docs: Build official documentation site by ganow · Pull Request #123 · KamitaniLab/bdpy

ganow · 2026-05-21T13:38:40Z

Summary

Refs #122.

This PR sets up the initial official documentation foundation for bdpy using MkDocs, Material for MkDocs, and mkdocstrings.

It includes:

MkDocs site configuration and documentation dependency setup
API reference pages generated mechanically with mkdocstrings from NumPy-style docstrings
Hierarchical documentation pages for a small set of frequently referenced API modules
A provisional getting started page, which is still mostly boilerplate and needs refinement
Contributor-facing documentation in CONTRIBUTING.md
Removal of the previous mostly-empty Jekyll docs setup

The API reference is the most complete part of this initial PR. Non-API pages are still generally sparse and should be expanded in follow-up work.

Behavior

This PR is intended to be documentation-only from a user-facing behavior perspective.

The Python source edits are limited to docstring/rendering cleanup and documentation support so that mkdocstrings can parse and display the API reference correctly. No runtime behavior changes are intended.

Local preview

Install the docs dependency group and run the MkDocs development server:

uv run --group docs mkdocs serve

Then open:

http://127.0.0.1:8000/

For a one-shot build check:

uv run --group docs mkdocs build

mkdocs build --strict is not clean yet because existing docstrings still produce griffe warnings. The non-strict build succeeds.

Notes

I have created a draft version of the bdpy documentation. I would appreciate it if you could check the documentation in your local environment.

Currently, I feel that various information is lacking for general package documentation, such as the Getting Started page (which is currently just a mockup written for the time being), as well as other user guides and tutorials.

Therefore, I believe we need to enrich the documentation by following one of these two approaches:

Create a topic branch before merging this PR, and then merge that topic branch into this branch.
Merge this PR into main, and then merge subsequent topic branches into main asynchronously.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Resolve symbol duplication, private method leakage, and section-style issues in the auto-generated API reference. - Add missing mkdocstrings handler options: docstring_section_style=list, merge_init_into_class, separate_signature, show_root_heading, show_symbol_type_heading, filters=["!^_"], and others - Drop global show_submodules to eliminate double-rendering of re-exported symbols (e.g. DataStore appeared twice under dataform) - Restructure stubs for packages with empty __init__.py (dl, evals, recon, opendata, dataset, pipeline, task) to target submodules directly, avoiding bdpy.recon.torch.__init__'s bare `import torch` pulling in the entire PyTorch namespace Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- bdata.py: retrun_index -> return_index (3 occurrences in BData.select) - utils.py: successsive -> successive (vstack, concat_dataset) - icnn.py: loss_function -> loss_func, display_interval -> disp_interval - preproc/interface.py: Mode/Baseline/ZeroThreshold -> mode/baseline/zero_threshold Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

numpydoc requires a blank line before each section header (Parameters, Returns, etc.) to recognize it as a section. Without it the entire docstring collapses to a prose paragraph in the API reference. - ml/learning.py: Classification class - fig/makeplots.py: Parameters and Returns sections - fig/makeplots2.py: Parameters and Returns sections Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

In BData's class docstring, a prose sentence was placed between the Parameters and Attributes sections, causing the numpydoc parser to generate phantom parameter rows in the API reference. Moved to a Notes section, which is the standard numpy docstring convention for supplementary information. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

corrcoef and corrmat had Returns entries without type annotations (e.g. bare 'r' instead of 'r : numpy.ndarray'), causing mkdocstrings to display the variable name in the Type column instead of the actual type. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Examples sections were written as plain indented text, causing mkdocstrings to render code as prose paragraphs. Prose text interspersed with code also triggered phantom headings via the markdown setext-heading pattern. - dataform/datastore.py: DataStore and DirStore.get examples - preproc/interface.py: shift_sample example (also fixes commented-out output) - fig/tile_images.py: all four layout diagram examples Also renames 'Example' headers to 'Examples' (numpy standard). Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- bdata/bdata.py: removed hand-maintained "API list" section with setext underline, which was being rendered as an H2 heading in the API reference - stats/__init__.py: removed redundant "Functions:" bullet list that duplicates what mkdocstrings generates automatically Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- recon/torch/icnn.py: fix typos numpy.ndarar/ndarary -> numpy.ndarray, remove (default: ...) suffix from type specs, fix crop_generator_output parameter name that had assignment syntax mixed in - ml/crossvalidation.py: fix unclosed parenthesis in array-like shape annotation (2 occurrences) - stats/corr.py: use numpy-standard {'row', 'col'} set notation instead of prose "str, 'row' or 'col'" (2 occurrences) Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

