rst
+++ b/docs/admin.rst
@@ -16,7 +16,7 @@ acces to the command line interface `geohc`. You can get help from the cli via :
 This will list all available commands. To get help with a specific command, run
 `geohc <<command>> --help`, e.g. ::
 
-    geohc db-adduser --help
+    geohc db adduser --help
 
 This will show you all the (required) options to add a user to the database.
 
@@ -32,7 +32,7 @@ To create the database execute the following:
 
 Open a command line, (if needed activate your virtualenv), and do ::
 
-    geohc db-create
+    geohc db create
 
 add user
 ........
@@ -41,9 +41,9 @@ To add a new user to the database:
 
 Open a command line, (if needed activate your virtualenv), and do ::
 
-    geohc db-adduser
+    geohc db adduser
     # or
-    geohc db-adduser -u username -p password -e email@address.com -r admin
+    geohc db adduser -u username -p password -e email@address.com -r admin
 
 drop db
 .......
@@ -52,7 +52,7 @@ To delete the database execute the following, however you will loose all your in
 
 Open a command line, (if needed activate your virtualenv), and do ::
 
-    geohc db-drop
+    geohc db drop
 
 Note: you need to create a Database again before you can start GHC again.
 
@@ -61,7 +61,7 @@ load data
 
 To load a JSON data file, do (WARN: deletes existing data!) ::
 
-    geohc db-load --file my_data.json
+    geohc db load --file my_data.json
 
 You will be asked for confirmation. You can also specify the `-y` or `--yes`
 flag to indicate you are sure and to skip the confirmation question.
@@ -73,14 +73,14 @@ flush
 
 To flush the old records from the system, you can flush the records ::
 
-    geohc db-flush
+    geohc db flush
 
 upgrade
 .......
 
 To upgrade the database structure (might be necessary with a new release of GeoHealthCheck) ::
 
-    geohc db-upgrade
+    geohc db upgrade
 
 export data
 ...........

From 14df3f03e700e9f7f6eb4359bfd56dee1bfa7eee Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 21:44:42 +0100
Subject: [PATCH 45/49] Fix flake8

---
 GeoHealthCheck/models.py | 13 +++++++------
 1 file changed, 7 insertions(+), 6 deletions(-)

diff --git a/GeoHealthCheck/models.py b/GeoHealthCheck/models.py
index b1289e69..33f65e51 100644
--- a/GeoHealthCheck/models.py
+++ b/GeoHealthCheck/models.py
@@ -894,8 +894,9 @@ def db_commit():
     if len(sys.argv) > 1:
         if sys.argv[1] == 'create':
             LOGGER.warning('models.py create is deprecated since 0.8.0. Please'
-                          ' use cli: `geohc db create` and `geohc db adduser`',
-                          DeprecationWarning)
+                           ' use cli: `geohc db create` and '
+                           '`geohc db adduser`',
+                           DeprecationWarning)
             print('Creating database objects')
             DB.create_all()
 
@@ -921,14 +922,14 @@ def db_commit():
 
         elif sys.argv[1] == 'drop':
             LOGGER.warning('models.py drop is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db drop`', DeprecationWarning)
+                           'use cli: `geohc db drop`', DeprecationWarning)
             print('Dropping database objects')
             DB.drop_all()
             db_commit()
 
         elif sys.argv[1] == 'load':
             LOGGER.warning('models.py load is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db load`', DeprecationWarning)
+                           'use cli: `geohc db load`', DeprecationWarning)
             print('Load database from JSON file (e.g. tests/fixtures.json)')
             if len(sys.argv) > 2:
                 file_path = sys.argv[2]
@@ -953,11 +954,11 @@ def db_commit():
 
         elif sys.argv[1] == 'run':
             LOGGER.warning('models.py run is deprecated. Please use `python '
-                          'healthcheck.py`', DeprecationWarning)
+                           'healthcheck.py`', DeprecationWarning)
 
         elif sys.argv[1] == 'flush':
             LOGGER.warning('models.py flush is deprecated since 0.8.0. Please '
-                          'use cli: `geohc db flush`', DeprecationWarning)
+                           'use cli: `geohc db flush`', DeprecationWarning)
             flush_runs()
 
         DB.session.remove()

From f9afdfe0f014454813ae8f101fd5950f0bce8558 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Mon, 13 Jan 2020 21:54:05 +0100
Subject: [PATCH 46/49] Fix version number in docs

