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Add release workflow (#699)
* Create Contents.m * Add workflow file for preparing new release * Update worflow to run on a matrix of platforms * Update CloneNwbTest.m Add ad hoc pc compatibility fix * Update requirements.txt Some requirements are not present by default on windows runners * Update prepare_release.yml Fix problems running tests on mac and windows runners * Update prepare_release.yml Update job name * Update prepare_release.yml Use deploy key as this will job will push back to protected branch * Add page in docs detailing how to create a release * Update releases.rst Fix rst formatting * Update prepare_release.yml
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‎+tests/+unit/+file/CloneNwbTest.m

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@@ -40,6 +40,9 @@ function testCloneNwbFile(testCase)
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function restoreNwbFileClass(classDefStr)
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fid = fopen( fullfile(misc.getMatnwbDir(), 'NwbFile.m'), 'wt' );
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if ispc % Ad hoc fix when saving to file using fwrite on pc
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classDefStr = strrep(classDefStr, newline, '');
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end
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fwrite(fid, classDefStr);
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fclose(fid);
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end

‎+tests/requirements.txt

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hdf5plugin
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scipy
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matplotlib
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hdf5plugin
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dataframe_image
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git+https://github.com/NeurodataWithoutBorders/nwbinspector.git@dev
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git+https://github.com/NeurodataWithoutBorders/pynwb.git@dev

‎.github/workflows/prepare_release.yml

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# Run MATLAB tests across multiple MATLAB versions and create a draft release
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name: Prepare release
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on:
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workflow_dispatch:
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inputs:
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version:
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description: 'Version number in major.minor.patch format, i.e 2.8.0'
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required: true
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type: string
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jobs:
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validate_version:
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runs-on: ubuntu-latest
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steps:
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- name: Check version format
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run: |
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version="${{ github.event.inputs.version }}"
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if [[ ! "$version" =~ ^[0-9]+\.[0-9]+\.[0-9]+$ ]]; then
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echo "Error: Input for 'version' ('$version') is not in the expected major.minor.patch format."
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exit 1
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fi
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echo "Version '$version' is valid."
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run_tests:
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name: Run MATLAB tests (${{ matrix.matlab-version }} on ${{ matrix.os }})
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runs-on: ${{ matrix.os }}
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needs: [validate_version]
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strategy:
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fail-fast: false
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matrix:
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os: [windows-latest, ubuntu-latest, macos-13]
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matlab-version: [R2021a, R2021b, R2022a, R2022b, R2023a, R2023b, R2024a, R2024b]
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include:
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- matlab-version: R2021a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2021b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '1'
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- matlab-version: R2022a
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2022b
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python-version: '3.9'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023a
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2023b
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python-version: '3.10'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024a
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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- matlab-version: R2024b
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python-version: '3.11'
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skip-pynwb-compatibilty-test-for-tutorial: '0'
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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: ${{ matrix.python-version }}
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- name: Install python dependencies
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run: |
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python -m pip install -U pip
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pip install -r +tests/requirements.txt
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python -m pip list
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- name: Configure python env (macOS, ubuntu)
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if: runner.os != 'Windows'
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run: |
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echo "HDF5_PLUGIN_PATH=$(python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)")" >> "$GITHUB_ENV"
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- name: Configure python env (Windows)
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if: runner.os == 'Windows'
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shell: pwsh
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run: |
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$pluginPath = python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)"
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Add-Content -Path $env:GITHUB_ENV -Value "HDF5_PLUGIN_PATH=$pluginPath"
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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: ${{ matrix.matlab-version }}
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- name: Run tests
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uses: matlab-actions/run-command@v2
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env:
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HDF5_PLUGIN_PATH: ${{ env.HDF5_PLUGIN_PATH }}
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with:
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command: |
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setenv("SKIP_PYNWB_COMPATIBILITY_TEST_FOR_TUTORIALS", ...
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num2str(${{ matrix.skip-pynwb-compatibilty-test-for-tutorial }}))
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pyenv("ExecutionMode", "OutOfProcess");
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results = assertSuccess(nwbtest('ReportOutputFolder', '.'));
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assert(~isempty(results), 'No tests ran');
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- name: Upload JUnit results
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if: always()
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uses: actions/upload-artifact@v4
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with:
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name: test-results-${{ matrix.os }}-${{ matrix.matlab-version }}
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path: testResults.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: Check out repository
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uses: actions/checkout@v4
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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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pattern: test-results-*
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merge-multiple: false
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- name: Publish test 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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update_version:
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name: Create new draft relase for given version
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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: Checkout repository using deploy key
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uses: actions/checkout@v4
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with:
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ref: refs/heads/main
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ssh-key: ${{ secrets.DEPLOY_KEY }}
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- name: Update Contents.m file
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run: |
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# Read the template file
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template=$(cat .github/workflows/templates/contents_header_template.txt)
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# Get current date in DD-MMM-YYYY format
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date_string=$(date +"%d-%b-%Y")
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# Get current year
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year_number=$(date +"%Y")
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# Replace placeholders in template
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header="${template/\{\{version_number\}\}/${{ github.event.inputs.version }}}"
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header="${header/\{\{date_string\}\}/$date_string}"
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header="${header/\{\{year_number\}\}/$year_number}"
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# Extract the content after the header from the current Contents.m file
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content=$(awk '/^% -{10,}/{flag=1;next} flag{print}' Contents.m)
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# Combine new header with existing content
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echo "$header" > Contents.m
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echo "$content" >> Contents.m
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- name: Commit updated Contents.m file
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continue-on-error: true
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run: |
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git config user.name "${{ github.workflow }} by ${{ github.actor }}"
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git config user.email "<>"
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git add Contents.m
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git commit -m "Update version number in Contents.m"
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git fetch
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git push
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- name: Set up Python
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uses: actions/setup-python@v4
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with:
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python-version: '3.12' # Pinned to 3.12 because of pybadges dependencies
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- name: Generate tested with badge
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run: |
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pip install --upgrade setuptools
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pip install pybadges
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mkdir -p .github/badges/v${{ inputs.version }}
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python -c "
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from pybadges import badge
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with open('.github/badges/v${{ inputs.version }}/tested_with.svg', 'w') as f:
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f.write(badge(
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left_text='tested with',
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right_text='R2021a | R2021b | R2022a | R2022b | R2023a | R2023b | R2024 | R2024b',
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right_color='green'
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))
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"
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- name: Tag repository with version tag
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if: always()
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run: |
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git fetch
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git config user.name "${{ github.workflow }} by ${{ github.actor }}"
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git config user.email "<>"
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# Create the tag with a message
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git tag -a "${{ inputs.version }}" -m "Release ${{ inputs.version }}"
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# Push the new tag to the remote repository
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git push origin "${{ inputs.version }}"
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# Commit the SVG for the MATLAB releases test badge to gh-badges branch
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- name: Checkout gh-badges branch
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uses: actions/checkout@v4
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with:
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ref: gh-badges
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path: gh-badges
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- name: Push to gh-badges
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run: |
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mkdir -p gh-badges/.github/badges/v${{ inputs.version }}
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cp .github/badges/v${{ inputs.version }}/tested_with.svg gh-badges/.github/badges/v${{ inputs.version }}/tested_with.svg
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cd gh-badges
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git config user.name "${{ github.workflow }} by ${{ github.actor }}"
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git config user.email "<>"
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# Only proceed with commit and push if changes are detected
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if [[ $(git add .github/badges/* --dry-run | wc -l) -gt 0 ]]; then
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git add .github/badges/*
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git commit -m "Update 'tested_with' badge for release v${{ inputs.version }}"
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git push -f
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else
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echo "Nothing to commit"
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fi
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# Create the release
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- name: Create GitHub release
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uses: ncipollo/release-action@v1
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with:
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draft: true
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tag: ${{ inputs.version }}
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generateReleaseNotes: true
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body: |
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![Tested On Platforms](https://raw.githubusercontent.com/NeurodataWithoutBorders/matnwb/refs/heads/gh-badges/.github/badges/tested_on.svg)
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![MATLAB Versions Tested](https://raw.githubusercontent.com/NeurodataWithoutBorders/matnwb/refs/heads/gh-badges/.github/badges/v${{ inputs.version }}/tested_with.svg)

