Merge pull request #8 from scipp/copier-update

Copier update with dependencies.
scipp · Dec 13, 2023 · 5bfcd7a · 5bfcd7a
2 parents 1628d4f + 1c613da
commit 5bfcd7a
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diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,7 +1,7 @@
 # Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
-_commit: ff7f76b
+_commit: ec09f73
 _src_path: gh:scipp/copier_template
-description: Data reduction for NMX at the European Spallation Source
+description: Data reduction for NMX at the European Spallation Source.
 max_python: '3.11'
 min_python: '3.9'
 namespace_package: ess

diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -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 }}
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -32,6 +32,11 @@ 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 }}
@@ -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 }}
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,9 @@ html
 
 *.sw?
 
+# Environments
+venv
+
 # Caches
 .clangd/
 *.ipynb_checkpoints

diff --git a/README.md b/README.md
@@ -7,7 +7,7 @@
 
 ## About
 
-Data reduction for NMX at the European Spallation Source
+Data reduction for NMX at the European Spallation Source.
 
 ## Installation
 

diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -18,6 +18,7 @@ requirements:
  - sciline>=23.9.1
  - scipp>=23.8.0
  - scippnexus>=23.9.0
+ - pooch
 
 test:
  imports:
@@ -33,12 +34,12 @@ test:
 build:
  noarch: python
  script:
- - pip install .
+ - python -m pip install .
 
 about:
  home: https://github.com/scipp/essnmx
  license: BSD-3-Clause
- summary: Data reduction for NMX at the European Spallation Source
- description: Data reduction for NMX at the European Spallation Source
+ summary: Data reduction for NMX at the European Spallation Source.
+ description: Data reduction for NMX at the European Spallation Source.
  dev_url: https://github.com/scipp/essnmx
  doc_url: https://scipp.github.io/essnmx
diff --git a/docs/conf.py b/docs/conf.py
@@ -25,7 +25,7 @@
  'sphinx.ext.napoleon',
  'sphinx_autodoc_typehints',
  'sphinx_copybutton',
- "sphinx_design",
+ 'sphinx_design',
  'nbsphinx',
  'myst_parser',
 ]
@@ -152,7 +152,7 @@
  },
  {
  "name": "Conda",
- "url": "https://anaconda.org/conda-forge/essnmx",
+ "url": "https://anaconda.org/scipp/essnmx",
  "icon": "fa-custom fa-anaconda",
  "type": "fontawesome",
  },
@@ -191,8 +191,29 @@
 
 # -- Options for doctest --------------------------------------------------
 
+# sc.plot returns a Figure object and doctest compares that against the
+# output written in the docstring. But we only want to show an image of the
+# figure, not its `repr`.
+# In addition, there is no need to make plots in doctest as the documentation
+# build already tests if those plots can be made.
+# So we simply disable plots in doctests.
 doctest_global_setup = '''
 import numpy as np
+
+try:
+ import scipp as sc
+
+ def do_not_plot(*args, **kwargs):
+ pass
+
+ sc.plot = do_not_plot
+ sc.Variable.plot = do_not_plot
+ sc.DataArray.plot = do_not_plot
+ sc.DataGroup.plot = do_not_plot
+ sc.Dataset.plot = do_not_plot
+except ImportError:
+ # Scipp is not needed by docs if it is not installed.
+ pass
 '''
 
 # Using normalize whitespace because many __str__ functions in scipp produce

diff --git a/docs/index.md b/docs/index.md
@@ -1,7 +1,7 @@
 # Essnmx
 
 <span style="font-size:1.2em;font-style:italic;color:#5a5a5a">
- Data reduction for NMX at the European Spallation Source
+ Data reduction for NMX at the European Spallation Source.
  </br></br>
 </span>
 

diff --git a/pyproject.toml b/pyproject.toml
@@ -7,7 +7,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "essnmx"
-description = "Data reduction for NMX at the European Spallation Source"
+description = "Data reduction for NMX at the European Spallation Source."
 authors = [{ name = "Scipp contributors" }]
 license = { file = "LICENSE" }
 readme = "README.md"
@@ -36,6 +36,7 @@ dependencies = [
  "sciline>=23.9.1",
  "scipp>=23.8.0",
  "scippnexus>=23.9.0",
+ "pooch",
 ]
 
 dynamic = ["version"]
@@ -49,7 +50,12 @@ dynamic = ["version"]
 
 [tool.pytest.ini_options]
 minversion = "7.0"
-addopts = "-ra -v"
+addopts = """
+--strict-config
+--strict-markers
+-ra
+-v
+"""
 testpaths = "tests"
 filterwarnings = [
  "error",

