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viewcode.py gives "list index out of range" #11016

Open
raar1 opened this issue Dec 5, 2022 · 9 comments
Open

viewcode.py gives "list index out of range" #11016

raar1 opened this issue Dec 5, 2022 · 9 comments
Labels
extensions:viewcode type:bug
Milestone
some future version

Comments

@raar1
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raar1 commented Dec 5, 2022

Describe the bug

When attempting to build the docs for our project at https://github.com/aiproteomics/aiproteomics we get an exception:

Exception occurred:
  File "/opt/hostedtoolcache/Python/3.9.15/x64/lib/python3.9/site-packages/sphinx/ext/viewcode.py", line 268, in collect_pages
    lines[start])
IndexError: list index out of range

This happens when running make coverage doctest html.

The full output is here:

  make coverage doctest html
  shell: /usr/bin/bash -e {0}
  env:
    pythonLocation: /opt/hostedtoolcache/Python/3.9.15/x64
    LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.15/x64/lib
Running Sphinx v5.3.0
making output directory... done
loading intersphinx inventory from https://docs.python.org/3/objects.inv...
[AutoAPI] Reading files... [  6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
[AutoAPI] Reading files... [ 12%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/__init__.py
[AutoAPI] Reading files... [ 18%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/transformer_rt.py
[AutoAPI] Reading files... [ 25%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/__init__.py
[AutoAPI] Reading files... [ 31%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/__init__.py
[AutoAPI] Reading files... [ 37%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/save_model.py
[AutoAPI] Reading files... [ 43%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1_gen.py
[AutoAPI] Reading files... [ 50%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/test_prosit_to_onnx.py
[AutoAPI] Reading files... [ 56%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/layers.py
[AutoAPI] Reading files... [ 62%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/__init__.py
[AutoAPI] Reading files... [ 68%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/losses.py
[AutoAPI] Reading files... [ 75%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/sanitize.py
[AutoAPI] Reading files... [ 81%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/constants.py
[AutoAPI] Reading files... [ 87%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/__init__.py
[AutoAPI] Reading files... [ 93%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/__init__.py
[AutoAPI] Reading files... [100%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/transformer_frag.py

[AutoAPI] Mapping Data... [  6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
[AutoAPI] Mapping Data... [ 12%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/__init__.py
[AutoAPI] Mapping Data... [ 18%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/transformer_rt.py
[AutoAPI] Mapping Data... [ 25%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/__init__.py
[AutoAPI] Mapping Data... [ 31%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/__init__.py
[AutoAPI] Mapping Data... [ 37%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/save_model.py
[AutoAPI] Mapping Data... [ 43%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1_gen.py
[AutoAPI] Mapping Data... [ 50%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/test_prosit_to_onnx.py
[AutoAPI] Mapping Data... [ 56%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/layers.py
[AutoAPI] Mapping Data... [ 62%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/__init__.py
[AutoAPI] Mapping Data... [ 68%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/losses.py
[AutoAPI] Mapping Data... [ 75%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/sanitize.py
[AutoAPI] Mapping Data... [ 81%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/constants.py
[AutoAPI] Mapping Data... [ 87%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/__init__.py
[AutoAPI] Mapping Data... [ 93%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/__init__.py
[AutoAPI] Mapping Data... [100%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/transformer_frag.py

[AutoAPI] Rendering Data... [  6%] aiproteomics
[AutoAPI] Rendering Data... [ 12%] aiproteomics.rt
[AutoAPI] Rendering Data... [ 18%] aiproteomics.rt.models.transformer_rt
[AutoAPI] Rendering Data... [ 25%] aiproteomics.rt.models
[AutoAPI] Rendering Data... [ 31%] aiproteomics.modelgen
[AutoAPI] Rendering Data... [ 37%] aiproteomics.modelgen.save_model
[AutoAPI] Rendering Data... [ 43%] aiproteomics.modelgen.prosit1_gen
[AutoAPI] Rendering Data... [ 50%] aiproteomics.modelgen.test_prosit_to_onnx
[AutoAPI] Rendering Data... [ 56%] aiproteomics.modelgen.prosit1.layers
[AutoAPI] Rendering Data... [ 62%] aiproteomics.modelgen.prosit1
[AutoAPI] Rendering Data... [ 68%] aiproteomics.modelgen.prosit1.losses
[AutoAPI] Rendering Data... [ 75%] aiproteomics.modelgen.prosit1.sanitize
[AutoAPI] Rendering Data... [ 81%] aiproteomics.modelgen.prosit1.constants
[AutoAPI] Rendering Data... [ 87%] aiproteomics.frag
[AutoAPI] Rendering Data... [ 93%] aiproteomics.frag.models
[AutoAPI] Rendering Data... [100%] aiproteomics.frag.models.transformer_frag

