Merge branch 'main' into i_atcorr_major_refactoring

.flake8

@@ -39,7 +39,7 @@ per-file-ignores =
     doc/python/vector_example_ctypes.py: F403, F405
     doc/python/m.distance.py: F403, F405, E501
     doc/gui/wxpython/example/dialogs.py: F401
-    locale/grass_po_stats.py: E122, E128, E231, E401, E722, E741
+    locale/grass_po_stats.py: E122, E128, E231, E401, E722
     gui/scripts/d.wms.py: E501
     gui/wxpython/core/gcmd.py: E402
     gui/wxpython/core/gthread.py: F841
@@ -71,8 +71,7 @@ per-file-ignores =
     gui/wxpython/gui_core/widgets.py: F841, E722, E266
     gui/wxpython/image2target/*: F841, E722, E265
     gui/wxpython/image2target/g.gui.image2target.py: E501, E265, F841
-    gui/wxpython/iscatt/*: F841, E722, E741, F405, F403
-    gui/wxpython/lmgr/giface.py: E741
+    gui/wxpython/iscatt/*: F841, E722, F405, F403
     gui/wxpython/lmgr/frame.py: F841, E722
     # layertree still includes some formatting issues (it is ignored by Black)
     gui/wxpython/lmgr/layertree.py: E722, E266, W504, E225
@@ -82,16 +81,15 @@ per-file-ignores =
     gui/wxpython/photo2image/*: F841, E722, E265
     gui/wxpython/photo2image/g.gui.photo2image.py: E501, F841
     gui/wxpython/psmap/*: F841, E266, E722, F405, F403
-    gui/wxpython/vdigit/*: F841, E722, E741, F405, F403
+    gui/wxpython/vdigit/*: F841, E722, F405, F403
     gui/wxpython/vnet/*: F841
     gui/wxpython/wxgui.py: F841
     gui/wxpython/animation/g.gui.animation.py: E501
     gui/wxpython/animation/mapwindow.py: F841
     gui/wxpython/animation/provider.py: F841
-    gui/wxpython/tplot/frame.py: F841, E722, E741
+    gui/wxpython/tplot/frame.py: F841, E722
     gui/wxpython/tplot/g.gui.tplot.py: E501
     gui/wxpython/rdigit/g.gui.rdigit.py: F841
-    gui/wxpython/iclass/dialogs.py: E741
     gui/wxpython/iclass/digit.py: F405, F403
     gui/wxpython/iclass/frame.py: F405, F403
     gui/wxpython/iclass/g.gui.iclass.py: E501
@@ -109,14 +107,12 @@ per-file-ignores =
     gui/wxpython/mapwin/buffered.py: E722
     gui/wxpython/mapwin/graphics.py: E722
     gui/wxpython/startup/locdownload.py: E722, E402
-    gui/wxpython/timeline/g.gui.timeline.py: E501, E741
-    gui/wxpython/timeline/frame.py: E741
+    gui/wxpython/timeline/g.gui.timeline.py: E501
     gui/wxpython/tools/build_modules_xml.py: E722
     gui/wxpython/web_services/cap_interface.py: E501
-    gui/wxpython/web_services/widgets.py: F841, E741, E402
-    gui/wxpython/rlisetup/frame.py: E741
+    gui/wxpython/web_services/widgets.py: F841, E402
     gui/wxpython/rlisetup/sampling_frame.py: F841
-    gui/wxpython/rlisetup/wizard.py: E722, E741
+    gui/wxpython/rlisetup/wizard.py: E722
     # Generated file
     gui/wxpython/menustrings.py: E501
     # F821 undefined name 'cmp'
@@ -130,7 +126,6 @@ per-file-ignores =
     python/grass/pygrass/vector/__init__.py: E402
     python/grass/pygrass/modules/interface/*.py: F401
     python/grass/pygrass/modules/grid/*.py: F401
-    python/grass/pygrass/raster/rowio.py: E741
     python/grass/pygrass/raster/category.py: E721
     python/grass/pygrass/rpc/__init__.py: F401, F403
     python/grass/pygrass/utils.py: E402
@@ -140,13 +135,11 @@ per-file-ignores =
     python/grass/temporal/datetime_math.py: F841, E722
     python/grass/temporal/open_stds.py: F841
     python/grass/temporal/spatial_topology_dataset_connector.py: E722
-    python/grass/temporal/temporal_algebra.py: E741, F841, E722
+    python/grass/temporal/temporal_algebra.py: F841, E722
     python/grass/temporal/temporal_granularity.py: F841, E722
-    python/grass/temporal/temporal_raster_algebra.py: E741
     python/grass/temporal/temporal_raster_base_algebra.py: F841, E722
-    python/grass/temporal/temporal_raster3d_algebra.py: E741
     python/grass/temporal/temporal_topology_dataset_connector.py: E722
-    python/grass/temporal/temporal_vector_algebra.py: E741, F841
+    python/grass/temporal/temporal_vector_algebra.py: F841
     python/grass/temporal/univar_statistics.py: E231
     # Current benchmarks/tests are changing sys.path before import.
     # Possibly, a different approach should be taken there anyway.
@@ -165,7 +158,7 @@ per-file-ignores =
     # E402 module level import not at top of file
     scripts/d.polar/d.polar.py: F841
     scripts/r.in.wms/wms_gdal_drv.py: F841, E722
-    scripts/r.in.wms/wms_cap_parsers.py: F841, E741
+    scripts/r.in.wms/wms_cap_parsers.py: F841
     scripts/r.in.wms/wms_drv.py: E402, E722
     scripts/r.in.wms/srs.py: E722
     scripts/r.semantic.label/r.semantic.label.py: F841, E501
@@ -174,8 +167,7 @@ per-file-ignores =
     scripts/g.extension/g.extension.py: F841, E722, E501
     scripts/v.unpack/v.unpack.py: F841, E722, E501
     scripts/v.import/v.import.py: F841, E722, E501
-    scripts/db.univar/db.univar.py: E741, E501
-    scripts/d.rast.leg/d.rast.leg.py: E741
+    scripts/db.univar/db.univar.py: E501
     scripts/d.frame/d.frame.py: E722
     scripts/i.pansharpen/i.pansharpen.py: E722, E501
     scripts/r.in.srtm/r.in.srtm.py: E722

