Merge branch 'main' into add_consume_file

oxli-bio · Oct 2, 2024 · 5d31c76 · 5d31c76
2 parents 556e6b5 + e5aac64
commit 5d31c76
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diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
@@ -1,4 +1,4 @@
-# This file is autogenerated by maturin v1.4.0
+# This file is autogenerated by maturin v1.7.1
 # To update, run
 #
 #    maturin generate-ci github
@@ -9,7 +9,6 @@ on:
   push:
     branches:
       - main
-      - master
     tags:
       - '*'
   pull_request:
@@ -20,71 +19,122 @@ permissions:
 
 jobs:
   linux:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+          - runner: ubuntu-latest
+            target: s390x
+          - runner: ubuntu-latest
+            target: ppc64le
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
+          target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
           manylinux: auto
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-linux-${{ matrix.platform.target }}
+          path: dist
+
+  musllinux:
+    runs-on: ${{ matrix.platform.runner }}
+    strategy:
+      matrix:
+        platform:
+          - runner: ubuntu-latest
+            target: x86_64
+          - runner: ubuntu-latest
+            target: x86
+          - runner: ubuntu-latest
+            target: aarch64
+          - runner: ubuntu-latest
+            target: armv7
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Build wheels
+        uses: PyO3/maturin-action@v1
+        with:
+          target: ${{ matrix.platform.target }}
+          args: --release --out dist --find-interpreter
+          sccache: 'true'
+          manylinux: musllinux_1_2
+      - name: Upload wheels
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheels-musllinux-${{ matrix.platform.target }}
           path: dist
 
   windows:
-    runs-on: windows-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x64, x86]
+        platform:
+          - runner: windows-latest
+            target: x64
+          - runner: windows-latest
+            target: x86
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
-          architecture: ${{ matrix.target }}
+          python-version: 3.x
+          architecture: ${{ matrix.platform.target }}
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
+          target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-windows-${{ matrix.platform.target }}
           path: dist
 
   macos:
-    runs-on: macos-latest
+    runs-on: ${{ matrix.platform.runner }}
     strategy:
       matrix:
-        target: [x86_64, aarch64]
+        platform:
+          - runner: macos-12
+            target: x86_64
+          - runner: macos-14
+            target: aarch64
     steps:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: '3.10'
+          python-version: 3.x
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          target: ${{ matrix.target }}
+          target: ${{ matrix.platform.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
       - name: Upload wheels
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-macos-${{ matrix.platform.target }}
           path: dist
 
   sdist:
@@ -97,24 +147,25 @@ jobs:
           command: sdist
           args: --out dist
       - name: Upload sdist
-        uses: actions/upload-artifact@v3
+        uses: actions/upload-artifact@v4
         with:
-          name: wheels
+          name: wheels-sdist
           path: dist
 
