[WIP] Added API link in examples #1013

percygautam · 2020-01-19T21:16:16Z

Fixes #1000 . Added API link in the examples.

percygautam · 2020-01-19T21:17:24Z

@OriolAbril The link is showing in generated docs when I use make html. But I don't how to check whether link will work in github or not?

OriolAbril · 2020-01-19T21:34:51Z

doc/sphinxext/gallery_generator.py

+ def apiname(self):
+ name = self.modulename.split("_")
+ name = name[1::]
+ return "_".join(name)


I think this will fail in many cases such as {backend}_plot_ess_evolution (or quantile or local), {backend}_plot_loo_pit_ecdf, {backend}_plot_pair_hex (or kde) and so on. There are several plots with more than one image in the gallery were some extra description is needed.

@OriolAbril I'll try to come up with a solution.

ahartikainen

Added some comments

doc/sphinxext/gallery_generator.py

ahartikainen · 2020-01-20T20:56:51Z

doc/sphinxext/gallery_generator.py

- name = self.modulename.split("_")
- name = name[1::]
- return "_".join(name)
+ name=""


Maybe just return None if nothing is found?

Okay, make sense.

ahartikainen · 2020-01-20T20:58:04Z

doc/sphinxext/gallery_generator.py

+ regex = r"az\.(plot\_[a-z_]+)\("
+ matches = re.finditer(regex, file.read(), re.MULTILINE)
+ for matchNum, match in enumerate(matches, start=1):
+ name = match.group(1)


will this return the last found plot_xyz? Should it return all the matches?

Do you think re.findall would work here? No need for looping?

I think the first is enough, there is only a couple of cases where more than a function is called, and in these cases the function called is always the same.

@ahartikainen @OriolAbril I worked some examples and let's say we have a hypothetical code as:

az.plot_compare(model_compare, figsize=(12, 4)) az.plot_forest(model_compare, figsize=(12, 4)) az.plot_density(model_compare, figsize=(12, 4))

If we run our code, it will return the last found match as 'plot_density'. As in our example files, we are only calling the function one time, so I don't think it'll be a problem.
As a possible solution for, when (in future) we have multiple plots in a single example, we can do something like:

for matchNum, match in enumerate(matches, start=1): api_name.append(match.group(1)) return api_name #returns the list

And then maybe check the length when rendering it in the template.
As suggested by @ahartikainen , re.findall() will work best for such case. For example, above code can be simplified as

with open("mpl_plot_compare.py", "r") as f: regex = r"az\.(plot\_[a-z_]+)\(" api_name = re.findall(regex, f.read()) return api_name #api_name will contain list

How should we do it?

I think using only the first function is good enough for that. Returning the list with all occurrences seems like an overkill which complicates the code without much gain

Okay, I'll do it.

…C3 predictive samples (arviz-devs#983) Adds from_pymc3_predictions to add predictions and constant_data_predictions groups of inference data objects. Co-authored-by: Oriol Abril <oriol.abril.pla@gmail.com>

* fix histogram, add rug * add rug to bokeh * remove redundant line, make bokeh plot looks closer to matplotlib, fix scale jitter

OriolAbril

Looks good, I only have one question, what happens to the styles example?

percygautam · 2020-01-21T20:25:33Z

@OriolAbril It would return API Documentation: None, with a link to az.None function which will give file not found error. I tried to give some condition to rst template so that it does not show the API documentation line, but supposedly rst doesn't support inline code snippets

OriolAbril · 2020-01-22T13:30:50Z

doc/sphinxext/gallery_generator.py

@@ -40,6 +40,7 @@ def execfile(filename, globals=None, locals=None):
 .. image:: {img_file}

 **Python source code:** :download:`[download source: {fname}]<{fname}>`
+**API documentation:** `{api_name} <../../generated/arviz.{api_name}>`_ 


Maybe this could be changed to {api_text} so that below, if api_name is None nothing is written?

@OriolAbril , I have done the changes, now it'll show None <None> and not the directory link.

