New data collected at 2025-09-22_00-03-44

actions-user · actions-user · commit 5f7535112fce · 2025-09-22T00:03:44.000Z
diff --git a/github-actions/ggplot2/R-CMD-check.yaml b/github-actions/ggplot2/R-CMD-check.yaml
@@ -58,7 +58,21 @@ jobs:
           http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
 
+      # TODO: remove this when R 4.6 is released
+      - name: Tweak for old Windows (R 4.1)
+        uses: r-lib/actions/setup-r-dependencies@v2
+        if: ${{ matrix.config.os == 'windows-latest' && matrix.config.r == 'oldrel-4' }}
+        with:
+          cache-version: 3
+          extra-packages: >
+            any::rcmdcheck,
+            ragg@1.4.0,
+            Hmisc=?ignore-before-r=4.2.0,
+            quantreg=?ignore-before-r=4.3.0
+          needs: check
+
       - uses: r-lib/actions/setup-r-dependencies@v2
+        if: ${{ matrix.config.os != 'windows-latest' || matrix.config.r != 'oldrel-4' }}
         with:
           cache-version: 3
           extra-packages: >
diff --git a/github-actions/igraph/arch-emu.yml b/github-actions/igraph/arch-emu.yml
@@ -18,13 +18,16 @@ env:
   CMAKE_COLOR_DIAGNOSTICS: ON
   CCACHE_MAXSIZE: 64M
   OMP_NUM_THREADS: 1
-  CTEST_PARALLEL_LEVEL: 0 # Since CMake 3.29, a setting of 0 will try to use all available resources
+  CTEST_PARALLEL_LEVEL: 2 # No more than two tests running at a time to prevent timeouts
 
 jobs:
 
   alpine:
     runs-on: ubuntu-latest
 
+    # Do not run in forks
+    if: github.repository == 'igraph/igraph'
+
     defaults:
       run:
         # Use emulated shell as default
@@ -50,7 +53,7 @@ jobs:
         uses: actions/checkout@v5
         with:
           fetch-depth: 0
-          ref: ${{ github.event_name == 'schedule' && 'develop' || github.ref_name }}
+          ref: ${{ github.event_name == 'schedule' && 'main' || github.ref_name }}
 
       - name: Install dependencies
         uses: jirutka/setup-alpine@v1
@@ -122,7 +125,7 @@ jobs:
 
       - name: Test
         # Need a longer timeout as emulated runs are slow.
-        run: cd build && ctest --output-on-failure --timeout 240
+        run: cd build && ctest --output-on-failure
 
       - name: Ccache statistics
         continue-on-error: true
diff --git a/github-actions/igraph/coverity.yml b/github-actions/igraph/coverity.yml
@@ -24,7 +24,7 @@ jobs:
       uses: actions/checkout@v5
       with:
         fetch-depth: 0
-        ref: ${{ github.event_name == 'schedule' && 'develop' || github.ref_name }}
+        ref: ${{ github.event_name == 'schedule' && 'main' || github.ref_name }}
 
     - name: Create build environment
       run: cmake -E make_directory ${{github.workspace}}/build
diff --git a/github-actions/lintr/ast-fuzz.yaml b/github-actions/lintr/ast-fuzz.yaml
@@ -23,6 +23,8 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          install-quarto: false
 
       - name: Ensure equivalent code generates equivalent lints
         run: |
diff --git a/github-actions/lintr/check-all-examples.yaml b/github-actions/lintr/check-all-examples.yaml
@@ -30,6 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           pak-version: devel
           extra-packages: |
             any::pkgload
diff --git a/github-actions/lintr/lint.yaml b/github-actions/lintr/lint.yaml
@@ -20,6 +20,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: |
             any::cyclocomp
             r-lib/lintr
diff --git a/github-actions/lintr/pkgdown.yaml b/github-actions/lintr/pkgdown.yaml
@@ -30,6 +30,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: any::pkgdown, local::.
           needs: website
 
diff --git a/github-actions/lintr/repo-meta-tests.yaml b/github-actions/lintr/repo-meta-tests.yaml
@@ -23,6 +23,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: |
             any::roxygen2
 
diff --git a/github-actions/lintr/test-coverage-examples.yaml b/github-actions/lintr/test-coverage-examples.yaml
@@ -21,6 +21,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: |
             any::covr
             local::.
diff --git a/github-actions/lintr/test-coverage.yaml b/github-actions/lintr/test-coverage.yaml
@@ -24,6 +24,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: any::covr, any::xml2
           needs: coverage
 
diff --git a/github-actions/lintr/test-package-vigilant.yaml b/github-actions/lintr/test-package-vigilant.yaml
@@ -22,6 +22,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
+          install-quarto: false
           extra-packages: local::.
 
