Fix CI for publishing

Author: chris-zen

.github/workflows/build.yaml

@@ -12,11 +12,29 @@ permissions:
 
 env:
   TERM: xterm
-  PYTHON_VERSION: 3.11
+  PYTHON_VERSION: 3.12
 
 jobs:
-  packages-build:
-    name: Build packages
+  check-version:
+    name: Check version
+    runs-on: ubuntu-latest
+    if: startsWith(github.ref, 'refs/tags/')
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: astral-sh/setup-uv@v4
+
+      - name: Check version matching the tag
+        run: make check-version
+
+  check-code:
+    name: Check code
     runs-on: ubuntu-latest
     env:
       RUFF_FORMAT: github
@@ -29,35 +47,27 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
 
       - name: Check format
         run: |
           make check-format || true
           BOLDRED=$(tput bold && tput setaf 1)
           RESET=$(tput sgr0)
-          echo "${BOLDRED}==> We won't fail on formatting errors for the time being, but we will in the future.${RESET}"
+          echo "${BOLDRED}==> We won't penalise formatting errors for the time being, but we will in the future.${RESET}"
 
       - name: Check lint
         run: |
           make check-lint || true
           BOLDRED=$(tput bold && tput setaf 1)
           RESET=$(tput sgr0)
-          echo "${BOLDRED}==> We won't fail on lint errors for the time being, but we will in the future.${RESET}"
-
-      - name: Build packages
-        run: make build-dist
+          echo "${BOLDRED}==> We won't enforce linting errors for the time being, but we will in the future.${RESET}"
 
-      - name: Upload packages
-        uses: actions/upload-artifact@v4
-        with:
-          name: python-packages
-          path: dist
-
-  docker-build:
-    name: Build Docker image
+  docs-build:
+    name: Build documentation
     runs-on: ubuntu-latest
+    needs:
+      - check-code
 
     steps:
       - uses: actions/checkout@v4
@@ -67,22 +77,23 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
-
-      - name: Check Dockerfile
-        run: make check-docker
+      - uses: astral-sh/setup-uv@v4
 
-      - name: Build Docker image
-        run: make build-image
+      - name: Build the docs
+        shell: bash
+        run: make docs
 
-      # TODO: Enable this when we figure out how to run it without having to download several Gigabytes of data.
-      # - name: Test Docker image
-      #   run: make run-example
+      - name: Upload documentation
+        uses: actions/upload-artifact@v4
+        with:
+          name: documentation
+          path: docs/build
 
-  docs-build:
-    name: Build documentation
+  sdist-build:
+    name: Build sdist
     runs-on: ubuntu-latest
+    needs:
+      - check-code
 
     steps:
       - uses: actions/checkout@v4
@@ -92,27 +103,26 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
 
-      - name: Check version matching the tag
-        shell: bash
-        run: make docs
+      - name: Build sdist
+        run: make build-sdist
 
-      - name: Upload documentation
+      - name: Upload packages
         uses: actions/upload-artifact@v4
         with:
-          name: documentation
-          path: docs/build
+          name: packages-sdist
+          path: dist
 
-  check-version:
-    name: Check version
-    runs-on: ubuntu-latest
-    if: startsWith(github.ref, 'refs/tags/')
+  wheels-build:
+    name: Build wheels
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
     needs:
-      - packages-build
-      - docker-build
-      - docs-build
+      - check-code
 
     steps:
       - uses: actions/checkout@v4
@@ -122,18 +132,25 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
 
-      - name: Check version matching the tag
-        run: make check-version
+      - name: Build wheels
+        run: make build-wheels
 
+      - name: Upload packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: packages-wheels-${{ matrix.os }}
+          path: dist
+          
   packages-publish:
     name: Publish packages
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/')
     needs:
       - check-version
+      - sdist-build
+      - wheels-build
 
     steps:
       - uses: actions/checkout@v4
@@ -143,37 +160,74 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
 
       - name: Download packages
         uses: actions/download-artifact@v4
         with:
-          name: python-packages
+          pattern: packages-*
+          merge-multiple: true
+          path: dist
 
       - name: Publish to PyPI
         env:
           PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
         run: make publish-dist
 
+  docker-build:
+    name: Build Docker image
+    runs-on: ubuntu-latest
+    needs:
+      - check-code
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: astral-sh/setup-uv@v4
+
+      - name: Check Dockerfile
+        run: make check-docker
+
+      - name: Build Docker image
+        run: make save-image
+
+      # TODO: Enable this when we figure out how to run it without having to download several Gigabytes of data.
+      # - name: Test Docker image
+      #   run: make run-example
+
+      - name: Upload Docker image
+        uses: actions/upload-artifact@v4
+        with:
+          name: docker-image
+          path: oncodrivefml.tar
+          
   docker-push:
     name: Push Docker image
     if: startsWith(github.ref, 'refs/tags/')
     runs-on: ubuntu-latest
     needs:
       - check-version
+      - docker-build
 
     steps:
-      - if: ${{ env.DOCKER_USERNAME != '' }}
-        uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
+
+      - name: Download Docker image
+        uses: actions/download-artifact@v4
+        with:
+          name: docker-image
 
       - name: Login to DockerHub
         env:
@@ -182,4 +236,4 @@ jobs:
         run: make docker-login
 
       - name: Push Docker image
-        run: make push-image
+        run: make load-image push-image

.gitignore

@@ -38,6 +38,9 @@ docs/build
 # External users tests
 external_checks
 
+# VSCode
+.vscode/
+
 .ruff_cache/
 .venv
 data/

.python-version

@@ -1 +1 @@
-3.11.9
+3.12

CHANGELOG.rst CHANGELOG.md

@@ -1,9 +1,11 @@
 
-Changelog
-=========
+# Changelog
 
-2.4.0
------
+## 2.5.0
+
+- Adopted uv as a build tool and added a CI/CD pipeline
+
+## 2.4.0
 
 - The ``--no-indels`` flags only discards indels, it cannot enable their
   analysis
@@ -13,19 +15,14 @@ Changelog
 - Added seed as option in the configuration file
 - Updated dependencies and dropped Python 3.5 support
 
-2.3.0
------
+## 2.3.0
 
 - Added option to set the size limit for the indels
 
-2.2.0
------
+## 2.2.0
 
 - Simplified signature computation using bgsignature.
   Complex options should be computed externally.
-
 - Adapted to bgparsers 0.9 that require a regions file with header.
-
 - Simplified indels computation as assuming everything in the positive strand.
-
-- Set by default the indels computation as substitutions.
+- Set by default the indels computation as substitutions.