Devel

.envrc

@@ -0,0 +1 @@
+source ./.venv/bin/activate

.gitattributes

@@ -1,18 +1,23 @@
 #
 # Special handling for binary files
-# See https://git-scm.com/book/tr/v2/Customizing-Git-Git-Attributes
-# Install doc2txt https://sourceforge.net/projects/docx2txt/?source=navbar
+# See https://git-scm.com/book/en/v2/Customizing-Git-Git-Attributes
 #
-*.npz binary
-*.xz binary
-*.zip binary
 *.bz2 binary
+*.dll binary
+*.docx binary
+*.duckdb binary
 *.gz binary
-*.zip binary
 *.npy binary
-*.docx binary
-#*.docx binary diff=word
+*.npz binary
 *.png binary
-#*.png diff=exif
+*.so binary
 *.dll binary
 *.pyd binary
+*.sqlite binary
+*.nc binary
+*.parquet binary
+*.xlsx binary
+*.xz binary
+*.zip binary
+# SCM syntax highlighting & preventing 3-way merges
+uv.lock merge=binary linguist-language=TOML linguist-generated=true

.github/dependabot.yml

@@ -1,50 +1,55 @@
+---
+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
 version: 2
 
 updates:
+- package-ecosystem: github-actions
+  directory: /  # Location of package manifests
+  schedule:
+    interval: monthly
+  labels:
+    - "ci"
+    - "github_actions"
+    - "bot"
+  groups:   # open a single pull-request for all GitHub actions updates
+    github-actions:
+      patterns:
+      - '*'
+  open-pull-requests-limit: 10
+  target-branch: devel
+  cooldown:
+    default-days: 7
 
-  - package-ecosystem: pip
-    directory: "/"
-    schedule:
-      interval: daily
-    labels:
-      - "kind/dependencies"
-      - "bot"
-    open-pull-requests-limit: 20
-    target-branch: devel
-
-  - package-ecosystem: "github-actions"
-    # Workflow files stored in the default location of `.github/workflows`
-    directory: "/"
-    schedule:
-      interval: weekly
-      day: tuesday
-    labels:
-      - "area/ci"
-      - "github_actions"
-      - "kind/dependencies"
-      - "bot"
-    open-pull-requests-limit: 10
-    target-branch: devel
+- package-ecosystem: uv
+  directory: /  # Location of package manifests
+  schedule:
+    interval: monthly
+  labels:
+    - "ci"
+    - "dependencies"
+    - "bot"
+  groups:
+    python-dependencies:
+      patterns:
+      - '*'
+  open-pull-requests-limit: 10
+  target-branch: devel
+  cooldown:
+    default-days: 7
 
-  - package-ecosystem: "gitsubmodule"
-    directory: "/"
-    schedule:
-      interval: weekly
-      day: wednesday
-    labels:
-      - "kind/dependencies"
-      - "bot"
-    open-pull-requests-limit: 10
-    target-branch: devel
+- package-ecosystem: "gitsubmodule"
+  directory: "/"
+  schedule:
+    interval: monthly
+  labels:
+    - "kind/dependencies"
+    - "bot"
+  open-pull-requests-limit: 10
+  target-branch: devel
+  cooldown:
+    default-days: 7
 
-  - package-ecosystem: "uv"
-    directory: "/"
-    schedule:
-      interval: weekly
-      day: thursday
-    labels:
-      - "area/ci"
-      - "kind/dependencies"
-      - "bot"
-    open-pull-requests-limit: 10
-    target-branch: devel

.github/workflows/combine-prs.yml

@@ -34,7 +34,7 @@ jobs:
 
     # Steps represent a sequence of tasks that will be executed as part of the job
     steps:
-      - uses: actions/github-script@v7
+      - uses: actions/github-script@v9
         id: fetch-branch-names
         name: Fetch branch names
         with:
@@ -100,7 +100,7 @@ jobs:
             console.log('Combined: ' + combined);
             return combined
       # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
-      - uses: actions/checkout@v4.1.2
+      - uses: actions/checkout@v5
         with:
           fetch-depth: 0
       # Creates a branch with other PR branches merged together
@@ -126,7 +126,7 @@ jobs:
           git pull origin $sourcebranches --no-edit
           git push origin $COMBINE_BRANCH_NAME
       # Creates a PR with the new combined branch
-      - uses: actions/github-script@v7
+      - uses: actions/github-script@v9
         name: Create Combined Pull Request
         env:
           PRS_STRING: ${{ steps.fetch-branch-names.outputs.prs-string }}

.github/workflows/labeler.yml

@@ -26,10 +26,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: Run labeler
-        uses: crazy-max/ghaction-github-labeler@v5
+        uses: crazy-max/ghaction-github-labeler@v6
         with:
           github-token: ${{ secrets.MCKIT_GITHUB_TOKEN }}
           skip-delete: true

.github/workflows/publish.yml

@@ -22,10 +22,10 @@ jobs:
       matrix:
         # ubuntu-20.04 is required to build wheels for older OS (clusters...)
         os: [ubuntu-20.04, ubuntu-latest, windows-latest]
-        python-version: ['3.11', '3.12', '3.13']
+        python-version: ['3.11', '3.12', '3.13', '3.14']
     steps:
       - name: Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
           submodules: 'true'

.github/workflows/release-drafter.yml

@@ -7,6 +7,6 @@ jobs:
   draft_release:
     runs-on: ubuntu-latest
     steps:
-      - uses: release-drafter/release-drafter@v6
+      - uses: release-drafter/release-drafter@v7
         env:
           GITHUB_TOKEN: ${{ secrets.MCKIT_GITHUB_TOKEN }}

