Merge pull request #466 from MiraGeoscience/release/0.8.0

GEOPY-1285 set version to 0.8.0

Author: andrewg-mira

.github/workflows/issue_to_jira.yml

@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "geoh5py"}]}'
     - name: Post JIRA link
-      uses: peter-evans/create-or-update-comment@v2
+      uses: peter-evans/create-or-update-comment@v3
       with:
         # The number of the issue or pull request in which to create a comment.
         issue-number: ${{ github.event.issue.number }}

.github/workflows/pytest-windows.yml

@@ -65,7 +65,7 @@ jobs:
       - name: Install dependencies
         run: poetry install -vvv
       - name: pytest
-        run: poetry run pytest --cov-report=xml
+        run: poetry run pytest --cov --cov-report=xml
       - name: Codecov
         if: ${{ success() && matrix.python_ver == '3.10' }}
         uses: codecov/codecov-action@v3

.lift.toml

@@ -0,0 +1,6 @@
+ignoreFiles = """
+    tests/
+    docs/
+    examples/
+    devtools/
+"""

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
+    rev: 23.7.0
     hooks:
     -   id: black
         types: [text]
@@ -22,27 +22,28 @@ repos:
         additional_dependencies: [tomli] # to read config from pyproject.toml
         types: [text]
         types_or: [python, pyi]
+        exclude: geoh5py/objects/__init__\.py
 -   repo: https://github.com/humitos/mirrors-autoflake
     rev: v1.1
     hooks:
     -   id: autoflake
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/PyCQA/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
     -   id: flake8
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.4.0
+    rev: v3.10.1
     hooks:
     -   id: pyupgrade
         args: [--py37-plus]
         types: [text]
         types_or: [python, pyi]
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.3.0
+    rev: v1.5.1
     hooks:
     -   id: mypy
         additional_dependencies: [
@@ -51,6 +52,12 @@ repos:
 #            'numpy>=1.23.5,<1.24.0'
         ]
         exclude: (geoh5py/interfaces/__init__\.py|geoh5py/handlers/__init__\.py|geoh5py/interfaces|geoh5py/handlers|tests)
+-   repo: https://github.com/codingjoe/relint
+    rev: 3.1.0
+    hooks:
+    -   id: relint
+        args: [-W]  # to fail on warnings
+        exclude: ^setup.py$
 -   repo: local
     hooks:
     -   id: pylint
@@ -69,7 +76,7 @@ repos:
         types_or: [python, pyi]
         exclude: ^(devtools/|docs/|setup.py)
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
+    rev: v2.2.5
     hooks:
     -   id: codespell
         exclude: (\.ipynb$|^\.github/workflows/issue_to_jira.yml$)

.readthedocs.yml

@@ -0,0 +1,19 @@
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "mambaforge-22.9"
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+conda:
+  environment: docs/environment.yml
+
+python:
+  install:
+    - method: pip
+      path: .

.relint.yml

@@ -0,0 +1,10 @@
+- name: No import os.path
+  pattern: 'from os import\b.*\bpath\b'
+  hint: Use from pathlib import Path
+  filePattern: .*\.pyi?
+  error: false
+- name: No os.path
+  pattern: '\bos\.path\b'
+  hint: Use pathlib.Path
+  filePattern: .*\.pyi?
+  error: false

README.rst

@@ -150,4 +150,13 @@ Third Party Software notices and/or additional terms and conditions are located
 
 Copyright
 ^^^^^^^^^
-Copyright (c) 2023 Mira Geoscience Ltd.
+Copyright (c) 2024 Mira Geoscience Ltd.
+
+
+Citing geoh5py
+^^^^^^^^^^^^^^
+
+If you use **geoh5py** in your research, please cite it as follows:
+
+.. image:: https://zenodo.org/badge/207860560.svg
+   :target: https://zenodo.org/badge/latestdoi/207860560

devtools/publish.py

@@ -1,26 +1,26 @@
 import os
 import shutil
+from pathlib import Path
 
 
 def copyImages():
     # get relevant directories
-    cwd = os.getcwd()
-    contentdir = cwd + "/content"
-    buildimagesdir = cwd + "/_build/html/_images"
+    cwd = Path()
+    contentdir = cwd / "content"
+    buildimagesdir = cwd / "_build" / "html" / "_images"
 
     # check if images directory exists
-    if not os.path.isdir(buildimagesdir):
-        os.mkdir(buildimagesdir)
+    buildimagesdir.mkdir(exist_ok=True)
 
     # images that have been copied
     imnames = os.listdir(buildimagesdir)
 
     # search for images that have been missed
-    for root, dirList, fileList in os.walk(contentdir):
+    for root, dirList, fileList in os.walk(str(contentdir)):
         if root.endswith("images"):
             for filename in fileList:
                 if filename not in imnames:
-                    shutil.copy(os.path.join(root, filename), buildimagesdir)
+                    shutil.copy(Path(root) / filename, buildimagesdir)
     return
 
 

docs/_ext/Add2Build.py

@@ -2,9 +2,9 @@
 
 import datetime
 import json
-import os
+from pathlib import Path
 
-fName = os.path.realpath(__file__)
+fName = Path(__file__).resolve()
 # info_list = ['title', 'date', 'author', 'url', 'pdf', 'jupyter']
 pdf_root = "https://storage.googleapis.com/simpeg/eosc350lectures/"
 jupyter_root = "http://mybinder.org/repo/ubcgif/gpgLabs/notebooks/"
@@ -31,8 +31,8 @@ def make_lectures_page(fpath=None, fout=None):
     if fout is None:
         fout = lecture_path + "lectures.rst"
 
