khanlab / khanlab/snakebids

Snakebids create docs

Open
#434 3 comments 0 reactions 0 assignees View on GitHub
Dominant language
Python
Stars
23
Forks
16
PR merge metrics
No merged PRs in 30d

Description

## The problem

The docs for the CLI (app and snakemake) don't build properly since the snakebids isn't in the requirements.txt for the docs.

Looks like simple fix is to add snakebids to the requirements.txt, any objections to that?

## Steps to reproduce

Create an app, say yes to docs:
`snakebids create test_snakebids`

Then make venv (python3.11) for docs/requirements.txt, install them, then from `docs/`:

```
sphinx-build . _build_docs
```

## Screenshots

```
(venv_docs) alik@AFI-CBS-H-10:/local/scratch/test_snakebids/docs$ sphinx-build . _build_docs
Running Sphinx v5.3.0
making output directory... done
myst v1.0.0: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=set(), disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, fence_as_directive=set(), number_code_blocks=[], title_to_header=False, heading_anchors=0, heading_slug_func=None, html_meta={}, footnote_transition=True, words_per_minute=200, substitutions={}, linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area', enable_checkboxes=False, suppress_warnings=[], highlight_code_blocks=True)
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 4 source files that are out of date
updating environment: [new config] 4 added, 0 changed, 0 removed
reading sources... [100%] usage/snakemake_cli
/local/scratch/test_snakebids/docs/usage/app_cli.md:3: ERROR: Failed to import "get_parser" from "test_snakebids.run".
No module named 'test_snakebids'
/local/scratch/test_snakebids/docs/usage/snakemake_cli.md:3: ERROR: Failed to import "get_argument_parser" from "snakebids.snakemake_compat".
No module named 'snakebids'
looking for now-outdated files... none found
pickling environment... done
checking consistency... done
preparing documents... done
writing output... [100%] usage/snakemake_cli
generating indices... genindex done
writing additional pages... search done
copying static files... done
copying extra files... done
dumping search index in English (code: en)... done
dumping object inventory... done
build succeeded, 2 warnings.
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with docs/requirements.txt and the generated documentation under docs/. Reproduce the issue by creating the documented Python 3.11 environment and running sphinx-build . _build_docs from docs/. Done means the CLI documentation builds without the missing snakebids and test_snakebids import warnings.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
build-system, documentation
Issue type
Bug
Difficulty
1/5
Estimated time
Under an hour
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
48/100

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