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merged 12 commits into from
Jan 22, 2022

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@yaaun yaaun commented Jan 19, 2022

PR Summary

Expanded documentation of Axis.set_ticks as per discussion in #22262 to help protect future users from pitfalls when trying to add special/custom ticks.

PR Checklist

Tests and Styling

  • [N/A] Has pytest style unit tests (and pytest passes).
  • Is Flake 8 compliant (install flake8-docstrings and run flake8 --docstring-convention=all).

Documentation

  • [N/A] New features are documented, with examples if plot related.
  • [N/A] New features have an entry in doc/users/next_whats_new/ (follow instructions in README.rst there).
  • [N/A] API changes documented in doc/api/next_api_changes/ (follow instructions in README.rst there).
  • Documentation is sphinx and numpydoc compliant (the docs should build without error). (I can't build the docs without installing from source, and there appears to be no way to finish the installation without VC++ which I cannot fit onto my old PC)

@yaaun yaaun marked this pull request as ready for review January 19, 2022 22:25
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yaaun commented Jan 19, 2022

Oops, some merge commit seems to have got caught in the PR, which wasn't intended...

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@QuLogic QuLogic added status: needs rebase status: needs workflow approval For PRs from new contributors, from which GitHub blocks workflows by default. labels Jan 20, 2022
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Thanks for the suggestions. There is a balance between brevity and clarity - I think this is too verbose for a method docstring...

Comment on lines 1826 to 1843
List of tick locations.
labels : list of str, optional
List of tick labels. If not set, the labels show the data value.

.. warning::
Setting *labels=None* does not guarantee that labels for all
set ticks will be automatically generated - this depends
on the :class:`~matplotlib.ticker.Formatter` of the axis.
Some tick label formatters, e.g.
:class:`~matplotlib.ticker.ScalarFormatter` (default for
plots made with :meth:`~.Axes.plot`) will make
labels for custom ticks, while
others like e.g.
:class:`~matplotlib.ticker.LogFormatterSciNotation`
(default for :meth:`~.Axes.semilogy` plots) may not.
Supply all tick labels in the *labels* parameter if you
want to be sure.

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The PR adds a lot of verbiage for a particular edge case. Suggest something more concise...

Suggested change
List of tick locations.
labels : list of str, optional
List of tick labels. If not set, the labels show the data value.
.. warning::
Setting *labels=None* does not guarantee that labels for all
set ticks will be automatically generated - this depends
on the :class:`~matplotlib.ticker.Formatter` of the axis.
Some tick label formatters, e.g.
:class:`~matplotlib.ticker.ScalarFormatter` (default for
plots made with :meth:`~.Axes.plot`) will make
labels for custom ticks, while
others like e.g.
:class:`~matplotlib.ticker.LogFormatterSciNotation`
(default for :meth:`~.Axes.semilogy` plots) may not.
Supply all tick labels in the *labels* parameter if you
want to be sure.
List of tick locations. The axis `.Locator` is replaced by a `.FixedLocator`. Some
default tick formatters will not label arbitrary ticks, so pass *label* if needed.
labels : list of str, optional
List of tick labels. If not set, the labels are generated with the axis tick `.Formatter`.

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Yes, I know my suggestion is quite verbose. I wanted to make the contradiction of actual behaviour with the claim that "If not set, the labels show the data value." very explicit to the reader, hence the big block of text.

At least for me, speaking from a user perspective, initially it was not at all comprehensible as to why without knowledge of the internals of tick labeling.

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I am thinking to perhaps change the last clause "if needed" to "to ensure labels are shown" to explicitly make the point of why labels are needed.

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This should be put into the right perspective. Most cases, in particular the defaults, are fine without labels. The main purpose for labels is putting explicit values that cannot be derived from the positions using a formatter.
Formatters not generating labels for certain values is quite an edge case (I didn't even know we have that). Do we know which formatters are affected at all? If so they should be listed explicitly.

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The LogFormatter will not label non-decade labels, unless you override labelOnlyBase. I don't know if there are others...

ticks = axes.get_yticks()
ticks_ext = np.append(ticklist, special_ticks)
axes.set_yticks(ticks_ext)

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I don't think this block of changes should go in. The first paragraph is in my suggested change above, and the rest is too specialized for a method docstring.