---
 docs/conf.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/docs/conf.py b/docs/conf.py
index b51008ec..dd91ba54 100644
--- a/docs/conf.py
+++ b/docs/conf.py
@@ -14,6 +14,7 @@
 
 import sys
 import os
+import re
 
 # indicate Sphinx is building (to replace @Config decorators)
 os.environ['SPHINX_BUILD'] = '1'
@@ -55,8 +56,10 @@
 # built documents.
 #
 # The short X.Y version.
-with open('../VERSION') as ff:
-    version = ff.read().strip()
+with open('../GeoHealthCheck/__init__.py') as ff:
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              ff.read(), re.M)
+    version = version_match.group(1)
 # The full version, including alpha/beta/rc tags.
 release = version
 

From 57383c063d255a1182a57dcc91c81403cedc3f44 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 15 Jan 2020 09:57:07 +0100
Subject: [PATCH 47/49] Remove references to paver

---
 GeoHealthCheck/cli.py               |   2 -
 GeoHealthCheck/migrations/README.md |   4 +-
 README.md                           |   2 +-
 docker/README.md                    |   2 +-
 docs/config.rst                     |   4 +-
 docs/install.rst                    |  13 +-
 pavement.py                         | 352 ----------------------------
 requirements-dev.txt                |   1 -
 requirements.txt                    |   1 -
 9 files changed, 16 insertions(+), 365 deletions(-)
 delete mode 100644 pavement.py

diff --git a/GeoHealthCheck/cli.py b/GeoHealthCheck/cli.py
index 35c5070b..9bd0ed40 100644
--- a/GeoHealthCheck/cli.py
+++ b/GeoHealthCheck/cli.py
@@ -72,8 +72,6 @@ def version(ctx):
               'install the instance data and help files.')
 def create_instance(ctx, basepath):
     """Create an instance of GeoHealthCheck App
-
-    This command is a copy of `paver setup`
     """
     verbose_echo(ctx, 'GeoHC: create instance')
     import glob
diff --git a/GeoHealthCheck/migrations/README.md b/GeoHealthCheck/migrations/README.md
index 81db6740..5f0d6527 100755
--- a/GeoHealthCheck/migrations/README.md
+++ b/GeoHealthCheck/migrations/README.md
@@ -6,7 +6,7 @@ and Flask-Script.
 Users should be able to upgrade existing installs via: 
 
 	# In top dir of installation
-	paver upgrade
+	geohc db upgrade
 	
 The `versions` dir contains the various upgrades. These were
 initially created using the Alembic `autogenerate` facility
@@ -39,7 +39,7 @@ Subsequently the upgrade can be performed using:
 
 	python manage.py db upgrade
 	# or the equivalent (for users) 
-	paver upgrade
+	geohc db upgrade
 
 ## Revisions
 
diff --git a/README.md b/README.md
index 22ed6048..0719b947 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ geohc create-secret-key
 # setup local configuration (overrides GeoHealthCheck/config_main.py)
 vi instance/config_site.py
 # edit at least secret key:
-# - SECRET_KEY  # copy/paste result string from paver create_secret_key
+# - SECRET_KEY  # copy/paste result string from geohc create-secret-key
 
