Merge pull request #80 from scipp/update

Update copier and deps
scipp · Aug 26, 2024 · 4f3f73d · 4f3f73d
2 parents 232d7db + d61cfd9
commit 4f3f73d
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Showing 34 changed files with 151 additions and 63 deletions.
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,11 +1,11 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: afbe5c7
+_commit: bd9d844
 _src_path: gh:scipp/copier_template
 description: Common data reduction tools for the ESS facility
 max_python: '3.12'
 min_python: '3.10'
 namespace_package: ess
-nightly_deps: ''
+nightly_deps: scippnexus,scipp,sciline,cyclebane
 orgname: scipp
 prettyname: ESSreduce
 projectname: essreduce

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -46,6 +46,7 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit
 
   docs:
     needs: tests
@@ -54,3 +55,4 @@ jobs:
       publish: false
       linkcheck: ${{ contains(matrix.variant.os, 'ubuntu') && github.ref == 'refs/heads/main' }}
       branch: ${{ github.head_ref == '' && github.ref_name || github.head_ref }}
+    secrets: inherit
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -42,6 +42,10 @@ jobs:
   docs:
     name: Build documentation
     runs-on: 'ubuntu-22.04'
+    env:
+        ESS_PROTECTED_FILESTORE_USERNAME: ${{ secrets.ESS_PROTECTED_FILESTORE_USERNAME }}
+        ESS_PROTECTED_FILESTORE_PASSWORD: ${{ secrets.ESS_PROTECTED_FILESTORE_PASSWORD }}
+
     steps:
       - run: sudo apt install --yes graphviz pandoc
       - uses: actions/checkout@v4
@@ -65,7 +69,7 @@ jobs:
           name: docs_html
           path: html/
 
-      - uses: JamesIves/github-pages-deploy-action@v4.6.0
+      - uses: JamesIves/github-pages-deploy-action@v4.6.3
         if: ${{ inputs.publish }}
         with:
           branch: gh-pages

diff --git a/.github/workflows/nightly_at_main.yml b/.github/workflows/nightly_at_main.yml
@@ -31,3 +31,4 @@ jobs:
       os-variant: ${{ matrix.os }}
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
+    secrets: inherit
diff --git a/.github/workflows/nightly_at_release.yml b/.github/workflows/nightly_at_release.yml
@@ -38,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -41,8 +41,26 @@ on:
         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

diff --git a/.github/workflows/unpinned.yml b/.github/workflows/unpinned.yml
@@ -38,3 +38,4 @@ jobs:
       python-version: ${{ matrix.python.version }}
       tox-env: ${{ matrix.python.tox-env }}
       checkout_ref: ${{ needs.setup.outputs.release_tag }}
+    secrets: inherit
diff --git a/.gitignore b/.gitignore
@@ -20,6 +20,7 @@ __pycache__/
 .pytest_cache
 .mypy_cache
 docs/generated/
+.ruff_cache
 
 # Editor settings
 .idea/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -21,7 +21,7 @@ repos:
         args: [ "--drop-empty-cells",
                 "--extra-keys 'metadata.language_info.version cell.metadata.jp-MarkdownHeadingCollapsed cell.metadata.pycharm'" ]
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.4.1
+    rev: v0.4.3
     hooks:
       - id: ruff
         args: [ --fix ]

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -9,6 +9,7 @@ source:
 
 {% set pyproject = load_file_data('pyproject.toml') %}
 {% set dependencies = pyproject.get('project', {}).get('dependencies', {}) %}
+{% set test_dependencies = pyproject.get('project', {}).get('optional-dependencies', {}).get('test', {}) %}
 
 
 requirements:
@@ -18,16 +19,23 @@ requirements:
   run:
     - python>=3.10
 
+  {# Conda does not allow spaces between package name and version, so remove them #}
   {% for package in dependencies %}
-    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package }}{% endif %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
   {% endfor %}
 
 
 test:
   imports:
     - ess.reduce
   requires:
-    - pytest
+
+  {# Conda does not allow spaces between package name and version, so remove them #}
+  {% for package in test_dependencies %}
+    - {% if package == "graphviz" %}python-graphviz{% else %}{{ package|replace(" ", "") }}{% endif %}
+  {% endfor %}
+
+
   source_files:
     - pyproject.toml
     - tests/

