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  • felix-hilden 7
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issue 1

  • Add sphinx-codeautolink extension to docs build · 15 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1407385267 https://github.com/pydata/xarray/pull/7011#issuecomment-1407385267 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85T4v6z felix-hilden 25202257 2023-01-28T12:06:59Z 2023-01-28T12:07:46Z NONE

I'm not familiar with how :suppress: works, other than the fact that the documentation states that warnings and errors are ignored. But I see that the whole block is invisible, so maybe it is executed only internally by IPython and all output is suppressed. If this is the case, consider adding something like:

```rst .. autolink-preface::

import numpy as np
import pandas as pd
import xarray as xr
...

`` or you can also set a [global preface](https://sphinx-codeautolink.readthedocs.io/en/latest/reference.html#confval-codeautolink_global_preface) inconf.py`!

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  Add sphinx-codeautolink extension to docs build 1366751031
1405520420 https://github.com/pydata/xarray/pull/7011#issuecomment-1405520420 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Txook dcherian 2448579 2023-01-26T19:39:12Z 2023-01-26T19:39:53Z MEMBER

It works! so on to the next issue :(

https://xray--7011.org.readthedocs.build/en/7011/user-guide/data-structures.html# has no links in the first cell.

Do you execute ipython cells that are "suppressed" (see https://github.com/pydata/xarray/blob/main/doc/user-guide/data-structures.rst). I think we "suppress" cells with imports at the top of all our doc pages.

Thanks again for all your work!

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  Add sphinx-codeautolink extension to docs build 1366751031
1405517779 https://github.com/pydata/xarray/pull/7011#issuecomment-1405517779 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Txn_T felix-hilden 25202257 2023-01-26T19:38:04Z 2023-01-26T19:38:04Z NONE

Wow, it's green! I still see some matching warnings though 🤔 I can have a closer look later if you care about them.

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1405482835 https://github.com/pydata/xarray/pull/7011#issuecomment-1405482835 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85TxfdT felix-hilden 25202257 2023-01-26T19:15:21Z 2023-01-26T19:15:21Z NONE

Yep we'll definitely follow what IPython does, now available in sphinx-codeautolink==0.13.2!

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1384528701 https://github.com/pydata/xarray/pull/7011#issuecomment-1384528701 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Shjs9 dcherian 2448579 2023-01-16T20:37:02Z 2023-01-16T20:37:15Z MEMBER

It's the second code block here and the source is