 # Optional: edit other settings or leave defaults
 # - SQLALCHEMY_DATABASE_URI
diff --git a/docker/README.md b/docker/README.md
index d188cae3..8c2ddbd4 100644
--- a/docker/README.md
+++ b/docker/README.md
@@ -244,5 +244,5 @@ geohc db-upgrade
 etc
 ```
 
-NB: database upgrades (`paver upgrade`)
+NB: database upgrades (`geohc db upgrade`)
 are always performed automatically when running GHC via Docker.
diff --git a/docs/config.rst b/docs/config.rst
index 5716f565..c4395ec6 100644
--- a/docs/config.rst
+++ b/docs/config.rst
@@ -14,7 +14,7 @@ a configuration file in the environment settings that will override settings in
 The configuration options are:
 
 - **SQLALCHEMY_DATABASE_URI**: the database configuration.  See the SQLAlchemy documentation for more info
-- **SECRET_KEY**: secret key to set when enabling authentication. Use the output of ``paver create_secret_key`` to set this value
+- **SECRET_KEY**: secret key to set when enabling authentication. Use the output of ``geohc create-secret-key`` to set this value
 - **GHC_RETENTION_DAYS**: the number of days to keep Run history
 - **GHC_PROBE_HTTP_TIMEOUT_SECS**: stop waiting for the first byte of a Probe response after the given number of seconds
 - **GHC_MINIMAL_RUN_FREQUENCY_MINS**: minimal run frequency for Resource that can be set in web UI
@@ -106,7 +106,7 @@ This is the preferred mode as each `Resource` can have its own schedule (configu
 via Dashboard) and `cron` has dependencies on local environment.
 Later versions may phase out cron-scheduling completely.
 
-The **GHC Runner** can be run via the command `paver runner_daemon` or can run internally within
+The **GHC Runner** can be run via the command `geohc runner-daemon` or can run internally within
 the **GHC Webapp** by setting the config variable **GHC_RUNNER_IN_WEBAPP** to `True` (the default).
 NB it is still possible to run GHC as in the pre-v0.5.0 mode using cron-jobs: just run the
 **GHC Webapp** with **GHC_RUNNER_IN_WEBAPP** set to `False` and have your cron-jobs scheduled.
diff --git a/docs/install.rst b/docs/install.rst
index a034413c..d2c85615 100644
--- a/docs/install.rst
+++ b/docs/install.rst
@@ -67,7 +67,7 @@ Install
   vi instance/config_site.py
   # edit:
   # - SQLALCHEMY_DATABASE_URI
-  # - SECRET_KEY  # from paver create_secret_key
+  # - SECRET_KEY  # from geohc create-secret-key
   # - GHC_RETENTION_DAYS
   # - GHC_SELF_REGISTER
   # - GHC_NOTIFICATIONS
@@ -118,8 +118,8 @@ An existing GHC database installation can be upgraded with:
 Notes:
 
 * **Always backup your database first!!**
-* make sure Flask-Migrate is installed (see requirements.txt), else:  `pip install Flask-Migrate==2.5.2`, but best is to run `paver setup` also for other dependencies
-* upgrading is "smart": you can always run `paver upgrade`, it has no effect when DB is already up to date
+* make sure Flask-Migrate is installed (see requirements.txt), else:  `pip install Flask-Migrate==2.5.2`, but best is to run `geohc create-instance` also for other dependencies
+* upgrading is "smart": you can always run `geohc db upgrade`, it has no effect when DB is already up to date
 * when upgrading from earlier versions without Plugin-support:
 
   - adapt your `config_site.py` to Plugin settings from `config_main.py`
@@ -144,6 +144,13 @@ the `paver upgrade` command. Also password recovery was changed: a user can crea
 a unique, personal URL that GHC sends by email. This requires a working email configuration and a reachable
 `SITE_URL` config value. See :ref:`admin_user_mgt` for solving password problems.
 
+Upgrade notes v0.8.0
+....................
+
+In previous version GHC used `paver` to control the setup and administration of
+the application. With this version GHC switched `click` and the cli commands
+changed to `geohc`. Type `geohc --help` to get more information.
+
 
 Running
 -------
diff --git a/pavement.py b/pavement.py
deleted file mode 100644
index ecd35738..00000000
--- a/pavement.py
+++ /dev/null
@@ -1,352 +0,0 @@
-# =================================================================
-#
-# Authors: Tom Kralidis <tomkralidis@gmail.com>
-#
-# Copyright (c) 2014 Tom Kralidis
