Skip to content

Fix citations

Fix citations #245

Workflow file for this run

name: Github Action
on: [push, pull_request]
jobs:
clean:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Black formatting
uses: lgeiger/black-action@v1.0.1
with:
args: "./"
- name: Check for modified files
id: git-check
run: echo ::set-output name=modified::$(if git diff-index --quiet HEAD --; then echo "false"; else echo "true"; fi)
- name: Push changes
if: steps.git-check.outputs.modified == 'true'
run: |
git config --global user.name "romainsacchi"
git config --global user.email "r_s@me.com"
git remote set-url origin https://x-access-token:${{ secrets.GITHUB_TOKEN }}@github.com/$GITHUB_REPOSITORY
git checkout $GITHUB_HEAD_REF
git commit -am "Black reformating"
git push
build:
runs-on: ${{matrix.os}}
strategy:
matrix:
os: [ubuntu-latest]
needs: clean
steps:
- uses: actions/checkout@v4
- name: Install system dependencies for pyenv
run: |
sudo apt-get update
sudo apt-get install build-essential zlib1g-dev libffi-dev libssl-dev \
libbz2-dev libreadline-dev libsqlite3-dev liblzma-dev \
libncurses-dev tk-dev
- name: Install python version
uses: gabrielfalcao/pyenv-action@v13
with:
default: 3.10.6
command: pip install -U pip
- name: create environment
run: pyenv local 3.10.6 && python -mvenv .venv390
- name: Install dependencies
run: |
pip install -r requirements.txt --upgrade pip
pip install .
pip install pytest
- name: Run tests
run: |
pip list
pytest
Pypi:
runs-on: ubuntu-latest
needs: build
strategy:
fail-fast: false
matrix:
os: [ "ubuntu-latest" ]
python-version: [ "3.11" ]
steps:
- uses: actions/checkout@v4
- name: Install pypa/build
run: >-
python -m
pip install
build
- name: Build a binary wheel and a source tarball
run: >-
python -m
build
--sdist
--wheel
--outdir dist/
.
- name: Publish distribution 📦 to PyPI if Release
if: startsWith(github.ref, 'refs/tags')
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }}
skip-existing: true
- name: Publish distribution 📦 to Test PyPI if Push
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.TEST_PYPI_API_TOKEN }}
repository-url: https://test.pypi.org/legacy/
skip-existing: true
conda:
name: (${{ matrix.python-version }}, ubuntu-latest)
runs-on: ubuntu-latest
needs: build
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: [ "3.11" ]
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
channels: conda-forge,cmutel,konstantinstadler,haasad,romainsacchi
allow-softlinks: true
auto-update-conda: true
activate-environment: test
- name: Conda info
shell: bash -l {0}
run: conda info
- name: Git checkout
uses: actions/checkout@v4
- name: Branch name
run: echo running on branch ${GITHUB_REF##*/}
- name: Publish distribution 📦 to Anaconda if Push from non-master branch
if: github.ref != 'refs/heads/master'
shell: bash -l {0}
run: |
conda clean --all
PKG_NAME=pathways
USER=romainsacchi
conda install anaconda-client
conda install conda-build
mkdir ~/conda-bld
conda config --set anaconda_upload no
export CONDA_BLD_PATH=~/conda-bld
export VERSION=`date +%Y.%m.%d`
conda build "conda/" --old-build-string
ls $CONDA_BLD_PATH/noarch/
anaconda -t ${{ secrets.ANACONDA_CLOUD }} upload -u $USER $CONDA_BLD_PATH/noarch/$PKG_NAME-$VERSION-py_0.tar.bz2 --force
testconda:
name: (${{ matrix.python-version }}, ${{ matrix.os }})
runs-on: ${{ matrix.os }}
needs: conda
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest"]
python-version: [ "3.11" ]
steps:
- uses: actions/checkout@v4
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
channels: conda-forge,cmutel,konstantinstadler,haasad,pascallesage,romainsacchi
allow-softlinks: true
channel-priority: strict
auto-update-conda: true
activate-environment: test
- name: Pull distribution 📦 from Anaconda and test it if master branch
if: github.ref == 'refs/heads/master'
shell: bash -l {0}
run: |
conda install -c romainsacchi pathways
conda update pathways
conda install pytest
pytest
- name: Pull distribution 📦 from Anaconda and test it if non-master branch
if: github.ref != 'refs/heads/master'
shell: bash -l {0}
run: |
conda install -c romainsacchi pathways
conda update pathways
conda install pytest
pytest