Packages whose __init__.py re-exports symbols via aliases are not rendered by mkdocstrings when show_submodules is off. Fix by pointing each ::: directive at the canonical submodule (e.g. bdpy.bdata.bdata) rather than the package root (bdpy.bdata), for bdata, stats, feature, util, mri, distcomp, dl, and recon. Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

- remove_nan_value: convert from non-numpy docstring format to numpy style Parameters/Returns sections - ImageDataset (__init__): add summary line so merge_init_into_class correctly renders the Parameters section - BaseCallback: wrap inline doctest example in a fenced code block to prevent >>> from being interpreted as markdown blockquotes Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Replace show_submodules:false + per-submodule ::: directives with show_submodules:true + single ::: bdpy.<pkg> per page. This prevents missing-module gaps when new submodules are added without updating the stubs. Previously absent modules (dl.torch.dataset, dl.torch.models, dl.torch.domain.feature_domain, dataform.utils, fig.makeplots family, ml.learning, ml.crossvalidation, ml.model, preproc.preprocessor) now appear automatically. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

- Split bdata, dl, ml, and recon API docs into submodule pages - Add overview pages for nested API reference sections - Update API index and MkDocs nav to point to the new structure - Adjust mkdocstrings options to reduce duplicate headings and submodule output

KenyaOtsuka

Thank you for this great update!

Overall, I think this looks good as a foundation version of the BdPy documentation. The API reference structure looks reasonable to me, and I think it is fine that the non-API pages are still sparse at this stage, since they can be improved in follow-up PRs.

I left a few comments. I would appreciate it if you could take a look.

One additional point:
I noticed that docs/bdata_api_examples.md and docs/dataform_features.md are removed in this PR.

For docs/bdata_api_examples.md, most of the basic BData examples seem to be covered by the new Getting Started page, so I think its removal is probably fine.

However, I could not find equivalent replacement content for docs/dataform_features.md. If this content was removed mainly because it does not fit the new MkDocs structure, I think it would be a bit unfortunate to lose it entirely. It may be better to keep it somewhere.

KenyaOtsuka · 2026-05-26T04:39:13Z

+        ...               dirs_pattern=['layer', 'subject', 'roi'],
+        ...               file_pattern='<image>.mat',
+        ...               variable='feat')
+        >>> data = ds.get(layer='conv1', subject='TH', roi='VC', image='Image_001')


I think TH should be replaced with something like sub-01.

KenyaOtsuka · 2026-05-26T04:43:38Z

-    group : array-like (shape =  (n_samples, )
+    group : array-like of shape (n_samples,)
        Group labels (e.g., run labels, block labels, ...)
    n_folds : int, optional


should be nfolds

I found a few other warnings that appear to be caused by simple docstring/signature mismatches. I think these should be easy to fix, so it would be good to address them in this PR.

WARNING - griffe: bdpy/mri/roi.py:159: Parameter 'roi_mask' does not appear in the function signature WARNING - griffe: bdpy/bdata/bdata.py:288: Parameter 'key' does not appear in the function signature WARNING - griffe: bdpy/ml/learning.py:183: No types or annotations for parameters ['None'] WARNING - griffe: bdpy/ml/learning.py:183: Parameter 'None' does not appear in the function signature

This reverts commit d4fe070.

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

… and nav - datastore.py: replace subject='TH' with 'sub-01' in example - crossvalidation.py: rename n_folds -> nfolds in docstring to match signature - roi.py: rename roi_mask -> label in add_roilabel docstring - bdata.py: rename key -> metakey in edit_metadatadescription docstring - learning.py: remove spurious Parameters/None section from CrossValidation.run - mkdocs.yml: add Features and DecodedFeatures page to nav Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

ganow · 2026-05-26T08:32:36Z

Thank you for the thorough review!