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Ok, I concede that I put in a lot here. If this is too much, maybe put it in an example titled "Adding custom ticks to an axis", or somewhere else where it would be appropriate, as official guidance for this kind of problem?

In honesty, I got to the doc for Axes.set_yticks from some accepted StackOverflow answer that proposes a flawed solution, e.g. this one in the second part when looking how to approach the task I had in mind.

Comment on lines 1827 to 1828
`.FixedLocator`. Some default tick formatters will not label
arbitrary ticks, so pass *label* to ensure labels are visible.
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I don't think we should add that second sentence. It's a workaround for another issue. Instead we should

  • Document at the respective formatters that they don't generate labels for certain positions.
  • In theory that would be enough. If people use a LogFormatterSciNotation they should refer to its docs if it does not format as expected. The issue is that plt.loglog implicitly switches to this formatter, so people won't know. One should investigate whether empty labels can also occur at positions issued from the corresponding formatter. If not, only special user-defined positions will run into the empty-label issue, which means we can issue a warning on empty labels without annoying regular users.

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Document at the respective formatters that they don't generate labels for certain positions.

Implementing your suggestions goes a bit further than the very small PR that I started from - should e.g. adding docs to Formatters be continued here or split off into some other PR?

In theory that would be enough. If people use a LogFormatterSciNotation they should refer to its docs if it does not format as expected. The issue is that plt.loglog implicitly switches to this formatter, so people won't know.

Yes, this implicit Formatter switching is the gotcha here, since it breaks the behaviour that the user (ignorant of the internals) would expect - namely I set the ticks, so I should get labels on them, which got me here in the first place.

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One should investigate whether empty labels can also occur at positions issued from the corresponding formatter.

Regarding the problem of Locator-Formatter correspondence (I hope I am understanding you correctly): from the issue discussion and my (limited) knowledge of the code, I grasp that is a "gentlemen's agreement" without any explicit mechanism ensuring Locator will not generate ticks that Formatter will not make labels for.

Digging through the code, I found that the choice of Locator and Formatter pairs is in the set_default_locators_and_formatters override methods of ScaleBase subclasses (in scale.py). Do you mean going through all possible combinations and analyzing their interactions...?

If not, only special user-defined positions will run into the empty-label issue, which means we can issue a warning on empty labels without annoying regular users.

I am not certain what you mean by "we can issue a warning on empty labels without annoying regular users." - in this docstring, that this is only relevant when setting ticks manually? Or somewhere else, or at runtime (?)

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I don't think we should add that second sentence. It's a workaround for another issue. Instead we should

  • Document at the respective formatters that they don't generate labels for certain positions.
  • In theory that would be enough. If people use a LogFormatterSciNotation they should refer to its docs if it does not format as expected. The issue is that plt.loglog implicitly switches to this formatter, so people won't know. One should investigate whether empty labels can also occur at positions issued from the corresponding formatter. If not, only special user-defined positions will run into the empty-label issue, which means we can issue a warning on empty labels without annoying regular users.

You can issue a runtime warning if you want, but I don't see that adding a sentence that says what to do if you don't get the expected results is a bad thing to do. The heuristics for such a runtime warning seem brittle to me.

Comment on lines 1845 to 1846
Do not mix automatically and manually placed ticks with this method.
See :ghissue:`22262` for discussion.
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Can try you write this down more explicitly? If we write down extra comment they must be easily understandable for the user. Without having looked at #22262, this doesn't make sense to me. I either have a Locator that automatically places ticks, or I have set tick positions explicitly, which results in a FixedLocator. How can I mix both? Generally, I'm 👎 on referring to GitHub issues for explanation. They are a historic record of a discussion but not a condensed and easy to understand description.

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The problem with mixing auto and manual ticks comes from a simple and very naive idea of how to add a special tick to an existing axis. Essentially getting and appending to the list of ticks already on the axis:

ticks = axes.get_yticks()
ticks_added = np.append(ticks, [1.234])
axes.set_yticks(ticks_added)

For an outside user, there is nothing to suggest that this shouldn't be done and in itself it doesn't look that unreasonable to do. But it turns out to be an edge case where the underlying implementation leaks through.

