Merge pull request #730 from MiraGeoscience/release/0.12.0-dev.1

[GEOPY-2095] Release/0.12.0

Author: domfournier

.flake8

@@ -1,5 +1,15 @@
 [flake8]
-ignore = E203, E266, E501, W503
+ignore =
+    E203,
+    E266,
+    E501,
+    W503,
+    # TODO: reduce complexity and restore this rule (Function is too complex)
+    C901,
+
+
 max-line-length = 80
 max-complexity = 16
 select = B,C,E,F,W,T4,B9
+per-file-ignores =
+    geoapps/clustering/driver.py: E402

.gitattributes

@@ -1,2 +1,5 @@
+*.pt filter=lfs diff=lfs merge=lfs -text
 *.geoh5 filter=lfs diff=lfs merge=lfs -text
+*.h5 filter=lfs diff=lfs merge=lfs -text
+*.min.js filter=lfs diff=lfs merge=lfs -text
 *.ipynb filter=lfs diff=lfs merge=lfs -text

.github/workflows/issue_to_jira.yml

@@ -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@v3
+      uses: peter-evans/create-or-update-comment@v4
       with:
         # The number of the issue or pull request in which to create a comment.
         issue-number: ${{ github.event.issue.number }}

.github/workflows/pr_add_jira_summary.yml

@@ -19,7 +19,13 @@ jobs:
         PR_TITLE: ${{ github.event.pull_request.title }}
       run: >
         echo $HEAD_REF $PR_TITLE
-        | echo "issue_key=$(grep -os "\b\(GA\|GEOPY\)-[0-9]\+" | head -n1)" >> $GITHUB_OUTPUT
+        | echo "issue_key=$(
+        grep -osi "\b\(GA\|GEOPY\|DEVOPS\)[ #-]*[0-9]\+"
+        | head -n1
+        | sed -E "s/([A-Z]+)[-# ]*([0-9]+)/\1-\2/i"
+        | tr [:lower:] [:upper:]
+        )"
+        >> $GITHUB_OUTPUT
     - name: Get JIRA summary
       id: get_jira_summary
       if: ${{ steps.find_jira_key.outputs.issue_key }}
@@ -31,18 +37,26 @@ jobs:
         -H "Authorization: Basic $JIRA_BASIC_AUTH"
         -H "Content-Type: application/json"
         "$JIRA_BASE_URL/rest/api/2/issue/${{ steps.find_jira_key.outputs.issue_key }}"
-        | echo "summary=$(jq -r '.fields.summary')" >> $GITHUB_OUTPUT
+        | echo "summary=$(jq -r '.fields.summary // empty')" >> $GITHUB_OUTPUT
+    - name: Extract PR title
+      id: get_pr_title
+      env:
+        PR_TITLE: ${{ github.event.pull_request.title }}
+      run: |
+        echo "text=$(echo $PR_TITLE | sed -E "s/^\s*[?[A-Z]+[-# ]*[0-9]+]?[-: ]*(.*)/\1/i")" >> $GITHUB_OUTPUT
     - name: Add comment
       if: ${{ steps.find_jira_key.outputs.issue_key }}
       env:
         ISSUE_SUMMARY: ${{ steps.get_jira_summary.outputs.summary }}
+        TITLE_TEXT: ${{ steps.get_pr_title.outputs.text }}
         PR_BODY: ${{ github.event.pull_request.body }}
       run: >
         jq
         --arg ISSUE_ID "${{ steps.find_jira_key.outputs.issue_key }}"
         --arg ISSUE_SUMMARY "$(cat <<< $ISSUE_SUMMARY)"
+        --arg TITLE_TEXT "$(cat <<< ${TITLE_TEXT:-$ISSUE_SUMMARY})"
         --arg PR_BODY "$(cat <<< $PR_BODY)"
-        -c '."body"="**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY' <<< {}
+        -c '{"title": ($ISSUE_ID + ": " + $TITLE_TEXT), "body": ("**" + $ISSUE_ID + " - " + $ISSUE_SUMMARY + "**\n" + $PR_BODY)}' <<< {}
         | curl -sS -X POST -d @-
         -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}"
         -H "Content-Type: application/json"

