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prjemian / spec2nexus

Converts SPEC data files and scans into NeXus HDF5 files
https://prjemian.github.io/spec2nexus/
4 stars 7 forks source link

missing documentation for standard plugins #287

Closed prjemian closed 2 years ago

prjemian commented 2 years ago

This page has no content: https://prjemian.github.io/spec2nexus/supplied_plugins/spec_common.html

prjemian commented 2 years ago

In local builds, the documentation is not missing, on-line is missing. Check the most recent build log on GitHub:

``` 2022-09-06T06:39:05.7723967Z Running Sphinx v5.1.1 2022-09-06T06:39:06.1660908Z [autosummary] generating autosummary for: api.rst, applications.rst, changes.rst, charts.rst, contents.rst, control_lines.rst, diffractometers.rst, example_data.rst, extractSpecScan.rst, eznx.rst, ..., supplied_plugins/XPCS.rst, supplied_plugins/apstools_specwriter.rst, supplied_plugins/fallback.rst, supplied_plugins/spec_common.rst, supplied_plugins/uim.rst, supplied_plugins/unicat.rst, supplied_plugins/uxml.rst, unit_testing.rst, utils.rst, writer.rst 2022-09-06T06:39:06.2306263Z Failed to import spec2nexus.charts. 2022-09-06T06:39:06.2307043Z Possible hints: 2022-09-06T06:39:06.2310287Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2311112Z * AttributeError: module 'spec2nexus' has no attribute 'charts' 2022-09-06T06:39:06.2314721Z Failed to import spec2nexus.plugins.uxml. 2022-09-06T06:39:06.2315177Z Possible hints: 2022-09-06T06:39:06.2315883Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'uxml' 2022-09-06T06:39:06.2318732Z * ModuleNotFoundError: No module named 'lxml' 2022-09-06T06:39:06.2319823Z Failed to import spec2nexus.specplot_gallery. 2022-09-06T06:39:06.2321343Z Possible hints: 2022-09-06T06:39:06.2322106Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2322869Z * AttributeError: module 'spec2nexus' has no attribute 'specplot_gallery' 2022-09-06T06:39:06.2323432Z Failed to import spec2nexus.control_lines. 2022-09-06T06:39:06.2323845Z Possible hints: 2022-09-06T06:39:06.2407875Z * AttributeError: module 'spec2nexus' has no attribute 'control_lines' 2022-09-06T06:39:06.2408686Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2410422Z Failed to import spec2nexus.diffractometers. 2022-09-06T06:39:06.2410738Z Possible hints: 2022-09-06T06:39:06.2411250Z * AttributeError: module 'spec2nexus' has no attribute 'diffractometers' 2022-09-06T06:39:06.2411707Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2412209Z Failed to import spec2nexus.extractSpecScan. 2022-09-06T06:39:06.2412501Z Possible hints: 2022-09-06T06:39:06.2420427Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2421040Z * AttributeError: module 'spec2nexus' has no attribute 'extractSpecScan' 2022-09-06T06:39:06.2421465Z Failed to import spec2nexus.plugins.spec_common. 2022-09-06T06:39:06.2421777Z Possible hints: 2022-09-06T06:39:06.2422144Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2422790Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'spec_common' 2022-09-06T06:39:06.2423238Z Failed to import spec2nexus.utils. 2022-09-06T06:39:06.2423490Z Possible hints: 2022-09-06T06:39:06.2423852Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2424303Z * AttributeError: module 'spec2nexus' has no attribute 'utils' 2022-09-06T06:39:06.2424619Z Failed to import spec2nexus.writer. 2022-09-06T06:39:06.2424887Z Possible hints: 2022-09-06T06:39:06.2425484Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2426079Z * AttributeError: module 'spec2nexus' has no attribute 'writer' 2022-09-06T06:39:06.2426642Z Failed to import spec2nexus.nexus. 2022-09-06T06:39:06.2426936Z Possible hints: 2022-09-06T06:39:06.2427329Z * AttributeError: module 'spec2nexus' has no attribute 'nexus' 2022-09-06T06:39:06.2427756Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2428086Z Failed to import spec2nexus.plugins.XPCS. 2022-09-06T06:39:06.2428368Z Possible hints: 2022-09-06T06:39:06.2428773Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'XPCS' 2022-09-06T06:39:06.2429224Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2429541Z Failed to import spec2nexus.eznx. 2022-09-06T06:39:06.2429785Z Possible hints: 2022-09-06T06:39:06.2430188Z * AttributeError: module 'spec2nexus' has no attribute 'eznx' 2022-09-06T06:39:06.2430612Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2430905Z Failed to import spec2nexus.spec. 2022-09-06T06:39:06.2431166Z Possible hints: 2022-09-06T06:39:06.2431568Z * AttributeError: module 'spec2nexus' has no attribute 'spec' 2022-09-06T06:39:06.2431979Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2432348Z Failed to import spec2nexus.plugins.apstools_specwriter. 