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I can try to reformulate this more explicitly in words, but I think it can't really get any better than the code. But then again, that is a bit verbose.

My intent is to warn any future users that could fall into this same trap when trying to approach the task in this deceptively simple way.

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There's more, actually, not limited to the edge case. The edge case just results in the Locator changing unilaterally without the Formatter changing to match it, as is normally the case when the plot is made, and extra ticks appearing in places not expected by the Formatter (the "gentlemen's agreement" is broken).

But in this case, even if all ticks are set manually, this will pop up whenever a tick is set to something other than what the Formatter is trained to expect from the default Locator for the type of plot.

The warning to not mix auto and manual ticks comes from the issue discussion, but the problem of unlabeled ticks is not directly related to the mixing itself, if one thinks about it carefully.

So I guess this last sentence can be deleted if it is made clear enough that the problem lies with the Formatter alone.

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So I guess this last sentence can be deleted if it is made clear enough that the problem lies with the Formatter alone.

Do you think the above description makes it clear enough?

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Yes, I believe so.

I have further tested to make sure that even this apparently discouraged mixing will work, so there is no need for this sentence.

The test:

xs = np.linspace(0, L, 101)
ys = 0.05 / np.abs(np.exp(-xs))

fig = plt.figure()
axes = fig.subplots()
axes.semilogy(xs, ys)

sticx = np.append(axes.get_yticks(), [0.1, 0.5, 1, 2, 4, 10])
sticlbl = [f"{tick:g}" for tick in sticx]
axes.set_yticks(sticx, labels=sticlbl)

gives
Figure 2022-01-21 113522
which is what we wanted.

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Test of the same "naive" method on both axes with loglog plot:

xs = np.linspace(0, L, 101)
ys = 0.05 / np.abs(np.exp(-xs))

fig = plt.figure()
axes = fig.subplots()
axes.loglog(xs, ys)

sticx = np.append(axes.get_xticks(), [0.1, 0.25, 0.5, 1, 2, 4, 6])
sticxlbl = [f"{tick:g}" for tick in sticx]
sticy = np.append(axes.get_yticks(), [0.1, 0.5, 1, 2, 4, 10])
sticylbl = [f"{tick:g}" for tick in sticy]
axes.set_xticks(sticx, labels=sticxlbl)
axes.set_yticks(sticy, labels=sticylbl)

gives
Figure 2022-01-21 114438

Comment on lines 1845 to 1846
Do not mix automatically and manually placed ticks with this method.
See :ghissue:`22262` for discussion.
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So I guess this last sentence can be deleted if it is made clear enough that the problem lies with the Formatter alone.

Do you think the above description makes it clear enough?

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yaaun commented Jan 21, 2022

Some cryptic issue is failing the docs build...?

Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>
@timhoffm timhoffm merged commit 695bc25 into matplotlib:main Jan 22, 2022
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Thanks @yaaun!

@timhoffm timhoffm removed the status: needs workflow approval For PRs from new contributors, from which GitHub blocks workflows by default. label Jan 22, 2022
@yaaun yaaun deleted the yaaun_doc branch January 22, 2022 23:34
@QuLogic QuLogic added this to the v3.6.0 milestone Jan 24, 2022
stanleyjs added a commit to stanleyjs/matplotlib that referenced this pull request Jan 26, 2022
_axstack whitespace

_parent._axstack

move clear functions into figurebase

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TEST: partial subfig clearing

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flake8

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TITLE UNDERLINE

Expire mathttext-related deprecations

Fixed review comments and a few more removals

Use PNG image as the icon for Tk plot windows

Fix loading user-defined icons for Tk toolbar

Co-Authored-By: Elliott Sales de Andrade <quantum.analyst@gmail.com>

Prevent tooltips from overlapping buttons in NavigationToolbar2Tk

Update doc/api/next_api_changes/behavior/22135-JSS3.rst

Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>

Fix loading user-defined icons for Qt plot window

Update both zoom/pan states on wx when triggering from keyboard.

Previously, typing "o" and "p" on a wx window would result in both the
zoom and the pan button being pressed at the same time.  Fix that by
relying on the same strategy as all other backends.

