Merge pull request #183 from scipp/drop-py38

Drop Python 3.8

.copier-answers.yml

@@ -1,12 +1,13 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: 13cf3e6
+_commit: ec09f73
 _src_path: gh:scipp/copier_template
 description: An h5py-like utility for NeXus files with seamless Scipp integration
 max_python: '3.12'
-min_python: '3.8'
+min_python: '3.9'
 namespace_package: ''
 nightly_deps: scipp
 orgname: scipp
+prettyname: ScippNexus
 projectname: scippnexus
 related_projects: Scipp,ScippNeutron
 year: 2023

.github/workflows/ci.yml

@@ -13,7 +13,7 @@ on:
 jobs:
   formatting:
     name: Formatting and static analysis
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       min_tox_env: ${{ steps.vars.outputs.min_tox_env }}
@@ -39,7 +39,7 @@ jobs:
     needs: formatting
     strategy:
       matrix:
-        os: ['ubuntu-20.04']
+        os: ['ubuntu-22.04']
         python:
           - version: '${{needs.formatting.outputs.min_python}}'
             tox-env: '${{needs.formatting.outputs.min_tox_env}}'
@@ -54,4 +54,5 @@ jobs:
     uses: ./.github/workflows/docs.yml
     with:
       publish: false
+      linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
       branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}

.github/workflows/docs.yml

@@ -32,14 +32,19 @@ on:
         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-20.04'
+    runs-on: 'ubuntu-22.04'
     steps:
       - run: sudo apt install --yes graphviz pandoc
       - uses: actions/checkout@v3
@@ -55,6 +60,8 @@ jobs:
         if: ${{ inputs.version != '' }}
       - run: tox -e docs
         if: ${{ inputs.version == '' }}
+      - run: tox -e linkcheck
+        if: ${{ inputs.linkcheck }}
       - uses: actions/upload-artifact@v3
         with:
           name: docs_html
@@ -66,4 +73,3 @@ jobs:
           branch: gh-pages
           folder: html
           single-commit: true
-          ssh-key: ${{ secrets.GH_PAGES_DEPLOY_KEY }}

.github/workflows/nightly_at_main.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
     steps:
@@ -25,7 +25,7 @@ jobs:
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-20.04']
+        os: ['ubuntu-22.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'nightly'

.github/workflows/nightly_at_release.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       release_tag: ${{ steps.release.outputs.release_tag }}
@@ -31,7 +31,7 @@ jobs:
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-20.04']
+        os: ['ubuntu-22.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'nightly'

.github/workflows/python-version-ci

@@ -1 +1 @@
-3.8
+3.9

.github/workflows/release.yml

@@ -15,7 +15,7 @@ defaults:
 jobs:
   build_conda:
     name: Conda build
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
 
     steps:
       - uses: actions/checkout@v3
@@ -38,7 +38,7 @@ jobs:
 
   build_wheels:
     name: Wheels
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
 
     steps:
       - uses: actions/checkout@v3
@@ -64,7 +64,7 @@ jobs:
   upload_pypi:
     name: Deploy PyPI
     needs: [build_wheels, build_conda]
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     environment: release
     permissions:
       id-token: write
@@ -76,7 +76,7 @@ jobs:
   upload_conda:
     name: Deploy Conda
     needs: [build_wheels, build_conda]
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     if: github.event_name == 'release' && github.event.action == 'published'
 
     steps:
@@ -100,7 +100,7 @@ jobs:
   assets:
     name: Upload docs
     needs: docs
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     permissions:
       contents: write  # This is needed so that the action can upload the asset
     steps:

.github/workflows/test.yml

@@ -7,7 +7,7 @@ on:
   workflow_dispatch:
     inputs:
       os-variant:
-        default: 'ubuntu-20.04'
+        default: 'ubuntu-22.04'
         type: string
       python-version:
         type: string
@@ -26,7 +26,7 @@ on:
   workflow_call:
     inputs:
       os-variant:
-        default: 'ubuntu-20.04'
+        default: 'ubuntu-22.04'
         type: string
       python-version:
         type: string

.github/workflows/unpinned.yml

@@ -11,7 +11,7 @@ on:
 jobs:
   setup:
     name: Setup variables
-    runs-on: 'ubuntu-20.04'
+    runs-on: 'ubuntu-22.04'
     outputs:
       min_python: ${{ steps.vars.outputs.min_python }}
       release_tag: ${{ steps.release.outputs.release_tag }}
@@ -31,7 +31,7 @@ jobs:
     needs: setup
     strategy:
       matrix:
-        os: ['ubuntu-20.04']
+        os: ['ubuntu-22.04']
         python:
           - version: '${{needs.setup.outputs.min_python}}'
             tox-env: 'unpinned'

.gitignore

@@ -1,13 +1,17 @@
+# Build artifacts
+build
 dist
 html
 .tox
-src/scippnexus.egg-info
+*.egg-info
 
 *.sw?
 
