Reorganize cuDF Python docs by shwina · Pull Request #10691 · NVIDIA/cudf

shwina · 2022-04-20T17:17:47Z

This PR is composed of two high-level changes:

Replaces the use of ReStructuredText with MyST Markdown. I used rst2myst for this and it worked pretty well. The rationale for this change is simple: we use myst-nb to render notebooks into documentation, and for consistency, it's nice to use myst-parser to parse the rest of our docs too. As a matter of opinion, I think Markdown is simpler and more familiar to most developers.
Reorganizes the docs (see below):

Prior to this PR, the cuDF documentation was divided into 3 sections:

A user guide
A "Basics" section
API reference

The distinction between the first two sections was never clear. I've gone ahead and merged those into a single section named "User Guide". This is also more consistent with Pandas.

This PR also makes a couple of other changes:

Renamed the "Basics" page under the previous "Basics" section to "Data Types", as that reflects its contents more accurately. I also modified the content here a bit.
Renamed the "10 minutes to CuPy and CuDF" notebook to "Interoperability between CuPy and CuDF" as that more accurately describes what that page is about.

Compare the TOC from this PR (below) with our currently published docs.

…reorg-docs

review-notebook-app · 2022-04-20T17:17:51Z

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codecov · 2022-04-20T18:34:26Z

Codecov Report

Merging #10691 (1857972) into branch-22.06 (84f88ce) will increase coverage by 0.02%.
The diff coverage is 100.00%.

❗ Current head 1857972 differs from pull request most recent head e68b86e. Consider uploading reports for the commit e68b86e to get more accurate results

@@               Coverage Diff                @@
##           branch-22.06   #10691      +/-   ##
================================================
+ Coverage         86.40%   86.43%   +0.02%     
================================================
  Files               143      143              
  Lines             22444    22448       +4     
================================================
+ Hits              19393    19402       +9     
+ Misses             3051     3046       -5

Impacted Files	Coverage Δ
python/cudf/cudf/_fuzz_testing/utils.py	`0.00% <ø> (ø)`
python/cudf/cudf/comm/gpuarrow.py	`79.76% <ø> (ø)`
python/cudf/cudf/core/column/string.py	`89.21% <ø> (+0.12%)`	⬆️
python/cudf/cudf/core/frame.py	`93.41% <ø> (ø)`
python/cudf/cudf/core/series.py	`95.16% <ø> (ø)`
python/custreamz/custreamz/kafka.py	`29.16% <ø> (ø)`
python/cudf/cudf/core/column/interval.py	`83.67% <100.00%> (ø)`
python/cudf/cudf/core/column/struct.py	`96.42% <100.00%> (ø)`
python/cudf/cudf/core/dataframe.py	`93.74% <100.00%> (+0.04%)`	⬆️
python/cudf/cudf/core/reshape.py	`90.11% <100.00%> (+0.11%)`	⬆️
... and 10 more

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…reorg-docs

shwina · 2022-04-26T15:03:03Z

@@ -2,15 +2,16 @@
 "cells": [


This looks to be an issue with the way ReviewNB diffs things. There's no ==================================== in the source. Ditto in many places below.

Reply via ReviewNB

shwina · 2022-04-26T15:05:30Z

@@ -2,46 +2,31 @@
 "cells": [


I removed the hardcoded table of contents below as Sphinx/myst-nb already generate one for us.

Reply via ReviewNB

galipremsagar

Overall looks great to me Ashwin. Except for a few rendering issues that I mentioned below.

galipremsagar · 2022-04-27T17:00:08Z

+    :class: io-supported-types-table special-table
    :widths: 15 10 10 10 10 10 10 10 10 10 10 10 10 10 10 10

    +-----------------------+--------+--------+--------+--------+---------+--------+--------+--------+--------+-------------------+--------+--------+---------+---------+


I like how GitHub thinks you only moved this and 2 more files while you also made similar file movements in this PR 🤣

Yeah what the heck is that about...

…reorg-docs

galipremsagar

Changes LGTM @shwina and all the issues are now fixed. Thank you!

bdice

Really nice job @shwina. I haven't had a chance to render the docs locally, but I thought I would take a peek. I left a handful of comments, but only one (on index.md) is probably blocking. Feel free to skip/ignore any comments or deal with them in future PRs. I recognize this PR is huge so I don't want to block it. Hope the feedback is helpful! :)

bdice · 2022-05-04T00:51:07Z

+also provide special data types for working with decimals, list-like,
+and dictionary-like data.
+
+All data types in cuDF are [nullable](/user_guide/missing-data).


This should use the MyST equivalent of Sphinx's :ref: rather than an absolute path. The absolute path won't work in rendered HTML unless it's being served at the root. That's prone to breakage. This piece of the documentation might help: https://myst-parser.readthedocs.io/en/latest/syntax/syntax.html#targets-and-cross-referencing

Used a relative path instead

A relative path is an improvement but not quite as good as ref syntax. If the page is moved or renamed, the ref will still pick it up as long as it's in the same Sphinx project. refs with missing referents will throw warnings, and refs are supported by non-HTML Sphinx outputs. An absolute/relative path won't be checked for correctness afaik.

With markdown syntax [nullable](mossing-data), I get:

cudf/docs/cudf/source/user_guide/data-types.md:8: WARNING: 'myst' reference target not found: mossing-data

The markdown syntax translates into Sphinx's any role, which seems pretty flexible in what it can do.

Nice to know! If it's translated to the any role, that's awesome. I thought it would be interpreted as a link, rather than a reference (any will match ref or any other role).

