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Merge pull request #225 from matchms/193-check-conda-package
WIP-193 check conda package
2 parents d1b21e8 + fbed102 commit 1a4bff3

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‎.github/workflows/build.yml‎

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@@ -36,7 +36,7 @@ jobs:
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shell: bash -l {0}
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run: python -m pip install -r conda/requirements-dev.txt
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- name: Conda list
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shell: pwsh
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shell: bash -l {0}
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run: conda list
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- name: Check style against standards using prospector
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shell: bash -l {0}

‎.github/workflows/anaconda.yml‎ renamed to ‎.github/workflows/conda_build.yml‎

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@@ -1,13 +1,11 @@
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name: 'Anaconda Build and Publish'
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name: Anaconda Build
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on:
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release:
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types: [published]
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on: [push, pull_request]
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jobs:
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publish:
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name: Publish conda (${{ matrix.python-version }}, ${{ matrix.os }})
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build:
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name: Build for (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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- uses: actions/checkout@v2
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- uses: goanpeca/setup-miniconda@v1
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with:
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miniconda-version: 'latest'
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activate-environment: matchms-build
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auto-activate-base: false
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auto-update-conda: true
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environment-file: conda/environment-build.yml
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miniconda-version: 'latest'
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python-version: ${{ matrix.python-version }}
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activate-environment: matchms
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auto-activate-base: false
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channels: conda-forge,bioconda,nlesc
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- name: Install required packages
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shell: bash -l {0}
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run: |
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conda install conda-build conda-verify anaconda
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- name: Show conda config
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shell: bash -l {0}
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run: |
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conda info
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conda list
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conda config --show-sources
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conda config --show
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- name: Python info
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shell: bash -l {0}
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run: |
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which python
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python --version
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- name: Build the conda package
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shell: bash -l {0}
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run: |
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conda config --set anaconda_upload no
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export BUILD_FOLDER=./output
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export BUILD_DATE=`date +%Y.%m.%d`
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export BUILD_FOLDER=/tmp/matchms/_build
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mkdir -p $BUILD_FOLDER
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conda build -c bioconda -c conda-forge -c nlesc --output-folder $BUILD_FOLDER .
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- name: Push the package to anaconda cloud
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shell: bash -l {0}
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run: |
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export BUILD_FOLDER=./output
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anaconda -t ${{ secrets.ANACONDA_TOKEN }} upload -u nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
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conda build --numpy 1.18.1 --no-include-recipe \
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--channel bioconda --channel conda-forge \
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--croot $BUILD_FOLDER \
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./conda

‎.github/workflows/conda_publish.yml‎

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name: Anaconda Publish
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on:
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release:
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types: [published]
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jobs:
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publish:
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name: Publish for (${{ matrix.python-version }}, ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: ['ubuntu-latest', 'macos-latest', 'windows-latest']
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python-version: ['3.7']
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steps:
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- uses: actions/checkout@v2
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- uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: matchms-build
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auto-activate-base: false
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auto-update-conda: true
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environment-file: conda/environment-build.yml
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miniconda-version: 'latest'
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python-version: ${{ matrix.python-version }}
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- name: Show conda config
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shell: bash -l {0}
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run: |
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conda info
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conda list
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conda config --show-sources
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conda config --show
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- name: Python info
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shell: bash -l {0}
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run: |
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which python
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python --version
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- name: Build the conda package
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shell: bash -l {0}
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run: |
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conda config --set anaconda_upload no
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export BUILD_FOLDER=/tmp/matchms/_build
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mkdir -p $BUILD_FOLDER
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conda build --numpy 1.18.1 --no-include-recipe \
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--channel bioconda --channel conda-forge \
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--croot $BUILD_FOLDER \
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./conda
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- name: Push the package to anaconda cloud
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shell: bash -l {0}
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run: |
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export BUILD_FOLDER=/tmp/matchms/_build
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anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
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- uses: goanpeca/setup-miniconda@v1
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with:
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activate-environment: matchms-test
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auto-activate-base: false
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auto-update-conda: true
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channels: conda-forge,bioconda,nlesc
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miniconda-version: 'latest'
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python-version: ${{ matrix.python-version }}
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- name: Show conda config
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shell: bash -l {0}
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run: |
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conda info
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conda list
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conda config --show-sources
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conda config --show
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- name: Install the conda package from anaconda repository
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shell: bash -l {0}
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run: |
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conda install conda build -c bioconda -c conda-forge -c nlesc matchms
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- name: Install development dependencies
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shell: bash -l {0}
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run: python -m pip install -r conda/requirements-dev.txt
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- name: Test the installed conda package
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shell: bash -l {0}
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run: |
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cd ${CONDA_PREFIX}/pkgs/matchms-*/site-packages/tests
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pytest --ignore-glob='test_version_string_consistency.py'

‎CHANGELOG.md‎

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## [Unreleased]
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## [0.3.1] - 2020-05-19
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### Added
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- improve conda package https://github.com/matchms/matchms/pull/225
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- Build scripts for Windows and Unix(MacOS and Linux) systems
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- verify conda package after uploading to anaconda repository by installing it
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- conda package also includes `matchms/data` folder
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### Changed
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- conda package fixes [#223](https://github.com/matchms/matchms/pull/223)
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- skip builds for Python 2.X
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- more flexible package versions
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- add deployment requirements to meta.yml
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- verify conda package https://github.com/matchms/matchms/pull/225
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- use conda/environment.yml when building the package
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- split anaconda workflow https://github.com/matchms/matchms/pull/225
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- conda build: tests conda packages on every push and pull request
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- conda publish: publish and test conda package on release
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- update the developer instructions
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- move conda receipe to conda folder
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## [0.3.0] - 2020-05-13
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‎README.rst‎

