Merge pull request #648 from MiraGeoscience/release/0.11.0

merge release/0.11.0 to main

Author: andrewg-mira

.coveragerc

@@ -28,7 +28,7 @@ jobs:
         # Additional fields in JSON format
         fields: '{"components": [{"name": "geoapps"}]}'
     - 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/create_env_file.yml

@@ -30,14 +30,15 @@ jobs:
       fail-fast: false
       matrix:
         python_ver: ['3.9', '3.10']
-        os: [ubuntu-latest, macos-latest]
+        os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     defaults:
       run:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
+      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/issue_to_jira.yml

@@ -37,6 +37,7 @@ jobs:
     env:
       PYTHONUTF8: 1
       CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
+      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
       - uses: actions/checkout@v3
         with:

.github/workflows/pytest-unix-os.yaml

@@ -33,6 +33,7 @@ jobs:
     env:
       PYTHONUTF8: 1
       CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-win-64-dev.lock.yml
+      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
     steps:
       - uses: actions/checkout@v3
       - name: Setup conda env

.github/workflows/pytest-windows.yaml

@@ -140,8 +140,11 @@ dmypy.json
 # customization
 get_custom_conda.bat
 
+# not using poetry here, but conda lock
+poetry.lock
+
 # cleanup after tests
-*.lock
+*.geoh5.lock
 /geoapps-assets/EM1DInversion_.json
 /geoapps-assets/Inversion_.json
 /geoapps-assets/SimPEG_PFInversion/

.github/workflows/static-analysis.yml

@@ -1,7 +1,7 @@
 
 default_language_version:
     python: python3
-exclude: (docs/(conf.py|_ext/)|(^geoapps/simpeg(PF|EM1D)/))
+exclude: (^docs/(conf.py|_ext/)|^geoapps/simpeg(PF|EM1D)/|^geoapps-assets/)
 default_stages: [commit,push]
 fail_fast: false
 
@@ -12,35 +12,41 @@ ci:
 
 repos:
 -   repo: https://github.com/psf/black
-    rev: 23.3.0
-
+    rev: 23.10.0
     hooks:
     -   id: black
 -   repo: https://github.com/PyCQA/isort
     rev: 5.12.0
     hooks:
     -   id: isort
-        additional_dependencies: [toml] # to read config from pyproject.toml
+        additional_dependencies: [tomli] # to read config from pyproject.toml
 -   repo: https://github.com/humitos/mirrors-autoflake
     rev: v1.1
     hooks:
     -   id: autoflake
-#-   repo: https://gitlab.com/pycqa/flake8
-#    rev: 3.8.4
+#-   repo: https://github.com/PyCQA/flake8
+#    rev: 6.1.0
 #    hooks:
 #    -   id: flake8
 -   repo: https://github.com/asottile/pyupgrade
-    rev: v3.3.2
-
+    rev: v3.15.0
     hooks:
     -   id: pyupgrade
         args: [--py39-plus]
 #-   repo: https://github.com/pre-commit/mirrors-mypy
-#    rev: v0.790
+#    rev: v1.6.1
 #    hooks:
 #    -   id: mypy
-#        args: ["--ignore-missing-imports", "--scripts-are-modules", "--show-error-context",
-#               "--show-column-numbers"]
+#        additional_dependencies: [
+#            types-toml,
+#            types-PyYAML,
+#            tomli # to read config from pyproject.toml
+#        ]
+-   repo: https://github.com/codingjoe/relint
+    rev: 3.1.0
+    hooks:
+    -   id: relint
+        args: [-W]  # to fail on warnings
 -   repo: local
     hooks:
     -   id: pylint
@@ -49,23 +55,32 @@ repos:
         language: system
         require_serial: true  # pylint does its own parallelism
         types: [python]
-        exclude: docs/
+        exclude: ^(devtools|docs)/
     -   id: check-copyright
         name: Check copyright
         entry: python devtools/check-copyright.py
         language: python
-        files: (^LICENSE|README.rst|\.py|\.pyi)$
         types: [text]
-        exclude: (^setup.py$|^\.|\b(docs|geoapps-assets)/)
+        files: (^LICENSE|^README(|-dev).rst|\.py|\.pyi)$
+        exclude: (^\.|^docs/)
+    -   id: prepare-commit-msg
+        stages: [prepare-commit-msg]
+        name: Prepare commit message
+        entry: python devtools/git_message_hook.py --prepare
+        language: python
+    -   id: check-commit-msg
+        stages: [commit-msg]
+        name: Check commit message
+        entry: python devtools/git_message_hook.py --check
+        language: python
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
-
+    rev: v2.2.6
     hooks:
     -   id: codespell
-        exclude: (-lock\.ya?ml|\benvironments/.*\.ya?ml|\.ipynb)$
+        exclude: (-lock\.ya?ml|\benvironments/.*\.ya?ml|\.ipynb|^THIRD_PARTY_SOFTWARE\.rst)$
         entry: codespell -I .codespellignore
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
     -   id: trailing-whitespace
         exclude: \.mdj$
@@ -81,12 +96,13 @@ repos:
     -   id: mixed-line-ending
     -   id: name-tests-test
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.1.2
-
+    rev: v6.2.0
     hooks:
     -   id: rstcheck
+        exclude: ^THIRD_PARTY_SOFTWARE.rst$
         additional_dependencies: [sphinx]
 -   repo: https://github.com/pre-commit/pygrep-hooks
     rev: v1.10.0
     hooks:
     -   id: rst-backticks
+        exclude: ^THIRD_PARTY_SOFTWARE.rst$

.gitignore

@@ -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

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2023 Mira Geoscience
+Copyright (c) 2024 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

.relint.yml

@@ -29,7 +29,7 @@
 Welcome to **geoapps** - Open-source applications in geosciences
 ================================================================
 
-.. image:: https://github.com/MiraGeoscience/geoapps/raw/v0.10.0-rc.3/docs/images/index_page.png
+.. image:: https://github.com/MiraGeoscience/geoapps/raw/v0.10.0-rc.2/docs/images/index_page.png
     :align: right
     :width: 50%
 
@@ -65,12 +65,21 @@ Current sponsors
 - `Teck <https://www.teck.com/>`_
 - `Vale <https://www.vale.com/canada>`_
 
+Third Party Software
+^^^^^^^^^^^^^^^^^^^^
+The geoapps Software may provide links to third party libraries or code (collectively “Third Party Software”)
+to implement various functions. Third Party Software does not comprise part of the Software.
+The use of Third Party Software is governed by the terms of such software license(s).
+Third Party Software notices and/or additional terms and conditions are located in the
+`THIRD_PARTY_SOFTWARE.rst`_ file.
+
+.. _THIRD_PARTY_SOFTWARE.rst: THIRD_PARTY_SOFTWARE.rst
 
 License
 ^^^^^^^
 MIT License
 
-Copyright (c) 2023 Mira Geoscience
+Copyright (c) 2024 Mira Geoscience
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal