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Convert Azure Pipeline to Github Actions (#543)
* add test python requirements * migrate azure pipeline to github actions * Fix test workflow syntax - properly embed bash calls - fix artifact reference name - try to fix MATLAB test discovery * attempt to fix python setup * switch run-test to run-command * try to upload to codecov * Fix CI testing Use version of MATLAB that supports hdf5 dynamically loaded filters. * check ci env setting * fix debug pipeline * more env fixing * fix expected error test id * remove debug prints from ci * add source files to download repo * try different test suite * try different test suite (again) * Try using MATLAB R2024a for tests in workflow * Give test workflow a shorter name * Add codecov settings file * Update versions of dependent actions to latest versions * Update test badge in README.md * Rename utilities folder to tools * Add codespell workflow --------- Co-authored-by: ehennestad <ehennestad@gmail.com> Co-authored-by: Ben Dichter <ben.dichter@gmail.com>
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‎+tests/requirements.txt

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pynwb
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hdf5plugin

‎.codespellrc

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[codespell]
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skip = *.html,*logo_matnwb.svg,*fastsearch.m,*.yaml,*UpdateThirdPartyFromUpstream.sh,*testResults.xml
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skip = *.html,*logo_matnwb.svg,*fastsearch.m,*.yaml,*testResults.xml
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ignore-words-list = DNE,nd,whos

‎.github/.codecov.yaml

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coverage:
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range: "90...100"
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status:
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project:
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default:
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target: 90 # Set the desired coverage target as 90%
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threshold: 1 # Allowable drop in coverage
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patch:
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default:
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# 75% of the changed code must be covered by tests
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threshold: 25
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only_pulls: true

‎.github/workflows/project_action.yml ‎.github/workflows/add_issues_to_projects.yml

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‎.github/workflows/run_codespell.yml

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# Note: This workflow allows specifying a custom location for the Codespell
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# configuration file by defining CONFIG_FILE as an environment variable.
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# A defined subset of options is extracted from this file and passed to the
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# Codespell action. This also ensures that the output of the codespell action
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# prints out the values of these options.
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# Todo: Generalize the extraction of codespell input arguments/options.
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name: Codespell
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on:
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pull_request:
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branches:
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- master
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push:
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branches-ignore:
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- master
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jobs:
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codespell:
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name: Check for spelling errors
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runs-on: ubuntu-latest
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env:
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CONFIG_FILE: .codespellrc
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Extract codespell configurations from configuration file
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id: config
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run: |
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# Extract 'skip' value from the config file, excluding 'skip = ' part
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skip=$(grep -E '^skip' "$CONFIG_FILE" | sed 's/^skip *= *//')
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# Extract 'ignore-words-list' value from the config file, excluding 'ignore-words-list = ' part
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ignore_words=$(grep -E '^ignore-words-list' "$CONFIG_FILE" | sed 's/^ignore-words-list *= *//')
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# Export values as environment variables
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echo "SKIP=$skip" >> $GITHUB_ENV
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echo "IGNORE_WORDS_LIST=$ignore_words" >> $GITHUB_ENV
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- name: Codespell
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uses: codespell-project/actions-codespell@v2
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with:
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skip: "${{ env.SKIP }}"
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ignore_words_list: "${{ env.IGNORE_WORDS_LIST }}"

‎.github/workflows/run_tests.yml

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# Run and publish MATLAB tests with coverage
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name: Run tests
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on:
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pull_request:
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branches:
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- master
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paths-ignore:
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- "*.md"
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- "*.codespellrc"
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- ".github/**"
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push:
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branches:
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- master
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jobs:
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run_tests:
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name: Run MATLAB tests
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runs-on: ubuntu-latest
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steps:
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- name: check out repository
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uses: actions/checkout@v4
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- name: install python
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uses: actions/setup-python@v5
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with:
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python-version: '3.10'
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- name: configure python env
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run: |
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python -m pip install -U pip
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pip install -r +tests/requirements.txt
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echo "HDF5_PLUGIN_PATH=$(python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)")" >> "$GITHUB_ENV"
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- name: install MATLAB
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uses: matlab-actions/setup-matlab@v2
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with:
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release: R2024a # this is necessary to test dynamic filters
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- name: run tests
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uses: matlab-actions/run-command@v2
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with:
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command: results = assertSuccess(nwbtest); assert(~isempty(results), 'No tests ran');
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- name: upload JUnit results
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uses: actions/upload-artifact@v4
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with:
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name: test-results
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path: testResults.xml
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retention-days: 1
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- name: upload coverage results
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uses: actions/upload-artifact@v4
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with:
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name: test-coverage
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path: ./coverage.xml
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publish_junit:
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name: Publish JUnit Test Results
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runs-on: ubuntu-latest
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if: ${{ always() }}
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needs: [run_tests]
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steps:
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- name: retrieve result files
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uses: actions/download-artifact@v4
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with:
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name: test-results
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- name: publish results
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uses: mikepenz/action-junit-report@v4
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with:
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report_paths: 'testResults.xml'
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publish_coverage:
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name: Publish Cobertura Test Coverage
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runs-on: ubuntu-latest
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needs: [run_tests]
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steps:
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- name: check out repository
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uses: actions/checkout@v4
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- name: retrieve code coverage files
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uses: actions/download-artifact@v4
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with:
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name: test-coverage
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- name: publish on Codecov
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uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }}
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files: coverage.xml
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name: codecov-matnwb
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verbose: true

‎README.md

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![MatNWB Logo](logo/logo_matnwb_small.png)
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[![Open in MATLAB Online](https://www.mathworks.com/images/responsive/global/open-in-matlab-online.svg)](https://matlab.mathworks.com/open/github/v1?repo=NeurodataWithoutBorders/matnwb&file=tutorials/basicUsage.mlx)
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[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/matnwb/branch/master/graph/badge.svg?token=apA7F24NsO)](https://codecov.io/gh/NeurodataWithoutBorders/matnwb) ![Azure DevOps tests](https://img.shields.io/azure-devops/tests/NeurodataWithoutBorders/matnwb/4)
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[![codecov](https://codecov.io/gh/NeurodataWithoutBorders/matnwb/branch/master/graph/badge.svg?token=apA7F24NsO)](https://codecov.io/gh/NeurodataWithoutBorders/matnwb)
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[![Run tests](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_tests.yml/badge.svg)](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_tests.yml?query=event%3Apush+branch%3Amaster)
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[![Codespell](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_codespell.yml/badge.svg?branch=master)](https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/run_codespell.yml?query=event%3Apush+branch%3Amaster)
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MatNWB is a Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.x files.
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‎azure-pipelines.yml

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This file was deleted.

‎tools/maintenance/validateCodecovSettings.m

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function validateCodecovSettings()
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% validateCodecovSettings Validate a codecov settings file.
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%
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% Note: This is a utility function developer's can use to check the
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% codecov settings file in .github/.codecov.yaml
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sysCommand = sprintf("curl -X POST --data-binary @%s https://codecov.io/validate", ...
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fullfile(misc.getMatnwbDir, '.github', '.codecov.yaml'));
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[status, message] = system(sysCommand);
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assert(status == 0, 'Curl command failed')
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assert(contains(message, 'Valid!'), ...
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'Codecov settings file is invalid')
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end

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