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Sphinx build hanging on file-formats.md #268

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Sphinx build hanging on file-formats.md#268

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@kinow
kinow
opened on Oct 11, 2022

I have this issue on my environment, but GH Actions is clearly not having the same problem. I'll document it here in case others have a similar issue, or if someone would like to dig into it to understand what's happening.

  1. I've synced my main branch,
kinow@ranma:~/Development/python/workspace/user_guide$ git log -n 1
commit 50d824f23edf76012d7d4002681e4f9f24927b4b (HEAD -> main, upstream/main, upstream/HEAD)
Author: Bruno P. Kinoshita <[email protected]>
Date:   Mon Oct 10 22:58:10 2022 +1300

    Add section about exclusive params with expressions, and emphasize command output lines (#247)
    
    * Highlight lines of interest in the command outputs
    * Rename "Advanced Inputs" to "Inclusive and Exclusive Inputs"
    * Add text about the exclusive input parameters and expressions
    * explain why itemC was chosen when both are provided
    
    Co-authored-by: Michael R. Crusoe <[email protected]>
  1. I've created a new environment with venv (used Mamba to start a dev env for CWL projects, but it's a fresh new env):
$ mamba create -n dev python==3.10 --quiet --yes

                  __    __    __    __
                 /  \  /  \  /  \  /  \
                /    \/    \/    \/    \
███████████████/  /██/  /██/  /██/  /████████████████████████
              /  / \   / \   / \   / \  \____
             /  /   \_/   \_/   \_/   \    o \__,
            / _/                       \_____/  `
            |/
        ███╗   ███╗ █████╗ ███╗   ███╗██████╗  █████╗
        ████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
        ██╔████╔██║███████║██╔████╔██║██████╔╝███████║
        ██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
        ██║ ╚═╝ ██║██║  ██║██║ ╚═╝ ██║██████╔╝██║  ██║
        ╚═╝     ╚═╝╚═╝  ╚═╝╚═╝     ╚═╝╚═════╝ ╚═╝  ╚═╝

        mamba (0.25.0) supported by @QuantStack

        GitHub:  https://github.com/mamba-org/mamba
        Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

  Package               Version  Build               Channel                    Size
──────────────────────────────────────────────────────────────────────────────────────
  Install:
──────────────────────────────────────────────────────────────────────────────────────

  + _libgcc_mutex           0.1  conda_forge         conda-forge/linux-64     Cached
  + _openmp_mutex           4.5  2_gnu               conda-forge/linux-64     Cached
  + bzip2                 1.0.8  h7f98852_4          conda-forge/linux-64     Cached
  + ca-certificates   2022.9.24  ha878542_0          conda-forge/linux-64     Cached
  + ld_impl_linux-64     2.36.1  hea4e1c9_2          conda-forge/linux-64     Cached
  + libffi                3.4.2  h7f98852_5          conda-forge/linux-64     Cached
  + libgcc-ng            12.1.0  h8d9b700_16         conda-forge/linux-64     Cached
  + libgomp              12.1.0  h8d9b700_16         conda-forge/linux-64     Cached
  + libnsl                2.0.0  h7f98852_0          conda-forge/linux-64     Cached
  + libsqlite            3.39.4  h753d276_0          conda-forge/linux-64     Cached
  + libuuid              2.32.1  h7f98852_1000       conda-forge/linux-64     Cached
  + libzlib              1.2.12  h166bdaf_4          conda-forge/linux-64     Cached
  + ncurses                 6.3  h27087fc_1          conda-forge/linux-64     Cached
  + openssl               3.0.5  h166bdaf_2          conda-forge/linux-64     Cached
  + pip                  22.2.2  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + python               3.10.0  h543edf9_3_cpython  conda-forge/linux-64     Cached
  + readline              8.1.2  h0f457ee_0          conda-forge/linux-64     Cached
  + setuptools           65.4.1  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + sqlite               3.39.4  h4ff8645_0          conda-forge/linux-64     Cached
  + tk                   8.6.12  h27826a3_0          conda-forge/linux-64     Cached
  + tzdata                2022d  h191b570_0          conda-forge/noarch       Cached
  + wheel                0.37.1  pyhd8ed1ab_0        conda-forge/noarch       Cached
  + xz                    5.2.6  h166bdaf_0          conda-forge/linux-64     Cached

  Summary:

