cram-archiver 1.0.0__tar.gz

cram_archiver-1.0.0/.github/PULL_REQUEST_TEMPLATE.md

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+
+### Checklist
+- [ ] Pull request details were added to CHANGELOG.rst

cram_archiver-1.0.0/.github/release_checklist.md

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+Release checklist
+- [ ] Check outstanding issues on JIRA and GitHub.
+- [ ] Check README looks fine.
+- [ ] Create a release branch.
+  - [ ] Change current development version in `CHANGELOG.rst` to stable version.
+- [ ] Merge the release branch into `main`.
+- [ ] Created an annotated tag with the stable version number. Include changes 
+from CHANGELOG.rst.
+- [ ] Create a pypi package from the master branch. 
+      (Use `pip install build` and `python -m build .`)
+- [ ] Install the build packages to see if they work.
+- [ ] Push tag to remote.
+- [ ] Push tested packages to pypi.
+- [ ] merge `main` branch back into `develop`.
+- [ ] Create a new release on GitHub.
+- [ ] Update the package on bioconda.

cram_archiver-1.0.0/.github/workflows/ci.yml

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+name: Continous integration
+
+on:
+  pull_request:
+  push:
+    branches:
+      - develop
+      - main
+    tags:
+      - "*"
+
+jobs:
+
+  package-checks:
+    strategy:
+      matrix:
+        tox_env:
+          - lint
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          submodules: recursive
+      - name: Set up Python 3.10
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+      - name: Install tox
+        run: pip install --upgrade tox
+      - name: Run tox -e ${{ matrix.tox_env }}
+        run: tox -e ${{ matrix.tox_env }}
+
+  test:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        python-version:
+          - "3.10"
+          - "3.11"
+          - "3.12"
+          - "3.13"
+        os: ["ubuntu-latest"]
+    steps:
+      - uses: actions/checkout@v4
+      - name: install miniconda
+        uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge,bioconda,defaults
+          channel-priority: strict
+          auto-activate-base: false
+      - name: Set up environment with Python ${{ matrix.python-version }}
+        shell: bash -el {0}
+        run:
+           conda install 'python=${{ matrix.python-version }}' tox 'samtools>=1.22'
+      - name: Run tests
+        shell: bash -el {0}
+        run: tox
+      - name: Upload coverage report
+        uses: codecov/codecov-action@v1

cram_archiver-1.0.0/.gitignore

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+src/cram_archiver/_version.py
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# 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/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

cram_archiver-1.0.0/.pre-commit-config.yaml

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+repos:
+-   repo: https://github.com/pycqa/flake8
+    rev: '7.1.0'
+    hooks:
+    -   id: flake8
+-   repo: https://github.com/pre-commit/mirrors-mypy
+    rev: 'v1.10.1'
+    hooks:
+    -   id: mypy

cram_archiver-1.0.0/CHANGELOG.rst

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+==========
+Changelog
+==========
+
+.. Newest changes should be on top.
+
+.. This document is user facing. Please word the changes in such a way
+.. that users understand how the changes affect the new version.
+
+1.0.0
+------------------
++ Create a samtools wrapper that can convert BAM files into CRAM and delete
+  them when the checksum tests pass.