       - name: Run Tests
diff --git a/github-actions/mlflow/autoformat.yml b/github-actions/mlflow/autoformat.yml
@@ -100,20 +100,15 @@ jobs:
       # pre-commit
       # ************************************************************************
       - run: |
-          pip install -r requirements/lint-requirements.txt
-          pre-commit install --install-hooks
-          pre-commit run install-bin -a -v
-          pre-commit run --all-files --color=always || true
+          uv run --only-group lint pre-commit install --install-hooks
+          uv run --only-group lint pre-commit run install-bin -a -v
+          uv run --only-group lint pre-commit run --all-files --color=always || true
       # ************************************************************************
       # protos
       # ************************************************************************
       - if: steps.diff.outputs.protos == 'true'
         env:
           DOCKER_BUILDKIT: 1
-        run: |
-          pip install --upgrade pip
-          pip install .
-      - if: steps.diff.outputs.protos == 'true'
         run: |
           # Run the script multiple times. The changes generated by the first run
           # may trigger additional changes, which need to be applied in subsequent runs.
@@ -125,7 +120,6 @@ jobs:
       # ************************************************************************
       - if: steps.diff.outputs.db == 'true'
         run: |
-          pip install .
           tests/db/update_schemas.sh
       # ************************************************************************
       # js
diff --git a/github-actions/mlflow/copilot-setup-steps.yml b/github-actions/mlflow/copilot-setup-steps.yml
@@ -15,6 +15,7 @@ jobs:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       - uses: ./.github/actions/setup-node
       - uses: ./.github/actions/setup-python
+      - uses: ./.github/actions/setup-java
       - name: Install dependencies
         run: |
           uv sync --only-group lint
diff --git a/github-actions/mlflow/cross-version-tests.yml b/github-actions/mlflow/cross-version-tests.yml
@@ -132,7 +132,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix: ${{ fromJson(needs.set-matrix.outputs.matrix1) }}
-    steps:
+    steps: &test-steps
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
         with:
           repository: ${{ github.event_name == 'schedule' && 'mlflow/mlflow' || github.event.inputs.repository }}
@@ -198,58 +198,4 @@ jobs:
     strategy:
       fail-fast: false
       matrix: ${{ fromJson(needs.set-matrix.outputs.matrix2) }}
-    steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
-        with:
-          repository: ${{ github.event_name == 'schedule' && 'mlflow/mlflow' || github.event.inputs.repository }}
-          ref: ${{ github.event.inputs.ref }}
-      - uses: ./.github/actions/free-disk-space
-        if: matrix.free_disk_space
-      - uses: ./.github/actions/setup-python
-        with:
-          python-version: ${{ matrix.python }}
-      - uses: ./.github/actions/setup-pyenv
-      - uses: ./.github/actions/setup-java
-        with:
-          java-version: ${{ matrix.java }}
-      - name: Remove constraints
-        run: |
-          # Remove any constraints for the current package to prevent installation conflicts
-          sed -i '/^${{ matrix.package }}/d' requirements/constraints.txt
-
-          if ! git diff --exit-code requirements/constraints.txt; then
-            git diff
-            git config user.name 'mlflow-app[bot]'
-            git config user.email 'mlflow-app[bot]@users.noreply.github.com'
-            git add requirements/constraints.txt
-            git commit -m "Remove constraints for testing"
-          fi
-      - name: Install mlflow & test dependencies
-        run: |
-          pip install -U pip wheel setuptools
-          # For tracing SDK test, install the tracing package from the local path and minimal test dependencies
-          if [[ "${{ matrix.category }}" == "tracing-sdk" ]]; then
-            pip install libs/tracing
-            pip install pytest pytest-asyncio pytest-cov
-          # Other two categories of tests (model/autologging)
-          else
-            pip install .[extras]
-            pip install -r requirements/test-requirements.txt
-          fi
-      - name: Install ${{ matrix.package }} ${{ matrix.version }}
-        run: |
-          ${{ matrix.install }}
-      - uses: ./.github/actions/show-versions
-      - uses: ./.github/actions/pipdeptree
-      - name: Pre-test
-        if: matrix.pre_test
-        run: |
-          ${{ matrix.pre_test }}
-      - name: Run tests
-        env:
-          MLFLOW_CONDA_HOME: /usr/share/miniconda
-          SPARK_LOCAL_IP: localhost
-          JOHNSNOWLABS_LICENSE_JSON: ${{ secrets.JOHNSNOWLABS_LICENSE_JSON }}
-          HF_HUB_ENABLE_HF_TRANSFER: 1
-        run: |
-          ${{ matrix.run }}
+    steps: *test-steps
diff --git a/github-actions/mlflow/master.yml b/github-actions/mlflow/master.yml
@@ -82,6 +82,9 @@ jobs:
           source ./dev/install-common-deps.sh --ml
           # transformers doesn't support Keras 3 yet. tf-keras needs to be installed as a workaround.
           pip install tf-keras
+          # Ensure `databricks-connect` and `databricks-agents` are not installed
+          pip uninstall -y databricks-connect databricks-agents
+          pip install --no-deps --force-reinstall pyspark
       - uses: ./.github/actions/show-versions
       - uses: ./.github/actions/pipdeptree
       - name: Import check
diff --git a/github-actions/mlflow/protos.yml b/github-actions/mlflow/protos.yml
@@ -43,21 +43,18 @@ jobs:
         with:
           repository: ${{ github.event.inputs.repository }}
           ref: ${{ github.event.inputs.ref }}
-      - name: Install dependencies
-        run: |
-          pip install --upgrade pip
-          pip install .
+      - uses: ./.github/actions/setup-python
       - name: Run tests
         run: |
           ./dev/test-generate-protos.sh
 