diff --git a/docs/_templates/doc_version.html b/docs/_templates/doc_version.html
@@ -1,2 +1,2 @@
 <!-- This will display the version of the docs -->
-Current {{ project }} version: {{ version }} (<a href="https://github.com/{{orgname}}/{{ project|lower }}/releases">older versions</a>).
+Current ESSreduce version: {{ version }} (<a href="https://github.com/scipp/essreduce/releases">older versions</a>).
diff --git a/docs/conf.py b/docs/conf.py
@@ -1,12 +1,15 @@
-# -*- coding: utf-8 -*-
-
 import doctest
 import os
 import sys
+from importlib.metadata import PackageNotFoundError
 from importlib.metadata import version as get_version
 
+from sphinx.util import logging
+
 sys.path.insert(0, os.path.abspath('.'))
 
+logger = logging.getLogger(__name__)
+
 # General information about the project.
 project = 'ESSreduce'
 copyright = '2024 Scipp contributors'
@@ -34,6 +37,8 @@
     import sciline.sphinxext.domain_types  # noqa: F401
 
     extensions.append('sciline.sphinxext.domain_types')
+    # See https://github.com/tox-dev/sphinx-autodoc-typehints/issues/457
+    suppress_warnings = ["config.cache"]
 except ModuleNotFoundError:
     pass
 
@@ -111,8 +116,15 @@
 # built documents.
 #
 
-release = get_version("essreduce")
-version = ".".join(release.split('.')[:3])  # CalVer
+try:
+    release = get_version("essreduce")
+    version = ".".join(release.split('.')[:3])  # CalVer
+except PackageNotFoundError:
+    logger.info(
+        "Warning: determining version from package metadata failed, falling back to "
+        "a dummy version number."
+    )
+    release = version = "0.0.0-dev"
 
 warning_is_error = True
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -37,6 +37,13 @@ dependencies = [
 
 dynamic = ["version"]
 
+[project.optional-dependencies]
+test = [
+    "ipywidgets",
+    "pooch",
+    "pytest",
+]
+
 [project.scripts]
 grow-nexus = "ess.reduce.scripts.grow_nexus:main"
 
@@ -70,14 +77,14 @@ extend-exclude = [
 
 [tool.ruff.lint]
 # See https://docs.astral.sh/ruff/rules/
-select = ["B", "C4", "DTZ", "E", "F", "G", "I", "PERF", "PGH", "PT", "PYI", "RUF", "S", "T20", "W"]
+select = ["B", "C4", "DTZ", "E", "F", "G", "I", "PERF", "PGH", "PT", "PYI", "RUF", "S", "T20", "UP", "W"]
 ignore = [
     # Conflict with ruff format, see
     # https://docs.astral.sh/ruff/formatter/#conflicting-lint-rules
     "COM812", "COM819", "D206", "D300", "E111", "E114", "E117", "ISC001", "ISC002", "Q000", "Q001", "Q002", "Q003", "W191",
 ]
 fixable = ["I001", "B010"]
-isort.known-first-party = ["essreduce"]
+isort.known-first-party = ["ess.reduce"]
 pydocstyle.convention = "numpy"
 
 [tool.ruff.lint.per-file-ignores]

diff --git a/requirements/base.txt b/requirements/base.txt
@@ -11,7 +11,7 @@ h5py==3.11.0
     # via scippnexus
 networkx==3.3
     # via cyclebane
-numpy==2.0.1
+numpy==2.1.0
     # via
     #   h5py
     #   scipp
@@ -20,13 +20,13 @@ python-dateutil==2.9.0.post0
     # via scippnexus
 sciline==24.6.2
     # via -r base.in
-scipp==24.6.0
+scipp==24.8.0
     # via
     #   -r base.in
     #   scippnexus
 scippnexus==24.8.1
     # via -r base.in
-scipy==1.14.0
+scipy==1.14.1
     # via scippnexus
 six==1.16.0
     # via python-dateutil
diff --git a/requirements/basetest.in b/requirements/basetest.in
@@ -1,7 +1,12 @@
 # Dependencies that are only used by tests.
 # Do not make an environment from this file, use test.txt instead!
+# Add more dependencies in the ``test`` list
+# under ``[project.optional-dependencies]`` section, in ``pyproject.toml``
 