.github/workflows/additional_checks.yml

@@ -59,7 +59,7 @@ jobs:
 
       - name: Generate release notes using git log
         run: |
-          python -m pip install PyYAML
+          python -m pip install PyYAML requests
           # Git works without any special permissions.
           # Using current branch or the branch against the PR is open.
           # Using the last 30 commits (for branches, tags, and PRs).

.github/workflows/clang-format-check.yml

@@ -8,8 +8,8 @@ on:
   pull_request:
   workflow_dispatch:
 concurrency:
-  group: ${{ github.workflow }}-${{ github.ref }}
-  cancel-in-progress: ${{ github.ref_protected != true }}
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
 permissions: {}
 jobs:
   formatting-check:
@@ -22,7 +22,7 @@ jobs:
       - uses: DoozyX/clang-format-lint-action@11b773b1598aa4ae3b32f023701bca5201c3817d # v0.17
         with:
           source: "."
-          clangFormatVersion: 15
+          clangFormatVersion: 17
           inplace: True
       - name: Create and uploads code suggestions to apply
         id: diff

.github/workflows/codeql-analysis.yml

@@ -56,7 +56,7 @@ jobs:
         if: ${{ matrix.language == 'c-cpp' }}
 
       - name: Initialize CodeQL
-        uses: github/codeql-action/init@23acc5c183826b7a8a97bce3cecc52db901f8251 # v3.25.10
+        uses: github/codeql-action/init@b611370bb5703a7efb587f9d136a52ea24c5c38c # v3.25.11
         with:
           languages: ${{ matrix.language }}
           config-file: ./.github/codeql/codeql-config.yml
@@ -81,6 +81,6 @@ jobs:
         run: .github/workflows/build_ubuntu-22.04.sh "${HOME}/install"
 
       - name: Perform CodeQL Analysis
-        uses: github/codeql-action/analyze@23acc5c183826b7a8a97bce3cecc52db901f8251 # v3.25.10
+        uses: github/codeql-action/analyze@b611370bb5703a7efb587f9d136a52ea24c5c38c # v3.25.11
         with:
           category: "/language:${{matrix.language}}"

.github/workflows/create_release_draft.yml

@@ -13,6 +13,11 @@ on:
       - .github/**
       - utils/**
 
+concurrency:
+  group: >-
+    ${{ github.workflow }}-${{ github.event_name == 'pull_request' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
 env:
   OUT_DIR: ${{ github.workspace }}/../grass_outdir
   GRASS: grass-${{ github.ref_name }}
@@ -68,7 +73,7 @@ jobs:
           sha256sum ${{ env.GRASS }}.tar.xz > ${{ env.GRASS }}.tar.xz.sha256
       - name: Publish draft distribution to GitHub (for tags only)
         if: startsWith(github.ref, 'refs/tags/')
-        uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
+        uses: softprops/action-gh-release@a74c6b72af54cfa997e81df42d94703d6313a2d0 # v2.0.6
         with:
           name: GRASS GIS ${{ github.ref_name }}
           body: |