-#
-# Permission is hereby granted, free of charge, to any person
-# obtaining a copy of this software and associated documentation
-# files (the "Software"), to deal in the Software without
-# restriction, including without limitation the rights to use,
-# copy, modify, merge, publish, distribute, sublicense, and/or sell
-# copies of the Software, and to permit persons to whom the
-# Software is furnished to do so, subject to the following
-# conditions:
-#
-# The above copyright notice and this permission notice shall be
-# included in all copies or substantial portions of the Software.
-#
-# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-# EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
-# OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-# NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
-# HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
-# WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
-# FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
-# OTHER DEALINGS IN THE SOFTWARE.
-#
-# =================================================================
-
-import codecs
-import glob
-import os
-import shutil
-import tempfile
-from io import BytesIO
-from urllib.request import urlopen
-import zipfile
-
-from paver.easy import (Bunch, call_task, cmdopts, info, options,
-                        path, pushd, sh, task)
-
-BASEDIR = os.path.abspath(os.path.dirname(__file__))
-
-options(
-    base=Bunch(
-        home=path(BASEDIR),
-        docs=path('%s/docs' % BASEDIR),
-        instance=path('%s/instance' % BASEDIR),
-        pot=path('%s/GeoHealthCheck/translations/en/LC_MESSAGES/messages.po' %
-                 BASEDIR),
-        static_docs=path('%s/GeoHealthCheck/static/docs' % BASEDIR),
-        static_lib=path('%s/GeoHealthCheck/static/lib' % BASEDIR),
-        tmp=path(tempfile.mkdtemp()),
-        translations=path('%s/GeoHealthCheck/translations' % BASEDIR)
-    ),
-)
-
-
-@task
-def setup():
-    """setup plugin dependencies"""
-
-    config_file = options.base.home / 'GeoHealthCheck/config_main.py'
-    config_site = options.base.instance / 'config_site.py'
-
-    # setup dirs
-    if not os.path.exists(options.base.static_lib):
-        options.base.static_lib.mkdir()
-    if not os.path.exists(options.base.instance):
-        options.base.instance.mkdir()
-        data_dir = options.base.instance / 'data'
-        data_dir.mkdir()
-        # data_dir.chmod(0777) gives failure on Python 2.7 Paver 1.2.1
-        os.chmod(path(data_dir), 0o777)
-        # setup config
-        config_file.copy(config_site)
-
-    # setup deps
-    sh('pip install -r requirements.txt')
-
-    skin = 'http://github.com/BlackrockDigital/startbootstrap-sb-admin-2/archive/v3.3.7+1.zip'  # noqa
-
-    skin_dirs = ['dist', 'vendor']
-    need_to_fetch = False
-
-    for skin_dir in skin_dirs:
-        skin_dir_path = os.sep.join(
-            ['startbootstrap-sb-admin-2-3.3.7-1', skin_dir])
-        if not os.path.exists(skin_dir_path):
-            need_to_fetch = True
-
-    if need_to_fetch:
-        zipstr = BytesIO(urlopen(skin).read())
-        zipfile_obj = zipfile.ZipFile(zipstr)
-        zipfile_obj.extractall(options.base.static_lib)
-
-        for zf_mem in skin_dirs:
-            src_loc = path(options.base.static_lib /
-                           'startbootstrap-sb-admin-2-3.3.7-1' / zf_mem)
-            dest_loc = path(options.base.static_lib / zf_mem)
-            if not os.path.exists(dest_loc):
-                src_loc.move(dest_loc)
-            else:
-                info('directory already exists.  Skipping')
-
-        shutil.rmtree(path(options.base.static_lib /
-                           'startbootstrap-sb-admin-2-3.3.7-1'))
-
-    # install sparklines to static/site/js
-    with open(path(options.base.static_lib / 'jspark.js'), 'w') as f:
-        content = urlopen('http://ejohn.org/files/jspark.js').read().decode()
-        content.replace('red', 'green')
-        f.write(content)
-
-    # install bootstrap-tagsinput to static/lib
-    info('Getting select2')
-    select2 = 'https://github.com/select2/select2/archive/4.0.3.zip'
