Fix emphasize-lines with runcmd

[kinow]

Closes #269

@swzCuroverse this PR changes should fix the emphasize-lines and hopefully make html works for you from this branch. Could you review it, please?

@mr-c told you it was one of those annoying issues that requires a single line to fix, but you spend way too long figuring out which line to change 😆

The issue was identified in this pull request review by @mr-c : #246 (comment)

The comment was on the troubleshooting.md file. Here's this file rendered on my local environment (reviewers can use the RTD preview 👇):

[kinow]

(worth going around the user guide when reviewing it too... it shouldn't break anything, but you never know! 👍 )

[kinow]

Huh, I just tried re-running everything after cleaning my environment, and it failed to find the lines for inputs.md. I think that the error you had @swzCuroverse could be caused by this issue actually?

(venv) kinow@ranma:~/Development/python/workspace/user_guide/src/_includes/cwl/inputs$ cwltool record.cwl record-job1.yml
INFO /home/kinow/Development/python/workspace/user_guide/venv/bin/cwltool 3.1.20221008225030
INFO Resolved 'record.cwl' to 'file:///home/kinow/Development/python/workspace/user_guide/src/_includes/cwl/inputs/record.cwl'
ERROR Workflow error, try again with --debug for more information:
Invalid job input record:
record-job1.yml:1:1: the `dependent_parameters` field is not valid because
                       missing required field `itemB`

Something changed somewhere (either in the example, or in cwltool) that broke that example. Let me see if I can adjust it.

[kinow]

I think it's fixed now. Let me know if the build passes for you now @swzCuroverse 👍

[swzCuroverse]

Let me see if it works for me :)

[swzCuroverse]

Hmm - It isn't working for me. I went to the fix-emphasize-lines-runcmd branch and ran make html, and I still see the same errors. I verified that I had the correct branch by comparing the changes listed here and the files I have in my branch. Still no luck. Let me see if some old html is hanging about and that is causing an issue.

Side note -- these are my configurations if different than yours MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist', 'substitution', 'replacements'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')

and sphinx versions:
sphinx==5.2.3
sphinx-autobuild==2021.3.14
sphinx-reredirects==0.1.1
sphinxcontrib-applehelp==1.0.2
sphinxcontrib-devhelp==1.0.2
sphinxcontrib-htmlhelp==2.0.0
sphinxcontrib-jsmath==1.0.1
sphinxcontrib-qthelp==1.0.3
sphinxcontrib-runcmd==0.2.0
sphinxcontrib-serializinghtml==1.1.5

[kinow]

Hi @swzCuroverse , do you still have the exact same error? Could you try:

• rm -rf _build (if you have a _build folder)
• make html again, or sphinx-build -b html src _build/html/
• Confirm if you still get the same error of lines out of range, please?

Side note -- these are my configurations if different than yours MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist', 'substitution', 'replacements'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')

Are these from src/conf.py?

and sphinx versions:

Our sphinx versions are the same 👍 so I think we can rule that out.

Thanks @swzCuroverse !
-Bruno

[swzCuroverse]

@kinow , I removed the _build and make sure I am up to date with the latest main branch, and I still get the error: Let me re-clone and see if that fixes the issue.

make html
Running Sphinx v5.2.3
making output directory... done
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist', 'substitution', 'replacements'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 33 source files that are out of date
updating environment: [new config] 33 added, 0 changed, 0 removed
reading sources... [100%] tutorials

Warning, treated as error:
/home/swz/user_guide/src/topics/inputs.md.rst:210:line number spec is out of range(1-1): '6-7'
make: *** [Makefile:50: html] Error 2

[swzCuroverse]

I recloned a new version and it still breaks for me.

make html
Running Sphinx v5.2.3
making output directory... done
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=['colon_fence', 'deflist', 'substitution', 'replacements'], disable_syntax=[], all_links_external=False, url_schemes=('http', 'https', 'mailto', 'ftp'), ref_domains=None, highlight_code_blocks=True, number_code_blocks=[], title_to_header=False, heading_anchors=4, heading_slug_func=None, footnote_transition=True, words_per_minute=200, sub_delimiters=('{', '}'), linkify_fuzzy_links=True, dmath_allow_labels=True, dmath_allow_space=True, dmath_allow_digits=True, dmath_double_inline=False, update_mathjax=True, mathjax_classes='tex2jax_process|mathjax_process|math|output_area')
building [mo]: targets for 0 po files that are out of date
building [html]: targets for 33 source files that are out of date
updating environment: [new config] 33 added, 0 changed, 0 removed
reading sources... [100%] tutorials
Warning, treated as error:
/home/swz/user_guide/src/topics/inputs.md.rst:210:line number spec is out of range(1-1): '6-7'
make: *** [Makefile:50: html] Error 2

[swzCuroverse]

Maybe there is something different in your config?

[tetron]

@swzCuroverse I was able to get this to work after doing this:

1. rm -rf _build
2. pip install -U pip setuptools wheel
3. pip install .[all]