Sphinx gallery #902

choldgraf · 2017-06-27T17:03:59Z

I was making my way through the cartopy documentation in preparation for a class I'm working on, and thought that it would be helpful if the gallery were built with Sphinx-Gallery. This lets you include text / short descriptions of examples, it's also a more stable / faster way of building galleries with sphinx.

I figured it would be worth putting in some time to do the conversion, contained in this PR. The only main changes should be some renaming etc to clean up broken links, as well as setting up the machinery to get sphinx-gallery building. Here's an example of the gallery hosted on my fork:

http://predictablynoisy.com/cartopy/gallery/index.html

This PR focuses only on getting the gallery built with sphinx-gallery, but for future reference it could be extended to auto-link functions with API stub pages, or to (one day) include mybinder.org links for jupyter notebooks that are generated by sphinx-gallery. I didn't implement this stuff so that the PR doesn't become overwhelming. LMK what you think.

choldgraf · 2017-06-27T17:05:03Z

docs/doc-requirements.txt

@@ -0,0 +1,3 @@
+netCDF4


I included an extra .txt file because getting the docs to build required several extra requirements I didn't have. I can either clean this up / add to it if folks have suggestions, or remove it if people prefer not to have it.

Shouldn't there be sphinx and sphinx-gallery in here at least?

choldgraf · 2017-06-27T17:05:27Z

.gitignore

@@ -21,6 +21,8 @@ lib/cartopy/tests/mpl/output/
 docs/source/cartopy_outline.rst
 docs/source/examples
 docs/source/gallery.rst
+docs/source/gallery
+docs/source/api


this api section is auto-generated by sphinx-gallery and can be used to build mini-galleries for specific functions / classes if desired

choldgraf · 2017-06-27T17:07:34Z

docs/source/conf.py

+# Sphinx gallery configuration
+sphinx_gallery_conf = {
+    'examples_dirs': ['../../lib/cartopy/examples'],
+    'filename_pattern': '^((?!sgskip).)*$',


Any file that includes sgskip in its title will not be run by sphinx-gallery. Right now this is only the geostationary example because it kept hanging on my computer and I couldn't debug it.

It just takes a long time to reproject things, about 2 minutes for me.

ah I see - I wonder if this is just because I'm working on a relatively underpowered laptop...I'll remove the sgskip and will add some print statements so it doesn't look like it's hanging

So we can now remove this line, right?

this line should stay in case you ever want to have an example that isn't run by sphinx-gallery...it's a configuration option so won't change the behavior of the docs unless "sgskip" is in a file name

choldgraf · 2017-06-27T17:07:57Z

docs/source/conf.py

@@ -363,10 +367,10 @@
                 'figure.subplot.top': 0.96,
                 'figure.subplot.left': 0.04,
                 'figure.subplot.right': 0.96}
-plot_formats = (('thumb.png', 20),
+plot_formats = [('thumb.png', 20),


This kept giving me a warning when building the site saying it should be a list, so I updated it

choldgraf · 2017-06-27T17:08:33Z

docs/source/index.rst

@@ -65,23 +66,23 @@ outlines recent changes, new features, and future development plans.
 Getting involved
 ================

-Cartopy was originally developed at the UK Met Office to allow scientists to visualise 
-their data on maps quickly, easily and most importantly, accurately. 
+Cartopy was originally developed at the UK Met Office to allow scientists to visualise


I believe all of these are just trailing whitespace updates that my editor apparently auto-corrected. LMK if you want me to revert these for some reason

choldgraf · 2017-06-27T17:09:19Z

docs/source/matplotlib/advanced_plotting.rst

@@ -139,16 +139,18 @@ visualising vector fields:
 :meth:`streamplots <cartopy.mpl.geoaxes.GeoAxes.streamplot>` (:ref:`example <examples-streamplot>`)
 each with their own benefits for displaying certain vector field forms.