I think it would be more clear replacing the whole line, so that when no match is fount (e.g. styles case) instead of **API doc... a white line is written. Or alternatively something like:

API Documentation: No API Documentation available for {api_name}

I see myself some months from now confusing the None <None> with a doc generation error.

@OriolAbril I understand your point. I have done the changes. Now, it'll show something like:

API Documentation: No API Documentation available

We can't specify the name of documentation available because api_name would be an open string and other params like modulename will be in the form of backend_xyz. If we must do this then we have to use regex again or split the name and then pass to the new variable.

OriolAbril · 2020-01-24T16:40:05Z

doc/sphinxext/gallery_generator.py

+ with open(op.join(self.target_dir, self.pyfilename), "r") as file:
+ regex = r"az\.(plot\_[a-z_]+)\("
+ name = re.findall(regex, file.read())
+ apitext = name[0] if len(name) > 0 else ""


I think if name acts the same as if len(name) > 0

OriolAbril · 2020-01-24T16:40:58Z

doc/sphinxext/gallery_generator.py

+ name = re.findall(regex, file.read())
+ apitext = name[0] if len(name) > 0 else ""
+ return (
+ "`" + apitext + " <../../generated/arviz." + apitext + ">`_"


.format can be used here instead of adding strings

Okay, I'll add it.

OriolAbril · 2020-01-25T23:15:41Z

@percygautam #990 has already been merged, so rebasing/merging the latest changes in master should fix the failing tests. After this it can be merged

percygautam · 2020-01-26T01:50:01Z

Okay, Thanks.

Added api link feature to gallery examples

956bf19

percygautam requested a review from OriolAbril January 19, 2020 21:17

Added api link feature to gallery examples

0dfb396

OriolAbril reviewed Jan 19, 2020

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aloctavodia changed the title ~~[WIP] Solve issue #1000 : Added API link in examples~~ [WIP] Added API link in examples Jan 20, 2020

Removed error for getting api links

2057b29

percygautam requested a review from OriolAbril January 20, 2020 18:14

ahartikainen reviewed Jan 20, 2020

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rpgoldman and others added 10 commits January 22, 2020 00:51

Populate InferenceData with out-of-sample prediction results from PyM…

1960c82

…C3 predictive samples (arviz-devs#983) Adds from_pymc3_predictions to add predictions and constant_data_predictions groups of inference data objects. Co-authored-by: Oriol Abril <oriol.abril.pla@gmail.com>

Violinplot: fix histogram, add rug (arviz-devs#997)

8b2b091

* fix histogram, add rug * add rug to bokeh * remove redundant line, make bokeh plot looks closer to matplotlib, fix scale jitter

Update CHANGELOG.md

4d3722c

Add group argument to plot_joint (arviz-devs#1012)

c3836bb

Integrate stats.ic_scale rcParam (arviz-devs#993)

cdbb491

Update changelog with some untracked changes (arviz-devs#1015)

f38487b

Add data_pairs usage example for plot_ppc (arviz-devs#1007)

2db39c2

changes

08f36a4

added the change in changlog.md

23fd65d

Merge branch 'master' into API_link

878e4e3

OriolAbril reviewed Jan 21, 2020

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OriolAbril reviewed Jan 22, 2020

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percygautam added 3 commits January 22, 2020 19:34

minor fixes

dc25a7b

linting fixes

d09f07c

Corrected api text format

c013176

percygautam requested review from OriolAbril and ahartikainen January 22, 2020 18:05

OriolAbril approved these changes Jan 24, 2020

View reviewed changes

percygautam added 2 commits January 25, 2020 00:42

final fixes

691d8af

final fixes

a2b9bfd

percygautam requested a review from OriolAbril January 24, 2020 19:15

Merge branch 'master' into API_link

0033ddf

OriolAbril merged commit 06f0153 into arviz-devs:master Jan 26, 2020

percygautam deleted the API_link branch January 26, 2020 02:37

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[WIP] Added API link in examples #1013

[WIP] Added API link in examples #1013

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[WIP] Added API link in examples #1013

[WIP] Added API link in examples #1013

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