Merge pull request #37 from complextissue/dev

Author: maltekuehl

.flake8

@@ -1,6 +1,7 @@
 name: Test & lint package & deploy documentation
 
 on:
+  workflow_dispatch:
   schedule:
     # run every Monday at 15:00 UTC
     - cron: "0 15 * * 1"
@@ -11,54 +12,49 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: true
       matrix:
         include:
-          - os: ubuntu-24.04
-            python: "3.12"
+          - os: ubuntu-latest
+            python: "3.13"
+
+    name: Python ${{ matrix.python }}
+
+    env:
+      OS: ${{ matrix.os }}
+      PYTHON: ${{ matrix.python }}
 
     steps:
-      - uses: actions/checkout@v3
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v3
+      - uses: actions/checkout@v5
+      - name: Install the latest version of uv and setup Python
+        uses: astral-sh/setup-uv@v6
         with:
+          version: "latest"
           python-version: ${{ matrix.python-version }}
-      - uses: actions/cache@v3
-        with:
-          path: ${{ env.pythonLocation }}
-          key: ${{ env.pythonLocation }}-${{ hashFiles('pyproject.toml') }}
+          enable-cache: true
       - name: Install dependencies
         run: |
-          export FLIT_ROOT_INSTALL=1
-          python -m pip install --upgrade pip
-          python -m pip install flit
-          python -m flit install --deps production
-          python -m pip install biocframe dolomite dolomite-se summarizedexperiment
-          python -m pip install bandit mypy==1.15.0 ruff==0.11.2
-          python -m pip install coverage pytest sphinx sphinx-autoapi \
-            myst-parser pygments sphinx-autodoc-typehints sphinx-rtd-theme furo sphinx_design sphinx-copybutton \
-            sphinxcontrib-bibtex sphinxcontrib-mermaid nbsphinx pandoc
-          sudo apt-get update
-          sudo apt-get install -y pandoc
+          uv sync --all-extras
       - name: Lint with ruff
         run: |
-          ruff check --fix --exit-non-zero-on-fix pytximport
+          uv run ruff check --fix --exit-non-zero-on-fix pytximport
       - name: Format with ruff
         run: |
-          ruff format --check pytximport
+          uv run ruff format --check pytximport
       - name: Type check with mypy
         run: |
-          python -m mypy -p pytximport
+          uv run mypy -p pytximport
       - name: Check security with bandit
         run: |
-          python -m bandit --verbose --ini .bandit.ini -ll --recursive pytximport
+          uv run bandit --verbose --ini .bandit.ini -ll --recursive pytximport
       - name: Test with pytest
         run: |
-          coverage run -m pytest --maxfail=10
-          coverage xml
-      - name: Upload coverage reports to Codecov
-        uses: codecov/codecov-action@v4.0.1
+          uv run coverage run -m pytest --maxfail=10 -m "not gpu" -m "not no_github_ci"
+          uv run coverage xml
+      - name: Upload coverage to Codecov
+        uses: codecov/codecov-action@v5
         with:
+          fail_ci_if_error: true
           token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/ci.yml

@@ -1,4 +1,4 @@
-name: Upload Python Package
+name: Publish Package
 
 on:
   release:
@@ -8,25 +8,25 @@ permissions:
   contents: read
 
 jobs:
-  deploy:
-
+  pypi-publish:
+    name: Upload release to PyPI
     runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      contents: read
+      id-token: write
 
     steps:
-    - uses: actions/checkout@v4
-    - name: Set up Python
-      uses: actions/setup-python@v3
-      with:
-        python-version: '3.11'
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install flit
-    - name: Build package
-      run: flit build
-    - name: Publish package
-      run: flit publish
-      env:
-        FLIT_USERNAME: '__token__'
-        FLIT_PASSWORD: ${{ secrets.FLIT_PASSWORD }}
-        FLIT_INDEX_URL: 'https://upload.pypi.org/legacy/'
+      - uses: actions/checkout@v5
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version-file: "pyproject.toml"
+      - name: Install the latest version of uv
+        uses: astral-sh/setup-uv@v6
+        with:
+          version: "latest"
+      - name: Build package
+        run: uv build
+      - name: Publish package
+        run: uv publish --trusted-publishing always

.github/workflows/publish.yml

@@ -2,7 +2,7 @@ default_stages: [pre-commit, pre-push]
 