-.. literalinclude:: /examples/arrows.py
-.. plot:: examples/arrows.py
+.. figure:: ../gallery/vector_data/images/sphx_glr_arrows_001.png


These are updated so that old figures generated with the plot directive are now linking to the sphinx-gallery image (the end result is basically the same)

choldgraf · 2017-06-27T17:10:21Z

lib/cartopy/examples/lines_and_polygons/README.txt

@@ -0,0 +1,4 @@
+Lines and polygons


All of these docstring changes are just to add a title + description (sometimes the description is an empty string), which gets rendered by sphinx-gallery

QuLogic

Looks good to me; cross linking in the example code is already a huge benefit. Hope that can be added for Cartopy code as well.

The deleted __init__.py needs to be restored for tests to work though.

QuLogic · 2017-06-27T21:16:22Z

docs/source/conf.py

+# Sphinx gallery configuration
+sphinx_gallery_conf = {
+    'examples_dirs': ['../../lib/cartopy/examples'],
+    'filename_pattern': '^((?!sgskip).)*$',


It just takes a long time to reproject things, about 2 minutes for me.

QuLogic · 2017-06-27T21:16:56Z

docs/source/conf.py

+    'doc_module': ('cartopy'),
+    'reference_url': {'matplotlib': 'http://matplotlib.org',
+                      'numpy': 'http://docs.scipy.org/doc/numpy/reference',
+                      'scipy': 'http://docs.scipy.org/doc/scipy/reference'},


https: on all links should work.

Might be a problem due to sphinx-gallery/sphinx-gallery#236, but it should be fixed with sphinx-gallery/sphinx-gallery#258.

QuLogic · 2017-06-27T21:19:41Z

docs/source/matplotlib/advanced_plotting.rst

+.. figure:: ../gallery/vector_data/images/sphx_glr_arrows_001.png
+   :target: ../gallery/vector_data/arrows.html
+   :align: center
+   :scale: 50


Seems too small.

QuLogic · 2017-06-27T21:20:04Z

docs/source/matplotlib/advanced_plotting.rst

+.. figure:: ../gallery/vector_data/images/sphx_glr_regridding_arrows_001.png
+   :target: ../gallery/vector_data/regridding_arrows.html
+   :align: center
+   :scale: 50


Also a bit small.

QuLogic · 2017-06-27T21:21:03Z

docs/source/matplotlib/feature_interface.rst

+.. figure:: ../gallery/lines_and_polygons/images/sphx_glr_feature_creation_001.png
+   :target: ../gallery/lines_and_polygons/feature_creation.html
+   :align: center
+   :scale: 50


Also small.

QuLogic · 2017-06-27T21:23:52Z

lib/cartopy/examples/README.txt

+
+The following examples show off the functionality of CartoPy. They
+illustrate the kinds of things you can do with this library. For
+more examples, tutorials, and guides on how to use CartoPy, see


QuLogic · 2017-06-27T21:25:18Z

lib/cartopy/examples/lines_and_polygons/always_circular_stereo.py

@@ -1,4 +1,8 @@
-__tags__ = ['Lines and polygons']
+"""
+Always Circular Stereo


A bit weird for a title; it's more like "Keep Boundary Circular" or something along those lines.

QuLogic · 2017-06-27T21:26:54Z

lib/cartopy/examples/miscellanea/un_flag.py

@@ -1,4 +1,8 @@
-__tags__ = ['Miscellanea']
+"""
+Un Flag


QuLogic · 2017-06-27T21:28:15Z

lib/cartopy/examples/scalar_data/eyja_volcano.py

 """
-__tags__ = ["Scalar data"]
+# -*- coding: utf-8 -*-


I don't think this works on this line.

ah you are right - I'm trying to remember how we fixed this in MPL...maybe we just removed those lines? Or it was fine w/o moving them?

