Merge branch 'main' into seqfetcher-test-blank-env

.github/workflows/python-package.yml

@@ -1,47 +1,48 @@
+# https://packaging.python.org/en/latest/guides/publishing-package-distribution-releases-using-github-actions-ci-cd-workflows/
 name: Python package
 
 on:
   push:
+    tags:
+      - '[0-9]+.[0-9]+.[0-9]+'            # release
+      - '[0-9]+.[0-9]+.[0-9]+a[0-9]+'     # alpha
+      - '[0-9]+.[0-9]+.[0-9]+b[0-9]+'     # beta
+      - '[0-9]+.[0-9]+.[0-9]+rc[0-9]+'    # release candidate
+      - '[0-9]+.[0-9]+.[0-9]+.dev[0-9]+'  # dev (not semver compliant)
+      - '[0-9]+.[0-9]+.[0-9]+.post[0-9]+' # post (not semver compliant)
   pull_request:
 
 jobs:
   cqa:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
+    - uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: zsh
+        version: 1.0
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-        python-version: "3.10"
+        python-version: "3.12"
         cache: pip
-        cache-dependency-path: '**/setup.cfg'
+        cache-dependency-path: '**/pyproject.yaml'
 
     - name: Install test dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install --use-deprecated=legacy-resolver -e .[dev]
+        pip install --use-deprecated=legacy-resolver -e .[dev,test]
 
-    - name: Lint with flake8
+    - name: Lint with Ruff
       run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
-
-    - name: Format check with isort
-      run: |
-        isort --check src
+        ruff check .
 
     - name: Format check with Ruff
       run: |
-        ruff format --check src
-
-    # Disable bandit until issues are resolved
-    # - name: Security check with bandit
-    #   run: |
-    #     bandit -ll -r src
+        ruff format --check .
 
   test:
     runs-on: ubuntu-latest
@@ -52,10 +53,15 @@ jobs:
         python-version: ["3.10", "3.11", "3.12"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
+
+    - uses: awalsh128/cache-apt-pkgs-action@latest
+      with:
+        packages: zsh
+        version: 1.0
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
         cache: pip
@@ -64,46 +70,70 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install --use-deprecated=legacy-resolver -e .[test]
+        make develop
 
     - name: Test with pytest
       run: |
         make test
 
-  deploy:
+    - name: Upload coverage data to Codecov
+      run: |
+        # Verify integrity of codecov download
+        curl https://uploader.codecov.io/verification.gpg | gpg --no-default-keyring --keyring trustedkeys.gpg --import
+        curl -Os https://uploader.codecov.io/latest/linux/codecov
+        curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
+        curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
+        gpgv codecov.SHA256SUM.sig codecov.SHA256SUM
+        shasum -a 256 -c codecov.SHA256SUM
+        # Upload coverage report
+        chmod +x codecov
+        ./codecov
+
+  build:
+    name: Build distribution
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
+    runs-on: ubuntu-latest
     needs:
     - cqa
     - test
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+          cache-dependency-path: '**/setup.cfg'
+      - name: Install pypa/build
+        run: >-
+          python3 -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: python3 -m build
+      - name: Store the distribution packages
+        uses: actions/upload-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+
+  publish-to-pypi:
+    name: >-
+      Publish Python distribution to PyPI
+    needs:
+      - build
     runs-on: ubuntu-latest
-
+    environment:
+      name: pypi
+      url: https://pypi.org/p/bioutils
+    permissions:
+      id-token: write # IMPORTANT: mandatory for trusted publishing
     steps:
-    - name: hello world
-      run: |
-        echo "::group::Environment info"
-        echo github.event_name = ${{ github.event_name }}
-        echo refs = ${{ github.ref }}
-        echo tags = ${{ startsWith(github.ref, 'refs/tags') }}
-        echo "::endgroup::"
-
-    - uses: actions/checkout@v3
-
-    - name: Set up Python
-      uses: actions/setup-python@v4
-      with:
-        python-version: "3.10"
-        cache: pip
-        cache-dependency-path: '**/setup.cfg'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install build
-
-    - name: Build package
-      run: python -m build --wheel
-
-    - name: Publish package
-      if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
-      uses: pypa/gh-action-pypi-publish@release/v1
-      with:
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      - name: Download all the dists
+        uses: actions/download-artifact@v4
+        with:
+          name: python-package-distributions
+          path: dist/
+      - name: Publish distribution to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

Makefile

@@ -9,7 +9,7 @@ SHELL:=/bin/bash -e -o pipefail
 SELF:=$(firstword $(MAKEFILE_LIST))
 
 PY_VERSION:=$(shell python3 --version | cut -d" " -f2 | cut -d. -f1-2)
-VE_DIR:=venv/${PY_VERSION}
+VE_DIR=venv
 
 $(info Using Python ${PY_VERSION})
 
@@ -46,10 +46,10 @@ ${VE_DIR}: venv/%:
 	pip install --upgrade pip setuptools wheel
 
 #=> develop: install package in develop mode
-.PHONY: develop install
+#=> develop: install package in develop mode
+.PHONY: develop
 develop:
-	@if [ -z "$${VIRTUAL_ENV}" ]; then echo "Not in a virtual environment; see README.md" 1>&2; exit 1; fi
-	pip install -e .[dev,test]
+	pip install -e ".[dev, test]"
 
 #=> install: install package
 install:

docs/source/conf.py

@@ -6,23 +6,31 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'bioutils'
-copyright = '2019, bioutils Contributors'
-author = 'bioutils Contributors'
+project = "bioutils"
+copyright = "2019, bioutils Contributors"
+author = "bioutils Contributors"
 
 
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
 # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
 # ones.
-extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx', 'sphinx.ext.todo',
-              'sphinx.ext.autosummary', 'sphinx.ext.viewcode', 'sphinx.ext.coverage',
-              'sphinx.ext.doctest', 'sphinx.ext.ifconfig', 'sphinx.ext.mathjax',
-              'sphinx.ext.napoleon']
+extensions = [
+    "sphinx.ext.autodoc",
+    "sphinx.ext.intersphinx",
+    "sphinx.ext.todo",
+    "sphinx.ext.autosummary",
+    "sphinx.ext.viewcode",
+    "sphinx.ext.coverage",
+    "sphinx.ext.doctest",
+    "sphinx.ext.ifconfig",
+    "sphinx.ext.mathjax",
+    "sphinx.ext.napoleon",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -35,9 +43,9 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = "alabaster"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]

src/bioutils/normalize.py

@@ -1,7 +1,6 @@
 # -*- coding: utf-8 -*-
 """Provides functionality for normalizing alleles, ensuring comparable representations."""
 
-import copy
 import enum
 import logging
 import math

tests/conftest.py

@@ -1,7 +1,6 @@
 import logging
 import os
 
-import pytest
 import vcr
 
 # set vcr logging level

tests/test_seqfetcher.py

@@ -6,7 +6,6 @@
 
 from bioutils.seqfetcher import (
     _add_eutils_api_key,
-    _fetch_seq_ensembl,
     _fetch_seq_ncbi,
     fetch_seq,
 )