Switch transOffset to offset_transform.

Note that most APIs *previously* already accepted *offset_transform* as
kwarg, due to the presence of the `set_offset_transform` setter.  Prefer
that name (shortening it to `offset_trf` for local variables).

Backcompat for the old `transOffset` name is kept in most places by
introducing a property alias.

Started deprecating tight_bbox and tight_layout

Recreated deprecated files and changed references

Fix drawing animated artists changed in selector callback

Fix getting tuple of animated artists; add comments and test

Use list comprehension instead of filter

Fix z_order

Improve docstring and add comments

Ensure log formatters use Unicode minus

Fixes matplotlib#21540

FIX: better repr for subgridspecs

FIX: add test for identical subgridspec

FIX

Use a fixture for widget test axes

Improved coverage of mathtext and removed unused code

Removed dev from 3.10-version

DOC: explain too many ticks

DOC: artist extent

Update doc/users/faq/howto_faq.rst

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Apply suggestions from code review

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FIX: streamline examples

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Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>

Apply suggestions from code review

Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>

FIX: macosx check case-insensitive app name

Only check for "python" case insensitive to match either Python
or pythonw.

Fix typo in `axhline` docstring

Removed unused variables etc.

Passed on sides and pad_to

Use standard toolbar in wx.

The previous approach manually positioned the toolbar to have it at the
bottom of the window, but this can in fact be achieved just with
style=wx.TB_BOTTOM.

Removing manual sizing of the toolbar also fixes a bug previously
present on Windows, whereby a `set_size_inches` reducing the size of the
canvas would *not* reduce the window width, likely because it was forced
to its max value by the toolbar's explicit size.

Expire axes_grid1/axisartist deprecations.

Clean up 3d plot box_aspect zooming

linting

Cleanup

Make zoom and dist private attrs

Deprecate Axes3D.dist

Deprecate Axes3D.dist

DOC: Fix upstream URL for merge in CircleCI

DOC: Add hatch API to reference

DOC: Document default cap styles

- remove '(default)' from cap style demo as this is only true for Line2D
  and the default rcParameters
- document default cap styles for Line2D and Patch in their cap style
  setters
- document default cap style for GraphicsContextBase in the same way as
  it's already done for joinstyle

Factor out underline-thickness lookups in mathtext.

Just adding a small helper function.

Fix merge

Update _formlayout.py

Bump minimum NumPy to 1.19

Fix name typo in API changes

DOC: git:// is deprecated.

See https://github.blog/2021-09-01-improving-git-protocol-security-github/

Today is a brownout day.

I removed the sentence that git:// is RO and https:// is RW as you soon
won't be able to use git://

Personally I use https:// as RO and ssh:// as RW, but I understand it
might not be convenient on windows.

Stop sorting artists in Figure Options dialog

With matplotlib#18216, the order that artists are added to an Axes is their
canonical order. The dialog should not be sorting them in some other
manner.

Additionally, this fixes a bug in that `apply_callback` indexes back to
the original list, which means that changes will be made to the *wrong*
artist if sorting actually occurred. It also makes the legend almost
entirely wrong as well.

See https://discourse.matplotlib.org/t/bug-on-re-generate-automatic-legend-of-matplotlib-figure-property/22511

Document ArtistList

DOC: Document default join style

in the same way as the default cap styles.

Jointly track x and y in PolygonSelector.

It's easier to track them in a single list.

Also init _selection_artist and _polygon_handles with empty arrays, as
there's no reason to pretend that they start with 0, 0.  On the other
hand, _xys does need to start as a non-empty array as the last point
gets updated as being the cursor position.

Verify that lib/src is not changed on -doc backports

ci: Use released version to build v*-doc branches

Fix typo in `tutorials/intermediate/arranging_axes.py`

Trivial doc fix to annotations tutorial.

Initially I just wanted to capitalize "matplotlib", but the wording was
a bit awkward too, so...

ENH: implement and use base layout_engine for more flexible layout.

FIX: typo

Remove some unnecessary getattrs.

Figures always have a canvas attached (even if it's just a
FigureCanvasBase), and canvases always have a "manager" attribute (which
may be None).