QuLogic · 2017-06-27T21:29:32Z

docs/doc-requirements.txt

@@ -0,0 +1,3 @@
+netCDF4


Shouldn't there be sphinx and sphinx-gallery in here at least?

choldgraf · 2017-06-28T19:32:43Z

working on changes now - re: the deleted __init__.py...this would mess up sphinx-gallery since it auto-runs any python files inside the examples folder. Do these examples get run as a part of the tests?

choldgraf · 2017-06-28T19:54:54Z

regarding auto-linking the API...the trick is that you'd need to do this with autosummary and jinja templates. This isn't hard to do but we'd basically have two options:

Manually list all of the objects in the autosummary (e.g., all of the coordinate classes)
Do something like "automodule" which would loop through all objects in a module like crs and build the proper sphinx-gallery template. The problem here is that it'd import all the public classes / functions in the module. IIRC the modules within cartopy have all kinds of imports etc in their public namespace, right?

QuLogic · 2017-06-29T02:08:08Z

You can change the regex to skip __init__.py, though? You can see that Travis is failing right now without it.

I think most of Cartopy is not auto(doc/module/summary/etc.)'d because they're simply not documented enough. Partly the reason is also #203, I think.

BTW, you'll need to fill out the CLA before this is merged.

choldgraf · 2017-06-29T03:35:33Z

yep the regex should be pretty easy to fix, it'd just be a bit hacky is all but I can make the change in the next push.

I'll sign the CLA - do you have a link to a tl;dr for what exactly it is that I'm signing away? I've never seen something like that for an open-source project before...

dopplershift · 2017-06-29T16:04:48Z

(IANAL, blah blah)

You have the rights to the contribution you're making (it doesn't belong to someone else, no IP infringement)
You grant the Met Office a permanent license to distribute it (i.e. You can't take it back)
The Met Office can distribute this contribution under the current or future versions of the LGPL
You retain the copyright of your contribution

It's more common for projects backstopped by larger organizations that have legal departments and want to try to avoid potential IP problems. The Python Software Foundation and Django (as well as my own MetPy project) are among many that do. Django has a nice FAQ on the agreements in general.

choldgraf · 2017-06-29T18:06:41Z

ok latest push adds example auto-linking. It doesn't generate any new API pages (e.g., stub pages) but links to the autofunction/class/module section that was already built.

e.g., see: http://predictablynoisy.com/cartopy/gallery/lines_and_polygons/global_map.html#sphx-glr-gallery-lines-and-polygons-global-map-py

I'm still not sure how to get __init__.py working, since the regex is only to tell sphinx-gallery whether to run the file, not whether to render the file (e.g., it will still try to create a little gallery slot for __init__.py). I have an issue open with them to see what's up with that.

Will get to the CLA once I can figure out how to insert a digital signature (spilled coffee on my computer so I'm operating off of an old crappy macbook air)

choldgraf · 2017-06-29T23:24:54Z

So it looks like there is no way to have sphinx gallery skip a python file entirely if it's within the examples directory. That gives us three options:

Remove init.py and refactor the tests so that they don't treat the examples as a module...this seems relatively straightforward on first glance and I can put some time into doing this if folks are friendly to it.
Embed an __init__.py file in each examples directory.
Turn all of the testing-related examples code into separate files in the tests directory, and leave the examples as-is.

Any thoughts on any of those? The examples are going to get run by sphinx-gallery each time the docs build, so that's a good way to test which of them are still building or not. If a particular example is crucial to have the same output each time, then perhaps it can just be incorporated into a test?

LMK

QuLogic · 2017-06-30T05:34:20Z

Maybe if we add a doc build to Travis, then that would be sufficient to drop the examples from the tests? @pelson?

choldgraf · 2017-06-30T05:46:55Z

FWIW you can tell sphinx-gallery to raise an error and fail if it fails to build.

pelson · 2017-07-04T11:51:21Z

Will get to the CLA once I can figure out how to insert a digital signature (spilled coffee on my computer so I'm operating off of an old crappy macbook air)

Don't need to overthink it - a scribble is perfectly fine. 😉 🖊 🐾

I didn't actually think cartopy tested any of the examples... that was a decision taken in Iris which I felt was unhealthy and vowed not to go down that path with cartopy. That said, the examples should be importable IMO (namespaces... they are a honking good idea!).

