DOC: fix PR02 errors in docstrings #57111

jordan-d-murphy · 2024-01-28T06:15:24Z

Pandas has a script for validating docstrings:

Lines 72 to 194 in 9008ee5

    
           MSG='Partially validate docstrings (PR02)' ;  echo $MSG 
        
           $BASE_DIR/scripts/validate_docstrings.py --format=actions --errors=PR02 --ignore_functions \ 
        
               pandas.io.formats.style.Styler.to_excel\ 
        
               pandas.CategoricalIndex.rename_categories\ 
        
               pandas.CategoricalIndex.reorder_categories\ 
        
               pandas.CategoricalIndex.add_categories\ 
        
               pandas.CategoricalIndex.remove_categories\ 
        
               pandas.CategoricalIndex.set_categories\ 
        
               pandas.IntervalIndex.set_closed\ 
        
               pandas.IntervalIndex.contains\ 
        
               pandas.IntervalIndex.overlaps\ 
        
               pandas.IntervalIndex.to_tuples\ 
        
               pandas.DatetimeIndex.round\ 
        
               pandas.DatetimeIndex.floor\ 
        
               pandas.DatetimeIndex.ceil\ 
        
               pandas.DatetimeIndex.month_name\ 
        
               pandas.DatetimeIndex.day_name\ 
        
               pandas.DatetimeIndex.to_period\ 
        
               pandas.DatetimeIndex.std\ 
        
               pandas.TimedeltaIndex.round\ 
        
               pandas.TimedeltaIndex.floor\ 
        
               pandas.TimedeltaIndex.ceil\ 
        
               pandas.PeriodIndex\ 
        
               pandas.PeriodIndex.strftime\ 
        
               pandas.Series.clip\ 
        
               pandas.Series.rename_axis\ 
        
               pandas.Series.interpolate\ 
        
               pandas.Series.dt.to_period\ 
        
               pandas.Series.dt.tz_localize\ 
        
               pandas.Series.dt.tz_convert\ 
        
               pandas.Series.dt.strftime\ 
        
               pandas.Series.dt.round\ 
        
               pandas.Series.dt.floor\ 
        
               pandas.Series.dt.ceil\ 
        
               pandas.Series.dt.month_name\ 
        
               pandas.Series.dt.day_name\ 
        
               pandas.Series.str.wrap\ 
        
               pandas.Series.cat.rename_categories\ 
        
               pandas.Series.cat.reorder_categories\ 
        
               pandas.Series.cat.add_categories\ 
        
               pandas.Series.cat.remove_categories\ 
        
               pandas.Series.cat.set_categories\ 
        
               pandas.Series.plot\ 
        
               pandas.Series.plot.bar\ 
        
               pandas.Series.plot.barh\ 
        
               pandas.Series.plot.line\ 
        
               pandas.Series.plot.pie\ 
        
               pandas.DataFrame.clip\ 
        
               pandas.DataFrame.plot\ 
        
               pandas.DataFrame.plot.bar\ 
        
               pandas.DataFrame.plot.barh\ 
        
               pandas.DataFrame.plot.line\ 
        
               pandas.DataFrame.plot.pie\ 
        
               pandas.tseries.offsets.DateOffset\ 
        
               pandas.tseries.offsets.BusinessDay\ 
        
               pandas.tseries.offsets.BDay\ 
        
               pandas.tseries.offsets.BusinessHour\ 
        
               pandas.tseries.offsets.CustomBusinessDay\ 
        
               pandas.tseries.offsets.CDay\ 
        
               pandas.tseries.offsets.CustomBusinessHour\ 
        
               pandas.tseries.offsets.MonthEnd\ 
        
               pandas.tseries.offsets.MonthBegin\ 
        
               pandas.tseries.offsets.BusinessMonthEnd\ 
        
               pandas.tseries.offsets.BMonthEnd\ 
        
               pandas.tseries.offsets.BusinessMonthBegin\ 
        
               pandas.tseries.offsets.BMonthBegin\ 
        
               pandas.tseries.offsets.CustomBusinessMonthEnd\ 
        
               pandas.tseries.offsets.CBMonthEnd\ 
        
               pandas.tseries.offsets.CustomBusinessMonthBegin\ 
        
               pandas.tseries.offsets.CBMonthBegin\ 
        
               pandas.tseries.offsets.SemiMonthEnd\ 
        