+# Environments
+venv
+
+# Caches
 .clangd/
-.idea/
-.vscode/
 *.ipynb_checkpoints
 __pycache__/
 .vs/
@@ -16,3 +20,20 @@ __pycache__/
 .pytest_cache
 .mypy_cache
 docs/generated/
+
+# Editor settings
+.idea/
+.vscode/
+
+# Data files
+*.data
+*.dat
+*.csv
+*.xye
+*.h5
+*.hdf5
+*.hdf
+*.nxs
+*.raw
+*.cif
+*.rcif

.pre-commit-config.yaml

@@ -1,10 +1,11 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.3.0
+    rev: v4.5.0
     hooks:
       - id: check-added-large-files
       - id: check-json
         exclude: asv.conf.json
+      - id: check-merge-conflict
       - id: check-toml
       - id: check-yaml
         exclude: conda/meta.yaml
@@ -18,7 +19,7 @@ repos:
       - id: isort
         name: isort (python)
   - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.9.0
+    rev: 23.11.0
     hooks:
       - id: black
   - repo: https://github.com/kynan/nbstripout
@@ -29,28 +30,27 @@ repos:
         args: [ "--drop-empty-cells",
                 "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 6.1.0
     hooks:
       - id: flake8
         types: ["python"]
-        additional_dependencies: ["flake8-bugbear==22.10.27"]
+        additional_dependencies: ["flake8-bugbear==23.9.16"]
   - repo: https://github.com/pycqa/bandit
-    rev: 1.7.4
+    rev: 1.7.5
     hooks:
       - id: bandit
         additional_dependencies: ["bandit[toml]"]
         args: ["-c", "pyproject.toml"]
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.2
+    rev: v2.2.6
     hooks:
       - id: codespell
         additional_dependencies:
           - tomli
   - repo: https://github.com/pre-commit/pygrep-hooks
-    rev: v1.9.0
+    rev: v1.10.0
     hooks:
       - id: python-no-eval
-        exclude: "object_list.py"
       - id: python-no-log-warn
       - id: python-use-type-annotations
       - id: rst-backticks

CONTRIBUTING.md

@@ -1,18 +1,18 @@
-## Contributing to Scippnexus
+## Contributing to ScippNexus
 
-Welcome to the developer side of Scippnexus!
+Welcome to the developer side of ScippNexus!
 
 Contributions are always welcome.
 This includes reporting bugs or other issues, submitting pull requests, requesting new features, etc.
 
-If you need help with using Scippnexus or contributing to it, have a look at the GitHub [discussions](https://github.com/scipp/scippnexus/discussions) and start a new [Q&A discussion](https://github.com/scipp/scippnexus/discussions/categories/q-a) if you can't find what you are looking for.
+If you need help with using ScippNexus or contributing to it, have a look at the GitHub [discussions](https://github.com/scipp/scippnexus/discussions) and start a new [Q&A discussion](https://github.com/scipp/scippnexus/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/scipp/scippnexus/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://scipp.github.io/scippnexus/developer/index.html) for details on how Scippnexus is developed.
+Check out the subsections of the [Developer documentation](https://scipp.github.io/scippnexus/developer/index.html) for details on how ScippNexus is developed.
 
 ## Code of conduct
 

conda/meta.yaml

@@ -11,7 +11,7 @@ requirements:
     - setuptools
     - setuptools_scm
   run:
-    - python>=3.8
+    - python>=3.9
     - python-dateutil
     - scipp>=23.07.0
     - scipy
@@ -31,7 +31,7 @@ test:
 build:
   noarch: python
   script:
-    - pip install .
+    - python -m pip install .
 
 about:
   home: https://github.com/scipp/scippnexus