Merge branch 'main' into test/msvc

.github/workflows/build-conan-deps.yml

@@ -45,7 +45,7 @@ jobs:
 
     env:
       CONAN_HOME: "${{ github.workspace }}/.conan2"
-      IMAGE: quay.io/pypa/manylinux_2_28_${{ inputs.arch }}
+      IMAGE: quay.io/pypa/manylinux_2_28_${{ inputs.arch }}:2024.11.09-1
 
     outputs:
       conan-key: ${{ steps.generate-cache-key.outputs.conan-key }}
@@ -107,6 +107,30 @@ jobs:
           path: ${{ env.CONAN_HOME }}/p
           lookup-only: true
 
+      - name: Configure Conan
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: |
+          cat << 'EOF' | tee script.sh > /dev/null
+          #!usr/bin/env bash
+          set -u
+          set -e
+
+          conan_version="$1"
+
+          PATH="/opt/python/cp312-cp312/bin:$PATH"
+          pip install "conan==$conan_version"
+
+          conan remote update conancenter --url https://center2.conan.io
+          EOF
+
+          chmod 755 script.sh
+
+          docker run \
+            -e "CONAN_HOME=$CONAN_HOME" \
+            -v "$PWD/script.sh:/tmp/script.sh:ro" \
+            -v "$CONAN_HOME:$CONAN_HOME" \
+            "$IMAGE" /tmp/script.sh '${{ inputs.conan-version }}'
+
       - name: Clean Conan cache (pre-build)
         if: steps.cache-conan.outputs.cache-hit != 'true'
         run: |
@@ -261,15 +285,17 @@ jobs:
       - uses: actions/setup-python@v5
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Update build deps
         if: steps.cache-conan.outputs.cache-hit != 'true'
         run: pip install "conan==${{ inputs.conan-version }}"
 
       - name: Configure Conan
         if: steps.cache-conan.outputs.cache-hit != 'true'
-        run: conan profile detect --force
+        run: |
+          conan profile detect --force
+          conan remote update conancenter --url https://center2.conan.io
 
       - name: Clean Conan cache (pre-build)
         if: steps.cache-conan.outputs.cache-hit != 'true'
@@ -366,7 +392,7 @@ jobs:
       - uses: actions/setup-python@v5
         if: steps.cache-conan.outputs.cache-hit != 'true'
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Update build deps
         if: steps.cache-conan.outputs.cache-hit != 'true'
@@ -380,6 +406,8 @@ jobs:
 
           sed -i 's/compiler\.cppstd=.*/compiler.cppstd=${{ inputs.cppstd }}/' "$conan_profile"
 
+          conan remote update conancenter --url https://center2.conan.io
+
       - name: Clean Conan cache (pre-build)
         if: steps.cache-conan.outputs.cache-hit != 'true'
         run: |

.github/workflows/fuzzy-testing.yml

@@ -11,8 +11,6 @@ on:
       - "cmake/**"
       - "src/**"
       - "test/scripts/fuzzer.py"
-      - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
@@ -22,8 +20,6 @@ on:
       - "cmake/**"
       - "src/**"
       - "test/scripts/fuzzer.py"
-      - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
@@ -147,6 +143,10 @@ jobs:
           key: conan-${{ steps.cache-key.outputs.key }}
           path: ${{ env.CONAN_HOME }}/p
 
+      - name: Configure Conan
+        if: steps.cache-conan.outputs.cache-hit != 'true'
+        run: conan remote update conancenter --url https://center2.conan.io
+
       - name: Clean Conan cache (pre-build)
         if: steps.cache-conan.outputs.cache-hit != 'true'
         run: |

.github/workflows/lint-cff.yml

@@ -0,0 +1,62 @@
+# Copyright (C) 2024 Roberto Rossini <[email protected]>
+# SPDX-License-Identifier: MIT
+
+name: Lint CITATION.cff
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - ".github/workflows/lint-cff.yml"
+      - "CITATION.cff"
+
+  pull_request:
+    paths:
+      - ".github/workflows/lint-cff.yml"
+      - "CITATION.cff"
+
+# https://stackoverflow.com/a/72408109
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+defaults:
+  run:
+    shell: bash
+
+jobs:
+  lint-cff:
+    runs-on: ubuntu-latest
+    name: Lint CITATION.cff
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          sparse-checkout: CITATION.cff
+          sparse-checkout-cone-mode: false
+
+      - name: Generate DESCRIPTION file
+        run: |
+          cat << EOF > DESCRIPTION
+          Package: hictkpy
+          Title: What the Package Does (One Line, Title Case)
+          Version: 0.0.0.9000
+          Authors@R:
+            person("First", "Last", , "[email protected]", role = c("aut", "cre"))
+          Description: What the package does (one paragraph).
+          License: MIT
+          Encoding: UTF-8
+          Roxygen: list(markdown = TRUE)
+          RoxygenNote: 7.3.2
+          Imports:
+            cffr
+          EOF
+
+      - name: Setup R
+        uses: r-lib/actions/setup-r@v2
+
+      - name: Add requirements
+        uses: r-lib/actions/setup-r-dependencies@v2
+
+      - name: Lint CITATION.cff
+        run: Rscript -e 'cffr::cff_validate("CITATION.cff")'

