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Merge branch 'master' into patch-default-literal
2 parents 24034d5 + 7742f14 commit 3054122

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‎.dockerignore

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@@ -91,7 +91,13 @@ src
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## Project process results
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workflows
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**/*.tif
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## build/release
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archive
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*.zip
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*.tar.gz
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**/*.zip
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**/*.tag.gz
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## Project local configurations
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!config/*.example

‎.github/workflows/tests.yml

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strategy:
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matrix:
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os: [ubuntu-latest]
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python-version: ["3.8", "3.9", "3.10", "3.11"]
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python-version: ["3.10", "3.11", "3.12"]
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allow-failure: [false]
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test-case: [test-unit-only, test-func-only]
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include:
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# experimental python
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- os: ubuntu-latest
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python-version: "3.12"
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python-version: "3.13"
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allow-failure: true
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test-case: test-unit-only
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- os: ubuntu-latest
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python-version: "3.12"
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python-version: "3.13"
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allow-failure: true
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test-case: test-func-only
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# linter tests
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- name: Run Tests
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run: make stop ${{ matrix.test-case }}
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# disable due to confusing and unhelpful messages created by codecov
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# (see )https://github.com/codecov/feedback/issues/304#issuecomment-2492675117)
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# - name: Upload test results to Codecov
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# if: ${{ !cancelled() && success() && matrix.test-case == 'test-coverage-only' }}
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# uses: codecov/test-results-action@v1
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# with:
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# files: reports/coverage-junit.xml,!./cache
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# flags: ${{ matrix.python-version }}
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# token: ${{ secrets.CODECOV_TOKEN }}
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# manually invoke reporting in case of test failure to still generate them
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# otherwise, they would have been generated automatically following the successful coverage run
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- name: Handle Failed Coverage Report
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if: ${{ failure() && matrix.test-case == 'test-coverage-only' }}
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run: make coverage-reports
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# flaky test analysis, which includes failed tests if applicable
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- name: Upload test results to Codecov
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if: ${{ !cancelled() && matrix.test-case == 'test-coverage-only' }}
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uses: codecov/test-results-action@v1
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with:
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files: reports/coverage-junit.xml,!./cache
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flags: ${{ matrix.python-version }}
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token: ${{ secrets.CODECOV_TOKEN }}
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# coverage test analysis
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- name: Upload coverage report
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uses: codecov/codecov-action@v2
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if: ${{ success() && matrix.test-case == 'test-coverage-only' }}

‎.github/workflows/zenodo.yml

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name: Zenodo Release
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on: [push]
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jobs:
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deploy:
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if: ${{ success() && contains(github.ref, 'refs/tags') }}
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runs-on: ubuntu-latest
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env:
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REPORTS_DIR: ${{ github.workspace }}/reports
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CHANGES_HTML: ${{ github.workspace }}/reports/CHANGES_${{ github.ref_name }}.html
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steps:
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- uses: actions/checkout@v3
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with:
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fetch-depth: "0"
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- name: Generate Archive
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# We don't use releases, but tags. Therefore, we have to make the zip ourselves.
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# env:
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# tarball: ${{ github.event.release.tarball_url }}
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# zipball: ${{ github.event.release.zipball_url }}
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# Add the suffix to the name of the file so type is recognized when
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# downloading from Zenodo .tar.gz for tarball and .zip for zipball.
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# Archiving the zipball will cause Zenodo to show a preview of the contents while using tarball will not.
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run: |
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make generate-archive
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name=$(basename *.zip)
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echo "ZENODO_ARCHIVE=${name}" >> $GITHUB_ENV
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# if changelogs fail to generate, silently ignore
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# prefer a partially generated release than none at all
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- name: Generate Changelog
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id: zenodo_metadata
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run: |
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make generate-changes-html VERSION=${{ github.ref_name }} || true
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cat ${{ env.CHANGES_HTML }}
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- name: Run Zenodo Publish
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id: deploy_zenodo
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uses: fmigneault/zenodo-release@main
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with:
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token: ${{ secrets.ZENODO_TOKEN }}
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version: ${{ github.ref_name }}
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zenodo_json: .zenodo.json
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html_url: ${{ github.server_url }}/${{ github.repository }}/tree/${{ github.ref_name }} # GitHub tag link
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archive: ${{ env.ZENODO_ARCHIVE }}
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description_file: ${{ env.CHANGES_HTML }}
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# DOI for all versions. Leaving this blank (the default) will create
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# a new DOI on every release. Use a DOI that represents all versions will
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# create a new version for this existing DOI.
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# Newer versions have their own DOIs, but they're also linked to this DOI
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# as a different version. When using this, use the DOI for all versions.
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doi: '10.5281/zenodo.14210717'
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- name: View Outputs
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env:
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doi: ${{ steps.deploy_zenodo.outputs.doi }}
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conceptdoi: ${{ steps.deploy_zenodo.outputs.conceptdoi }}
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conceptbadge: ${{ steps.deploy_zenodo.outputs.conceptbadge }}
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badge: ${{ steps.deploy_zenodo.outputs.badge }}
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bucket: ${{ steps.deploy_zenodo.outputs.bucket }}
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latest: ${{ steps.deploy_zenodo.outputs.latest }}
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latest_html: ${{ steps.deploy_zenodo.outputs.latest_html }}
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record: ${{ steps.deploy_zenodo.outputs.record }}
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record_html: ${{ steps.deploy_zenodo.outputs.record_html }}
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run: |
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echo "doi ${doi}"
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echo "conceptdoi ${conceptdoi}"
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echo "conceptbadge ${conceptbadge}"
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echo "badge ${badge}"
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echo "bucket ${bucket}"
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echo "latest ${latest}"
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echo "latest html ${latest_html}"
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echo "record ${record}"
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echo "record html ${record_html}"