+# Anything above "--- END OF CUSTOM SECTION ---"
+# will not be touched by ``make_base.py``
+# --- END OF CUSTOM SECTION ---
+# The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
+ipywidgets
 pooch
 pytest
-numpy
-ipywidgets
diff --git a/requirements/basetest.txt b/requirements/basetest.txt
@@ -1,4 +1,4 @@
-# SHA1:5532a168d5d263d81330479c8860b4b7b399de9b
+# SHA1:d69d994ed83cc9e89ad349f490a0f8f41d18d8bf
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
@@ -21,22 +21,20 @@ exceptiongroup==1.2.2
     #   pytest
 executing==2.0.1
     # via stack-data
-idna==3.7
+idna==3.8
     # via requests
 iniconfig==2.0.0
     # via pytest
 ipython==8.26.0
     # via ipywidgets
-ipywidgets==8.1.3
+ipywidgets==8.1.5
     # via -r basetest.in
 jedi==0.19.1
     # via ipython
-jupyterlab-widgets==3.0.11
+jupyterlab-widgets==3.0.13
     # via ipywidgets
 matplotlib-inline==0.1.7
     # via ipython
-numpy==2.0.1
-    # via -r basetest.in
 packaging==24.1
     # via
     #   pooch
@@ -81,5 +79,5 @@ urllib3==2.2.2
     # via requests
 wcwidth==0.2.13
     # via prompt-toolkit
-widgetsnbextension==4.0.11
+widgetsnbextension==4.0.13
     # via ipywidgets
diff --git a/requirements/ci.txt b/requirements/ci.txt
@@ -5,7 +5,7 @@
 #
 #    pip-compile-multi
 #
-cachetools==5.4.0
+cachetools==5.5.0
     # via tox
 certifi==2024.7.4
     # via requests
@@ -25,7 +25,7 @@ gitdb==4.0.11
     # via gitpython
 gitpython==3.1.43
     # via -r ci.in
-idna==3.7
+idna==3.8
     # via requests
 packaging==24.1
     # via

diff --git a/requirements/dev.txt b/requirements/dev.txt
@@ -119,7 +119,7 @@ terminado==0.18.1
     #   jupyter-server-terminals
 toposort==1.10
     # via pip-compile-multi
-types-python-dateutil==2.9.0.20240316
+types-python-dateutil==2.9.0.20240821
     # via arrow
 uri-template==1.3.0
     # via jsonschema

diff --git a/requirements/docs.txt b/requirements/docs.txt
@@ -54,7 +54,7 @@ fastjsonschema==2.20.0
     # via nbformat
 graphviz==0.20.3
     # via -r docs.in
-idna==3.7
+idna==3.8
     # via requests
 imagesize==1.4.1
     # via sphinx
@@ -65,7 +65,7 @@ ipython==8.26.0
     #   -r docs.in
     #   ipykernel
     #   ipywidgets
-ipywidgets==8.1.3
+ipywidgets==8.1.5
     # via -r docs.in
 jedi==0.19.1
     # via ipython
@@ -92,7 +92,7 @@ jupyter-core==5.7.2
     #   nbformat
 jupyterlab-pygments==0.3.0
     # via nbconvert
-jupyterlab-widgets==3.0.11
+jupyterlab-widgets==3.0.13
     # via ipywidgets
 markdown-it-py==3.0.0
     # via
@@ -160,7 +160,7 @@ pygments==2.18.0
     #   sphinx
 pyyaml==6.0.2
     # via myst-parser
-pyzmq==26.1.0
+pyzmq==26.2.0
     # via
     #   ipykernel
     #   jupyter-client
@@ -240,5 +240,5 @@ webencodings==0.5.1
     # via
     #   bleach
     #   tinycss2
-widgetsnbextension==4.0.11
+widgetsnbextension==4.0.13
     # via ipywidgets