               pandas.tseries.offsets.SemiMonthBegin\ 
        
               pandas.tseries.offsets.Week\ 
        
               pandas.tseries.offsets.WeekOfMonth\ 
        
               pandas.tseries.offsets.LastWeekOfMonth\ 
        
               pandas.tseries.offsets.BQuarterEnd\ 
        
               pandas.tseries.offsets.BQuarterBegin\ 
        
               pandas.tseries.offsets.QuarterEnd\ 
        
               pandas.tseries.offsets.QuarterBegin\ 
        
               pandas.tseries.offsets.BYearEnd\ 
        
               pandas.tseries.offsets.BYearBegin\ 
        
               pandas.tseries.offsets.YearEnd\ 
        
               pandas.tseries.offsets.YearBegin\ 
        
               pandas.tseries.offsets.FY5253\ 
        
               pandas.tseries.offsets.FY5253Quarter\ 
        
               pandas.tseries.offsets.Easter\ 
        
               pandas.tseries.offsets.Day\ 
        
               pandas.tseries.offsets.Hour\ 
        
               pandas.tseries.offsets.Minute\ 
        
               pandas.tseries.offsets.Second\ 
        
               pandas.tseries.offsets.Milli\ 
        
               pandas.tseries.offsets.Micro\ 
        
               pandas.tseries.offsets.Nano\ 
        
               pandas.describe_option\ 
        
               pandas.reset_option\ 
        
               pandas.get_option\ 
        
               pandas.set_option\ 
        
               pandas.Timestamp.max\ 
        
               pandas.Timestamp.min\ 
        
               pandas.Timestamp.resolution\ 
        
               pandas.Timedelta.max\ 
        
               pandas.Timedelta.min\ 
        
               pandas.Timedelta.resolution\ 
        
               pandas.Interval\ 
        
               pandas.Grouper\ 
        
               pandas.core.groupby.SeriesGroupBy.apply\ 
        
               pandas.core.groupby.SeriesGroupBy.transform\ 
        
               pandas.core.groupby.DataFrameGroupBy.transform\ 
        
               pandas.core.groupby.DataFrameGroupBy.nth\ 
        
               pandas.core.groupby.DataFrameGroupBy.rolling\ 
        
               pandas.core.groupby.SeriesGroupBy.idxmax\ 
        
               pandas.core.groupby.SeriesGroupBy.idxmin\ 
        
               pandas.core.groupby.SeriesGroupBy.nth\ 
        
               pandas.core.groupby.SeriesGroupBy.rolling\ 
        
               pandas.core.groupby.DataFrameGroupBy.hist\ 
        
               pandas.core.groupby.DataFrameGroupBy.plot\ 
        
               pandas.core.groupby.SeriesGroupBy.plot\ 
        
               pandas.read_hdf\ 
        
               pandas.HDFStore.append\ 
        
               pandas.core.window.rolling.Rolling.quantile\ 
        
               pandas.core.window.expanding.Expanding.quantile\ 
        
               pandas.api.extensions.ExtensionArray.argsort # There should be no backslash in the final line, please keep this comment in the last ignored function 
        
           RET=$(($RET + $?)) ; echo $MSG "DONE"

Currently, some methods fail the PR02 check.

The task here is:

take 2-4 methods
run: scripts/validate_docstrings.py --format=actions --errors=PR02 method-name
check if validation docstrings passes for those methods, and if it’s necessary fix the docstrings according to whatever error is reported
remove those methods from code_checks.sh
commit, push, open pull request

Please don't comment take as multiple people can work on this issue. You also don't need to ask for permission to work on this, just comment on which methods are you going to work.

If you're new contributor, please check the contributing guide

thanks @natmokval @mroeschke for the inspiration for this issue

The text was updated successfully, but these errors were encountered:

jordan-d-murphy · 2024-01-28T08:55:49Z

I'll take

pandas.Series.interpolate
pandas.read_hdf
pandas.HDFStore.append

jrmylow · 2024-01-28T10:37:56Z

I'll get started with:

pandas.describe_option
pandas.reset_option
pandas.get_option
pandas.set_option

jordan-d-murphy · 2024-01-30T05:06:06Z

I'll take:

pandas.core.groupby.SeriesGroupBy.idxmax
pandas.core.groupby.SeriesGroupBy.idxmin

