issue_comments

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`!

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!

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

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

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?

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 😄

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!

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

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

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

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

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.

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*

```

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

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...