Perhaps when we build the docs we can simply blow away the __init__ (assuming that doesn't have other, unforeseen, impacts)...

FWIW you can tell sphinx-gallery to raise an error and fail if it fails to build.

Sounds like a good option for our CI testing.

ajdawson · 2017-07-04T12:17:23Z

I didn't actually think cartopy tested any of the examples... that was a decision taken in Iris which I felt was unhealthy and vowed not to go down that path with cartopy. That said, the examples should be importable IMO (namespaces... they are a honking good idea!).

We don't test the examples, but lib/cartopy/tests/mpl/test_caching.py imports the sample_data function from cartopy.examples.waves, thus it fails when the __init__.py file is removed from the examples package. It probably shouldn't be doing this really... Regardless, having the examples importable is useful and this should be preserved.

choldgraf · 2017-07-04T15:10:01Z

The function that's imported from the examples into the tests is quite small, so that's easy to move to a different spot. More generally I'm curious what's the benefit of having the examples be importable. I've never seen this done in another package, so wondering what gains it provides?

it would be possible to obliterate that file temporarily as a part of the docs makefile, though that's a little bit clunky :-)

pelson · 2017-07-05T04:59:57Z

More generally I'm curious what's the benefit of having the examples be importable.

Mostly:

from cartopy.examples.hurricane_katrina import main

main()

# Celebrate

Anybody with an installation of cartopy is able to run an example easily from their python interpreter. I've long intended to advertise this feature in the example pages, but seem to have never gotten around to it... 😄

choldgraf · 2017-07-05T17:41:49Z

That makes sense - that's cool that you can run things interactively!

I can edit the make html command so that it recursively deletes the __init__.py file from each folder, then re-creates them. Though requiring everything to be inside of a main function does limit the benefits of sphinx-gallery as it makes it harder to write examples in a narrative style. I guess at the end of the day, the question is: what is the ratio of "users looking at examples on the website" to "users running examples interactively in python".

FWIW, in the near future you'll be able to automatically generate links for mybinder.org with sphinx-gallery, which means any example will have a link that takes users to a live jupyter notebook where they can run the code. Just a thought!

choldgraf · 2017-07-06T03:20:08Z

Also here's the CLA, does that work?

https://www.dropbox.com/s/icgc3wrwgh7i4o4/cla_form.pdf?dl=0

choldgraf · 2017-07-06T05:09:22Z

Latest push adds a little script at the end of the docs build that inserts a noshow class to each of the gallery examples that link to the __init__.py files. That way they don't show up in the gallery and the examples can stay in there.

choldgraf · 2017-08-09T19:37:32Z

hey all - other than the now-conflicting files, what's blocking on this PR? I'm trying to remember if this ball is in my court or in the devs court :-)

would be good to get this merged before a next release if it's happening soon (@QuLogic)

QuLogic · 2017-08-10T01:52:33Z

Well, the tests are failing and I think you still need to submit the CLA, at least.

choldgraf · 2017-08-10T15:59:29Z

@QuLogic I put a link to the CLA here: #902 (comment)

ajdawson · 2017-08-10T17:38:44Z

You need to send the CLA to the email address given in the document.

choldgraf · 2017-08-10T19:18:02Z

gotcha, done

choldgraf · 2017-09-15T23:59:32Z

ok I think I figured out what was going with travis, so let's see if it builds now.

I see there's a CLA checker in there...I emailed the CLA on August 10th.

choldgraf · 2017-09-16T00:12:00Z

I'm not sure what the travis test failures are about - in one case it seems to be because there's a fortran library that's not linked properly, in another its an image comparison in one of the tests. But neither of those seem related to this PR...

pelson

This is definitely close. I'm 100% behind using sphinx-gallery. I'd like the ability to continue using the plot directive in some situations (such as inline/contextual examples that aren't destined for the gallery). I'd also like to step back from autosummary as a means for getting 100% documentation coverage - I think in the next few months there will be development effort to improve the coverage in a contexual/richer form that will be more beneficial to the user.