jrmylow · 2024-01-30T06:40:43Z

Would it be helpful to add the good-first-issue label to this? Seems the previous iteration (for EX03?) had that

jordan-d-murphy · 2024-01-30T06:53:33Z

I think so, but I can't add the label myself. Feel free to add if you have permissions 🙂

manlattan · 2024-01-30T14:02:57Z

/take

thiphan94 · 2024-01-31T08:27:12Z

I worked on:

pandas.Series.clip
pandas.DataFrame.clip
pandas.api.extensions.ExtensionArray.argsort

jordan-d-murphy · 2024-02-02T06:39:07Z

I'll take

pandas.core.groupby.SeriesGroupBy.transform
pandas.core.groupby.DataFrameGroupBy.transform

jordan-d-murphy · 2024-02-02T07:56:58Z

Note - a new method was added to the list in ci/code_checks.sh

pandas.core.groupby.DataFrameGroupBy.corrwith

See:

#57109
#57158

jordan-d-murphy · 2024-02-02T07:59:15Z

I'll work on

pandas.core.window.rolling.Rolling.quantile
pandas.core.window.expanding.Expanding.quantile

jordan-d-murphy · 2024-02-03T21:20:20Z

I got a fix for pandas.io.formats.style.Styler.to_excel

nkasing · 2024-02-04T00:39:46Z

I'll take

pandas.Series.plot.bar / pandas.DataFrame.plot.bar
pandas.Series.plot.barh / pandas.DataFrame.plot.barh
pandas.Series.plot.line / pandas.DataFrame.plot
pandas.Series.plot.pie / pandas.DataFrame.plot.pie

jordan-d-murphy · 2024-02-04T01:09:42Z

got a fix for pandas.Series.rename_axis

nkasing · 2024-02-04T01:53:50Z

"Unknown parameters" arises from parameters in the docstring that do not appear in the function signatures.

Often, this happens because the parameter is buried in **kwargs. For example, in the docstring for bar and line plots, color is specified as a parameter, but the function signature does not include it.

In these cases, the only thing I can think of is to copy the default color value, adding it to the function signature (note this wouldn't be updated if matplotlib's defaults update) and then override it in the function if it is found in kwargs, but I really don't like this solution.

What would be a better method?

jordan-d-murphy · 2024-02-04T03:15:36Z

I've noticed this too, and I've been thinking about this a lot over the last week or so, but I'm not sure yet what the best approach would be. Whatever we end up choosing as the best approach, there are quite a few docstrings in the list that exhibit this behavior and could be resolved with the solution we decide on.

jrmylow · 2024-02-04T07:12:34Z

As a suggestion, I've implemented something that might work in: #57235, open to suggestions on whether this reads well to people

jrmylow · 2024-02-06T12:50:04Z

hi all, would like to get some opinions around the difficulty I'm having with the pd.tseries.offsets. Note in this case the problem is due to how the objects are generated, and not necessarily that the docstrings are bad.

Currently, the offsets are generated using cython. Cython unfortunately does not support inspect (nor does it plan to) [1]. As I understand it, the signatures generated don't even have parameters attached to them (despite having parameters in the wrong code).

The numpydoc test suite that runs uses inspect under the hood [2] and returns no parameters if the underlying object doesn't support introspection (e.g. a C object).

I suspect there are libraries out there that would allow introspection of c objects and their signatures, is it alright to just import one of them? Alternatively I can go and look at whether we can expose this via tinkering with the Cython flags but that's new territory for me.

[1] - https://cython.readthedocs.io/en/latest/src/userguide/limitations.html#inspect-support
[2] - https://github.com/numpy/numpydoc/blob/8e2d545131fc2a124dd01d749c385f827bb1072b/numpydoc/validate.py#L422

jordan-d-murphy · 2024-02-07T06:51:37Z

I got a fix for pandas.core.groupby.SeriesGroupBy.apply

jordan-d-murphy · 2024-02-08T17:56:29Z

I got a fix for pandas.core.groupby.DataFrameGroupBy.hist

jordan-d-murphy · 2024-02-09T21:08:44Z

I'll open a PR for pandas.Series.str.wrap

Dxuian · 2024-02-10T03:01:58Z

Im new to open source , apologies in advance when i run the command to check which methods fail the PR02 check even the methods that other people have dealt with and merged show up ?
are these the default errors that show up ? or does that suggest some error in the PR02 validation checker ?

