merged main

.github/labels.yml

@@ -0,0 +1,35 @@
+- name: "bug"
+  color: "d73a4a"
+  description: "Something isn't working"
+
+- name: "documentation"
+  color: "0075ca"
+  description: "Improvements or additions to documentation"
+
+- name: "duplicate"
+  color: "cfd3d7"
+  description: "This issue or pull request already exists"
+
+- name: "enhancement"
+  color: "a2eeef"
+  description: "New feature or request"
+
+- name: "good first issue"
+  color: "7057ff"
+  description: "Good for newcomers"
+
+- name: "help wanted"
+  color: "008672"
+  description: "Extra attention is needed"
+
+- name: "invalid"
+  color: "e4e669"
+  description: "This doesn't seem right"
+
+- name: "question"
+  color: "d876e3"
+  description: "Further information is requested"
+
+- name: "wontfix"
+  color: "ffffff"
+  description: "This will not be worked on"

.github/workflows/labels.yml

@@ -0,0 +1,26 @@
+name: github
+
+on:
+  push:
+    branches:
+      - 'main'
+    paths:
+      - '.github/labels.yml'
+      - '.github/workflows/labels.yml'
+
+jobs:
+  labeler:
+    runs-on: ubuntu-latest
+    steps:
+      -
+        name: Checkout
+        uses: actions/checkout@v3
+      -
+        name: Run Labeler
+        uses: crazy-max/ghaction-github-labeler@v4
+        with:
+          github-token: ${{ secrets.GITHUB_TOKEN }}
+          yaml-file: .github/labels.yml
+          exclude: |
+            help*
+            *issue

.github/workflows/python-package.yml

@@ -0,0 +1,111 @@
+name: Python package
+
+on:
+  push:
+
+jobs:
+  # cqa:
+  #   runs-on: ubuntu-latest
+
+  #   steps:
+  #   - 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 test dependencies
+  #     run: |
+  #       python -m pip install --upgrade pip
+  #       pip install --use-deprecated=legacy-resolver -e .[dev]
+
+  #   - name: Lint with flake8
+  #     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
+
+  #   - name: Format check with black
+  #     run: |
+  #       black --check src
+
+  #   - name: Security check with bandit
+  #     run: |
+  #       bandit -ll -r src
+
+  test:
+    runs-on: ubuntu-latest
+
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+    - name: Install packages
+      run: |
+        sudo apt install libhts-dev libhts3 libhtscodecs-dev libhtscodecs2 tabix
+
+    - uses: actions/checkout@v3
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+        cache: pip
+        cache-dependency-path: '**/setup.cfg'
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        make develop
+
+    - name: Test with pytest
+      run: |
+        make test
+        
+  deploy:
+    needs:
+    # - cqa
+    - test
+    runs-on: ubuntu-latest
+
+    steps:
+    - name: Environment
+      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 twine
+
+    - name: Build package
+      run: python -m build
+
+    - 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 }}

.github/workflows/stale.yml

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+# https://github.com/actions/stale
+
+name: 'Close stale issues and PRs'
+on:
+  schedule:
+    - cron: '1 1 * * *'
+
+jobs:
+  stale:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/stale@v8
+        with:
+          days-before-issue-stale: 30
+          days-before-issue-close: 7
+          stale-issue-message: 'This issue is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-issue-message: 'This issue was closed because it has been stalled for 7 days with no activity.'
+
+          days-before-pr-stale: 30
+          days-before-pr-close: 7
+          stale-pr-message: 'This PR is stale because it has been open 30 days with no activity. Remove stale label or comment or this will be closed in 7 days.'
+          close-pr-message: 'This PR was closed because it has been stalled for 7 days with no activity.'
+
+          exempt-all-pr-assignees: true

.gitignore

@@ -1,110 +1,22 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*$py.class
-
-# C extensions
-*.so
-
-# Distribution / packaging
-.Python
-env/
-build/
-develop-eggs/
-dist/
-downloads/
-eggs/
-.eggs/
-lib/
-lib64/
-parts/
-sdist/
-var/
-*.egg-info/
-.installed.cfg
+*.bak
 *.egg
-
-# PyInstaller
-#  Usually these files are written by a python script from a template
-#  before PyInstaller builds the exe, so as to inject date/other infos into it.
-*.manifest
-*.spec
-
-# Installer logs
-pip-log.txt
-pip-delete-this-directory.txt
-
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.coverage
-.coverage.*
-.cache
-nosetests.xml
-coverage.xml
-*,cover
-.hypothesis/
-
-# Translations
-*.mo
-*.pot
-
-# Django stuff:
+*.egg-info
 *.log
-local_settings.py
-
-# Flask stuff:
-instance/
-.webassets-cache
-
-# Scrapy stuff:
-.scrapy
-
-# Sphinx documentation
-docs/_build/
-
-# PyBuilder
-target/
-
-# IPython Notebook
-.ipynb_checkpoints
-
-# pyenv
-.python-version
-
-# celery beat schedule file
-celerybeat-schedule
-
-# dotenv
-.env
-
-# virtualenv
-venv/
-ENV/
-
-# Spyder project settings
-.spyderproject
-
-# Rope project settings
-.ropeproject
-
-# PyCharm
-.idea
-
-*~
-*.bak
+*.manifest
 *.orig
-doc/_build
+*.sqlite3
+*~
+.cache
+.coverage
 .eggs
-archive
-misc/docker
-.pytest_cache
-
-doc/changelog/*/.tags
-doc/changelog/*/.tags.mk
-doc/changelog/*/hg-git-remap.pl
+.idea
+.ipynb_checkpoints
+.tox
 .vscode
-
-
-.tags
-.tags.mk
+__pycache__
+archive
+build
+dist
+docs/_build
+nosetests.xml
+venv

CITATION.cff

@@ -0,0 +1,27 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+title: SeqRepo
+type: software
+authors:
+  - given-names: Reece K.
+    family-names: Hart
+  - given-names: Andreas
+    family-names: Prlić
+repository-code: 'https://github.com/biocommons/biocommons.seqrepo'
+license: Apache-2.0
+
+preferred-citation:
+  type: article
+  title: "SeqRepo: A system for managing local collections of biological sequences"
+  authors:
+  - family-names: "Hart"
+    given-names: "Reece K."
+  - family-names: "Prlić"
+    given-names: "Andreas"
+  doi: "10.1371/journal.pone.0239883"
+  journal: "PLoS One"
+  year: 2020
+  month: 12
+  volume: 15
+  issue: 12
+  start: "e0239883"