2022-09-06T06:39:06.2432660Z Possible hints: 2022-09-06T06:39:06.2433107Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'apstools_specwriter' 2022-09-06T06:39:06.2433586Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2433904Z Failed to import spec2nexus.specplot. 2022-09-06T06:39:06.2434176Z Possible hints: 2022-09-06T06:39:06.2434565Z * AttributeError: module 'spec2nexus' has no attribute 'specplot' 2022-09-06T06:39:06.2434995Z * ModuleNotFoundError: No module named 'numpy' 2022-09-06T06:39:06.2435514Z Failed to import spec2nexus.plugins.fallback. 2022-09-06T06:39:06.2435793Z Possible hints: 2022-09-06T06:39:06.2436321Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'fallback' 2022-09-06T06:39:06.2436923Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2437255Z Failed to import spec2nexus.plugins.unicat. 2022-09-06T06:39:06.2437555Z Possible hints: 2022-09-06T06:39:06.2437999Z * AttributeError: module 'spec2nexus.plugins' has no attribute 'unicat' 2022-09-06T06:39:06.2438444Z * ModuleNotFoundError: No module named 'h5py' 2022-09-06T06:39:06.2438800Z building [mo]: targets for 0 po files that are out of date 2022-09-06T06:39:06.2439173Z building [html]: targets for 52 source files that are out of date 2022-09-06T06:39:06.2439550Z updating environment: [new config] 52 added, 0 changed, 0 removed 2022-09-06T06:39:06.2439987Z reading sources... [ 1%] api ```

Summary: Failed to import lots of parts, thus documentation is missing.

prjemian commented 2 years ago

act is a great tool for testing GitHub Actions workflows. First problem it finds:

[Publish Sphinx Docs to GitHub Pages/build-docs]   🐳  docker exec cmd=[bash --noprofile --norc -e -o pipefail /var/run/act/workflow/1] user= workdir=
| /var/run/act/workflow/1: line 2: pip: command not found
prjemian commented 2 years ago

With pip installed, the next problem:

[Publish Sphinx Docs to GitHub Pages/build-docs]   ❓  ::group:: Running Sphinx builder
| Running Sphinx v5.1.1
| 
| Configuration error:
| There is a programmable error in your configuration file:
| 
| Traceback (most recent call last):
|   File "/usr/local/lib/python3.8/dist-packages/sphinx/config.py", line 347, in eval_config_file
|     exec(code, namespace)
|   File "/home/zorinvm/Documents/projects/prjemian/spec2nexus/docs/source/conf.py", line 13, in <module>
|     import spec2nexus
| ModuleNotFoundError: No module named 'spec2nexus'
| 
| Error: Invalid status code: 2

Note the workflow uses sphinx-notes/pages@master which is not the latest sphinx-notes/pages@v2

prjemian commented 2 years ago

With the workflow action update, the next problem is:

| ERROR: Could not find a version that satisfies the requirement matplotlib-base (from -r /home/zorinvm/Documents/projects/prjemian/spec2nexus/././requirements.txt (line 3)) (from versions: none)
| ERROR: No matching distribution found for matplotlib-base (from -r /home/zorinvm/Documents/projects/prjemian/spec2nexus/././requirements.txt (line 3))

That's true so change to matplotlib.

prjemian commented 2 years ago

This error again:

[Publish Sphinx Docs to GitHub Pages/build-docs]   ❓  ::group:: Running Sphinx builder
| Running Sphinx v5.1.1
| 
| Configuration error:
| There is a programmable error in your configuration file:
| 
| Traceback (most recent call last):
|   File "/usr/local/lib/python3.8/dist-packages/sphinx/config.py", line 347, in eval_config_file
|     exec(code, namespace)
|   File "/home/zorinvm/Documents/projects/prjemian/spec2nexus/docs/source/conf.py", line 13, in <module>
|     import spec2nexus
| ModuleNotFoundError: No module named 'spec2nexus'
|
prjemian commented 2 years ago

The root cause was the source file rearrangement of src/spec2nexus -> spec2nexus.