jordan-d-murphy · 2024-02-10T03:08:32Z

@Dxuian - try running this with some of the ones that haven't been fixed yet
scripts/validate_docstrings.py --format=actions --errors=PR02 <method-name>
for example:
scripts/validate_docstrings.py --format=actions --errors=PR02 pandas.Series.dt.to_period

Dxuian · 2024-02-10T03:18:37Z

@Dxuian - try running this with some of the ones that haven't been fixed yet scripts/validate_docstrings.py --format=actions --errors=PR02 <method-name> for example: scripts/validate_docstrings.py --format=actions --errors=PR02 pandas.Series.dt.to_period

the checks fail for pandas.Series.dt.to_periods as is expected , what im trying to say is that the checks also fail for pandas.read_hdf

which was previously fixed and merged or does that happen because pandas.read_hdf is no longer in code_checks.sh
thank you in advance

jordan-d-murphy · 2024-02-10T03:22:57Z

Ah I see, @Dxuian

Running scripts/validate_docstrings.py --format=actions --errors=PR02 pandas.read_hdf on my branch outputs the following,

################################################################################
################################## Validation ##################################
################################################################################

Docstring for "pandas.read_hdf" correct. :)

which makes me think what might be going on is your branch might be out of sync with main.

I've been using these commands to keep my env and branches in sync with the latest updates. Can you try updating your branch with the latest changes from main?

Updating the development environment

git checkout main
git merge upstream/main
mamba activate pandas-dev
mamba env update -f environment.yml --prune

Creating a feature branch

git checkout main
git pull upstream main --ff-only
git checkout -b shiny-new-feature

Pre-commit

pre-commit install
pre-commit run --files
pre-commit run --from-ref=upstream/main --to-ref=HEAD --all-files
pre-commit run --hook-stage manual --all-files

Updating your pull request

git checkout shiny-new-feature
git fetch upstream
git merge upstream/main

jordan-d-murphy · 2024-02-10T07:59:15Z

I got fixes for these:

pandas.core.groupby.DataFrameGroupBy.rolling
pandas.core.groupby.SeriesGroupBy.rolling

Dxuian · 2024-02-10T18:22:07Z

Ah I see, @Dxuian

Running scripts/validate_docstrings.py --format=actions --errors=PR02 pandas.read_hdf on my branch outputs the following,
################################################################################
################################## Validation ##################################
################################################################################

Docstring for "pandas.read_hdf" correct. :)
which makes me think what might be going on is your branch might be out of sync with main.

I've been using these commands to keep my env and branches in sync with the latest updates. Can you try updating your branch with the latest changes from main?

Updating the development environment

git checkout main git merge upstream/main mamba activate pandas-dev mamba env update -f environment.yml --prune

Creating a feature branch

git checkout main git pull upstream main --ff-only git checkout -b shiny-new-feature

Pre-commit

pre-commit install pre-commit run --files pre-commit run --from-ref=upstream/main --to-ref=HEAD --all-files pre-commit run --hook-stage manual --all-files

Updating your pull request

git checkout shiny-new-feature git fetch upstream git merge upstream/main

so i've been trying to wrestle what going on wrong since yesterday but i cant seem to pin it down even after i've pulled from the latest main branch i still get the same PR02 errors on issues that should've been fixed after checking out this issue page.

I've reset all env tried different dev configs
I want to confirm has anyone who's not worked on the issue been able replicate this or is it just me ?
so far ive redownloaded docker containers , used the pip venv method even tried the mamba method but nothing seems to work. can someone confirm if
the issue still persists for commits that have been merged

thanks in advance

jordan-d-murphy · 2024-02-11T01:06:58Z

EDIT: this suggestion didn't end up panning out, I am going to close the PR.

jordan-d-murphy · 2024-02-19T20:52:56Z

for anyone interested, I've opened some similar issues:
DOC: fix RT03 errors in docstrings
DOC: fix SA01 errors in docstrings
DOC: fix PR07 errors in docstrings
DOC: fix PR01 errors in docstrings
DOC: fix ES01 errors in docstrings
DOC: fix GL08 errors in docstrings

pmhatre1 · 2024-03-08T05:47:33Z

Got fixes for
pandas.DatetimeIndex.day_name
pandas.DatetimeIndex.month_name

jordan-d-murphy · 2024-03-17T00:23:09Z

Hi all, if CI: speedup docstring check consecutive runs #57826 gets merged in, I might be reworking our approach here; this would look like closing the following issues:

