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publish to Pypi (#260)
* drop libsqlite pin (pks seems fixed) * updates to CI/CD * drop the venv * fix norns: pkg_resources * test pip and conda installs * fix conda action * fix pip action
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‎.github/workflows/ci-cd.yml‎

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name: CI/CD
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on:
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push:
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branches: [ "master", "develop" ]
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pull_request:
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branches: [ "master", "develop" ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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ci_pip:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Cleanup build folder 🧹
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run: |
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ls -la ./
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rm -rf ./* || true
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rm -rf ./.??* || true
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ls -la ./
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- name: Setup Python 3.12 🐍
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- name: Setup backend 🏗️
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run: |
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pip install uv
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uv pip install --system hatch pytest pytest-rerunfailures autoflake==1.7 isort==6.0 black==25.1
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- name: Checkout 🛎️
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uses: actions/checkout@v4
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# Builds a wheel needed for the CD
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- name: Build wheel 🎡
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run: hatch build -t wheel
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# Store the wheel in GitHub Actions
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- name: Upload artifact ❄️
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uses: actions/upload-artifact@v4
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with:
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name: genomepy_wheel
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path: dist/
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# Test if the created wheel can be installed
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- name: Install 🛠️
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run: uv pip install --system dist/*.whl --force-reinstall
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- name: Unit tests 📜
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run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py
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- name: Integration tests 📚
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run: |
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genomepy --help
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genomepy annotation --help
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genomepy install --help
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genomepy search --help
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ci_conda:
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runs-on: ubuntu-latest
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defaults:
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run:
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shell: bash -l {0}
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steps:
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- name: Cleanup build folder 🧹
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run: |
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ls -la ./
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rm -rf ./* || true
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rm -rf ./.??* || true
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ls -la ./
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- name: Checkout 🛎️
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uses: actions/checkout@v4
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- name: Setup backend 🏗️
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uses: conda-incubator/setup-miniconda@v3
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with:
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environment-file: environment.yml
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miniforge-version: latest
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- name: Install 🛠️
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run: pip install . --no-deps --ignore-installed
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- name: Unit tests 📜
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run: pytest -vvv --reruns 1 --reruns-delay 10 tests/test_01_basic.py
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- name: Integration tests 📚
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run: |
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genomepy --help
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genomepy annotation --help
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genomepy install --help
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genomepy search --help
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cd:
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needs: ci_pip
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runs-on: ubuntu-latest
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# Only run this job if new work is pushed to "master"
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if: github.event_name == 'push' && github.ref == 'refs/heads/master'
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# # Only run this job on a tagged commit
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# if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags')
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steps:
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- name: Cleanup build folder 🧹
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run: |
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ls -la ./
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rm -rf ./* || true
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rm -rf ./.??* || true
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ls -la ./
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- name: Setup Python 3.12 🐍
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uses: actions/setup-python@v5
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with:
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python-version: 3.12
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- run: mkdir -p dist
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- name: Download artifact ❄️
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uses: actions/download-artifact@v4
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with:
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name: genomepy_wheel
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path: dist/
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- name: Publish to PyPI 🚀
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uses: pypa/gh-action-pypi-publish@release/v1
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with:
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user: __token__
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password: ${{ secrets.PYPI_API_TOKEN }}

‎.github/workflows/docs.yml‎

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name: Build and Deploy
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name: Documentation
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on:
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push:
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branches:
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- master
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- docs # backdoor branch to update docs
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branches: [ "master" ]
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# Allows you to run this workflow manually from the Actions tab
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workflow_dispatch:
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jobs:
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build-and-deploy:
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runs-on: ubuntu-latest
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steps:
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- name: Checkout 🛎️
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uses: actions/checkout@v3
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uses: actions/checkout@v4
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- name: Install & Build 📜
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run: |

‎.travis.yml‎

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before_install:
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# setup mambaforge
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- wget -q -O Mambaforge.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
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- bash Mambaforge.sh -b -p "${HOME}/conda" > /dev/null
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- wget -O Miniforge3.sh "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
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- bash Miniforge3.sh -b -p "${HOME}/conda" > /dev/null
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- source "${HOME}/conda/etc/profile.d/conda.sh"
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- source "${HOME}/conda/etc/profile.d/mamba.sh"
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- mamba activate

‎environment.yml‎

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- click
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- colorama
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- filelock >=3.5
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- libsqlite <3.49 # v3.49.1: no column "size" (this is a diskcache requirement)
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# - libsqlite <3.49 # v3.49.1: no column "size" (this is a diskcache requirement)
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- loguru
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- mygene
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- mysql <=8.4 # 9.3: 'mysql_native_password' cannot be loaded
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# Testing
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- autoflake =1.7
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- black =25.1
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- flake8 =4.0
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- flake8-bugbear =23.3
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# - flake8 =4.0
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# - flake8-bugbear =23.3
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# - flakeheaven # v3.3.0 does not work with python 3.12
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- isort =6.0
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- pytest

‎pyproject.toml‎

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"mygene",
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"mysql-connector-python",
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"norns >=0.1.6",
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"setuptools; python_version >= '3.12'", # norns uses pkg_resources
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"numpy",
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"pandas",
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"pyfaidx >=0.7.2.1",

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