I've addressed all the points you raised:

subject='TH' → replaced with 'sub-01' in datastore.py
n_folds → nfolds in crossvalidation.py
griffe warnings (roi.py, bdata.py, learning.py) — all four parameter/signature mismatches fixed

Regarding dataform_features.md: I reverted the deletion commit and re-deleted only _config.yml and bdata_api_examples.md. dataform_features.md is now kept as a non-API page and added to the site navigation under "Features and DecodedFeatures".

github-actions · 2026-05-26T08:32:56Z

Coverage Report

File	Stmts	Miss	Cover	Missing
bdpy/bdata
bdata.py	399	195	51%	62, 87, 92, 96, 101, 105, 115–117, 173, 216–222, 235–245, 259–260, 293, 297, 301–339, 388–394, 402–403, 408–409, 426–433, 451–452, 458, 491, 522, 531, 543, 572–581, 593, 608, 644, 666–674, 679–712, 721, 733–740, 744–750, 754–782, 786–807, 811–845, 849–851, 855–857, 861–870
featureselector.py	64	12	81%	62–67, 69–74
metadata.py	67	1	99%	84
utils.py	113	37	67%	71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
datastore.py	107	85	21%	60–76, 91–94, 98–99, 103–114, 117–120, 123–128, 132–133, 138–159, 191–198, 219–256, 259–262
features.py	298	165	45%	31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
kvs.py	177	13	93%	21, 24, 114, 118, 127–131, 171, 173, 185, 254, 282
pd.py	9	5	44%	25–27, 43–44
sparse.py	67	7	90%	29, 52–58, 74, 109, 123
utils.py	12	12	0%	3–18
bdpy/dataset
utils.py	45	45	0%	3–98
bdpy/distcomp
distcomp.py	92	18	80%	33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
caffe.py	60	60	0%	4–129
bdpy/dl/torch
base.py	43	24	44%	31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
dataset.py	74	40	46%	37–39, 67–72, 75, 78–88, 122–130, 133, 136–149, 196, 199
models.py	333	226	32%	148–169, 297–316, 327–331, 345–350, 442–494, 515–517, 528–587, 611–614, 625–684, 708–711, 722–771, 790–793, 804–853, 872–875
torch.py	121	55	55%	189–226, 229, 232–244, 247–282
bdpy/dl/torch/domain
core.py	46	2	96%	47, 63
feature_domain.py	24	1	96%	30
image_domain.py	81	3	96%	91, 94, 257
bdpy/evals
metrics.py	95	45	53%	49–53, 82–112, 130–142, 151–152, 157, 184–191
bdpy/feature
feature.py	30	2	93%	69–70
bdpy/fig
__init__.py	5	5	0%	6–10
draw_group_image_set.py	90	90	0%	3–182
fig.py	88	88	0%	16–164
makeplots2.py	263	263	0%	1–610
makeplots.py	336	336	0%	1–731
tile_images.py	59	59	0%	1–187
bdpy/ml
crossvalidation.py	59	27	54%	47–48, 113–114, 117–118, 138, 164–196
learning.py	313	97	69%	9, 47–48, 52, 56, 63, 96–109, 114–130, 133, 163–175, 185–210, 294, 310, 314–316, 319–320, 330, 340–341, 346–347, 357–365, 368–369, 377, 412–419, 440, 453, 461, 470, 502–504, 543, 556, 559, 568, 577, 582, 603
model.py	140	120	14%	29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
searchlight.py	16	13	19%	32–51
bdpy/mri
fmriprep.py	497	451	9%	25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862
glm.py	40	36	10%	46–95
image.py	24	19	21%	29–54
load_epi.py	28	18	36%	36–50, 56–63, 82–88
load_mri.py	19	16	16%	16–36
roi.py	248	217	12%	37–100, 165–235, 241–314, 320–387, 399–466, 473–499
spm.py	158	139	12%	26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
__init__.py	1	1	0%	1
openneuro.py	210	210	0%	1–329
bdpy/pipeline
config.py	36	2	94%	37–38
bdpy/preproc
interface.py	52	16	69%	111–123, 148–157
preprocessor.py	129	69	47%	35, 44, 112–114, 121–128, 138–189, 196–227
select_top.py	23	1	96%	55
bdpy/recon
utils.py	55	55	0%	4–146
bdpy/recon/torch
icnn.py	161	161	0%	15–480
bdpy/recon/torch/modules
critic.py	44	2	95%	58, 132
encoder.py	29	1	97%	29
generator.py	72	5	93%	47, 52, 68, 128, 309
latent.py	34	3	91%	16, 21, 32
bdpy/recon/torch/task
inversion.py	83	11	87%	22, 40, 45, 50, 57, 62, 67, 72, 96, 210, 225
bdpy/stats
corr.py	43	3	93%	57, 68, 102
bdpy/task
callback.py	71	4	94%	114, 163, 168, 236
core.py	16	1	94%	50
bdpy/util
info.py	47	36	23%	19–79
utils.py	36	8	78%	60, 116–121, 140–142
TOTAL	5981	3636	39%