DOC: fix GL08 errors in docstrings
DOC: fix PR01 errors in docstrings
DOC: fix PR07 errors in docstrings
DOC: fix SA01 errors in docstrings
DOC: fix RT03 errors in docstrings
DOC: fix PR02 errors in docstrings

And opening a new issue to address these based on the new approach.

tl;dr

the work can still be done, but probably under a new ticket once #57826 is merged in

jordan-d-murphy · 2024-03-18T02:01:11Z

Closed by:
CI: speedup docstring check consecutive runs #57826
CI: Better error control in the validation of docstrings #57879

Opening a new issue to fix docstring errors.

jordan-d-murphy · 2024-03-29T06:46:32Z

Opened DOC: Enforce Numpy Docstring Validation (Parent Issue) #58063 as a parent issue for fixing docstrings based on the refactoring in code_checks.sh

Feel free to swing by and help out! 🙂

jordan-d-murphy mentioned this issue Jan 28, 2024

DOC: Add docstrings for fixtures defined from pandas.tests.io.conftest #57047

Closed

5 tasks

jordan-d-murphy mentioned this issue Jan 28, 2024

DOC: fix PR02 errors in docstrings - pandas.Series.interpolate, pandas.read_hdf, pandas.HDFStore.append #57114

Merged

5 tasks

jrmylow mentioned this issue Jan 28, 2024

DOC: fix PR02 errors in docstrings - pandas.describe_option, pandas.get_option, pandas.reset_option #57117

Merged

5 tasks

rhshadrach added Docs CI Continuous Integration labels Jan 30, 2024

jordan-d-murphy mentioned this issue Jan 30, 2024

DOC: fix PR02 errors in docstrings - pandas.core.groupby.SeriesGroupBy.idxmax, pandas.core.groupby.SeriesGroupBy.idxmin #57145

Merged

5 tasks

natmokval added the good first issue label Jan 30, 2024

jrmylow mentioned this issue Jan 30, 2024

DOC: discrepancy between pandas.set_option docstring and supported API #57148

Closed

1 task

thiphan94 mentioned this issue Jan 31, 2024

Fix docstring #57167

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 2, 2024

DOC: fix PR02 errors in docstrings - pandas.core.groupby.SeriesGroupBy.transform and pandas.core.groupby.DataFrameGroupBy.transform #57210

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 2, 2024

DOC: fix PR02 errors in docstrings - pandas.core.window.rolling.Rolling.quantile, pandas.core.window.expanding.Expanding.quantile #57211

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 3, 2024

DOC: fix PR02 errors in docstring for pandas.io.formats.style.Styler.to_excel #57230

Merged

5 tasks

jrmylow mentioned this issue Feb 3, 2024

DOC: Updated docstring for set_option #57235

Merged

3 tasks

jordan-d-murphy mentioned this issue Feb 4, 2024

DOC: fix PR02 errors in docstring for pandas.Series.rename_axis #57239

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 7, 2024

DOC: fix PR02 errors in docstring for pandas.core.groupby.SeriesGroupBy.apply #57288

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 8, 2024

DOC: fix PR02 errors in docstring for pandas.core.groupby.DataFrameGroupBy.hist #57304

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 9, 2024

DOC: fix PR02 errors in docstring for pandas.Series.str.wrap #57321

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 10, 2024

DOC: fix PR02 errors in docstring for pandas.core.groupby.DataFrameGroupBy.rolling and pandas.core.groupby.SeriesGroupBy.rolling #57334

Merged

5 tasks

jordan-d-murphy mentioned this issue Feb 11, 2024

DOC: fix PR02 errors in docstring for pandas.tseries.offsets.DateOffset #57350

Closed

5 tasks

pmhatre1 mentioned this issue Mar 9, 2024

Updated the pandas.DatetimeIndex.day_name and pandas.DatetimeIndex.month_name docstring #57790

Closed

This was referenced Mar 10, 2024

DOC: fix GL08 errors in docstrings #57443

Closed

CI: speedup docstring check consecutive runs #57826

Merged

jordan-d-murphy closed this as completed Mar 18, 2024

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DOC: fix PR02 errors in docstrings #57111

DOC: fix PR02 errors in docstrings #57111

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DOC: fix PR02 errors in docstrings #57111

DOC: fix PR02 errors in docstrings #57111

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