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* - **Other best practices**
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-
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* - Continuous integration
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- |Python Build| |Anaconda Build and Publish|
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- |Python Build| |Anaconda Build| |Anaconda Publish|
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* - Documentation
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- |ReadTheDocs Badge|
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* - Code Quality
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:target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Python%20Build%22
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:alt: Python Build
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.. |Anaconda Build and Publish| image:: https://github.com/matchms/matchms/workflows/Anaconda%20Build%20and%20Publish/badge.svg
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:target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Anaconda%20Build%20and%20Publish%22
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:alt: Anaconda Build and Publish
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.. |Anaconda Build| image:: https://github.com/matchms/matchms/workflows/Anaconda%20Build/badge.svg
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:target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Anaconda%20Build%22
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:alt: Anaconda Build
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.. |Anaconda Publish| image:: https://github.com/matchms/matchms/workflows/Anaconda%20Publish/badge.svg
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:target: https://github.com/matchms/matchms/actions?query=workflow%3A%22Anaconda%20Publish%22
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:alt: Anaconda Publish
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***********************
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Documentation for users
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conda deactivate
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conda env create --file conda/environment-build.yml
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conda activate matchms-build
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rm -rfv output;mkdir ./output
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BUILD_FOLDER=/tmp/matchms/_build
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rm -rfv $BUILD_FOLDER;mkdir -p $BUILD_FOLDER
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conda build --numpy 1.18.1 --no-include-recipe -c bioconda -c conda-forge \
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--croot /tmp/matchms/_build --output-folder ./output ./conda
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--croot $BUILD_FOLDER ./conda
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The package will saved in ``/tmp/matchms/_build`` folder.
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To install local anaconda package, do:
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.. code-block:: console
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conda install \
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--channel bioconda \
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--channel conda-forge \
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--channel file://${CONDA_PREFIX}/output/noarch/ \
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matchms
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where ``$PATH_TO_TARBALL`` is the path to local conda package with ``tar.bz2`` extension.
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To publish the package on anaconda cloud, do:
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.. code-block:: console
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anaconda --token ${{ secrets.ANACONDA_TOKEN }} upload --user nlesc --force $BUILD_FOLDER/noarch/*.tar.bz2
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where secrets.ANACONDA_TOKEN is a token to be gererated on anaconda cloud website. This secret should be added to repository.
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To remove matchms package:
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.. code-block:: console
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conda remove matchms
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To remove environment:
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To remove matchms-build environment:
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.. code-block:: console
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‎conda/bld.bat‎

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"%PYTHON%" -m pip install --no-deps --ignore-installed . -vv
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mkdir %PREFIX%\site-packages\matchms\data
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copy matchms\data\* %PREFIX%\site-packages\matchms\data\
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if errorlevel 1 exit 1

‎conda/build.sh‎

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#!/bin/bash
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# Show environment variables
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env
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$PYTHON -m pip install --no-deps --ignore-installed . -vv
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# Copy data folder
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mkdir -p $PREFIX/site-packages/matchms/data
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cp matchms/data/* $PREFIX/site-packages/matchms/data/

‎conda/conda_build_config.yaml‎

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numpy:
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- 1.18.4 # [unix]
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- 1.18.4 # [win]

‎conda/meta.yaml‎

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{% set name = "matchms" %}
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{% set version = "0.3.0" %}
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{% set version = "0.3.1" %}
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package:
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name: {{ name|lower }}
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preserve_egg_dir: True
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number: 0
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skip: True # [py2k]
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script: {{PYTHON}} -m pip install --no-deps --ignore-installed . -vv
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requirements:
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build:
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dev_url: https://github.com/matchms/matchms
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extra:
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deploy:
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- anaconda-client
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- setuptools >=0.39
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recipe-maintainers:
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- fdiblen

‎conda/run_tests.sh‎

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#!/bin/bash
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echo ${PREFIX}
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echo ${RECIPE_DIR}
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pip install -r ${RECIPE_DIR}/conda/requirements-dev.txt
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prospector -o grouped -o pylint:pylint-report.txt
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isort --check-only --diff --conda-env matchms --recursive --wrap-length 79 --lines-after-imports 2 --force-single-line --no-lines-before FUTURE --no-lines-before STDLIB --no-lines-before THIRDPARTY --no-lines-before FIRSTPARTY --no-lines-before LOCALFOLDER matchms/ tests/ integration-tests/
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cat readthedocs/_build/coverage/python.txt
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UNCOVERED_MEMBERS=$(grep '*' readthedocs/_build/coverage/python.txt | wc -l)
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UNCOVERED_MEMBERS_ALLOWED=25
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if (( $UNCOVERED_MEMBERS > $UNCOVERED_MEMBERS_ALLOWED )) ; then echo "There are currently ${UNCOVERED_MEMBERS} uncovered members in the documentation, which is more than the ${UNCOVERED_MEMBERS_ALLOWED} allowed."; exit 1;fi
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echo "The code is sufficiently documented with ${UNCOVERED_MEMBERS} uncovered members out of ${UNCOVERED_MEMBERS_ALLOWED} allowed.";
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python setup.py test
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pytest --cov --cov-report term --cov-report xml --junitxml=xunit-result.xml

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