Set up minimum CI actions.

.copier-answers.yml

@@ -0,0 +1,17 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: 3f79959
+_src_path: gh:scipp/copier_template
+description: 'Python package to read McStas data and export as python objects in different
+    formats or as other files.
+
+
+    '
+max_python: '3.12'
+min_python: '3.10'
+namespace_package: ''
+nightly_deps: scipp,scippnexus,mcstasscript
+orgname: mccode-dev
+prettyname: McStasToX
+projectname: mcstastox
+related_projects: Scipp,ScippNexus
+year: 2025

.github/dependabot.yml

@@ -1,7 +1,16 @@
 version: 2
 updates:
-  - package-ecosystem: "github-actions"
-    directory: "/"
+  # Note: We are not listing package-ecosystem: "github-actions". This causes
+  # noise in all template instances. Instead dependabot.yml in scipp/copier_template
+  # triggers updates of github-actions in the *template*. We then use `copier update`
+  # in template instances.
+  - package-ecosystem: "pip"
+    directory: "/requirements"
     schedule:
       interval: "weekly"
     target-branch: "main"
+    allow:
+      - dependency-name: "scipp"
+        dependency-type: "direct"
+      - dependency-name: "mcstasscript"
+        dependency-type: "direct"

.github/workflows/ci.yml

@@ -0,0 +1,58 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+      - release
+  pull_request:
+
+jobs:
+  # formatting:
+  #   name: Formatting and static analysis
+  #   runs-on: 'ubuntu-24.04'
+  #   outputs:
+  #     min_python: ${{ steps.vars.outputs.min_python }}
+  #     min_tox_env: ${{ steps.vars.outputs.min_tox_env }}
+  #   steps:
+  #     - uses: actions/checkout@v4
+  #     - name: Get Python version for other CI jobs
+  #       id: vars
+  #       run: |
+  #         echo "min_python=$(< .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+  #         echo "min_tox_env=py$(sed 's/\.//g' < .github/workflows/python-version-ci)" >> "$GITHUB_OUTPUT"
+  #     - uses: actions/setup-python@v5
+  #       with:
+  #         python-version-file: '.github/workflows/python-version-ci'
+  #     - uses: pre-commit/[email protected]
+  #       with:
+  #         extra_args: --all-files
+  #     - uses: pre-commit-ci/[email protected]
+  #       if: always()
+  #       with:
+  #         msg: Apply automatic formatting
+
+  # tests:
+  #   name: Tests
+  #   needs: formatting
+  #   strategy:
+  #     matrix:
+  #       os: ['ubuntu-24.04']
+  #       python:
+  #         - version: '${{needs.formatting.outputs.min_python}}'
+  #           tox-env: '${{needs.formatting.outputs.min_tox_env}}'
+  #   uses: ./.github/workflows/test.yml
+  #   with:
+  #     os-variant: ${{ matrix.os }}
+  #     python-version: ${{ matrix.python.version }}
+  #     tox-env: ${{ matrix.python.tox-env }}
+  #   secrets: inherit
+
+  docs:
+    # needs: tests
+    uses: ./.github/workflows/docs.yml
+    with:
+      publish: false
+      linkcheck: ${{ github.ref == 'refs/heads/main' }}
+      branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
+    secrets: inherit