Tests	Skipped	Failures	Errors	Time
218	0 💤	1 ❌	0 🔥	16.794s ⏱️

github-actions · 2026-05-26T08:32:56Z

Coverage Report

File	Stmts	Miss	Cover	Missing
bdpy/bdata
bdata.py	399	195	51%	62, 87, 92, 96, 101, 105, 115–117, 173, 216–222, 235–245, 259–260, 293, 297, 301–339, 388–394, 402–403, 408–409, 426–433, 451–452, 458, 491, 522, 531, 543, 572–581, 593, 608, 644, 666–674, 679–712, 721, 733–740, 744–750, 754–782, 786–807, 811–845, 849–851, 855–857, 861–870
featureselector.py	64	12	81%	62–67, 69–74
metadata.py	67	1	99%	84
utils.py	113	37	67%	71, 82, 85–86, 95, 127–173, 201, 246, 258, 263
bdpy/dataform
datastore.py	107	85	21%	60–76, 91–94, 98–99, 103–114, 117–120, 123–128, 132–133, 138–159, 191–198, 219–256, 259–262
features.py	298	165	45%	31–32, 43–46, 90–92, 101–103, 107, 111, 115, 119, 152–153, 157–161, 168–197, 214–215, 224–225, 232–236, 274, 288, 305–319, 323, 327, 331, 335, 339, 343, 347, 351, 355, 359, 364–394, 398–418, 422–462, 465, 470–477, 491–493, 496–499, 502–505, 508–512, 515–516, 536–549
kvs.py	177	13	93%	21, 24, 114, 118, 127–131, 171, 173, 185, 254, 282
pd.py	9	5	44%	25–27, 43–44
sparse.py	67	7	90%	29, 52–58, 74, 109, 123
utils.py	12	12	0%	3–18
bdpy/dataset
utils.py	45	45	0%	3–98
bdpy/distcomp
distcomp.py	92	18	80%	33, 35, 49, 53, 55, 66–70, 74, 76, 81–82, 89–93, 97
bdpy/dl
caffe.py	60	60	0%	4–129
bdpy/dl/torch
base.py	43	24	44%	31–41, 48, 54, 60, 63, 73–83, 90, 96, 102, 105
dataset.py	74	40	46%	37–39, 67–72, 75, 78–88, 122–130, 133, 136–149, 196, 199
models.py	333	226	32%	148–169, 297–316, 327–331, 345–350, 442–494, 515–517, 528–587, 611–614, 625–684, 708–711, 722–771, 790–793, 804–853, 872–875
torch.py	121	55	55%	189–226, 229, 232–244, 247–282
bdpy/dl/torch/domain
core.py	46	2	96%	47, 63
feature_domain.py	24	1	96%	30
image_domain.py	81	3	96%	91, 94, 257
bdpy/evals
metrics.py	95	45	53%	49–53, 82–112, 130–142, 151–152, 157, 184–191
bdpy/feature
feature.py	30	2	93%	69–70
bdpy/fig
__init__.py	5	5	0%	6–10
draw_group_image_set.py	90	90	0%	3–182
fig.py	88	88	0%	16–164
makeplots2.py	263	263	0%	1–610
makeplots.py	336	336	0%	1–731
tile_images.py	59	59	0%	1–187
bdpy/ml
crossvalidation.py	59	27	54%	47–48, 113–114, 117–118, 138, 164–196
learning.py	315	97	69%	9, 47–48, 52, 56, 63, 96–109, 114–130, 133, 163–175, 185–210, 294, 310, 314–316, 319–320, 330, 340–341, 346–347, 357–365, 368–369, 377, 412–419, 440, 453, 461, 470, 502–504, 543, 556, 559, 568, 577, 582, 603
model.py	140	120	14%	29–39, 54–70, 86–144, 156–169, 184–222, 225, 230–250, 254–258, 271–285
searchlight.py	16	13	19%	32–51
bdpy/mri
fmriprep.py	497	451	9%	25–34, 38, 44–62, 65–75, 78–89, 92–160, 163–194, 230–360, 367–380, 384, 388–390, 394, 398–400, 410–434, 437–454, 457–464, 471–472, 475–491, 494, 498, 502–815, 819–831, 842–862
glm.py	40	36	10%	46–95
image.py	24	19	21%	29–54
load_epi.py	28	18	36%	36–50, 56–63, 82–88
load_mri.py	19	16	16%	16–36
roi.py	248	217	12%	37–100, 165–235, 241–314, 320–387, 399–466, 473–499
spm.py	158	139	12%	26–155, 162–166, 170, 174–179, 183–300
bdpy/opendata
__init__.py	1	1	0%	1
openneuro.py	210	210	0%	1–329
bdpy/pipeline
config.py	36	2	94%	37–38
bdpy/preproc
interface.py	52	16	69%	111–123, 148–157
preprocessor.py	129	69	47%	35, 44, 112–114, 121–128, 138–189, 196–227
select_top.py	23	1	96%	55
bdpy/recon
utils.py	55	55	0%	4–146
bdpy/recon/torch
icnn.py	161	161	0%	15–480
bdpy/recon/torch/modules
critic.py	44	2	95%	58, 132
encoder.py	29	1	97%	29
generator.py	72	5	93%	47, 52, 68, 128, 309
latent.py	34	3	91%	16, 21, 32
optimizer.py	22	9	59%	8–26
bdpy/recon/torch/task
inversion.py	88	15	83%	11–16, 22, 40, 45, 50, 57, 62, 67, 72, 96, 210, 225
bdpy/stats
corr.py	43	3	93%	57, 68, 102
bdpy/task
callback.py	71	4	94%	114, 163, 168, 236
core.py	16	1	94%	50
bdpy/util
info.py	47	36	23%	19–79
utils.py	36	8	78%	60, 116–121, 140–142
TOTAL	5998	3649	39%

