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[DOC] deal with several warnings and errors in the doc build #1061

Merged
merged 3 commits into from
May 8, 2024
Merged

[DOC] deal with several warnings and errors in the doc build #1061

merged 3 commits into from
May 8, 2024

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Remi-Gau
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@Remi-Gau Remi-Gau commented May 8, 2024 •
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Remi-Gau
Remi-Gau commented May 8, 2024
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doc/api.rst
@@ -24,8 +24,6 @@ API Reference

.. currentmodule:: bids

.. _calibration_ref:
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duplicate ref

Remi-Gau
Remi-Gau commented May 8, 2024
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doc/examples/statsmodels_tutorial.md
@@ -11,7 +11,7 @@ kernelspec:
name: python3
---

## Executing and inspecting StatsModels with `pybids.modeling`
# Executing and inspecting StatsModels with `pybids.modeling`
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fix heading level

Remi-Gau
Remi-Gau commented May 8, 2024
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doc/layout/index.rst
@@ -1,4 +1,4 @@
.. _reports:
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duplicae ref

Remi-Gau
Remi-Gau commented May 8, 2024
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bids/variables/variables.py
Possible args:
- sampling_rate (int, str): The sampling rate to use if resampling
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fix indentation error

Remi-Gau
Remi-Gau commented May 8, 2024
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bids/reports/report.py
@@ -18,16 +18,20 @@ class BIDSReport:
(str), a dictionary, or None. If None, loads and uses default
configuration information.
Keys in the dictionary include:
'dir': a dictionary for converting encoding direction strings
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fix indentation error and ensure better HTML rendering

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codecov bot commented May 8, 2024 •
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Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 89.80%. Comparing base (235cd25) to head (e2343e4).

Additional details and impacted files 
@@           Coverage Diff           @@
##           master    #1061   +/-   ##
=======================================
  Coverage   89.80%   89.80%           
=======================================
  Files          63       63           
  Lines        7178     7178           
  Branches     1374     1374           
=======================================
  Hits         6446     6446           
  Misses        532      532           
  Partials      200      200

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

Remi-Gau
Remi-Gau commented May 8, 2024
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doc/conf.py
@@ -68,6 +68,7 @@
autosummary_generate = True
autodoc_default_flags = ['members', 'inherited-members']
add_module_names = False
numpydoc_class_members_toctree = False
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see https://stackoverflow.com/a/66139873

This feels a bit like a nuclear option but have not found a better way to deal with those warnings

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Remi-Gau commented May 8, 2024

I can deal with the intersphinx mapping config format mentioned here: https://github.com/bids-standard/pybids/actions/runs/8958443748/job/24602669575#step:5:29

but this would require bumping up the minimum required sphinx version

@Remi-Gau Remi-Gau requested a review from effigies May 8, 2024 11:32
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effigies commented May 8, 2024

Sure, we can bump the minimum sphinx no problem.

Remi-Gau
Remi-Gau commented May 8, 2024
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doc/analysis/index.rst
@@ -15,7 +15,7 @@
.. _overview:

An overview of the analysis module
===========================================
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I suspect there are more like this but I decided not to start looking to give my inner marie kondo a break.

Remi-Gau
Remi-Gau commented May 8, 2024
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doc/includes/big_toc_css.rst
@@ -2,6 +2,8 @@
File to ..include in a document with a big table of content, to give
it 'style'

:orphan:
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to silence 'not included in toc tree' warnings

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Remi-Gau commented May 8, 2024

not a consequence of this PR but noticed some funky layout in a tuto:

https://bids-standard.github.io/pybids/examples/pybids_tutorial.html#exporting-a-bidslayout-to-a-pandas-dataframe

image

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effigies commented May 8, 2024

This looks good. I'm still getting

/home/chris/Projects/bids/pybids/doc/api.rst:9: WARNING: autosummary: stub file not found 'bids.layout'. Check your autosummary_generate setting.
/home/chris/Projects/bids/pybids/doc/api.rst:31: WARNING: autosummary: stub file not found 'bids.modeling'. Check your autosummary_generate setting.
/home/chris/Projects/bids/pybids/doc/api.rst:47: WARNING: autosummary: stub file not found 'bids.reports'. Check your autosummary_generate setting.
/home/chris/Projects/bids/pybids/doc/api.rst:61: WARNING: autosummary: stub file not found 'bids.variables'. Check your autosummary_generate setting.
/home/chris/Projects/bids/pybids/doc/api.rst:83: WARNING: autosummary: stub file not found 'bids.config'. Check your autosummary_generate setting.
/home/chris/Projects/bids/pybids/doc/api.rst:98: WARNING: autosummary: stub file not found 'bids.utils'. Check your autosummary_generate setting.

Are those out of scope, or is there something wrong with my setup?

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Remi-Gau commented May 8, 2024

Are those out of scope, or is there something wrong with my setup?

yeah I noticed that but if I rerun the doc build the error goes away: do you get the same thing?

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effigies commented May 8, 2024

If I make -C doc clean html, it shows up consistently. Doesn't seem new, though. There are no references for the API summary to link to: https://bids-standard.github.io/pybids/api.html#bids-layout-querying-bids-datasets

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Remi-Gau commented May 8, 2024

tempted to leave it there for now , merge and and get back to it later.

@effigies effigies merged commit 09448ad into bids-standard:master May 8, 2024
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@Remi-Gau Remi-Gau deleted the doc_fix branch May 8, 2024 13:55
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