.github/workflows/stale.yml

@@ -10,7 +10,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-      - uses: actions/stale@v9
+      - uses: actions/stale@v10
         with:
           repo-token: ${{ secrets.MCKIT_GITHUB_TOKEN }}
           stale-issue-message: 'Stale issue message'

.github/workflows/tests.yml

@@ -8,6 +8,8 @@ on:
       - "master"
       - "devel"
       - "main"
+      - "feat/*"
+      - "pixi-2"
     paths:
       - "**.py"
       - "**.c"
@@ -53,10 +55,10 @@ jobs:
       !contains(github.event.head_commit.message, '[skip_ci]')
     steps:
       - name: ✅ Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
 
       - name: 📦 Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ env.DEFAULT_PYTHON }}
           enable-cache: true
@@ -66,7 +68,7 @@ jobs:
 
       - name: Run pre commit checks
         run: |
-          uv run --no-dev --group pre-commit pre-commit run -a
+          uv run --no-dev --group pre-commit pre-commit run --show-diff-on-failure --color=always --all-files
 
 
   # typing:
@@ -75,7 +77,7 @@ jobs:
   #     !contains(github.event.head_commit.message, '[skip_ci]')
   #   steps:
   #     - name: ✅ Check out the repository
-  #       uses: actions/checkout@v4
+  #       uses: actions/checkout@v5
 
   #     - name: 📦 Install uv
   #       uses: astral-sh/setup-uv@v6
@@ -100,13 +102,13 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: ✅ Check out the repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
         with:
           fetch-depth: 1
           submodules: 'true'
 
       - name: 📦 Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ env.DEFAULT_PYTHON }}
           enable-cache: true
@@ -125,27 +127,26 @@ jobs:
 
   tests:
     name: "Python ${{ matrix.python-version }} on ${{ matrix.os }}"
-    needs: [lint, docs]
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest ]
-        python-version: [ '3.11', '3.12', '3.13' ]
+        python-version: [ '3.11', '3.12', '3.13', '3.14' ]
         include: 
           - os: windows-latest
             python-version: '3.13'  # Windows runner is too slow
 
     steps:
 
       - name: ✅ Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v6
         with:
           fetch-depth: 1
           submodules: 'true'
 
       - name: 📦 Install uv
-        uses: astral-sh/setup-uv@v6
+        uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}
           enable-cache: true
@@ -157,49 +158,11 @@ jobs:
         run: uv sync --all-extras --no-dev --group test
 
       - name: ✅ Run tests
-        run: uv run coverage run --parallel -m pytest
-
-      - name: 🔃 Upload coverage data
-        uses: actions/upload-artifact@v4
-        with:
-          name: coverage-data-${{ runner.os }}-${{ matrix.python-version }}
-          path: ".coverage.*"
-          include-hidden-files: true
-          if-no-files-found: error
-
-  coverage:
-    runs-on: ubuntu-latest
-    needs: tests
-    steps:
-
-      - name: ✅ Check out the repository
-        uses: actions/checkout@v4
-
-      - name: 📦 Install uv
-        uses: astral-sh/setup-uv@v6
-        with:
-          python-version: ${{ env.DEFAULT_PYTHON }}
-          enable-cache: true
-          cache-dependency-glob: |
-            **/uv.lock
-            **/pyproject.toml      
-
-      - name: 🔃 Download coverage data
-        uses: actions/download-artifact@v4
-        with:
-          pattern: coverage-data-*
-          merge-multiple: true
-
-      - name: 📦 Combine coverage data and display human readable report
-        run: |
-          uv run --no-dev --group coverage coverage combine
-          uv run --no-dev --group coverage coverage report
-
-      - name: 📦 Create coverage report
         run: |
-          uv run --no-dev --group coverage coverage xml
+          uv run --group test pytest --cov --cov-report term-missing:skip-covered --cov-report xml
 
       - name: 📤 Upload coverage report
-        uses: codecov/codecov-action@v5
+        uses: codecov/codecov-action@v7
         with:
+          files: coverage.xml
           token: ${{ secrets.CODECOV_TOKEN }}

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
 
   # Standard hooks
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v5.0.0"
+    rev: "v6.0.0"
     hooks:
       - id: check-added-large-files
         exclude: uv.lock
@@ -52,23 +52,21 @@ repos:
       - id: pretty-format-json
         args: [--autofix, --no-ensure-ascii, --no-sort-keys]
         exclude: data|\.ipynb$
-      - id: requirements-txt-fixer
 
 
   - repo: https://github.com/fredrikaverpil/creosote
-    rev: v4.0.3
+    rev: v5.2.0
     hooks:
       - id: creosote
 
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.7.19
+    rev: 0.11.15
     hooks:
       - id: uv-lock 
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.2
+    rev: v0.15.14
     hooks:
-      # linter
       - id: ruff-check
         exclude: ^notebooks|^extern
       # formatter 
@@ -78,7 +76,7 @@ repos:
 
   # Check for common shell mistakes
   - repo: https://github.com/shellcheck-py/shellcheck-py
-    rev: "v0.10.0.1"
+    rev: "v0.11.0.1"
     hooks:
       - id: shellcheck
         args: [ --external-sources ]
@@ -96,7 +94,7 @@ repos:
 
   # Clang format the codebase automatically
   - repo: https://github.com/pre-commit/mirrors-clang-format
-    rev: "v20.1.4"
+    rev: "v22.1.5"
     hooks:
       - id: clang-format
         types_or: [c++, c, cuda]