-
-    zipstr = BytesIO(urlopen(select2).read())
-    zipfile_obj = zipfile.ZipFile(zipstr)
-    zipfile_obj.extractall(options.base.static_lib)
-    dirname = glob.glob(options.base.static_lib / 'select2-*')[0]
-    dstdir = ''.join(dirname.rsplit('-', 1)[:-1])
-    try:
-        os.rename(dirname, dstdir)
-    except OSError:
-        shutil.rmtree(dstdir)
-        os.rename(dirname, dstdir)
-
-    # install leafletjs to static/lib
-    info('Getting leaflet')
-    leafletjs = 'http://cdn.leafletjs.com/downloads/leaflet-0.7.5.zip'
-
-    zipstr = BytesIO(urlopen(leafletjs).read())
-    zipfile_obj = zipfile.ZipFile(zipstr)
-    zipfile_obj.extractall(options.base.static_lib / 'leaflet')
-
-    # install html5shiv to static/lib
-    with open(path(options.base.static_lib / 'html5shiv.min.js'), 'w') as f:
-        url = 'http://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js'
-        content = urlopen(url).read().decode()
-        f.write(content)
-
-    # install respond to static/lib
-    with open(path(options.base.static_lib / 'respond.min.js'), 'w') as f:
-        url = 'http://oss.maxcdn.com/respond/1.4.2/respond.min.js'
-        content = urlopen(url).read().decode()
-        f.write(content)
-
-    # build i18n .mo files
-    call_task('compile_translations')
-
-    # build local docs
-    call_task('refresh_docs')
-
-    # message user
-    info('GeoHealthCheck is now built. Edit settings in %s' % config_site)
-    info('before deploying the application. Alternatively, you can start a')
-    info('development instance with "python GeoHealthCheck/app.py"')
-
-
-@task
-@cmdopts([
-    ('email=', 'e', 'email'),
-    ('username=', 'u', 'username'),
-    ('password=', 'p', 'password')
-])
-def create(options):
-    """create database objects and superuser account"""
-    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use '
-         'cli: `geohc db-create` and `geohc db-adduser`')
-    args = ''
-    username = options.get('username', None)
-    password = options.get('password', None)
-    email = options.get('email', None)
-    info(username)
-    if all([username, password, email]):
-        args = '%s %s %s' % (username, password, email)
-    sh('python %s create %s' % (path('GeoHealthCheck/models.py'), args))
-
-
-@task
-def create_secret_key():
-    """create secret key for SECRET_KEY in instance/config_site.py"""
-    info('Warning!: create_secret_key is deprecated since 0.8.0. Please use '
-         'cli: `geohc create-secret-key`')
-    info('Secret key: \'%s\'' % codecs.encode(os.urandom(24), 'hex').decode())
-    info('Copy/paste this key to set the SECRET_KEY')
-    info('value in instance/config_site.py')
-
-
-@task
-@cmdopts([
-    ('password=', 'p', 'password')
-])
-def create_hash(options):
-    """
-    Create hash, mainly for passwords.
-    Usage: paver create_hash -p mypass
-    """
-    info('Warning!: create_hash is deprecated since 0.8.0. Please use cli: '
-         '`geohc create-hash`')
-    import sys
-    sys.path.insert(0, BASEDIR + '/GeoHealthCheck')
-    from util import create_hash
-    token = create_hash(options.get('password', None))
-    info('Copy/paste the entire token below for example to set password')
-    info(token)
-
-
-@task
-def upgrade():
-    """upgrade database if changed; be sure to backup first!"""
-    info('Warning!: upgrade is deprecated since 0.8.0. Please use cli: '
-         '`geohc db-upgrade`')
-    info('Upgrading database...')
-    with pushd(path('%s/GeoHealthCheck' % BASEDIR)):
-        sh('python manage.py db upgrade')
-
-
-@task
-def create_wsgi():
-    """create WSGI wrapper and Apache2 configuration"""
-    info('Warning!: create_wsgi is deprecated since 0.8.0. Please use cli: '
-         '`geohc create-wsgi`')
-    wsgi_script = '%s%sGeoHealthCheck.wsgi' % (options.base.instance, os.sep)
-    with open(wsgi_script, 'w') as ff:
-        ff.write('import sys\n')
-        ff.write('sys.path.insert(0, \'%s\')\n' % BASEDIR)
-        ff.write('from GeoHealthCheck.app import APP as application')
-
-    wsgi_conf = '%s%sGeoHealthCheck.conf' % (options.base.instance, os.sep)