``` rst .. ipython:: python

# only one argument has the 'x' coordinate
arr[0] + 1
# both arguments have the same 'x' coordinate
arr[0] - arr[0]

```

It's rendering properly so it seems like this should just work.

So In/Out won't be expected.

The source block doesn't have In/Out but I guess the extension is receiving the output after IPython has executed the block?

I tried moving the comments around which seems to work, but we do this in a lot of places. Is it easy for you to handle it?

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1383282969 https://github.com/pydata/xarray/pull/7011#issuecomment-1383282969 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85SczkZ felix-hilden 25202257 2023-01-15T23:24:05Z 2023-01-15T23:24:05Z NONE

That actually might be something for you to change. See the issue and in particular this IPython doc on the lexer implementation. It states that blocks not starting with a console prompt should be considered ordinary (IPython) code. So In/Out won't be expected. Now maybe comments are or should be an exception, but I suspect by moving the comment elsewhere you might get it to pass!

If you refuse, I'll have a look at IPython's implementation and how they handle comments 😄

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1383279041 https://github.com/pydata/xarray/pull/7011#issuecomment-1383279041 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85ScynB dcherian 2448579 2023-01-15T23:10:07Z 2023-01-15T23:10:07Z MEMBER

Ah now a different one ``` Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/block.py", line 213, in parse_source names = parse_names(modified_source, node) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/parse.py", line 20, in parse_names tree = ast.parse(source) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/ast.py", line 50, in parse return compile(source, filename, mode, flags, File "<unknown>", line 638 Out[125]: ^ SyntaxError: invalid syntax

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/init.py", line 43, in wrapper return func(args, *kwargs) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/init.py", line 135, in parse_blocks doctree.walkabout(visitor) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/docutils/nodes.py", line 227, in walkabout if child.walkabout(visitor): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/docutils/nodes.py", line 227, in walkabout if child.walkabout(visitor): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/docutils/nodes.py", line 227, in walkabout if child.walkabout(visitor): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/docutils/nodes.py", line 219, in walkabout visitor.dispatch_visit(self) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/docutils/nodes.py", line 2021, in dispatch_visit return method(node) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/block.py", line 166, in visit_literal_block return self.parse_source(node, node.get("language", None)) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/block.py", line 215, in parse_source show_source = self._format_source_for_error(source, prefaces) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/block.py", line 246, in _format_source_for_error guides[ix] = "block source:" IndexError: list assignment index out of range ```

Thanks for be patient with us!

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  Add sphinx-codeautolink extension to docs build 1366751031
1383271546 https://github.com/pydata/xarray/pull/7011#issuecomment-1383271546 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Scwx6 felix-hilden 25202257 2023-01-15T22:35:54Z 2023-01-15T22:35:54Z NONE

Oh yikes, that should also be fixed now! I hope the parsing logic is finally sound.

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1383181409 https://github.com/pydata/xarray/pull/7011#issuecomment-1383181409 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Scaxh dcherian 2448579 2023-01-15T15:33:22Z 2023-01-15T15:33:37Z MEMBER

We now have a different error where a error message is being treated as code: Traceback (most recent call last): File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/extension/block.py", line 204, in parse_source names = parse_names(modified_source, node) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/site-packages/sphinx_codeautolink/parse.py", line 20, in parse_names tree = ast.parse(source) File "/home/docs/checkouts/readthedocs.org/user_builds/xray/conda/7011/lib/python3.9/ast.py", line 50, in parse return compile(source, filename, mode, flags, File "<unknown>", line 638 ValueError: arguments without labels along dimension 'x' cannot be aligned because they have different dimension size(s) {2} than the size of the aligned dimension labels: 3 ^ SyntaxError: invalid syntax

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  Add sphinx-codeautolink extension to docs build 1366751031
1335512306 https://github.com/pydata/xarray/pull/7011#issuecomment-1335512306 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85Pmkzy dcherian 2448579 2022-12-02T16:36:16Z 2022-12-02T16:36:16Z MEMBER

@felix-hilden Looks like we still have the same issue with sphinx-codeautolink 0.12.1 pypi_0 pypi

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1304540480 https://github.com/pydata/xarray/pull/7011#issuecomment-1304540480 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85NwbVA felix-hilden 25202257 2022-11-05T12:47:14Z 2022-11-05T12:47:14Z NONE

Yep, a weird interaction between rST processing and the IPython transformer. This class of issues fixed in sphinx-codeautolink==0.12.1!

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  Add sphinx-codeautolink extension to docs build 1366751031
1304497912 https://github.com/pydata/xarray/pull/7011#issuecomment-1304497912 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85NwQ74 felix-hilden 25202257 2022-11-05T11:01:52Z 2022-11-05T11:01:52Z NONE

Hi, it looks like the print output is recognised as Python code and parsed. This shouldn't be happening since your what's-new correctly contains the Out [...]: prefixes which we use to ignore lines for parsing (although I couldn't find the specific case you presented). I'll test the multiline outputs and provide an update to you.

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  Add sphinx-codeautolink extension to docs build 1366751031
1304327461 https://github.com/pydata/xarray/pull/7011#issuecomment-1304327461 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85NvnUl dcherian 2448579 2022-11-04T23:09:21Z 2022-11-04T23:09:21Z MEMBER

There are a lot of these warnings: `` /home/docs/checkouts/readthedocs.org/user_builds/xray/checkouts/7011/doc/whats-new.rst:1: WARNING: invalid syntax (<unknown>, line 6) in document "whats-new" Parsed source inipython` block: block source: In [66]: ds = xray.Dataset({"x": np.arange(1000)})

          In [67]: with xray.set_options(display_width=40):
             ....:     print(ds)
             ....: 
          <xarray.Dataset>
          Dimensions:  (x: 1000)
          Coordinates:
            * x        (x) int64 0 1 2 ... 998 999
          Data variables:
              *empty*

```

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  Add sphinx-codeautolink extension to docs build 1366751031
1241283540 https://github.com/pydata/xarray/pull/7011#issuecomment-1241283540 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85J_HvU keewis 14808389 2022-09-08T22:05:00Z 2022-09-08T22:05:00Z MEMBER

did you compare the versions? If it works locally, maybe you have a different version of sphinx or sphinx-codeautolink (or any other dependency?)

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  Add sphinx-codeautolink extension to docs build 1366751031
1241137483 https://github.com/pydata/xarray/pull/7011#issuecomment-1241137483 https://api.github.com/repos/pydata/xarray/issues/7011 IC_kwDOAMm_X85J-kFL TomNicholas 35968931 2022-09-08T19:29:43Z 2022-09-08T19:29:43Z MEMBER

I don't understand why this failed - it works when I build the docs locally, but the RTD build doesn't give me a useful error message...

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