.github/workflows/docker.yml

@@ -76,7 +76,7 @@ jobs:
           password: ${{ secrets.DOCKERHUB_TOKEN  }}
       - name: Build and push
         id: docker_build
-        uses: docker/build-push-action@ca052bb54ab0790a636c9b5f226502c73d547a25 # v5.4.0
+        uses: docker/build-push-action@15560696de535e4014efeff63c48f16952e52dd1 # v6.2.0
         with:
           push: true
           pull: true

.github/workflows/label.yml

@@ -13,6 +13,10 @@ on:
 
 permissions: {}
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event_name == 'pull_request_target' && github.head_ref || github.sha }}
+  cancel-in-progress: true
+
 jobs:
   labeler:
     permissions:

.github/workflows/periodic_update.yml

@@ -33,7 +33,7 @@ jobs:
         run: git status --ignored
       - name: Create Pull Request
         id: cpr
-        uses: peter-evans/create-pull-request@6d6857d36972b65feb161a90e484f2984215f83e # v6.0.5
+        uses: peter-evans/create-pull-request@c5a7806660adbe173f04e3e038b0ccdcd758773c # v6.1.0
         with:
           commit-message: "config.guess + config.sub: updated from http://git.savannah.gnu.org/cgit/config.git/plain/"
           branch: periodic/update-configure

.github/workflows/post-pr-reviews.yml

@@ -47,6 +47,7 @@ jobs:
           INPUT_TOOL_NAMES: >-
             black
             clang-format
+            ruff
       - name: Post Black suggestions
         if: ${{ steps.tools.outputs.black == 'true' }}
         run: |
@@ -83,3 +84,21 @@ jobs:
           CI_REPO_OWNER: ${{ github.event.workflow_run.repository.owner.login }}
           CI_REPO_NAME: ${{ github.event.workflow_run.repository.name }}
           # CI_PULL_REQUEST: "" # Populated from reviewdog's "-guess" flag since hard to get
+      - name: Post Ruff suggestions
+        if: ${{ steps.tools.outputs.black == 'true' }}
+        run: |
+          TMPFILE="diff-${INPUT_TOOL_NAME}.patch"
+          GITHUB_ACTIONS="" reviewdog \
+              -name="${INPUT_TOOL_NAME:-reviewdog-suggester}" \
+              -f=diff \
+              -f.diff.strip=1 \
+              -filter-mode=nofilter \
+              -guess \
+              -reporter="github-pr-review" < "${TMPFILE}"
+        env:
+          INPUT_TOOL_NAME: ruff
+          REVIEWDOG_GITHUB_API_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          CI_COMMIT: ${{ github.event.workflow_run.head_sha }}
+          CI_REPO_OWNER: ${{ github.event.workflow_run.repository.owner.login }}
+          CI_REPO_NAME: ${{ github.event.workflow_run.repository.name }}
+          # CI_PULL_REQUEST: "" # Populated from reviewdog's "-guess" flag since hard to get

.github/workflows/pytest.yml

@@ -53,7 +53,7 @@ jobs:
           python -m pip install --upgrade pip
           pip install -r .github/workflows/python_requirements.txt
           pip install -r .github/workflows/optional_requirements.txt
-          pip install pytest pytest-timeout pytest-github-actions-annotate-failures pytest-xdist
+          pip install pytest pytest-timeout pytest-github-actions-annotate-failures pytest-xdist pytest-cov
 
       - name: Create installation directory
         run: |
@@ -70,18 +70,38 @@ jobs:
         run: |
           echo "$HOME/install/bin" >> $GITHUB_PATH
 
+      - name: Print installed versions
+        if: always()
+        run: .github/workflows/print_versions.sh
+
       - name: Test executing of the grass command
         run: .github/workflows/test_simple.sh
 
-      - name: Run pytest
+      - name: Run pytest with multiple workers in parallel
         run: |
           export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
           export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
-          pytest --verbose --color=yes --durations=0 --durations-min=0.5 --numprocesses auto -ra .
+          pytest --verbose --color=yes --durations=0 --durations-min=0.5 \
+            --numprocesses auto -ra . \
+            -m 'not needs_solo_run'
+
+      - name: Run pytest with a single worker (for tests marked with needs_solo_run)
+        run: |
+          export PYTHONPATH=`grass --config python_path`:$PYTHONPATH
+          export LD_LIBRARY_PATH=$(grass --config path)/lib:$LD_LIBRARY_PATH
+          pytest --verbose --color=yes --durations=0 --durations-min=0.5 \
+            --cov \
+            -ra . \
+            -m 'needs_solo_run'
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@e28ff129e5465c2c0dcc6f003fc735cb6ae0c673 # v4.5.0
+        with:
+          verbose: true
+          flags: pytest-python-${{ matrix.python-version }}
+          name: pytest-python-${{ matrix.python-version }}
+          token: ${{ secrets.CODECOV_TOKEN }}
 