.github/workflows/docs.yml

@@ -0,0 +1,100 @@
+name: Docs
+
+on:
+  workflow_dispatch:
+    inputs:
+      publish:
+        default: false
+        type: boolean
+      version:
+        default: ''
+        required: false
+        type: string
+      branch:
+        description: 'Branch/tag with documentation source. If not set, the current branch will be used.'
+        default: ''
+        required: false
+        type: string
+  workflow_call:
+    inputs:
+      publish:
+        default: false
+        type: boolean
+      version:
+        default: ''
+        required: false
+        type: string
+      branch:
+        description: 'Branch/tag with documentation source. If not set, the current branch will be used.'
+        default: ''
+        required: false
+        type: string
+      linkcheck:
+        description: 'Run the link checker. If not set the link checker will not be run.'
+        default: false
+        required: false
+        type: boolean
+
+env:
+  VERSION: ${{ inputs.version }}
+
+jobs:
+  docs:
+    name: Build documentation
+    runs-on: 'ubuntu-24.04'
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+        DOCSWORKDIR: ".tox/docs"
+    steps:
+      # - run: sudo apt install --yes graphviz pandoc
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.branch == '' && github.ref_name || inputs.branch }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 0  # history required so cmake can determine version
+      - uses: actions/setup-python@v5
+        with:
+          python-version-file: '.github/workflows/python-version-ci'
+      - uses: mamba-org/setup-micromamba@v2
+        with:
+          init-shell: bash
+          environment-name: mcstas
+          create-args: >-
+            python=3.10
+
+      # Manually building the docs.
+      # We(I) couldn't figure out how we do it with `tox` yet...
+      - run: mkdir -p ${DOCSWORKDIR}
+      # - run: python -m pip install -r requirements/ci.txt
+      - run: |
+          which python
+          python -m pip install --upgrade pip
+          python -m pip install -r requirements/docs.txt
+          micromamba install -c conda-forge mcstas=3.5 -y
+        shell: micromamba-shell {0}
+      - run: |
+          mcstas --version
+          python -m sphinx -j2 -v -b html -d ${DOCSWORKDIR}/docs_doctrees docs html
+          python -m sphinx -j2 -v -b doctest -d ${DOCSWORKDIR}/docs_doctrees docs html
+          # tox -e releasedocs -- "${VERSION}"
+          find html -type f -name "*.ipynb" -not -path "html/_sources/*" -delete
+        shell: micromamba-shell {0}
+      # Cleaned up the docs.
+      # - run: tox -e docs
+      #   if: ${{ inputs.version == '' }}
+      - run: tox -e linkcheck
+        if: ${{ inputs.linkcheck }}
+      - uses: actions/upload-artifact@v4
+        id: artifact-upload-step
+        with:
+          name: docs_html
+          path: html/
+      - run: echo "::notice::https://remote-unzip.deno.dev/${{ github.repository }}/artifacts/${{ steps.artifact-upload-step.outputs.artifact-id }}"
+
+      - uses: JamesIves/[email protected]
+        if: ${{ inputs.publish }}
+        with:
+          branch: gh-pages
+          folder: html
+          single-commit: true

.github/workflows/python-version-ci

@@ -0,0 +1 @@
+3.10

.github/workflows/test.yml

@@ -0,0 +1,79 @@
+name: Test
+
+on:
+  workflow_dispatch:
+    inputs:
+      os-variant:
+        default: 'ubuntu-24.04'
+        type: string
+      python-version:
+        type: string
+      tox-env:
+        default: 'test'
+        type: string
+      pip-recipe:
+        default: 'requirements/ci.txt'
+        type: string
+      coverage-report:
+        default: false
+        type: boolean
+      checkout_ref:
+        default: ''
+        type: string
+  workflow_call:
+    inputs:
+      os-variant:
+        default: 'ubuntu-24.04'
+        type: string
+      python-version:
+        type: string
+      tox-env:
+        default: 'test'
+        type: string
+      pip-recipe:
+        default: 'requirements/ci.txt'
+        type: string
+      coverage-report:
+        default: false
+        type: boolean
+      checkout_ref:
+        default: ''
+        type: string
+
+jobs:
+  package-test:
+    runs-on: ${{ inputs.os-variant }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.checkout_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ inputs.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install .
+      - run: python tests/package_test.py
+        name: Run package tests
+
+  test:
+    runs-on: ${{ inputs.os-variant }}
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          ref: ${{ inputs.checkout_ref }}
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ inputs.python-version }}
+      - run: python -m pip install --upgrade pip
+      - run: python -m pip install -r ${{ inputs.pip-recipe }}
+      - run: tox -e ${{ inputs.tox-env }}
+      - uses: actions/upload-artifact@v4
+        if: ${{ inputs.coverage-report }}
+        with:
+          name: CoverageReport
+          path: coverage_html/

.gitignore

@@ -51,3 +51,4 @@ docs/generated/
 *.c
 *.instr
 *.out
+*.dSYM

CONTRIBUTING.md

@@ -5,16 +5,16 @@ Welcome to the developer side of McStasToX!
 Contributions are always welcome.
 This includes reporting bugs or other issues, submitting pull requests, requesting new features, etc.
 
-If you need help with using McStasToX or contributing to it, have a look at the GitHub [discussions](https://github.com/mccode-dev/McStasToX/discussions) and start a new [Q&A discussion](https://github.com/mccode-dev/McStasToX/discussions/categories/q-a) if you can't find what you are looking for.
+If you need help with using McStasToX or contributing to it, have a look at the GitHub [discussions](https://github.com/mccode-dev/mcstastox/discussions) and start a new [Q&A discussion](https://github.com/mccode-dev/mcstastox/discussions/categories/q-a) if you can't find what you are looking for.
 
-For bug reports and other problems, please open an [issue](https://github.com/mccode-dev/McStasToX/issues/new) in GitHub.
+For bug reports and other problems, please open an [issue](https://github.com/mccode-dev/mcstastox/issues/new) in GitHub.
 
 You are welcome to submit pull requests at any time.
 But to avoid having to make large modifications during review or even have your PR rejected, please first open an issue first to discuss your idea!
 
-Check out the subsections of the [Developer documentation](https://mccode-dev.github.io/McStasToX/developer/index.html) for details on how McStasToX is developed.
+Check out the subsections of the [Developer documentation](https://mccode-dev.github.io/mcstastox/developer/index.html) for details on how McStasToX is developed.
 