       - name: Test
         run: |
-          python -c "from google.protobuf.internal import api_implementation; assert api_implementation.Type() != 'python'"
-          python -c "import mlflow"
+          uv run python -c "from google.protobuf.internal import api_implementation; assert api_implementation.Type() != 'python'"
+          uv run python -c "import mlflow"
 
           # Ensure mlflow works fine with the python backend. See the following link for more details:
           # https://github.com/protocolbuffers/protobuf/tree/main/python#implementation-backends
           export PROTOCOL_BUFFERS_PYTHON_IMPLEMENTATION=python
-          python -c "from google.protobuf.internal import api_implementation; assert api_implementation.Type() == 'python'"
-          python -c "import mlflow"
+          uv run python -c "from google.protobuf.internal import api_implementation; assert api_implementation.Type() == 'python'"
+          uv run python -c "import mlflow"
diff --git a/github-actions/mlflow/requirements.yml b/github-actions/mlflow/requirements.yml
@@ -24,6 +24,7 @@ env:
   MLFLOW_CONDA_HOME: /usr/share/miniconda
   SPARK_LOCAL_IP: localhost
   PYTHON_VERSION: "3.10" # minimum supported version + 1
+  PIP_EXTRA_INDEX_URL: https://download.pytorch.org/whl/cpu
   PIP_CONSTRAINT: ${{ github.workspace }}/requirements/constraints.txt
   _MLFLOW_TESTING_TELEMETRY: "true"
 
diff --git a/github-actions/mlflow/review.yml b/github-actions/mlflow/review.yml
@@ -19,7 +19,7 @@ jobs:
       contents: read
       models: read
       pull-requests: write
-    timeout-minutes: 10
+    timeout-minutes: 20
     # Run on pull_request events from mlflow/mlflow (not forks) or when anyone comments '/review' on a pull request
     if: >
       (github.event_name == 'pull_request' &&
@@ -78,11 +78,9 @@ jobs:
           sparse-checkout: |
             dev
       - uses: astral-sh/setup-uv@f0ec1fc3b38f5e7cd731bb6ce540c5af426746bb # v6.1.0
-        with:
-          version: 0.7.8
       - name: Install codex
         run: |
-          curl -L -o codex.tar.gz https://github.com/openai/codex/releases/download/rust-v0.25.0/codex-x86_64-unknown-linux-musl.tar.gz
+          curl -L -o codex.tar.gz https://github.com/openai/codex/releases/download/rust-v0.39.0/codex-x86_64-unknown-linux-musl.tar.gz
           tar -xzf codex.tar.gz
           mv codex-x86_64-unknown-linux-musl codex
           chmod +x codex
@@ -162,9 +160,9 @@ jobs:
 
