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preparation for new release (#390)
* Refl1d fix (#302) * assure refl1d actually runs from the GUI * don't fail on codecov upload * Improved limits for certain parameters (#304) * set `disable` status on relevant sub/super-phase parameters * Mighell transform (#303) * initial implementation of the mighell algorithm for data with zero variances * fixed chi2 reporting, added MD file with description * unit test update * added docs about Mighell * chi -> chi2 * version bump. dependency fix for release. * modified release version * updated docs * include plopp as a doc dependency
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‎.badgery.yaml‎

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default_branch: master
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develop_branch: develop
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cards:
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- group: Tests
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type: gh_action
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title: Code/package tests (GitHub)
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file: test.yml
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enabled: true
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- group: Tests
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type: gh_action
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title: Tutorial tests (GitHub)
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file: tutorial-tests.yml
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enabled: true
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- group: Tests
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type: gh_action
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title: Package tests (PyPI)
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file: pypi-test.yml
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enabled: true
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- group: Code Quality
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type: codefactor
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title: Code quality (CodeFactor)
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enabled: true
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- group: Code Quality
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type: radon_mi
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title: Maintainability index (radon)
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report: reports/{branch}/maintainability-index.json
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enabled: true
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- group: Code Quality
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type: radon_cc
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title: Cyclomatic complexity (radon)
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report: reports/{branch}/cyclomatic-complexity.json
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enabled: true
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- group: Size
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type: radon_loc
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title: Source/Logical lines of code (radon)
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report: reports/{branch}/raw-metrics.json
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enabled: true
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- group: Size
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type: radon_ff
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title: Functions/Files count (radon)
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report: reports/{branch}/cyclomatic-complexity.json
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enabled: true
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- group: Coverage
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type: codecov
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title: Unit test coverage (Codecov)
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flag: unittests
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enabled: true
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- group: Coverage
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type: interrogate
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title: Docstring coverage (interrogate)
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report: reports/{branch}/coverage-docstring.txt
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enabled: true
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- group: Build & Release
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type: gh_action
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title: Publishing (PyPI)
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workflow: pypi-publish.yml
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enabled: true
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- group: Build & Release
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type: gh_action
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title: Docs build/deployment
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workflow: docs.yml
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enabled: true

‎.codecov.yml‎

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github_checks:
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annotations: true
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annotations: true
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comment:
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layout: "reach, diff, flags, files"
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layout: 'reach, diff, flags, files'
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behavior: default
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require_changes: false # if true: only post the comment if coverage changes
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require_base: no # [yes :: must have a base report to post]
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require_head: yes # [yes :: must have a head report to post]
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require_changes: false # if true: only post the comment if coverage changes
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require_base: no # [yes :: must have a base report to post]
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require_head: yes # [yes :: must have a head report to post]

‎.copier-answers.yml‎

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# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
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_commit: 8bdcedc
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_src_path: gh:/EasyScience/EasyProjectTemplate
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description: A reflectometry python package built on the EasyScience framework.
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max_python: '3.13'
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min_python: '3.9'
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orgname: EasyScience
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packagename: easyreflectometry
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prettyname: Easy Reflectometry Library
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projectname: easyreflectometry
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year: 2024
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# WARNING: Do not edit this file manually.
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# Any changes will be overwritten by Copier.
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_commit: v0.11.2-3-ge3f42a1
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_src_path: gh:easyscience/templates
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lib_docs_url: https://easyscience.github.io/reflectometry-lib
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lib_doi: 10.5281/zenodo.18163581
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lib_package_name: easyreflectometry
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lib_python_max: '3.13'
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lib_python_min: '3.11'
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lib_repo_name: reflectometry-lib
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project_contact_email: support@easyreflectometry.org
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project_copyright_years: 2021-2026
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project_extended_description: A software for performing reflectometry calculations
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based on a layer model and refining its parameters against reflectometry data
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project_name: EasyReflectometry
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project_short_description: Reflectometry data analysis
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project_shortcut: ER
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project_type: lib
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template_type: lib

‎.gitattributes‎

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# SCM syntax highlighting & preventing 3-way merges
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pixi.lock merge=binary linguist-language=YAML linguist-generated=true -diff

‎.github/actions/download-artifact/action.yml‎

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name: 'Download artifact'
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description: 'Wrapper for actions/download-artifact'
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inputs:
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name:
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description: 'Name of the artifact to download'
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required: true
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path:
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description: 'Destination path'
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required: false
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default: '.'
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pattern:
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description: 'Glob pattern to match artifact names (optional)'
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required: false
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default: ''
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merge-multiple:
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description: 'Merge multiple artifacts into the same directory'
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required: false
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default: 'false'
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github-token:
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description: 'GitHub token for cross-repo download (optional)'
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required: false
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default: ''
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repository:
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description: 'owner/repo for cross-repo download (optional)'
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required: false
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default: ''
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run-id:
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description: 'Workflow run ID for cross-run download (optional)'
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required: false
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default: ''
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runs:
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using: 'composite'
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steps:
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- name: Download artifact
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uses: actions/download-artifact@v8
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with:
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name: ${{ inputs.name }}
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path: ${{ inputs.path }}
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pattern: ${{ inputs.pattern }}
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merge-multiple: ${{ inputs.merge-multiple }}
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github-token: ${{ inputs.github-token }}
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repository: ${{ inputs.repository }}
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run-id: ${{ inputs.run-id }}