.github/workflows/pip.yml

@@ -13,7 +13,6 @@ on:
       - "src/**"
       - "test/**"
       - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
@@ -25,7 +24,6 @@ on:
       - "src/**"
       - "test/**"
       - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
@@ -49,7 +47,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [windows-2022, macos-latest, ubuntu-latest]
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.9", "3.13"]
 
     runs-on: ${{ matrix.os }}
 
@@ -62,7 +60,7 @@ jobs:
           python-version: ${{ matrix.python-version }}
 
       - name: Add requirements
-        run: python -m pip install --upgrade wheel setuptools
+        run: python -m pip install --upgrade conan wheel setuptools
 
       - name: Generate cache key
         id: cache-key
@@ -71,6 +69,9 @@ jobs:
 
           echo "conan-key=pip-${{ matrix.os }}-$hash" >> $GITHUB_OUTPUT
 
+      - name: Configure Conan
+        run: conan remote update conancenter --url https://center2.conan.io
+
       - name: Restore Conan cache
         id: cache-conan
         uses: actions/cache/restore@v4

.github/workflows/wheels.yml

@@ -14,12 +14,9 @@ on:
       - "src/**"
       - "test/**"
       - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
-    tags:
-      - "v*.*.*"
 
   pull_request:
     paths:
@@ -29,7 +26,6 @@ on:
       - "src/**"
       - "test/**"
       - "utils/devel/stubgen.py"
-      - "utils/devel/symlink_pyarrow_libs.py"
       - "CMakeLists.txt"
       - "conanfile.py"
       - "pyproject.toml"
@@ -56,11 +52,13 @@ jobs:
     steps:
       - name: Checkout repo
         uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Setup Python
         uses: actions/setup-python@v5
         with:
-          python-version: "3.12"
+          python-version: "3.13"
 
       - name: Install cibuildwheel
         run: pip install 'cibuildwheel>=2.21'
@@ -177,6 +175,8 @@ jobs:
 
     steps:
       - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
 
       - name: Set up QEMU
         if: startsWith(matrix.os, 'ubuntu')
@@ -228,10 +228,11 @@ jobs:
           fail-on-cache-miss: true
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.21
+        uses: pypa/cibuildwheel@v2.22
         with:
           only: ${{ matrix.wheel-config }}
         env:
+          CIBW_BUILD_VERBOSITY: 1
           CIBW_ENVIRONMENT_LINUX: >
             PIP_VERBOSE=1
             HICTK_CI=1
@@ -249,8 +250,6 @@ jobs:
           CIBW_ENVIRONMENT_PASS_LINUX: >
             CONAN_HOME
             HICTKPY_CONAN_INSTALL_ARGS
-          CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
-          CIBW_MANYLINUX_AARCH64_IMAGE: manylinux_2_28
 
       - name: Verify clean directory
         run: git diff --exit-code
@@ -290,7 +289,37 @@ jobs:
           name: dist
           path: dist.tar
           if-no-files-found: error
-          retention-days: 30
+          retention-days: 7
+
+  pypi-publish:
+    name: Upload release to PyPI
+    if: github.event_name == 'release' && github.event.action == 'published'
+    needs: [package-artifacts]
+    environment:
+      name: PyPI
+      url: https://pypi.org/p/hictkpy
+    permissions:
+      id-token: write
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Download artifacts
+        uses: actions/download-artifact@v4
+        with:
+          name: dist
+          merge-multiple: true
+
+      - name: Extract dist.tar
+        run: |
+          tar -xf dist.tar
+          rm dist.tar
+
+      - name: Upload wheels to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          attestations: true
+          print-hash: true
+          verbose: true
 
   build-wheels-status-check:
     name: Status Check (Build wheels)
@@ -300,11 +329,16 @@ jobs:
       - build-sdist
       - build-wheels
       - package-artifacts
+      - pypi-publish
 
     steps:
       - name: Collect job results
         if: |
-          needs.build-sdist.result != 'success'  ||
-          needs.build-wheels.result != 'success' ||
-          needs.package-artifacts.result != 'success'
+          needs.build-sdist.result != 'success'        ||
+          needs.build-wheels.result != 'success'       ||
+          needs.package-artifacts.result != 'success'  ||
+          (
+           needs.pypi-publish.result != 'success'      &&
+           needs.pypi-publish.result != 'skipped'
+          )
         run: exit 1

.readthedocs.yaml

@@ -5,18 +5,20 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
-  apt_packages:
-    - librsvg2-bin
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
-sphinx:
-  configuration: docs/conf.py
-
-python:
-  install:
-    - requirements: docs/requirements.txt
+  commands:
+    - pip install -r docs/requirements.txt
+    - pip install . -v
+    - docs/update_index_links.py --root-dir "$PWD" --inplace
+    - make -C docs linkcheck
+    - make -C docs html
+    - make -C docs latexpdf
+    - mkdir -p "$READTHEDOCS_OUTPUT/pdf"
+    - cp -r docs/_build/html "$READTHEDOCS_OUTPUT/"
+    - cp docs/_build/latex/hictkpy.pdf "$READTHEDOCS_OUTPUT/pdf/"
 
 formats:
   - pdf