 ## Code of conduct
 
 This project is a community effort, and everyone is welcome to contribute.
-Everyone within the community is expected to abide by our [code of conduct](https://github.com/mccode-dev/McStasToX/blob/main/CODE_OF_CONDUCT.md).
+Everyone within the community is expected to abide by our [code of conduct](https://github.com/mccode-dev/mcstastox/blob/main/CODE_OF_CONDUCT.md).

README.md

@@ -1,6 +1,6 @@
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-2.1-4baaaa.svg)](CODE_OF_CONDUCT.md)
-[![PyPI badge](http://img.shields.io/pypi/v/McStasToX.svg)](https://pypi.python.org/pypi/McStasToX)
-[![Anaconda-Server Badge](https://anaconda.org/mccode-dev/McStasToX/badges/version.svg)](https://anaconda.org/mccode-dev/McStasToX)
+[![PyPI badge](http://img.shields.io/pypi/v/mcstastox.svg)](https://pypi.python.org/pypi/mcstastox)
+[![Anaconda-Server Badge](https://anaconda.org/mccode-dev/mcstastox/badges/version.svg)](https://anaconda.org/mccode-dev/mcstastox)
 [![License: BSD 3-Clause](https://img.shields.io/badge/License-BSD%203--Clause-blue.svg)](LICENSE)
 
 # McStasToX
@@ -34,7 +34,7 @@ pip install mcstastox
 > Note that still an early version of the package is on pip, but the API is not stable yet.
 
 ```sh
-python -m pip install McStasToX
+python -m pip install mcstastox
 ```
 
 ## Basic use

docs/_templates/doc_version.html

@@ -1,2 +1,2 @@
 <!-- This will display the version of the docs -->
-Current McStasToX version: {{ version }} (<a href="https://github.com/mccode-dev/McStasToX/releases">older versions</a>).
+Current McStasToX version: {{ version }} (<a href="https://github.com/mccode-dev/mcstastox/releases">older versions</a>).

docs/about/index.md

@@ -18,9 +18,9 @@ To cite a specific version of McStasToX, select the desired version on Zenodo to
 
 ## Older versions of the documentation
 
-Older versions of the documentation pages can be found under the assets of each [release](https://github.com/mccode-dev/McStasToX/releases).
+Older versions of the documentation pages can be found under the assets of each [release](https://github.com/mccode-dev/mcstastox/releases).
 Simply download the archive, unzip and view locally in a web browser.
 
 ## Source code and development
 
-McStasToX is hosted and developed [on GitHub](https://github.com/mccode-dev/McStasToX).
+McStasToX is hosted and developed [on GitHub](https://github.com/mccode-dev/mcstastox).

docs/api-reference/index.md

@@ -3,7 +3,7 @@
 ## Classes
 
 ```{eval-rst}
-.. currentmodule:: McStasToX
+.. currentmodule:: mcstastox
 
 .. autosummary::
    :toctree: ../generated/classes

docs/conf.py

@@ -99,7 +99,7 @@
 #
 
 try:
-    release = get_version("McStasToX")
+    release = get_version("mcstastox")
     version = ".".join(release.split('.')[:3])  # CalVer
 except PackageNotFoundError:
     logger.info(
@@ -151,19 +151,19 @@
     "icon_links": [
         {
             "name": "GitHub",
-            "url": "https://github.com/mccode-dev/McStasToX",
+            "url": "https://github.com/mccode-dev/mcstastox",
             "icon": "fa-brands fa-github",
             "type": "fontawesome",
         },
         {
             "name": "PyPI",
-            "url": "https://pypi.org/project/McStasToX/",
+            "url": "https://pypi.org/project/mcstastox/",
             "icon": "fa-brands fa-python",
             "type": "fontawesome",
         },
         {
             "name": "Conda",
-            "url": "https://anaconda.org/mccode-dev/McStasToX",
+            "url": "https://anaconda.org/mccode-dev/mcstastox",
             "icon": "fa-custom fa-anaconda",
             "type": "fontawesome",
         },
@@ -192,7 +192,7 @@
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.
-htmlhelp_basename = 'McStasToXdoc'
+htmlhelp_basename = 'mcstastoxdoc'
 
 # -- Options for Matplotlib in notebooks ----------------------------------
 
@@ -241,4 +241,7 @@ def do_not_plot(*args, **kwargs):
 linkcheck_ignore = [
     # Specific lines in Github blobs cannot be found by linkcheck.
     r'https?://github\.com/.*?/blob/[a-f0-9]+/.+?#',
+    # Linkcheck seems to be denied access by some DOI resolvers.
+    # Since DOIs are supposed to be permanent, we don't need to check them.'
+    r'https://doi\.org/',
 ]