.github/workflows/pytest-unix-os.yaml renamed to .github/workflows/pytest-unix-os.yml

@@ -2,6 +2,7 @@ name: pytest on Unix OS
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -20,25 +21,24 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: geoapps
-
 jobs:
   pytest:
     name: pytest (Unix)
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.9', '3.10']
+        python_ver: ['3.10']
         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 }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-${{ matrix.python_ver }}-${{ startsWith(matrix.os, 'macos') && 'osx' || 'linux' }}-64-dev.conda.lock.yml
     steps:
       - uses: actions/checkout@v4
         with:
@@ -50,5 +50,4 @@ jobs:
           environment-name: test_env
           cache-downloads: true
       - name: pytest
-        run: |
-          pytest --cov=${source_dir} --cov-report=xml --cov-branch
+        run: pytest --cov --cov-report=xml

.github/workflows/pytest-windows.yaml renamed to .github/workflows/pytest-windows.yml

@@ -2,6 +2,7 @@ name: pytest on Windows
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -20,24 +21,23 @@ concurrency:
   group: ${{ github.workflow }}-${{ github.head_ref || github.run_id }}
   cancel-in-progress: true
 
-env:
-  source_dir: geoapps
-
 jobs:
   pytest:
     name: pytest (Windows)
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     strategy:
       fail-fast: false
       matrix:
-        python_ver: ['3.9', '3.10']
+        python_ver: ['3.10']
     defaults:
       run:
         shell: powershell
     runs-on: windows-latest
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-${{ matrix.python_ver }}-win-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-${{ matrix.python_ver }}-win-64-dev.conda.lock.yml
     steps:
       - uses: actions/checkout@v4
         with:
@@ -50,10 +50,11 @@ jobs:
           init-shell: powershell
           cache-downloads: true
       - name: pytest
-        run: |
-          pytest --cov=${source_dir} --cov-report=xml --cov-branch
+        run: pytest --cov --cov-report=xml
       - name: Codecov
-        if: ${{ success() && matrix.python_ver == '3.9' }}
-        uses: codecov/codecov-action@v3
+        if: ${{ success() && matrix.python_ver == '3.10' }}
+        uses: codecov/codecov-action@v4
         with:
           name: GitHub
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/static-analysis.yml

@@ -2,6 +2,7 @@ name: static analysis
 
 on:
   pull_request:
+    types: [opened, synchronize, reopened, ready_for_review]
     branches:
       - develop
       - main
@@ -26,14 +27,16 @@ env:
 jobs:
   pylint:
     name: pylint
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     runs-on: ubuntu-latest
     defaults:
       run:
         shell: bash -l {0}
     env:
       PYTHONUTF8: 1
-      CONDA_LOCK_ENV_FILE: environments/conda-py-3.9-linux-64-dev.lock.yml
-      PIP_EXTRA_INDEX_URL: https://test.pypi.org/simple/
+      CONDA_CHANNEL_PRIORITY: strict
+      PIP_NO_DEPS: 1 # all dependencies are installed from conda
+      CONDA_LOCK_ENV_FILE: environments/py-3.10-linux-64-dev.conda.lock.yml
     steps:
       - uses: actions/checkout@v4
       - name: Setup conda env

.idea/copyright/Mira_Geoscience___MIT.xml

@@ -1,8 +1,8 @@
 
 default_language_version:
     python: python3
-exclude: (^docs/(conf.py|_ext/)|^geoapps/simpeg(PF|EM1D)/|^geoapps-assets/)
-default_stages: [commit,push]
+exclude: (^docs/(conf.py|_ext/))
+default_stages: [pre-commit,pre-push]
 fail_fast: false
 