-    with open(wsgi_conf, 'w') as ff:
-        ff.write('WSGIScriptAlias / %s%sGeoHealthCheck.wsgi\n' %
-                 (options.base.instance, os.sep))
-        ff.write('<Directory %s%s>\n' % (BASEDIR, os.sep))
-        ff.write('Order deny,allow\n')
-        ff.write('Allow from all\n')
-        ff.write('</Directory>')
-
-
-@task
-def refresh_docs():
-    """Build sphinx docs from scratch"""
-    info('Warning!: refresh_docs is deprecated since 0.8.0. Please use cli: '
-         '`geohc refresh-docs`')
-
-    make = sphinx_make()
-
-    if os.path.exists(options.base.static_docs):
-        shutil.rmtree(options.base.static_docs)
-
-    with pushd(options.base.docs):
-        sh('%s clean' % make)
-        sh('%s html' % make)
-        source_html_dir = path('%s/docs/_build/html' % BASEDIR)
-        source_html_dir.copytree(options.base.static_docs)
-
-
-@task
-def clean():
-    """clean environment"""
-    info('Warning!: clean is deprecated since 0.8.0. Please use cli: '
-         '`geohc clean`')
-
-    if os.path.exists(options.base.static_lib):
-        shutil.rmtree(options.base.static_lib)
-    if os.path.exists(options.base.tmp):
-        shutil.rmtree(options.base.tmp)
-    if os.path.exists(options.base.static_docs):
-        shutil.rmtree(options.base.static_docs)
-
-
-@task
-def extract_translations():
-    """extract translations wrapped in _() or gettext()"""
-
-    info('Warning!: extract_translations is deprecated since 0.8.0. Please use'
-         ' cli: `geohc lang-extract-translations`')
-    pot_dir = path('GeoHealthCheck/translations/en/LC_MESSAGES')
-    if not os.path.exists(pot_dir):
-        pot_dir.makedirs()
-
-    sh('pybabel extract -F babel.cfg -o %s GeoHealthCheck' % options.base.pot)
-
-
-@task
-@cmdopts([
-    ('lang=', 'l', '2-letter language code'),
-])
-def add_language_catalogue(options):
-    """adds new language profile"""
-
-    info('Warning!: add_language_catalogue is deprecated since 0.8.0. Please '
-         'use cli: `geohc lang-add-language-catalogue`')
-    lang = options.get('lang', None)
-
-    if lang is None:
-        raise RuntimeError('missing lang argument')
-
-    sh('pybabel init -i %s -d %s -l %s' % (
-       options.base.pot, options.base.translations, lang))
-
-
-@task
-def compile_translations():
-    """build .mo files"""
-    info('Warning!: compile_translations is deprecated since 0.8.0. Please use'
-         ' cli: `geohc lang-compile-translations`')
-    sh('pybabel compile -d %s' % options.base.translations)
-
-
-@task
-def update_translations():
-    """update language strings"""
-    info('Warning!: update_translations is deprecated since 0.8.0. Please use '
-         'cli: `geohc lang-update-translations`')
-    call_task('extract_translations')
-    sh('pybabel update -i %s -d %s' % (
-        options.base.pot, options.base.translations))
-
-
-@task
-def runner_daemon():
-    """Run the HealthCheck runner daemon scheduler"""
-    info('Warning!: runner_daemon is deprecated since 0.8.0. Please use cli: '
-         '`geohc runner-daemon`')
-    sh('python %s' % path('GeoHealthCheck/scheduler.py'))
-
-
-@task
-def run_healthchecks():
-    """Run all HealthChecks directly"""
-    info('Warning!: run_healthchecks is deprecated since 0.8.0. Please use '
-         'cli: `geohc run-healthchecks`')
-    sh('python %s' % path('GeoHealthCheck/healthcheck.py'))
-
-
-def sphinx_make():
-    """return what command Sphinx is using for make"""
-
-    if os.name == 'nt':
-        return 'make.bat'
-    return 'make'
-
-
-@task
-def run_tests():
-    """Run all tests"""
-    info('Warning!: run_tests is deprecated since 0.8.0. Please use cli: '
-         '`geohc run-tests`')
-    sh('python %s' % path('tests/run_tests.py'))
diff --git a/requirements-dev.txt b/requirements-dev.txt
index 095bdec7..d4d8edf7 100644
--- a/requirements-dev.txt
+++ b/requirements-dev.txt
@@ -1,5 +1,4 @@
 click==7.0
 flake8
-Paver==1.3.4
 pylint
 wheel==0.33.6
diff --git a/requirements.txt b/requirements.txt
index 7736133f..a937e4ce 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -15,4 +15,3 @@ requests>=2.20.0
 WTForms==2.2.1