   release:
     name: Release
     runs-on: ubuntu-latest
-    if: "startsWith(github.ref, 'refs/tags/')"
-    needs: [linux, windows, macos, sdist]
+    if: "startsWith(github.ref, 'refs/tags/v')"
+    needs: [linux, musllinux, windows, macos, sdist]
+    # Specifying a GitHub environment is optional, but strongly encouraged
+    environment: release
+    permissions:
+    # IMPORTANT: this permission is mandatory for trusted publishing
+      id-token: write
     steps:
       - uses: actions/download-artifact@v4
-        with:
-          name: wheels
       - name: Publish to PyPI
         uses: PyO3/maturin-action@v1
-        env:
-          MATURIN_PYPI_TOKEN: ${{ secrets.PYPI_API_TOKEN }}
         with:
           command: upload
-          args: --non-interactive --skip-existing *
+          args: --non-interactive --skip-existing wheels-*/*
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
@@ -0,0 +1,34 @@
+name: Python Tests
+
+on: [pull_request]
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      matrix:
+        python-version: ["3.10", "3.11", "3.12"]  # Test with Python 3.10 to the latest available version
+
+    steps:
+      # Checkout the latest commit associated with the PR
+      - uses: actions/checkout@v4
+
+      - name: Debug matrix value
+        run: echo "Python version is ${{ matrix.python-version }}"
+
+      # Set up Python based on the matrix version
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      # Install dependencies, including test dependencies from pyproject.toml
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install '.[test]'  # Install all dependencies, including test-specific ones
+
+      # Run pytest on the specified directory
+      - name: Run tests
+        run: pytest src/python/tests
diff --git a/.github/workflows/ruff.yml b/.github/workflows/ruff.yml
@@ -1,5 +1,5 @@
 name: Ruff Formatting
-on: [push, pull_request]
+on: [pull_request]
 jobs:
   ruff:
     runs-on: ubuntu-latest
@@ -10,6 +10,7 @@ jobs:
       - uses: actions/checkout@v4
         with:
           ref: ${{ github.sha }}
+          token: ${{ secrets.ACTION_TOKEN }}
       - uses: chartboost/ruff-action@v1
         with:
           src: './src/python'

diff --git a/.gitpod.Dockerfile b/.gitpod.Dockerfile
@@ -0,0 +1,34 @@
+# Image source code: https://github.com/axonasif/workspace-images/tree/tmp
+# Also see https://github.com/gitpod-io/workspace-images/issues/1071
+FROM axonasif/workspace-base@sha256:8c057b1d13bdfe8c279c68aef8242d32110c8d5310f9a393f9c0417bc61367d9
+
+# Set user
+USER gitpod
+
+# Install Miniconda
+RUN wget --quiet https://repo.anaconda.com/miniconda/Miniconda3-py311_24.1.2-0-Linux-x86_64.sh -O ~/miniconda.sh && \
+    /bin/bash ~/miniconda.sh -b -p $HOME/miniconda && \
+    rm ~/miniconda.sh
+
+# Add Miniconda to PATH
+ENV PATH="$HOME/miniconda/bin:$PATH"
+
+# Initialize conda in bash config files:
+RUN conda init bash
+
+# Set up Conda channels
+RUN conda config --add channels conda-forge && \
+    conda config --add channels bioconda && \
+    conda config --set channel_priority strict
+
+# Set libmamba as solver
+RUN conda config --set solver libmamba
+
+# Persist ~/ (HOME) and lib
+RUN echo 'create-overlay $HOME /lib' > "$HOME/.runonce/1-home-lib_persist"
+
+# Referenced in `.vscode/settings.json`
+ENV PYTHON_INTERPRETER="$HOME/miniconda/bin/python"
+
+# Pycharm recognizes this variables
+ENV PYCHARM_PYTHON_PATH="${PYTHON_INTERPRETER}"
diff --git a/.gitpod.yml b/.gitpod.yml
@@ -0,0 +1,25 @@
+image:
+  file: .gitpod.Dockerfile
+
+tasks:
+  - name: Init Gitpod Workspace
+    init: |
+      conda install --yes --solver=libmamba -c conda-forge -c bioconda "compilers" "maturin>=1,<2" "pytest" "rust" "scipy" "toml"
+      conda clean --all --yes
+    command: |
+      echo "Running: $GITPOD_WORKSPACE_URL"
+
+ports:
+  - name: Jupyter Notebook
+    port: 8888
+    onOpen: open-browser
+
+vscode:
+  extensions:
+    - eamodio.gitlens
+    - github.vscode-pull-request-github
+    - janisdd.vscode-edit-csv
+    - mechatroner.rainbow-csv
+    - ms-python.debugpy
+    - ms-python.python
+
diff --git a/Cargo.lock b/Cargo.lock
diff --git a/Cargo.toml b/Cargo.toml
@@ -1,6 +1,6 @@
 [package]
 name = "oxli"
-version = "0.2.3"
+version = "0.3.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html