Canvases also always have a "toolbar" attribute (which also may be
None).

Altogether this allows avoiding a couple of getattrs.

FIX: Return value instead of enum in get_capstyle/_joinstyle

for MarkerStyle and Patch (as do Line2D, Collections and GraphicsContextBase)

(1) turn off the grid after creating colorbar axes (2) added a test

Cleanup "anatomy of a figure"

No visual change.

Improve formatting of "Anatomy of a figure"

- Adapt margins
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Run wheel builds on PRs when requested by a label

Fix typos

Deprecate cleared kwarg to get_renderer.

This makes it easier for to mock the agg backend (e.g., in mplcairo).
Note that this is anyways only a shorthand for calling a method
(`.clear()`) on the renderer itself, so just issuing that call is just
as simple, more explicit, and can be done even when one just has access
to the renderer and not to the canvas (an admittedly rather hypothetical
case).

Improve ft2font error reporting.

This prints out human-readable error messages for failures.

As an example, `FT2Font("setup.py")` now raises
```
RuntimeError: In FT2Font: Can not load face (unknown file format; error code 0x2)
```

Ensure that all toolbar (old/new) subclasses can be init'ed consistently

i.e. with the same signature: with `canvas` as sole arg for the
old-style toolbars, with `toolmanager` as sole arg for the new ones.

Subclasses that explicitly support setting a parent widget keep that
support (except for gtk, which stashed that in the `.win` attribute but
never used it), but that argument is always optional now; the default is
the canvas' parent.

The goal is to later replace all _get_toolbar implementations by a
simple call (always with the same signature (dependent on the value of
rcParams["toolbar"])) to the correct class in the FigureManagerBase
constructor.

DOC: More capitalization of Axes

In line with matplotlib#18726.

Triggered by matplotlib#22242.

Started deprecating afm, fontconfig_pattern, and type1font

Recreated deprecated files and changed references

DOC: add dropdown

DOC: add dropdown

Fix topbar

DOC: Add all the releases

Just last point releases before 3.0

DOC: update release_guide

DOC: rename versions [skip azp] [skip appveyor] [skip actions]

BLD: pin sphinx data theme [skip actions] [skip appveyor] [skip azp]

Add some tests for minspan{x,y} in RectangleSelector

Skip tests on the -doc branches

DOC: fix version switcher json [skip actions] [skip appveyor] [skip azp]

DOC: fix version switcher [skip actions] [skip appveyor] [skip azp]

FIX

Fix Qt enum access.

This was missed in the global fixing of enums for PyQt6 (now using
_enum everywhere).  To trigger, try to interactively save a figure but
input an invalid format, e.g. "foo.bar".

MNT: deprecate filled parameter to colorbar

The *filled* kwarg doesn't directly do anything and filling is
completely controlled by the mappable.

OTOH, maybe we want to reinstate the ability of *filled* to fill
contours?

Deprecate colorbar.draw_all.

Merge main and "other" params docs in colorbar.make_axes.

`colorbar.make_axes` (and `make_axes_gridspec`) are low-level enough
that it's not worth the complexity in docstring interpolation to split
out "main" parameters and "other" parameters, when the docstring of
the more commonly used `plt.colorbar` smashes them together.  (Also,
`pad` is not really much more low-level than `shrink` or `aspect`...)

Numpydocify _colormap_kw_doc and use it in Colorbar too.

Specify the focal length for 3d plots

Create a gallery example showing the different proj_type options

Typo

Test fix, example fix, and linting

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swap plot order

Enforce a positive focal length

focal lentgh tests

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linting

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Disalbe showing cursor data on a QuadMesh by default

Give the Tk toolbar buttons a flat look

Simplify FontProperties.copy().

Expanded documentation of Axis.set_ticks as per discussion in issue matplotlib#22262 (matplotlib#22270)

* Expanded documentation of Axis.set_ticks()

* Fix flake8 W293 (blank line contains whitespace) warnings

* Expanded the documentation even more based on discussion in issue matplotlib#22262

* Update lib/matplotlib/axis.py - @jklymak rewording

Co-authored-by: Jody Klymak <jklymak@gmail.com>

* Reduced verbosity of doc by @jklymak 's suggestion.

