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* Version bump 3.0.0rc2 * Fix master / main branch naming in GH action * Fix typos in README file * Add pypi GH action * Fix PyPI linting errors * Reduce version to 3.0.0rc1 * Add a changelog * Install changelog with package * Change PyPI CD trigger to published release * Add rank metric #15 (#42) * Push all changes made on fork * Set Setuptools version also for external yml * Fixed erroneous variable names in matrix files * deleted A_2601_9 matrix for now. Caused troubles * Add A2601_9 syf matrix for debugging * Fixed bug in test caused by addition of A*26:01 matrix * Change solver from cbc to glpk to investigate if macOS dependant env problems in github actions can be solved * Corrected after review * Adjust tutorials to new structure * Change filter_result as discussed * Adjusted filter method and tutorials according to #12 * Fixed a bug occuring for netMHCfamily tools when peptide input has multiple lengths * remove logging * Alter filter_result method as discussed * Fixed issues #38, #44 and #45 (#46) * Fixed issues #44 and #45 * Fix #48, include review suggestions * Improve/update documentation (#50) * Update CHANGELOG * Extend README * Change framework name in code comment * Remove logging warning * Change file ending in tutorial * Add docstrings, minor formatting * Update CHANGELOG version and setup.py * Update date Co-authored-by: Leon Kuchenbecker <[email protected]> Co-authored-by: Jonas Scheid <[email protected]>
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name: PyPI | ||
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on: | ||
release: | ||
types: [published] | ||
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jobs: | ||
pypi-publish: | ||
name: Publish tagged release on PyPI | ||
runs-on: ubuntu-18.04 | ||
steps: | ||
- uses: actions/checkout@master | ||
- name: Install utilities | ||
run: sudo apt-get install -y mmv | ||
- name: Set up Python 3.7 | ||
uses: actions/setup-python@v1 | ||
with: | ||
python-version: 3.7 | ||
- name: Install pypa/build | ||
run: >- | ||
python -m | ||
pip install | ||
build | ||
--user | ||
- name: Build a binary wheel and a source tarball | ||
run: >- | ||
python -m | ||
build | ||
--sdist | ||
--wheel | ||
--outdir dist/ | ||
. | ||
- name: Create timestamp | ||
run: echo timestamp=$(date +%s) >> $GITHUB_ENV | ||
- name: Rename built files to include timestamp | ||
run: | | ||
mmv -v dist/'*.*.*-*' dist/'#1.#2.#3-'$timestamp'-#4' | ||
mmv -v dist/'*.tar.gz' dist/'#1-'$timestamp.tar.gz | ||
- name: Publish distribution package to PyPI (test) | ||
uses: pypa/gh-action-pypi-publish@master | ||
with: | ||
password: ${{ secrets.TEST_PYPI_API_TOKEN }} | ||
repository_url: https://test.pypi.org/legacy/ | ||
- name: Publish distribution package to PyPI (production) | ||
uses: pypa/gh-action-pypi-publish@master | ||
with: | ||
password: ${{ secrets.PYPI_API_TOKEN }} |
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# epytope: Changelog | ||
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The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | ||
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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## v3.0.0 - 2022-01-26 | ||
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Initial release of `epytope`. `epytope` is the successor project of [`FRED2`](https://github.com/FRED-2/Fred2), which was renamed to a more versioning friendly base name. | ||
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### `Added` | ||
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- [#6](https://github.com/KohlbacherLab/epytope/pull/6) - Add CI for external tools | ||
- [#24](https://github.com/KohlbacherLab/epytope/pull/24) - Add `keras` dependency | ||
- [#26](https://github.com/KohlbacherLab/epytope/pull/26) - Add a license file | ||
- [#31](https://github.com/KohlbacherLab/epytope/pull/31) - Add deployment to `PyPI` | ||
- [#42](https://github.com/KohlbacherLab/epytope/pull/42) - Add new `Syfpeithi` matrices | ||
- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Add support for `NetMHCII 2.3` and `NetMHCIIpan 4.0` | ||
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### `Changed` | ||
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- [#1](https://github.com/KohlbacherLab/epytope/pull/1) - Switch CI/CD from Travis to GitHub Actions | ||
- [#9](https://github.com/KohlbacherLab/epytope/pull/9) - Initial `Python 2` to `Python 3` conversion based on 2to3conv | ||
- [#20](https://github.com/KohlbacherLab/epytope/pull/20) - Use logging module rather than print calls across the library | ||
- [#23](https://github.com/KohlbacherLab/epytope/pull/23) - Rename the package from `FRED-2` to `epytope` | ||
- [#25](https://github.com/KohlbacherLab/epytope/pull/25) - Refactor CI to use more `pip` and less `conda` | ||
- [#42](https://github.com/KohlbacherLab/epytope/pull/42) - Extend `EpitopePredictionResult` structure to store `rank`-based scores | ||
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### `Fixed` | ||
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- [#11](https://github.com/KohlbacherLab/epytope/pull/11) - Fix `Python` version matrix in CI, remove versions that fail | ||
- [#16](https://github.com/KohlbacherLab/epytope/pull/16) - Fix epitope prediction 2to3 bugs and tests | ||
- [#17](https://github.com/KohlbacherLab/epytope/pull/17) - Fix Invalid subprocess handling and `mhcflurry` polluting stdout | ||
- [#18](https://github.com/KohlbacherLab/epytope/pull/18) - Fix external (`NetMHC` tool family) epitope prediction error and temp file handling | ||
- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Fix issues with MHC class-II `CombinedAlleles` [#45](https://github.com/KohlbacherLab/epytope/issues/45) | ||
- [#46](https://github.com/KohlbacherLab/epytope/pull/46) - Do not override `Allele` objects [#38](https://github.com/KohlbacherLab/epytope/issues/38) |
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