       - name: Run codex
         env:
-          OPENAI_API_KEY: ${{ secrets.OPENAI_API_KEY }}
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           PR_URL: ${{ github.event.issue.pull_request.html_url || github.event.pull_request.html_url}}
         run: |
+          ./codex login --api-key "${{ secrets.OPENAI_API_KEY }}"
           # Use timeout in case codex hangs
-          timeout 5m ./codex exec --skip-git-repo-check "Can you review $PR_URL?" || true
+          timeout 10m ./codex exec --skip-git-repo-check "Can you review $PR_URL?" || true
diff --git a/github-actions/mlflow/tracing.yaml b/github-actions/mlflow/tracing.yaml
@@ -33,6 +33,7 @@ jobs:
     permissions:
       contents: read
     timeout-minutes: 30
+    if: github.event_name != 'pull_request' || github.event.pull_request.draft == false
     steps:
       - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
       - uses: ./.github/actions/setup-python
diff --git a/github-actions/rayshader/pkgdown.yaml b/github-actions/rayshader/pkgdown.yaml
@@ -43,7 +43,7 @@ jobs:
         shell: Rscript {0}
           
       - name: Restore R package cache
-        uses: actions/cache@v2
+        uses: actions/cache@v4
         with:
           path: ${{ env.R_LIBS_USER }}
           key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-7-${{ hashFiles('.github/depends.Rds') }}
diff --git a/github-actions/xgboost/python_wheels_winarm64.yml b/github-actions/xgboost/python_wheels_winarm64.yml
@@ -46,7 +46,7 @@ jobs:
       - name: Build XGBoost Python wheel for Win-ARM64
         run: |
           # Patch to rename pkg to xgboost-cpu
-          python ops/script/pypi_variants.py --use-cpu-suffix=1 --require-nccl-dep=0
+          python ops/script/pypi_variants.py --use-suffix=cpu --require-nccl-dep=na
           cd python-package
           mkdir -p wheelhouse
           pip wheel --no-deps -v . --wheel-dir wheelhouse/
diff --git a/gitignore/igraph.gitignore b/gitignore/igraph.gitignore
@@ -8,3 +8,4 @@
 /build
 /build-*
 /tools/**/*.pyc
+/include/igraph_version.h
diff --git a/gitignore/xtensor.gitignore b/gitignore/xtensor.gitignore
@@ -63,3 +63,6 @@ __pycache__
 # Generated files
 *.pc
 .vscode/settings.json
+
+# Allow tag JSONs under etc/xeus-cpp
+!etc/xeus-cpp/tags.d/
diff --git a/gitlab-ci/data.table.gitlab-ci.yml b/gitlab-ci/data.table.gitlab-ci.yml
@@ -314,6 +314,8 @@ test-win-old:
   tags:
     - saas-macos-medium-m1
   before_script:
+    - curl -LO https://github.com/XQuartz/XQuartz/releases/download/XQuartz-2.8.5/XQuartz-2.8.5.pkg
+    - sudo installer -pkg "$(ls -1t XQuartz-*.pkg | head -n 1)" -target /
     - curl -O $R_BIN
     - sudo installer -pkg "$(ls -1t R-*-arm64.pkg | head -n 1)" -target /
     - sudo Rscript -e "source('https://mac.R-project.org/bin/install.R'); install.libs('gettext')"
diff --git a/pkgdown/forecast_pkgdown.yml b/pkgdown/forecast_pkgdown.yml
@@ -92,6 +92,7 @@ reference:
       - baggedModel
       - bats
       - tbats
+      - mean_model
       - nnetar
       - stlm
       - tslm
@@ -120,6 +121,7 @@ reference:
       - forecast.fracdiff
       - forecast.HoltWinters
       - forecast.lm
+      - forecast.mean_model
       - forecast.mlm
       - forecast.modelAR
       - forecast.mts
diff --git a/pkgdown/rlang_pkgdown.yml b/pkgdown/rlang_pkgdown.yml
@@ -336,5 +336,6 @@ reference:
   - subtitle: Operators
     contents:
       - "`%||%`"
+      - "`%&&%`"
       - "`%|%`"
       - "`%@%`"
diff --git a/rbuildignore/forecast.Rbuildignore b/rbuildignore/forecast.Rbuildignore
@@ -21,3 +21,4 @@ vignettes/*_cache
 ^\.vscode$
 ^rstudio$
 rstudio
+.history