(also "mossing data" 😆 )

bdice · 2022-05-04T00:53:50Z

+## NumPy data types
+
+We use NumPy data types for integer, floating, datetime, timedelta,
+and string data types.  Thus, just like in NumPy,


Is it weird that this always uses two spaces between sentences? Personally I prefer one space between sentences.

This is just Emacs'Emacs' auto-fill at work. Personally, I think Semantic Linefeeds are the best convention for documentation source, but it's hard to incorporate them in anything but personal projects :(

Vim’s “gq” does the same thing with two spaces. I would be open to rewriting this with semantic lines (or the easier to enforce “one sentence per line”). I have had no issues in practice with using that style on other projects. This word wrap is pretty harsh right now - it’s wrapping at less than 80 chars (74?), so I think it is unlikely that this word wrapped formatting will survive more than one or two revisions anyway.

Perhaps a discussion to have offline/as part of the dev guide?

I would not oppose making that change in this PR, since all the files are being rewritten anyway. If you don't want to make that decision in this PR, this would be a good topic for tomorrow's cuDF Python meeting.

+1 for semantic linefeeds

bdice · 2022-05-04T00:59:36Z

+`np.dtype("float32")`, `np.float32`, and `"float32"` are all acceptable
+ways to specify the `float32` data type:
+
+```python


I discovered recently that code blocks using >>> are (depending on the renderer) supposed to be rendered as pycon: Python console, rather than python.

That applies to GitHub Flavored Markdown via Linguist and also content highlighted with Pygments. It appears that MyST uses Pygments.

TIL! I can confirm that it works, but are there any advantages to using pycon over python (either ways, I'd prefer to change this in a follow up)

Ah I see, things like keywords in output/tracebacks aren't syntax highlighted by mistake. That's really cool!

Yep! It was definitely a "TIL" thing for me too. I think a lot of projects just use python and don't know the difference.

Co-authored-by: Bradley Dice <bdice@bradleydice.com>

bdice

Thanks @shwina for your dedication to this!

shwina · 2022-05-04T18:53:22Z

Rerun tests

shwina · 2022-05-04T21:39:23Z

@gpucibot merge

mmccarty and others added 5 commits April 19, 2022 15:26

Migrated user guide notebooks to MyST-NB and added sphinx extension

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Reorg

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Change CuPy notebook name

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Merge branch 'branch-22.06' of https://github.com/rapidsai/cudf into …

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…reorg-docs

Remove duplicate

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github-actions Bot added the conda label Apr 20, 2022

Change title

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shwina mentioned this pull request Apr 20, 2022

Migrated user guide notebooks to MyST-NB and added sphinx extension #10685

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mmccarty and others added 15 commits April 21, 2022 10:19

Using MyST-NB sphinx extension for Notebook execution and rendering

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Add Pandas comparison docs

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Move back to ipynb

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Deletee md

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Merge branch 'myst-nb' of github.com:mmccarty/cudf into reorg-docs

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Merge branch 'reorg-docs' into add-pandas-comparison

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Add more Pandas comparison notes

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Run notebooks

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Merge branch 'add-pandas-comparison' into reorg-docs

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set overflow for notebook output

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Update docs/cudf/source/_static/params.css

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Move from .rst to .md

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Merge branch 'myst-nb' of github.com:mmccarty/cudf into reorg-docs

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Cache notebook runs

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Improvements to pandas comparison docs

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shwina mentioned this pull request Apr 25, 2022

Add a "comparison with Pandas" section to user guide #10708

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shwina added 2 commits April 25, 2022 13:16

Remove Pandas comparison doc for now

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Merge branch 'branch-22.06' of https://github.com/rapidsai/cudf into …

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…reorg-docs

github-actions Bot removed the conda label Apr 26, 2022

Merge artefact

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Merge io sources into one

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shwina commented Apr 26, 2022

View reviewed changes

Comment thread docs/cudf/source/user_guide/io.md

shwina added 3 commits April 26, 2022 10:49

Use a wrapper to make special-table scrollable

da86dc0

Undo change to jupyter_execute_notebooks in conf.py

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Remove duplicate TOC in missing data notebook

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shwina added doc Documentation non-breaking Non-breaking change labels Apr 26, 2022

shwina marked this pull request as ready for review April 26, 2022 14:58

shwina commented Apr 26, 2022

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shwina requested a review from galipremsagar April 26, 2022 15:06

galipremsagar reviewed Apr 27, 2022

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shwina added 5 commits April 29, 2022 06:40

Merge branch 'branch-22.06' of https://github.com/rapidsai/cudf into …

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…reorg-docs

Improve data-types table

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[skip-ci] Add the result of gsr.dtype

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[skip-ci] Fix warning render

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[skip-ci] or -> and

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galipremsagar approved these changes May 3, 2022

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bdice reviewed May 4, 2022

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mmccarty approved these changes May 4, 2022

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shwina and others added 5 commits May 4, 2022 13:27

Changes after review

52fc1bf

Update docs/cudf/source/user_guide/internals.md

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Co-authored-by: Bradley Dice <bdice@bradleydice.com>

[skip-ci] More suggestions from review

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gramar

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Merge branch 'reorg-docs' of github.com:shwina/cudf into reorg-docs

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bdice approved these changes May 4, 2022

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rapids-bot Bot merged commit dd68db3 into NVIDIA:branch-22.06 May 4, 2022

isVoid mentioned this pull request May 18, 2022

Update Documentation with Pydata Sphinx Theme, and more rapidsai/cuspatial#523

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