diff --git a/.github/workflows/pypi-publish.yml b/.github/workflows/pypi-publish.yml index 7b591a2..53b4a88 100644 --- a/.github/workflows/pypi-publish.yml +++ b/.github/workflows/pypi-publish.yml @@ -9,43 +9,64 @@ on: jobs: build: - runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.9 - uses: actions/setup-python@v2 - with: - python-version: 3.9 - - name: Install dependencies - run: | - python -m pip install --upgrade pip - pip install flake8 pytest tox - # - 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: Test with tox - run: | - tox - - name: Build docs - run: | - tox -e docs - - run: touch ./docs/_build/html/.nojekyll - - name: GH Pages Deployment - uses: JamesIves/github-pages-deploy-action@4.1.3 - with: - branch: gh-pages # The branch the action should deploy to. - folder: ./docs/_build/html - clean: true # Automatically remove deleted files from the deploy branch - - name: Build Project and Publish - run: | - python -m tox -e clean,build - - name: Publish package - uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 - with: - user: __token__ - password: ${{ secrets.PYPI_PASSWORD }} + - uses: actions/checkout@v2 + + - name: Set up Python 3.9 + uses: actions/setup-python@v2 + with: + python-version: 3.9 + + # build SQLite from source, because I need 3.35<= + - name: Download SQLite3 + run: | + wget https://www.sqlite.org/2024/sqlite-autoconf-3450300.tar.gz + tar -xvf sqlite-autoconf-3450300.tar.gz + + - name: Install SQLite3 + run: | + ./configure + make + sudo make install + export PATH="/usr/local/lib:$PATH" + working-directory: sqlite-autoconf-3450300 + + - name: Install dependencies + run: | + python -m pip install --upgrade pip + pip install flake8 pytest tox + # - 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: Test with tox + run: | + tox + + - name: Build docs + run: | + tox -e docs + + - run: touch ./docs/_build/html/.nojekyll + + - name: GH Pages Deployment + uses: JamesIves/github-pages-deploy-action@4.1.3 + with: + branch: gh-pages # The branch the action should deploy to. + folder: ./docs/_build/html + clean: true # Automatically remove deleted files from the deploy branch + + - name: Build Project and Publish + run: | + python -m tox -e clean,build + + - name: Publish package + uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29 + with: + user: __token__ + password: ${{ secrets.PYPI_PASSWORD }} diff --git a/README.md b/README.md index 44d1501..d77bbc7 100644 --- a/README.md +++ b/README.md @@ -15,7 +15,7 @@ # scrnaseq -The `scRNAseq` package provides convenient access to several publicly available single-cell datasets in the form of [SingleCellExperiment](https://github.com/biocpy/singlecellexperiment) objects. Users can obtain a `SingleCellExperiment` and transform it into analysis-ready representations for immediate use. +The `scrnaseq` package provides convenient access to several publicly available single-cell datasets in the form of [SingleCellExperiment](https://github.com/biocpy/singlecellexperiment) objects. Users can obtain a `SingleCellExperiment` and transform it into analysis-ready representations for immediate use. To enable discovery, each dataset is decorated with metadata such as the study title/abstract, the species, the number of cells, etc. Users can also contribute their own published datasets to enable re-use by the wider Bioconductor/BiocPy community. @@ -23,7 +23,7 @@ To enable discovery, each dataset is decorated with metadata such as the study t ## Installation -package is published to [PyPI](https://pypi.org/project/scrnaseq/), +Package is published to [PyPI](https://pypi.org/project/scrnaseq/), ```shell pip install scrnaseq