‎.github/workflows/templates/contents_header_template.txt

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% MatNWB : NWB For MATLAB
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% Version {{version_number}} (R2019b+) {{date_string}}
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%
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% Copyright (c) {{year_number}}, Neurodata Without Borders
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% ---------------------------------------------

‎Contents.m

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% MatNWB : NWB For MATLAB
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% Version 2.7.0 (R2019b+) 19-Nov-2024
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%
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% Copyright (c) 2024, Neurodata Without Borders
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% ---------------------------------------------
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%
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% Functions:
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%
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% NwbFile - Root object representing an NWB file.
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% generateCore - Generate Matlab classes from NWB core schema files
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% generateExtension - Generate Matlab classes from NWB extension schema file
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% inspectNwbFile - Run nwbinspector on the specified NWB file
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% nwbClearGenerated - Clear generated class files.
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% nwbExport - Writes an NWB file.
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% nwbInstallExtension - Installs a specified NWB extension.
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% nwbRead - Read an NWB file.
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% nwbtest - Run MatNWB test suite.
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%
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% Namespaces:
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% types - Namespace containing classes for neurodata types.
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% util - Namespace containing utility functions.
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%
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% Folders:
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%
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% tutorials - Livescript tutorials demonstrating how to work with MatNWB
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% namespaces - Cached namespace specifications
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% nwb-schema - Source NWB specification schemas for different NWB versions

‎docs/source/index.rst

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pages/developer/contributing
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pages/developer/documentation
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pages/developer/releases
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‎docs/source/pages/developer/releases.rst

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.. _how-to-create-release:
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How to Create a New Release
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===========================
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1. **Navigate to the** `"Actions" <https://github.com/NeurodataWithoutBorders/matnwb/actions/workflows/prepare_release.yml>`_ **tab** in the MatNwb repository on GitHub.
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2. **Click "Run workflow"**, then:
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- Enter the desired version number in ``major.minor.patch`` format (e.g., ``2.8.0``).
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- Click the **Run workflow** button to start the process.
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3. **Monitor the workflow** as it runs across multiple MATLAB and OS configurations. The workflow is successful if:
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- The version string is valid.
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- All tests pass successfully.
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4. **Confirm the draft release** once the workflow completes:
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- A new tag (matching your version number) is pushed to the repository.
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- A draft release is automatically generated with updated badges and the revised ``Contents.m`` file.
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5. **(Optional) Finalize the release** by editing the draft release in GitHub’s "Releases" section, adding any additional details, and clicking **"Publish release"**.

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