Other than that, I'll double check to see where the administration is at wrt. your CLA. It all looks good to me.

Cheers,

pelson · 2017-10-11T04:50:33Z

docs/source/matplotlib/feature_interface.rst

@@ -3,7 +3,7 @@
 The cartopy Feature interface
 =============================

-The :ref:`data copyright, license and attribution  <referencing_copyright>` can be blended on the map using `text annotations (mpl docs) <http://matplotlib.org/users/annotations_intro.html>`_ as shown in `feature_creation <../examples/feature_creation.html>`_. 
+The :ref:`data copyright, license and attribution  <referencing_copyright>` can be blended on the map using `text annotations (mpl docs) <http://matplotlib.org/users/annotations_intro.html>`_ as shown in `feature_creation <../gallery/lines_and_polygons/feature_creation.html>`_.


It isn't ideal to change the URL of the examples (because of StackOverflow/Google links etc.). Any way of avoiding it?

hmmm, not without changing the directory structure of the examples. In other projects where we've implemented sphinx gallery we just kinda took a "rip the band-aid off" approach...I agree that's unfortunate :-/

pelson · 2017-10-11T04:55:29Z

docs/source/matplotlib/feature_interface.rst


 ------------


 Example of using the Feature class with the matplotlib interface
 ----------------------------------------------------------------

-.. literalinclude:: /examples/feature_creation.py


I definitely think we need to have a separation between what should live in the gallery, and what is useful as inline examples within the context of a chapter.

Cartopy hasn't got this completely right though - for example, there are a number of inline examples that really should be in the gallery: http://scitools.org.uk/cartopy/docs/v0.15/matplotlib/advanced_plotting.html#block-plots

Could we do the promotion of inline/contextual examples -> gallery examples as a separate PR?

I could also include the literalinclude in there as well if that's preferred, but if you don't want that in this PR I can take them out.

pelson · 2017-10-11T04:58:52Z

lib/cartopy/examples/__init__.py

@@ -0,0 +1,5 @@
+"""


Can we have just a blank file?
If not, then we need some copyright headers.

The problem is that sphinx-gallery will auto-detect any .py files and try to run them as examples, and if a file doesn't have a header, e.g.:

""" My Header ---------

then it'll error. So there needs to be something like that in there I believe. I could try to get away with something like

""" . -

so it's as minimal as possible...

pelson · 2017-10-11T04:59:39Z

lib/cartopy/examples/lines_and_polygons/__init__.py

@@ -0,0 +1,5 @@
+"""


Ditto (and for all other REMOVE type files)

pelson · 2017-10-11T05:08:55Z

docs/source/conf.py

              'sphinx.ext.autodoc',
              'sphinx.ext.doctest',
              'sphinx.ext.intersphinx',
              'sphinx.ext.coverage',
              'sphinx.ext.viewcode',
              'sphinx.ext.extlinks',
+              'sphinx.ext.autosummary',


Would you mind removing this from the PR? My prior experience suggests that in certain situations having autogenerated docs is worse than having no docs at all - cartopy is no shining start wrt its docs, but what is documented is generally more readable than most autogenerated API summary (e.g. http://scitools.org.uk/iris/docs/latest/iris/iris.html. To be clear - I implemented that autosummary generation for iris, so I'm explicitly not bad-mouthing anybody else 😉 ). I'm expecting to be able to invest some significant effort on cartopy's manually crafted docs over the coming months, and so keeping the autosummary would mask the shortcomings.

the main reason for autosummary is that it lets you auto-generate mini-galleries for functions etc with sphinx-gallery. In conjunction with the template files in this PR, that will generate pages like this matplotlib example. Usually I don't use automodule either, but instead do it class-by-class (or function-by-function) to get the most modularity over my docs

@pelson what's the decision on this? Do you want the autosummary removed or not? IMO it should be removed; I'm not convinced enough by @choldgraf's justification for keeping it in.