-      - name: Print installed versions
-        if: always()
-        run: .github/workflows/print_versions.sh
   pytest-success:
     name: pytest Result
     needs:

.github/workflows/python-code-quality.yml

@@ -30,11 +30,13 @@ jobs:
       # renovate: datasource=pypi depName=black
       BLACK_VERSION: "24.4.2"
       # renovate: datasource=pypi depName=flake8
-      FLAKE8_VERSION: "5.0.4"
+      FLAKE8_VERSION: "7.1.0"
       # renovate: datasource=pypi depName=pylint
       PYLINT_VERSION: "2.12.2"
       # renovate: datasource=pypi depName=bandit
       BANDIT_VERSION: "1.7.9"
+      # renovate: datasource=pypi depName=ruff
+      RUFF_VERSION: "0.5.0"
 
     runs-on: ${{ matrix.os }}
     permissions:
@@ -50,6 +52,7 @@ jobs:
           echo Flake8: ${{ env.FLAKE8_VERSION }}
           echo Pylint: ${{ env.PYLINT_VERSION }}
           echo Bandit: ${{ env.BANDIT_VERSION }}
+          echo Ruff: ${{ env.RUFF_VERSION }}
 
       - uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
 
@@ -61,6 +64,19 @@ jobs:
       - name: Upgrade pip
         run: python -m pip install --upgrade pip
 
+      - name: Install Ruff
+        run: pip install ruff==${{ env.RUFF_VERSION }}
+      - name: Run Ruff
+        run: ruff check --output-format=github . --preview --fix
+      - name: Create and uploads code suggestions to apply for Ruff
+        # Will fail fast here if there are changes required
+        id: diff-ruff
+        uses: ./.github/actions/create-upload-suggestions
+        with:
+          tool-name: ruff
+          # To keep repo's file structure in formatted changes artifact
+          extra-upload-changes: pyproject.toml
+
       - name: Install Black only
         run: pip install black[jupyter]==${{ env.BLACK_VERSION }}
 
@@ -87,9 +103,13 @@ jobs:
         run: |
           pip install -r .github/workflows/python_requirements.txt
           pip install -r .github/workflows/optional_requirements.txt
-          pip install flake8==${{ env.FLAKE8_VERSION }}
-          pip install pylint==${{ env.PYLINT_VERSION }} pytest-github-actions-annotate-failures
-          pip install bandit[sarif]==${{ env.BANDIT_VERSION }}
+          pip install --user pipx
+          pipx ensurepath
+          pipx install flake8==${{ env.FLAKE8_VERSION }}
+          pipx install pylint==${{ env.PYLINT_VERSION }}
+          pipx inject pylint -r .github/workflows/python_requirements.txt -r .github/workflows/optional_requirements.txt
+          # The extra toml is only needed before Python 3.11
+          pipx install bandit[sarif,toml]==${{ env.BANDIT_VERSION }}
 
       - name: Run Flake8
         run: |
@@ -110,7 +130,7 @@ jobs:
           path: bandit.sarif
 
       - name: Upload SARIF File into Security Tab
-        uses: github/codeql-action/upload-sarif@23acc5c183826b7a8a97bce3cecc52db901f8251 # v3.25.10
+        uses: github/codeql-action/upload-sarif@b611370bb5703a7efb587f9d136a52ea24c5c38c # v3.25.11
         with:
           sarif_file: bandit.sarif
 
@@ -146,7 +166,8 @@ jobs:
 
       - name: Run Pylint on other files using pytest
         run: |
-          pip install pytest==7.4.4 pytest-pylint==0.19
+          pipx inject --include-apps pylint pytest==7.4.4
+          pipx inject pylint pytest-pylint==0.19 pytest-github-actions-annotate-failures
           echo "::warning file=.github/workflows/python-code-quality.yml,line=149,col=42,endColumn=48::\
             Temporarily downgraded pytest-pylint and pytest to allow merging other PRs.\
             The errors reported with a newer version seem legitimite and should be fixed \

.github/workflows/super-linter.yml

@@ -36,6 +36,10 @@ jobs:
           DEFAULT_BRANCH: main
           # To report GitHub Actions status checks
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          # By default, super-linter expect all linters to have their config
+          # files inside .github/linters.
+          # Setting it to the root of the repo for easier configuration here.
+          LINTER_RULES_PATH: .
           # Listed but commented out linters would be nice to have.
           # (see https://github.com/github/super-linter#environment-variables)
           #
@@ -52,3 +56,5 @@ jobs:
           VALIDATE_POWERSHELL: true
           # VALIDATE_XML: true
           VALIDATE_YAML: true
+          MARKDOWN_CONFIG_FILE: .markdownlint.yml
+          YAML_CONFIG_FILE: .yamllint