-    fpath = os.path.sep.join(fName.split(os.path.sep)[:-2] + [fpath])
-    fout = os.path.sep.join(fName.split(os.path.sep)[:-2] + [fout])
+    fpath = Path(fName).parents(2) / fpath
+    fout = Path(fName).parents(2) / fout
 
     fpath = open(fpath)  # file to write to
     lectures = json.load(fpath)  # lecture json
@@ -61,7 +61,7 @@ def make_lectures_page(fpath=None, fout=None):
         date = datetime.date(year=date[0], month=date[1], day=date[2])
 
         if "pdf" in lecture.keys():
-            pdf_name = lecture["pdf"].split(".")[0].split(os.path.sep)[-1]
+            pdf_name = Path(lecture["pdf"]).stem
             if "_" in pdf_name:
                 pdf_name = " ".join(pdf_name.split("_")[1:])
             lecture_slides = """

docs/_ext/autodoc.py

@@ -5,7 +5,7 @@
 Loosely based on https://github.com/astropy/astropy/pull/347
 """
 
-import os
+from pathlib import Path
 import warnings
 
 __licence__ = "BSD (3 clause)"
@@ -37,9 +37,9 @@ def html_page_context(app, pagename, templatename, context, doctree):
         warnings.warn("edit_on_github_project not specified")
         return
 
-    path = os.path.relpath(doctree.get("source"), app.builder.srcdir)
-    show_url = get_github_url(app, "blob", path)
-    edit_url = get_github_url(app, "edit", path)
+    path = Path(doctree.get("source")).relative(Path(app.builder.srcdir))
+    show_url = get_github_url(app, "blob", str(path))
+    edit_url = get_github_url(app, "edit", str(path))
 
     # context['show_on_github_url'] = show_url
     context["edit_on_github_url"] = edit_url

docs/_ext/edit_on_github.py

@@ -22,9 +22,9 @@
 """
 
 import json
-import os
 import sys
 import zipfile
+from pathlib import Path
 
 import StringIO
 import urllib2
@@ -45,7 +45,7 @@ def get_gae_versions():
 
 
 def _version_tuple(v):
-    version_string = os.path.splitext(v["name"])[0].rpartition("_")[2]
+    version_string = Path(v["name"]).stem.rpartition("_")[2]
     return tuple(int(x) for x in version_string.split("."))
 
 
@@ -61,11 +61,10 @@ def main(argv):
     if len(argv) > 2:
         print("Usage: {} [<destination_dir>]".format(argv[0]))
         return 1
-    dest_dir = argv[1] if len(argv) > 1 else "."
-    if not os.path.exists(dest_dir):
-        os.makedirs(dest_dir)
+    dest_dir = Path(argv[1]) if len(argv) > 1 else Path()
+    dest_dir.mkdir(exist_ok=True)
 
-    if os.path.exists(os.path.join(dest_dir, "google_appengine")):
+    if (dest_dir / "google_appengine").exists():
         print(f"GAE SDK already installed at {dest_dir}, exiting.")
         return 0
 

docs/_ext/fetch_gae_sdk.py

@@ -15,15 +15,15 @@
 import os
 import sys
 
-# import geoh5py
+from pathlib import Path
 
-sys.path.append(os.path.abspath("./_ext"))
-sys.path.append(os.path.abspath(".."))
+sys.path.append(str(Path("_ext").resolve()))
+sys.path.append(str(Path().parent.resolve()))
 
 # If extensions (or modules to document with autodoc) are in another directory,
 # add these directories to sys.path here. If the directory is relative to the
-# documentation root, use os.path.abspath to make it absolute, like shown here.
-# sys.path.insert(0, os.path.abspath('.'))
+# documentation root, use pathlib.Path.resolve to make it absolute, like shown here.
+# sys.path.insert(0, Path().resolve())
 
 # -- General configuration ------------------------------------------------
 
@@ -80,9 +80,9 @@
 project = "geoh5py"
 
 # The short X.Y version.
-version = "0.7.1"
+version = "0.8.0"
 # The full version, including alpha/beta/rc tags.
-release = "0.7.1"
+release = "0.8.0"
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -161,6 +161,11 @@
 
 check_meta = False
 
+html_theme_options = {
+    "navigation_depth": 5,
+    "collapse_navigation": False,
+}
+
 # Add any paths that contain custom themes here, relative to this directory.
 # html_theme_path = []
 
@@ -345,26 +350,28 @@ def clean_state():
     for root, dirList, fileList in os.walk(cwd):
         if "Workspace" not in root:
             for filename in fileList:
-                if "ipynb" in filename:
-                    os.system("nbstripout " + os.path.join(root, filename))
-                if ".geoh5" in filename:
-                    os.remove(os.path.join(root, filename))
+                filepath = Path(root) / filename
+                if filepath.suffix == ".ipynb":
+                    os.system("nbstripout " + str(filepath))
+                if filepath.suffix == ".geoh5":
+                    filepath.unlink()
 
 
 clean_state()
 # # Build the API
-# dirname, filename = os.path.split(os.path.abspath(__file__))
+# dirpath = Path(__file__).parent.resolve()
 # subprocess.run(
 #     [
 #         "sphinx-autogen",
 #         "-i",
 #         "-t",
-#         os.path.sep.join([dirname, "_templates"]),
+#         str(dirpath / "_templates"),
 #         "-o",
-#         os.path.sep.join([dirname, "content/api/generated"]),
-#         os.path.sep.join([dirname, "content/api/index.rst"]),
+#         str(dirpath / "content" / "api" / "generated"),
+#         str(dirpath / "content" / "api" / "index.rst"),
 #     ]
 # )
 
+
 # TODO: build the source
 # sphinx-apidoc --templatedir templates/ -o content/api/ ../geoh5py