pelson · 2017-10-11T05:09:49Z

docs/source/conf.py

+# Sphinx gallery configuration
+sphinx_gallery_conf = {
+    'examples_dirs': ['../../lib/cartopy/examples'],
+    'filename_pattern': '^((?!sgskip).)*$',


So we can now remove this line, right?

pelson · 2017-10-11T05:10:25Z

docs/source/conf.py

+                      'numpy': 'http://docs.scipy.org/doc/numpy/reference',
+                      'scipy': 'http://docs.scipy.org/doc/scipy/reference',
+                      'shapely': 'http://toblerity.org/shapely',
+                      'cartopy': None},


These two lines should be removable at this point?

(the second line is the backreferences_dir one)

you want to remove the backreferences_dir line? I'm not sure which you're referring to

choldgraf · 2017-11-27T20:54:17Z

@corinnebosley thanks for giving a ping to get this going. Regarding autosummary you can take it or leave it, just trying to incorporate features that have proven useful in other projects.

TBH I'm not spending a lot more time on this PR as I've already put in a lot of effort and the iterations on feedback are going extremely slowly. I understand we've all got other stuff going on so no hard feelings, I just can't keep re-orienting myself to this PR once every month. If you (or someone with merge rights) wants to make a push on this then I can spend some time on it as well.

pp-mo · 2017-11-29T12:31:03Z

Replaced by #969

sphinx gallery init

fb52ad0

choldgraf commented Jun 27, 2017

View reviewed changes

updating paths and SG files

9617fc8

choldgraf force-pushed the sphinx_gallery branch from 7b2b366 to 9617fc8 Compare June 27, 2017 17:06

choldgraf commented Jun 27, 2017

View reviewed changes

QuLogic reviewed Jun 27, 2017

View reviewed changes

QuLogic added the Pending CLA label Jun 28, 2017

choldgraf force-pushed the sphinx_gallery branch from 0fd86a1 to b621060 Compare June 29, 2017 17:46

adding auto-linking

74e241f

choldgraf force-pushed the sphinx_gallery branch from b621060 to 74e241f Compare June 29, 2017 18:01

updating sphinx gallery builds

0c98fa6

choldgraf force-pushed the sphinx_gallery branch from b5ebb45 to 2e24247 Compare July 6, 2017 05:10

adding CSS to remote init.py files

2f5b9de

choldgraf force-pushed the sphinx_gallery branch from 2e24247 to 2f5b9de Compare July 6, 2017 05:39

choldgraf force-pushed the sphinx_gallery branch from 2c2987d to e86a76f Compare September 15, 2017 23:53

pelson added the Blocked: CLA needed See https://scitools.org.uk. Submit the form at: https://scitools.org.uk/cla/v4/form label Sep 15, 2017

choldgraf force-pushed the sphinx_gallery branch from e86a76f to 1e31ffc Compare September 16, 2017 00:03

pelson added the Blocked: CLA needed See https://scitools.org.uk. Submit the form at: https://scitools.org.uk/cla/v4/form label Sep 16, 2017

Merge branch 'master' into sphinx_gallery

b4d77ac

choldgraf force-pushed the sphinx_gallery branch from 1e31ffc to b4d77ac Compare September 16, 2017 00:11

pelson added the Blocked: CLA needed See https://scitools.org.uk. Submit the form at: https://scitools.org.uk/cla/v4/form label Sep 16, 2017

pelson requested changes Oct 11, 2017

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pelson removed Pending CLA Blocked: CLA needed See https://scitools.org.uk. Submit the form at: https://scitools.org.uk/cla/v4/form labels Oct 17, 2017

pelson added the Type: Documentation label Nov 20, 2017

pp-mo closed this Nov 29, 2017

pp-mo mentioned this pull request Dec 11, 2017

Fresher sphinx gallery #969

Merged

QuLogic mentioned this pull request Jul 25, 2020

Upgrading sphinx gallery requirement #1614

Merged

Sphinx gallery #902

Sphinx gallery #902

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choldgraf commented Nov 27, 2017

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