Tests	Skipped	Failures	Errors	Time
218	0 💤	0 ❌	0 🔥	16.458s ⏱️

KenyaOtsuka

I confirmed that all griffe warnings have been resolved.
This looks good to me!

PeerHerholz · 2026-05-28T08:31:35Z

Hey @ganow,

sorry, I'm getting to this so late. Should I still have a look at the docs even though the PR is already merged?

ganow · 2026-05-29T01:42:36Z

@PeerHerholz Thank you for checking this PR! I apologize for merging it without waiting for your review. If there are any points of concern, I would appreciate your comments. I know you are busy, so please feel free to skip the review if you prefer. I believe this PR has established the foundation for building the official documentation, so I would be very happy if you could cooperate with us in the future regarding documentation creation from the perspective of a new user.

PeerHerholz · 2026-05-29T10:12:14Z

Hey @ganow,

no worries or problems at all. I'm very sorry for not responding in a timely manner.
Yes, I would definitely like to support this endeavor and assign dedicated time to work and focus on this.

ganow and others added 20 commits May 21, 2026 18:12

fix: make bdpy.pipeline a proper Python package

9a14039

chore: remove legacy Jekyll docs setup

d4fe070

build: set up MkDocs with docs dependency group

bee7437

docs: add landing page and getting started guide

627bc65

docs: add API reference pages

749ab5f

docs: add CONTRIBUTING.md

d465afd

docs: enable hot reload and footer navigation in MkDocs

dedf0fe

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

docs: add syntax highlighting for code blocks

66c6cef

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

ganow requested review from KenyaOtsuka and PeerHerholz May 21, 2026 13:40

ganow added the enhancement label May 21, 2026

ganow mentioned this pull request May 22, 2026

typo #113

Closed

ganow marked this pull request as ready for review May 26, 2026 04:54

ganow changed the title ~~WIP: Build official documentation site~~ docs: Build official documentation site May 26, 2026

ganow changed the base branch from main to dev May 26, 2026 07:00

KenyaOtsuka reviewed May 26, 2026

View reviewed changes

ganow and others added 2 commits May 26, 2026 17:12

Revert "chore: remove legacy Jekyll docs setup"

f88efac

This reverts commit d4fe070.

chore: re-remove legacy Jekyll files, keep dataform_features.md

476171a

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

ganow and others added 3 commits May 26, 2026 17:16

fix: correct confusing indentation in docstring continuation lines

04a498b

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

docs: wrap example code block in icnn.py docstring with ```python fence

8de522b

Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>

KenyaOtsuka self-requested a review May 26, 2026 09:40

KenyaOtsuka approved these changes May 26, 2026

View reviewed changes

KenyaOtsuka merged commit 89b867c into dev May 26, 2026
3 of 6 checks passed

ganow deleted the docs/site-setup branch May 26, 2026 09:54

ganow mentioned this pull request May 26, 2026

docs: Investigate and clean up non-standard docstring formatting after PR #123 #128

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KenyaOtsuka May 26, 2026

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ganow commented May 26, 2026

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ganow commented May 21, 2026 •

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