‎.gitignore

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## project process results
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*.tif
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*.zip
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./workflow[s]
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## build/release
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archive
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*.zip
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*.tar.gz
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**/*.zip
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**/*.tag.gz
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## old project sources
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[Bb]in

‎.pylintrc

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R0901,too-many-ancestors,
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R0902,too-many-instance-attributes,
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R0904,too-many-public-methods,
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R0911,too-many-return-statements,
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R0912,too-many-branches,
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R0913,too-many-arguments,
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R0914,too-many-locals,

‎.zenodo.json

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{
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"upload_type": "software",
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"title": "crim-ca/weaver:6.2.0",
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"description": "Weaver: Workflow Execution Management Service (EMS); Application, Deployment and Execution Service (ADES); OGC API - Processes; WPS; CWL Application Package",
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"version": "6.2.0",
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"creators": [
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{
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"name": "Charette-Migneault, Francis",
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"orcid": "0000-0003-4862-3349",
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"affiliation": "Computer Research Institute of Montréal"
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}
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],
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"contributors": [
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{
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"name": "Computer Research Institute of Montréal",
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"type": "HostingInstitution"
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},
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{
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"name": "Charette-Migneault, Francis",
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"orcid": "0000-0003-4862-3349",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectLeader"
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},
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{
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"name": "Byrns, David",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Caron, David",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Pelletier, Francis",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Gagnon-Grenier, Félix",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Azeli, Nazim",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Perron, Louis-David",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Cummings, Charles-William",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Trapsida, Nadir",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Lacoursière, Éric",
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"affiliation": "Computer Research Institute of Montréal",
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"type": "ProjectMember"
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},
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{
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"name": "Schwartz, Misha",
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"affiliation": "University of Toronto",
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"type": "ProjectMember"
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}
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],
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"communities": [
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{
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"identifier": "crim"
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},
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{
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"identifier": "birdhouse"
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}
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],
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"related_identifiers": [
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{
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"identifier": "10.5281/zenodo.14210717",
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"relation": "isPartOf",
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"scheme": "doi"
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},
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{
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"identifier": "https://github.com/crim-ca/weaver",
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"scheme": "url",
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"relation": "isMetadataFor",
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"resource_type": "software"
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},
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{
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"identifier": "https://osf.io/d3esv/",
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"scheme": "url",
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"relation": "isVariantFormOf",
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"resource_type": "other"
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},
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{
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"identifier": "https://pavics-weaver.readthedocs.io/",
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"scheme": "url",
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"relation": "isDocumentedBy",
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"resource_type": "other"
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}
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],
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"custom": {
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"code:codeRepository": "https://github.com/crim-ca/weaver",
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"code:programmingLanguage": [
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{
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"id": "python",
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"title": {"en": "Python"}
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}
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],
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"code:developmentStatus": [
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{
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"id": "active",
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"title": {"en": "Active"}
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}
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]
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},
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"language": "eng",
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"keywords": [
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"OGC",
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"OGC API - Processes",
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"CWL",
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"Common Workflow Language",
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"WPS",
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"Web Processing Service",
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"Workflow",
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"Remote Execution",
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"Web API",
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"bird-house"
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],
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"access_right": "open",
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"license": "Apache-2.0"
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}

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