 ci:
@@ -11,42 +11,46 @@ ci:
     autoupdate_schedule: monthly
 
 repos:
--   repo: https://github.com/psf/black
-    rev: 23.10.0
+-   repo: https://github.com/hadialqattan/pycln
+    rev: v2.5.0
     hooks:
-    -   id: black
--   repo: https://github.com/PyCQA/isort
-    rev: 5.12.0
+    -   id: pycln
+        args: [--config=pyproject.toml]
+-   repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.9.1
     hooks:
-    -   id: isort
-        additional_dependencies: [tomli] # to read config from pyproject.toml
--   repo: https://github.com/humitos/mirrors-autoflake
-    rev: v1.1
-    hooks:
-    -   id: autoflake
-#-   repo: https://github.com/PyCQA/flake8
-#    rev: 6.1.0
-#    hooks:
-#    -   id: flake8
--   repo: https://github.com/asottile/pyupgrade
-    rev: v3.15.0
-    hooks:
-    -   id: pyupgrade
-        args: [--py39-plus]
-#-   repo: https://github.com/pre-commit/mirrors-mypy
-#    rev: v1.6.1
+    -   id: ruff
+        args:
+        -   --fix
+        -   --exit-non-zero-on-fix
+#        -   --unsafe-fixes
+        exclude_types: [jupyter]
+    -   id: ruff-format
+        exclude_types: [jupyter]
+#-   repo: https://github.com/pre-commit/mirrors-mypy  # TODO: fix mypy errors
+#    rev: v1.10.0
 #    hooks:
 #    -   id: mypy
 #        additional_dependencies: [
+#            numpy==1.26.*,
 #            types-toml,
 #            types-PyYAML,
-#            tomli # to read config from pyproject.toml
+#            tomli  # to read config from pyproject.toml
 #        ]
+#        exclude: ^(docs|geoapps-assets)/
 -   repo: https://github.com/codingjoe/relint
-    rev: 3.1.0
+    rev: 3.3.1
     hooks:
     -   id: relint
         args: [-W]  # to fail on warnings
+-   repo: https://github.com/MiraGeoscience/pre-commit-hooks
+    rev: v1.1.0
+    hooks:
+    -   id: check-copyright
+        files: (^package\.rst|^LICENSE|^README(|-dev)\.rst|\.py|\.pyi)$
+        exclude: (^\.|^docs/)
+    -   id: prepare-commit-msg
+    -   id: check-commit-msg
 -   repo: local
     hooks:
     -   id: pylint
@@ -56,47 +60,43 @@ repos:
         require_serial: true  # pylint does its own parallelism
         types: [python]
         exclude: ^(devtools|docs)/
-    -   id: check-copyright
-        name: Check copyright
-        entry: python devtools/check-copyright.py
-        language: python
-        types: [text]
-        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: v2.2.6
+    rev: v2.3.0
     hooks:
     -   id: codespell
         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: v4.5.0
+    rev: v5.0.0
     hooks:
     -   id: trailing-whitespace
         exclude: \.mdj$
+    -   id: check-json
+        exclude_types: [jupyter]
     -   id: check-toml
     -   id: check-yaml
-#    -   id: check-added-large-files # crashing on some configuration. To be investigated
+    -   id: check-added-large-files
+#        args: [--enforce-all]
     -   id: check-case-conflict
     -   id: check-merge-conflict
     -   id: debug-statements
     -   id: detect-private-key
     -   id: end-of-file-fixer
-        exclude: \.mdj$
+        exclude: (^\.idea/.*\.xml|\.mdj)$
     -   id: mixed-line-ending
+        exclude: ^\.idea/.*\.xml$
     -   id: name-tests-test
+    -   id: pretty-format-json
+        args:
+            - --autofix
+            - --indent=4
+            - --no-sort-keys
+            - --top-keys
+            - version,title,icon,documentation,conda_environment,run_command,geoh5,monitoring_directory,workspace_geoh5
+        exclude_types: [jupyter]
+        exclude: ^docs/.*/images/
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.0
+    rev: v6.2.4
     hooks:
     -   id: rstcheck
         exclude: ^THIRD_PARTY_SOFTWARE.rst$