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v6.0.0
     hooks:
       - id: check-yaml
         stages: [pre-commit]
@@ -21,33 +21,34 @@ repos:
         stages: [pre-commit]
       - id: mixed-line-ending
         stages: [pre-commit]
+      - id: no-commit-to-branch
+        args: [--branch=main]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.2
+    rev: v0.13.2
     hooks:
-      - id: ruff
-        args: [--select, I, --fix]
+      - id: ruff-check
+        args: [--select, "I,RUF022", --fix, --exit-non-zero-on-fix]
       - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.15.0
+    rev: "v1.18.2"
     hooks:
       - id: mypy
         stages: [pre-commit]
         language: system
         pass_filenames: false
         args: [-p, pytximport]
   - repo: https://github.com/PyCQA/bandit
-    rev: 1.7.5
+    rev: 1.8.6
     hooks:
       - id: bandit
         stages: [pre-commit]
         args: [--verbose, --ini, .bandit.ini, -ll, --recursive, pytximport]
-  # run the unittests
   - repo: local
     hooks:
       - id: unittests
         stages: [pre-commit]
         name: unittests
-        entry: python -m coverage run -m pytest --maxfail=10
+        entry: uv run coverage run -m pytest --maxfail=10
         language: system
         types: [python]
         pass_filenames: false

.pre-commit-config.yaml

@@ -1,16 +1,18 @@
 version: 2
 build:
-  os: ubuntu-22.04
+  os: ubuntu-24.04
   tools:
-    python: "3.11"
+    python: "3.12"
+  jobs:
+    create_environment:
+      - asdf plugin add uv
+      - asdf install uv latest
+      - asdf global uv latest
+      - uv venv $READTHEDOCS_VIRTUALENV_PATH
+      - UV_PROJECT_ENVIRONMENT=$READTHEDOCS_VIRTUALENV_PATH uv sync --all-extras --link-mode=copy
+    install:
+      - "true"
 
 sphinx:
-   configuration: docs/source/conf.py
-   fail_on_warning: false
-
-python:
-  install:
-  - method: pip
-    path: .
-    extra_requirements:
-    - dev
+  configuration: docs/source/conf.py
+  fail_on_warning: false

.readthedocs.yaml

@@ -1,48 +1,33 @@
 .DEFAULT_GOAL := test
 
-#
-# Virtual environment setup
-# You may want to replace python3 with the path to your python3 executable,
-# e.g. the output of `pyenv which python3`when using pyenv
-#
-create-venv:
-	python3 -m venv '.venv'
-	echo "Don't forget to activate with 'source .venv/bin/activate'"
-
 #
 # Install requirements
 #
 install:
-	python3 -m pip install --upgrade pip
-	python3 -m pip install flit poetry
-	python3 -m flit install --deps production
+	uv sync
 
-install-dev: install
-	python3 -m pip install '.[dev]'
-	python3 -m certifi
+install-dev:
+	uv sync --all-extras
 	pre-commit install --hook-type pre-commit --hook-type pre-push
 	echo "Please also install pandoc to create the documentation."
 
 #
-# Checks & package upload
+# Checks
 #
 check: install-dev
-	ruff format --check pytximport
-	ruff check pytximport
-	mypy -p pytximport
-	bandit -ll --recursive pytximport
-
-upload: check
-	flit publish
+	uv run ruff format --check pytximport
+	uv run ruff check pytximport
+	uv run mypy -p pytximport
+	uv run bandit -ll --recursive pytximport
 
 #
 # Testing
 #
 unittest:
-	coverage run -m pytest --maxfail=10
+	uv run coverage run -m pytest --maxfail=10
 
 coverage-report: unittest
-	coverage report
-	coverage html
+	uv run coverage report
+	uv run coverage html
 
 test: check unittest

Makefile

@@ -29,12 +29,16 @@ The recommended way to install `pytximport` is through Bioconda:
 mamba install -c bioconda pytximport
 ```
 
-`pytximport` can also be installed via pip:
+`pytximport` can also be installed via `pip` or added to your project via `uv`:
 
 ```bash
 pip install pytximport
 ```
 
+```bash
+uv add pytximport
+```
+
 While not required, we recommend users also install `pyarrow` for faster import of tab-separated value-based quantification files:
 
 ```bash
@@ -120,6 +124,7 @@ Generally, outputs from `pytximport` correspond to the outputs from `tximport` w
 While the outputs are identical within floating point tolerance for the same configuration, there remain some differences between the packages:
 
 Features unique to `pytximport`:
+
 - Generating transcript-to-gene maps, either from a BioMart server or an `annotation.gtf` file. Use `create_transcript_gene_map` or `create_transcript_gene_map_from_annotation` from `pytximport.utils`.
 - Command line interface. Type `pytximport --help` into your terminal to explore all options.
 - `AnnData`-support, enabling seamless integration with the `scverse`.
@@ -129,6 +134,7 @@ Features unique to `pytximport`:
 - Post-hoc biotype-filtering using `pytximport.utils.filter_by_biotype`.
 
 Features unique to `tximport`:
+
 - Alevin single-cell RNA-seq data support
 
 Argument order and argument defaults may differ between the implementations.
@@ -142,8 +148,7 @@ To set up `pytximport` for development on your machine, we recommend to git clon
 ```bash
 git clone --depth 1 -b dev https://github.com/complextissue/pytximport.git
 cd pytximport
-pyenv local 3.12
-make create-venv
+uv venv --python 3.13
 source .venv/source/activate
 make install-dev
 ```