diff --git a/requirements/base.in b/requirements/base.in
@@ -1,4 +1,8 @@
-
+# Temporary until questionary (dep of copier) updates
+# See https://github.com/tmbo/questionary/blob/2df265534f3eb77aafcf70902e53e80beb1793e0/pyproject.toml#L36C43-L36C110
+prompt-toolkit==3.0.36
+# Temporary pinned until prompt-tookit conflict is resolved.
+ipython==8.9.0
 # --- END OF CUSTOM SECTION ---
 # The following was generated by 'tox -e deps', DO NOT EDIT MANUALLY!
 dask
@@ -7,3 +11,4 @@ plopp
 sciline>=23.9.1
 scipp>=23.8.0
 scippnexus>=23.9.0
+pooch
diff --git a/requirements/base.txt b/requirements/base.txt
@@ -1,10 +1,18 @@
-# SHA1:d319e96fc4fdca56b4aa64fcfe16d5daa656be7a
+# SHA1:dc8a3b216315f3203ec4048ef1930f26643a833e
 #
 # This file is autogenerated by pip-compile-multi
 # To update, run:
 #
 # pip-compile-multi
 #
+asttokens==2.4.1
+ # via stack-data
+backcall==0.2.0
+ # via ipython
+certifi==2023.11.17
+ # via requests
+charset-normalizer==3.3.2
+ # via requests
 click==8.1.7
  # via dask
 cloudpickle==3.0.0
@@ -13,11 +21,15 @@ contourpy==1.2.0
  # via matplotlib
 cycler==0.12.1
  # via matplotlib
-dask==2023.11.0
+dask==2023.12.0
  # via -r base.in
-fonttools==4.45.1
+decorator==5.1.1
+ # via ipython
+executing==2.0.1
+ # via stack-data
+fonttools==4.46.0
  # via matplotlib
-fsspec==2023.10.0
+fsspec==2023.12.2
  # via dask
 graphlib-backport==1.0.3
  # via
@@ -27,16 +39,24 @@ graphviz==0.20.1
  # via -r base.in
 h5py==3.10.0
  # via scippnexus
-importlib-metadata==6.8.0
+idna==3.6
+ # via requests
+importlib-metadata==7.0.0
  # via dask
 importlib-resources==6.1.1
  # via matplotlib
+ipython==8.9.0
+ # via -r base.in
+jedi==0.19.1
+ # via ipython
 kiwisolver==1.4.5
  # via matplotlib
 locket==1.0.0
  # via partd
 matplotlib==3.8.2
  # via plopp
+matplotlib-inline==0.1.6
+ # via ipython
 numpy==1.26.2
  # via
  # contourpy
@@ -48,12 +68,33 @@ packaging==23.2
  # via
  # dask
  # matplotlib
+ # pooch
+parso==0.8.3
+ # via jedi
 partd==1.4.1
  # via dask
+pexpect==4.9.0
+ # via ipython
+pickleshare==0.7.5
+ # via ipython
 pillow==10.1.0
  # via matplotlib
+platformdirs==4.1.0
+ # via pooch
 plopp==23.11.0
  # via -r base.in
+pooch==1.8.0
+ # via -r base.in
+prompt-toolkit==3.0.36
+ # via
+ # -r base.in
+ # ipython
+ptyprocess==0.7.0
+ # via pexpect
+pure-eval==0.2.2
+ # via stack-data
+pygments==2.17.2
+ # via ipython
 pyparsing==3.1.1
  # via matplotlib
 python-dateutil==2.8.2
@@ -62,22 +103,36 @@ python-dateutil==2.8.2
  # scippnexus
 pyyaml==6.0.1
  # via dask
-sciline==23.9.1
+requests==2.31.0
+ # via pooch
+sciline==23.12.0
  # via -r base.in
 scipp==23.11.0
  # via
  # -r base.in
  # scippnexus
-scippnexus==23.11.1
+scippnexus==23.12.0
  # via -r base.in
 scipy==1.11.4
  # via scippnexus
 six==1.16.0
- # via python-dateutil
+ # via
+ # asttokens
+ # python-dateutil
+stack-data==0.6.3
+ # via ipython
 toolz==0.12.0
  # via
  # dask
  # partd
+traitlets==5.14.0
+ # via
+ # ipython
+ # matplotlib-inline
+urllib3==2.1.0
+ # via requests
+wcwidth==0.2.12
+ # via prompt-toolkit
 zipp==3.17.0
  # via
  # importlib-metadata

diff --git a/requirements/basetest.in b/requirements/basetest.in
@@ -0,0 +1,4 @@
+# Dependencies that are only used by tests.
+# Do not make an environment from this file, use test.txt instead!
+
+pytest
diff --git a/requirements/basetest.txt b/requirements/basetest.txt
@@ -0,0 +1,19 @@
+# SHA1:0eaa389e1fdb3a1917c0f987514bd561be5718ee
+#
+# This file is autogenerated by pip-compile-multi
+# To update, run:
+#
+# pip-compile-multi
+#
+exceptiongroup==1.2.0
+ # via pytest
+iniconfig==2.0.0
+ # via pytest
+packaging==23.2
+ # via pytest
+pluggy==1.3.0
+ # via pytest
+pytest==7.4.3
+ # via -r basetest.in
+tomli==2.0.1
+ # via pytest
diff --git a/requirements/ci.txt b/requirements/ci.txt
@@ -15,7 +15,7 @@ charset-normalizer==3.3.2
  # via requests
 colorama==0.4.6
  # via tox
-distlib==0.3.7
+distlib==0.3.8
  # via virtualenv
 filelock==3.13.1
  # via
@@ -32,7 +32,7 @@ packaging==23.2
  # -r ci.in
  # pyproject-api
  # tox
-platformdirs==4.0.0
+platformdirs==4.1.0
  # via
  # tox
  # virtualenv
@@ -52,5 +52,5 @@ tox==4.11.4
  # via -r ci.in
 urllib3==2.1.0
  # via requests
-virtualenv==20.24.7
+virtualenv==20.25.0
  # via tox