  Install: 23 packages

  Total download: 0 B

──────────────────────────────────────────────────────────────────────────────────────

Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
$ mamba activate dev
(dev) $ python -m venv venv
(dev) $ source venv/bin/activate
(dev) $ pip install -U pip
Requirement already satisfied: pip in ./venv/lib/python3.10/site-packages (21.2.3)
Collecting pip
  Using cached pip-22.2.2-py3-none-any.whl (2.0 MB)
Installing collected packages: pip
  Attempting uninstall: pip
    Found existing installation: pip 21.2.3
    Uninstalling pip-21.2.3:
      Successfully uninstalled pip-21.2.3
Successfully installed pip-22.2.2
(dev) $ pip install -e .[all]
# (...)
  Running setup.py install for livereload ... done
  Running setup.py install for cwl-runner ... done
Successfully installed CacheControl-0.12.11 MarkupSafe-2.1.1 alabaster-0.7.12 argcomplete-2.0.0 babel-2.10.3 bagit-1.8.1 beautifulsoup4-4.11.1 certifi-2022.9.24 charset-normalizer-2.1.1 colorama-0.4.5 coloredlogs-15.0.1 cwl-runner-1.0 cwl-upgrader-1.2.4 cwl-user-guide-0.1 cwl-utils-0.20 cwltest-2.2.20220521103021 cwltool-3.1.20221008225030 defusedxml-0.7.1 docutils-0.19 humanfriendly-10.0 idna-3.4 imagesize-1.4.1 isodate-0.6.1 jinja2-3.1.2 junit-xml-1.9 livereload-2.6.3 lockfile-0.12.2 lxml-4.9.1 markdown-it-py-2.1.0 mdit-py-plugins-0.3.1 mdurl-0.1.2 mistune-0.8.4 msgpack-1.0.4 mypy-extensions-0.4.3 myst-parser-0.18.1 networkx-2.8.7 packaging-21.3 prov-1.5.1 psutil-5.9.2 pydata-sphinx-theme-0.11.0 pydot-1.4.2 pygments-2.13.0 pyparsing-3.0.9 python-dateutil-2.8.2 pytz-2022.4 pyyaml-6.0 rdflib-6.2.0 requests-2.28.1 ruamel.yaml-0.17.21 ruamel.yaml.clib-0.2.6 schema-salad-8.3.20220916115321 shellescape-3.8.1 six-1.16.0 snowballstemmer-2.2.0 soupsieve-2.3.2.post1 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 tornado-6.2 typing-extensions-4.4.0 udocker-1.3.4 urllib3-1.26.12
  1. Now with all the dependencies installed in my environment, I tried the following:
(dev) $ rm -rf _build/ && make build
Running Sphinx v5.2.3
^C
Interrupted!
make: *** [Makefile:50: build] Interrupt

(venv) (dev) kinow@ranma:~/Development/python/workspace/user_guide$ rm -rf _build/ && 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... [ 57%] topics/file-formats
  1. That was at 14:52. Still at 14:52 it showed the message “reading sources... [57&] topics/file-formats”, as in the screenshot below.

image

  1. At 14:55, I took this screenshot of htop (configured to Display tree, then scrolling down to locate the make html command entry):

image

  1. I stopped the command at 15:00.
  2. This also hangs:
(dev) $  cd src/_includes/cwl/file-formats/
(dev) $ cwltool --debug metadata_example.cwl sample.yml 
INFO /home/kinow/Development/python/workspace/user_guide/venv/bin/cwltool 3.1.20221008225030
INFO Resolved 'metadata_example.cwl' to 'file:///home/kinow/Development/python/workspace/user_guide/src/_includes/cwl/file-formats/metadata_example.cwl'

I haven't had time to dig really deep into the issue, but this makes the workflow run in about 1 second, so it might be something with how $schemas is handled, and maybe my cwltool version (above), or my environment.

$ git diff
diff --git a/src/_includes/cwl/file-formats/metadata_example.cwl b/src/_includes/cwl/file-formats/metadata_example.cwl
index 9485522..f4b9482 100644
--- a/src/_includes/cwl/file-formats/metadata_example.cwl
+++ b/src/_includes/cwl/file-formats/metadata_example.cwl
@@ -24,5 +24,5 @@ outputs:
 
 $namespaces:
   edam: http://edamontology.org/
-$schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+#$schemas:
+#  - http://edamontology.org/EDAM_1.18.owl

Thanks!

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