* On second thought, the previous wording could be seen as very ambiguous.

* Update set_ticks docstring by @timhoffm compromise suggestion

Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>

* Removed extra sentence as per @timhoffm review

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MNT: make colorbars locators and formatters properties

TST: test setters and getters in colorbar

DOC: improve crosslinking for docs

FIX: small fixes

DOC: fix property docstrings

FIX: minorformatter None

Removed unused code

Fixed repr for SecondaryAxis

and increase coverage for axes/_base.py

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Co-authored-by: Tim Hoffmann <2836374+timhoffm@users.noreply.github.com>

Display bad format string in error message.

I had something like `for i in range(n): plot(..., f"oC{i}")` which
works for n up to 10, but for greater values one gets "oC10" which is
not supported (which is reasonable, as some single-digit strings are
actually *marker* abbreviations); mentioning the full format string in
the error message ("Unrecognized character 0 in format string 'oC10'")
makes it clearer.

FIX: bury import of matplotlib.font_manager

We need to ensure that the sub-module matplotlib.font_manager is imported when
it is used in SclarFormater, however if we import it at the top level we will
get circular imports.

closes matplotlib#22305

In mpl_toolkits, use the same floating point slop as for standard ticks.

Standard ticks use _interval_contains_close (in Axis._update_ticks); do
the same in mpl_toolkits and deprecate the custom slops delta1, delta2
(if such knobs are really needed, we should try to have the same API in
the main library anyways).

FIX: use window_extent instead

Add set_cursor method to FigureCanvasTk

Don't warn on grid removal deprecation is grid is hidden

Fixes matplotlib#21723.

See matplotlib#21723 (comment)
for a full desciption of motivation and edge cases.

Modify example for x-axis tick labels at the top

Primarily describe how to do this for a single Axes (using `tick_params`).
Only mention the `rcParams` in a note. Globally changing `rcParams` is
usually not a good idea and should not be demonstrated. The whole
topic of `rcParams` (global, context, matplotlibrc) is too long to
be discussed here and not the focus of the example.

Remove Axes sublist modification from docs

Make bar of pie example more explicit

... by saving and using the results from Axes method calls. Also,
replace the colour palette in the bar chart.

Respect `position` argument in Tk toolmanager

Set focus properly to ensure mouse events get delivered to Tk canvas

Rework/fix Text layout cache.

Instead of caching the text layout based on a bunch of properties, only
cache the computation of the text's metrics, which 1) should be the most
expensive part (everything else in _get_layout is relatively simple
iteration and arithmetic) and 2) depends on fewer implicit parameters.

In fact, the old cache key was insufficient in that it would conflate
usetex and non-usetex strings together, even though they have different
metrics; e.g. with the (extremely artificial) example
```python
figtext(.1, .5, "foo\nbar", size=32)  # (0)
figtext(.1, .5, "foo\nbar", usetex=True, size=32, c="r", alpha=.5)  # (1)
figtext(.3, .5, "foo\nbar", usetex=True, size=32, c="r", alpha=.5)  # (2)
```
the linespacing of the first usetex string (1) would be "wrong": it is
bigger that the one of the second usetex string (2), because it instead
reuses the layout computed for the non-usetex string (0).

The motivation is also to in the future let the renderer have better
control on cache invalidation (with a yet-to-be-added renderer method),
e.g. multiple instances of the same renderer cache could share the same
layout info.

Rename outdated seaborn styles.

They are kept available under a versioned name for backcompat.

dangling clf

Silently discard blits if bbox is outside canvas

Custom cap widths in box and whisker plots in bxp() and boxplot()

Add pre-commit config and dev instructions

Update pre-commit hooks

rst format

Disable autofixes on PRs

Unless manually triggered. See https://pre-commit.ci/#configuration

add pre-commit to environment.yml

Slow down autoupdate schedule

alphabetize

Add sentence about where pre-commit config is

Add excludes to pre-commit config

Otherwise end of lines of test images will get fixed,
this also ignores all the prev_whats_new and prev_api_changes
as well as vendored components (agg, gitwash)

pre-comit config

CI: ban coverage 6.3 that may be causing random hangs in fork test
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4 participants