 APScheduler==3.6.1
 passlib==1.7.1
-paver==1.3.4

From 9675b12f579fc7b7e63327eda5264415af7a7056 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Tue, 21 Jan 2020 19:18:24 +0100
Subject: [PATCH 48/49] Fix paths in setup script

---
 GeoHealthCheck/cli.py | 12 +++++++-----
 1 file changed, 7 insertions(+), 5 deletions(-)

diff --git a/GeoHealthCheck/cli.py b/GeoHealthCheck/cli.py
index 9bd0ed40..db1b3919 100644
--- a/GeoHealthCheck/cli.py
+++ b/GeoHealthCheck/cli.py
@@ -92,12 +92,14 @@ def create_instance(ctx, basepath):
     # setup dirs
     if not os.path.exists(os.path.normpath('%s/static/lib' % basedir)):
         os.mkdir(os.path.normpath('%s/static/lib' % basedir))
-    if not os.path.exists(os.path.normpath('%s/instance' % basedir)):
+    if not os.path.exists(os.path.normpath('%s/instance' % basedir_parent)):
         os.mkdir(os.path.normpath('%s/instance' % basedir_parent))
-        data_dir = os.path.normpath('%s/instance/data' % basedir_parent)
-        os.mkdir(data_dir, mode=0o777)
         # setup config
         shutil.copy(config_file, config_site)
+    if not os.path.exists(os.path.normpath('%s/instance/data'
+                          % basedir_parent)):
+        data_dir = os.path.normpath('%s/instance/data' % basedir_parent)
+        os.mkdir(data_dir, mode=0o777)
 
     skin = 'http://github.com/BlackrockDigital/startbootstrap-sb-admin-2/archive/v3.3.7+1.zip'  # noqa
 
@@ -181,8 +183,8 @@ def create_instance(ctx, basepath):
     update_documentation(ctx, basepath=basedir_parent)
 
     # message user
-    click.echo('GeoHealthCheck is now built. Edit settings in %s'
-               % config_site)
+    click.echo('GeoHealthCheck is now built. Edit settings like the secret-key'
+               ' and the database connection string in %s' % config_site)
     click.echo('before deploying the application. Alternatively, you can')
     click.echo('start a development instance with ')
     click.echo('"python GeoHealthCheck/app.py"')

From d52e6a9315b49a5a47fdd476c68c69aaecd5adb5 Mon Sep 17 00:00:00 2001
From: Rob van Loon <borrob@me.com>
Date: Wed, 22 Jan 2020 16:55:02 +0100
Subject: [PATCH 49/49] Fix docker daemon

---
 GeoHealthCheck/cli.py        | 12 +++++++++---
 docker/scripts/run-runner.sh |  3 ---
 2 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/GeoHealthCheck/cli.py b/GeoHealthCheck/cli.py
index db1b3919..1d26a97e 100644
--- a/GeoHealthCheck/cli.py
+++ b/GeoHealthCheck/cli.py
@@ -409,7 +409,9 @@ def runner_daemon(ctx):
     verbose_echo(ctx, 'GeoHC: going to run the scheduler daemon. Press ctrl-c '
                       'to stop.')
     import os
-    os.system('python %s' % os.path.normpath('GeoHealthCheck/scheduler.py'))
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    scheduler = basedir + '/scheduler.py'
+    os.system('python %s' % os.path.normpath(scheduler))
 
 
 @cli.command()
@@ -418,7 +420,9 @@ def run_healthchecks(ctx):
     """Run all HealthChecks directly"""
     verbose_echo(ctx, 'GeoHC: going to run all the healthchecks once.')
     import os
-    os.system('python %s' % os.path.normpath('GeoHealthCheck/healthcheck.py'))
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    healtcheck = basedir + '/healtcheck.py'
+    os.system('python %s' % os.path.normpath(healtcheck))
     click.echo('GeoHC: Finished running the healthchecks.')
 
 
@@ -427,7 +431,9 @@ def run_healthchecks(ctx):
 def run_tests(ctx):
     """Run all tests"""
     import os
-    os.system('python %s' % os.path.normpath('tests/run_tests.py'))
+    basedir = os.path.abspath(os.path.dirname(__file__))
+    tests = basedir + '/run_tests.py'
+    os.system('python %s' % os.path.normpath(tests))
 
 
 @cli.command()
diff --git a/docker/scripts/run-runner.sh b/docker/scripts/run-runner.sh
index d8c3e24f..f34ee4fe 100755
--- a/docker/scripts/run-runner.sh
+++ b/docker/scripts/run-runner.sh
@@ -12,9 +12,6 @@ echo "START /run-runner.sh"
 # that schedules healthcheck jobs
 source /venv/bin/activate .
 
-# Make sure PYTHONPATH includes GeoHealthCheck
-export PYTHONPATH=/GeoHealthCheck/GeoHealthCheck:$PYTHONPATH
-
 geohc runner-daemon
 
 echo "END /run-runner.sh"