‎.github/actions/github-script/action.yml‎

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name: 'GitHub Script'
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description: 'Wrapper for actions/github-script'
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inputs:
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script:
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description: 'JavaScript to run'
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required: true
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github-token:
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description: 'GitHub token (defaults to github.token)'
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required: false
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default: ${{ github.token }}
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runs:
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using: 'composite'
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steps:
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- uses: actions/github-script@v9
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with:
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script: ${{ inputs.script }}
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github-token: ${{ inputs.github-token }}

‎.github/actions/setup-easyscience-bot/action.yml‎

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name: 'Setup EasyScience bot for pushing'
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description: 'Create GitHub App token and configure git identity + origin remote'
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inputs:
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app-id:
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description: 'GitHub App ID'
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required: true
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private-key:
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description: 'GitHub App private key (PEM)'
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required: true
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repositories:
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description: 'Additional repositories to grant access to (newline-separated)'
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required: false
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default: ''
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outputs:
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token:
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description: 'Installation access token'
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value: ${{ steps.app-token.outputs.token }}
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runs:
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using: 'composite'
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steps:
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- name: Create GitHub App installation token
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id: app-token
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uses: actions/create-github-app-token@v3
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with:
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client-id: ${{ inputs.app-id }}
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private-key: ${{ inputs.private-key }}
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repositories: ${{ inputs.repositories }}
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- name: Configure git for pushing
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shell: bash
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run: |
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git config user.name "easyscience[bot]"
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git config user.email "${{ inputs.app-id }}+easyscience[bot]@users.noreply.github.com"
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- name: Configure origin remote to use the bot token
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shell: bash
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run: |
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git remote set-url origin https://x-access-token:${{ steps.app-token.outputs.token }}@github.com/${{ github.repository }}.git

‎.github/actions/setup-pixi/action.yml‎

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name: 'Setup Pixi Environment'
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description: 'Wrapper for prefix-dev/setup-pixi'
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inputs:
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environments:
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description: 'Pixi environments to setup'
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required: false
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default: 'default'
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activate-environment:
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description: 'Environment to activate'
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required: false
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default: 'default'
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run-install:
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description: 'Whether to run pixi install'
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required: false
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default: 'true'
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locked:
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description: 'Whether to run pixi install --locked'
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required: false
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default: 'false'
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frozen:
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description: 'Whether to run pixi install --frozen'
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required: false
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default: 'true'
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cache:
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description: 'Whether to use cache'
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required: false
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default: 'false'
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post-cleanup:
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description: 'Whether to run post cleanup'
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required: false
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default: 'false'
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runs:
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using: 'composite'
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steps:
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- uses: prefix-dev/setup-pixi@v0.9.4
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with:
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environments: ${{ inputs.environments }}
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activate-environment: ${{ inputs.activate-environment }}
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run-install: ${{ inputs.run-install }}
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locked: ${{ inputs.locked }}
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frozen: ${{ inputs.frozen }}
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cache: ${{ inputs.cache }}
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post-cleanup: ${{ inputs.post-cleanup }}

‎.github/actions/upload-artifact/action.yml‎

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name: 'Upload artifact'
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description: 'Wrapper for actions/upload-artifact'
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inputs:
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name:
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description: 'Artifact name'
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required: true
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path:
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description: 'File(s)/dir(s)/glob(s) to upload (newline-separated)'
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required: true
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include-hidden-files:
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description: 'Include hidden files'
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required: false
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default: 'true'
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if-no-files-found:
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description: 'warn | error | ignore'
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required: false
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default: 'error'
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compression-level:
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description: '0-9 (0 = no compression)'
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required: false
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default: '0'
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retention-days:
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description: 'Retention in days (optional)'
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required: false
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default: ''
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overwrite:
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description: 'Overwrite an existing artifact with the same name'
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required: false
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default: 'false'
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runs:
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using: 'composite'
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steps:
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- name: Upload artifact
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uses: actions/upload-artifact@v7
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with:
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name: ${{ inputs.name }}
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path: ${{ inputs.path }}
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include-hidden-files: ${{ inputs.include-hidden-files }}
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if-no-files-found: ${{ inputs.if-no-files-found }}
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compression-level: ${{ inputs.compression-level }}
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retention-days: ${{ inputs.retention-days }}
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overwrite: ${{ inputs.overwrite }}

‎.github/actions/upload-codecov/action.yml‎

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name: 'Upload coverage to Codecov'
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description: 'Wrapper for codecov/codecov-action'
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inputs:
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name:
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description: 'Codecov upload name'
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required: true
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flags:
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description: 'Codecov flags'
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required: false
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default: ''
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files:
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description: 'Coverage report files'
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required: true
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fail_ci_if_error:
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description: 'Fail CI if upload fails'
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required: false
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default: 'true'
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verbose:
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description: 'Enable verbose output'
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required: false
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default: 'true'
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token:
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description: 'Codecov token'
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required: true
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runs:
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using: composite
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steps:
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- uses: codecov/codecov-action@v6
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with:
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name: ${{ inputs.name }}
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flags: ${{ inputs.flags }}
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files: ${{ inputs.files }}
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fail_ci_if_error: ${{ inputs.fail_ci_if_error }}
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verbose: ${{ inputs.verbose }}
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token: ${{ inputs.token }}

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