Fix CI for publishing

Author: chris-zen

.github/workflows/build.yaml

@@ -15,8 +15,8 @@ env:
   PYTHON_VERSION: 3.11
 
 jobs:
-  packages-build:
-    name: Build packages
+  checks:
+    name: Check code
     runs-on: ubuntu-latest
     env:
       RUFF_FORMAT: github
@@ -29,30 +29,70 @@ 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}"
+          echo "${BOLDRED}==> We won't enforce linting errors for the time being, but we will in the future.${RESET}"
 
-      - name: Build packages
-        run: make build-dist
+  sdist-build:
+    name: Build sdist
+    runs-on: ubuntu-latest
+
+    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: Build sdist
+        run: make build-sdist
 
       - name: Upload packages
         uses: actions/upload-artifact@v4
         with:
-          name: python-packages
+          name: sdist
+          path: dist
+
+  wheels-build:
+    name: Build wheels
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - uses: astral-sh/setup-uv@v4
+
+      - name: Build wheels
+        run: make build-wheels
+
+      - name: Upload packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-${{ matrix.os }}
           path: dist
 
   docker-build:
@@ -67,19 +107,24 @@ jobs:
         with:
           python-version: ${{ env.PYTHON_VERSION }}
 
-      - name: Prepare virtual environment
-        run: make create-env
+      - uses: astral-sh/setup-uv@v4
 
       - name: Check Dockerfile
         run: make check-docker
 
       - name: Build Docker image
-        run: make build-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
+
   docs-build:
     name: Build documentation
     runs-on: ubuntu-latest
@@ -92,10 +137,9 @@ 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
+      - name: Build the docs
         shell: bash
         run: make docs
 
@@ -109,10 +153,6 @@ jobs:
     name: Check version
     runs-on: ubuntu-latest
     if: startsWith(github.ref, 'refs/tags/')
-    needs:
-      - packages-build
-      - docker-build
-      - docs-build
 
     steps:
       - uses: actions/checkout@v4
@@ -122,8 +162,7 @@ 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
@@ -134,6 +173,8 @@ jobs:
     if: startsWith(github.ref, 'refs/tags/')
     needs:
       - check-version
+      - sdist-build
+      - wheels-build
 
     steps:
       - uses: actions/checkout@v4
@@ -143,14 +184,15 @@ 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
+          path: dist
 
+      - run: find ./dist -iname "oncodrive*"
+      
       - name: Publish to PyPI
         env:
           PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
@@ -162,18 +204,22 @@ jobs:
     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 +228,4 @@ 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/

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.