[autosummary] generating autosummary for: index.rst
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], 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=None, 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 [coverage]: coverage overview
updating environment: [new config] 18 added, 0 changed, 0 removed
reading sources... [  5%] autoapi/aiproteomics/frag/index
reading sources... [ 11%] autoapi/aiproteomics/frag/models/index
reading sources... [ 16%] autoapi/aiproteomics/frag/models/transformer_frag/index
reading sources... [ 22%] autoapi/aiproteomics/index
reading sources... [ 27%] autoapi/aiproteomics/modelgen/index
reading sources... [ 33%] autoapi/aiproteomics/modelgen/prosit1/constants/index
reading sources... [ 38%] autoapi/aiproteomics/modelgen/prosit1/index
reading sources... [ 44%] autoapi/aiproteomics/modelgen/prosit1/layers/index
reading sources... [ 50%] autoapi/aiproteomics/modelgen/prosit1/losses/index
reading sources... [ 55%] autoapi/aiproteomics/modelgen/prosit1/sanitize/index
reading sources... [ 61%] autoapi/aiproteomics/modelgen/prosit1_gen/index
reading sources... [ 66%] autoapi/aiproteomics/modelgen/save_model/index
reading sources... [ 72%] autoapi/aiproteomics/modelgen/test_prosit_to_onnx/index
reading sources... [ 77%] autoapi/aiproteomics/rt/index
reading sources... [ 83%] autoapi/aiproteomics/rt/models/index
reading sources... [ 88%] autoapi/aiproteomics/rt/models/transformer_rt/index
reading sources... [ 94%] autoapi/index
reading sources... [100%] index
[AutoAPI] Adding AutoAPI TOCTree [autoapi/index] to index.rst

/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:109: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:143: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:124: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:125: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:148: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:146: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:146: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:198: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:220: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:262: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:282: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:32: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/index.rst: WARNING: document isn't included in any toctree
pickling environment... done
checking consistency... done
2022-12-05 10:23:43.792507: W tensorflow/stream_executor/platform/default/dso_loader.cc:64] Could not load dynamic library 'libcudart.so.11.0'; dlerror: libcudart.so.11.0: cannot open shared object file: No such file or directory; LD_LIBRARY_PATH: /opt/hostedtoolcache/Python/3.9.15/x64/lib
2022-12-05 10:23:43.792537: I tensorflow/stream_executor/cuda/cudart_stub.cc:29] Ignore above cudart dlerror if you do not have a GPU set up on your machine.
build succeeded, 26 warnings.

Testing of coverage in the sources finished, look at the results in _build/coverage/python.txt.
Running Sphinx v5.3.0
making output directory... done
loading pickled environment... done
[AutoAPI] Reading files... [  6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
[AutoAPI] Reading files... [ 12%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/__init__.py
[AutoAPI] Reading files... [ 18%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/transformer_rt.py
[AutoAPI] Reading files... [ 25%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/__init__.py
[AutoAPI] Reading files... [ 31%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/__init__.py
[AutoAPI] Reading files... [ 37%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/save_model.py
[AutoAPI] Reading files... [ 43%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1_gen.py
[AutoAPI] Reading files... [ 50%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/test_prosit_to_onnx.py
[AutoAPI] Reading files... [ 56%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/layers.py
[AutoAPI] Reading files... [ 62%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/__init__.py
[AutoAPI] Reading files... [ 68%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/losses.py
[AutoAPI] Reading files... [ 75%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/sanitize.py
[AutoAPI] Reading files... [ 81%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/constants.py
[AutoAPI] Reading files... [ 87%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/__init__.py
[AutoAPI] Reading files... [ 93%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/__init__.py
[AutoAPI] Reading files... [100%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/transformer_frag.py

[AutoAPI] Mapping Data... [  6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
[AutoAPI] Mapping Data... [ 12%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/__init__.py
[AutoAPI] Mapping Data... [ 18%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/transformer_rt.py
[AutoAPI] Mapping Data... [ 25%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/__init__.py
[AutoAPI] Mapping Data... [ 31%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/__init__.py
[AutoAPI] Mapping Data... [ 37%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/save_model.py
[AutoAPI] Mapping Data... [ 43%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1_gen.py
[AutoAPI] Mapping Data... [ 50%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/test_prosit_to_onnx.py
[AutoAPI] Mapping Data... [ 56%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/layers.py
[AutoAPI] Mapping Data... [ 62%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/__init__.py
[AutoAPI] Mapping Data... [ 68%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/losses.py
[AutoAPI] Mapping Data... [ 75%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/sanitize.py
[AutoAPI] Mapping Data... [ 81%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/modelgen/prosit1/constants.py
[AutoAPI] Mapping Data... [ 87%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/__init__.py
[AutoAPI] Mapping Data... [ 93%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/__init__.py
[AutoAPI] Mapping Data... [100%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/frag/models/transformer_frag.py

[AutoAPI] Rendering Data... [  6%] aiproteomics
[AutoAPI] Rendering Data... [ 12%] aiproteomics.rt
[AutoAPI] Rendering Data... [ 18%] aiproteomics.rt.models.transformer_rt
[AutoAPI] Rendering Data... [ 25%] aiproteomics.rt.models
[AutoAPI] Rendering Data... [ 31%] aiproteomics.modelgen
[AutoAPI] Rendering Data... [ 37%] aiproteomics.modelgen.save_model
[AutoAPI] Rendering Data... [ 43%] aiproteomics.modelgen.prosit1_gen
[AutoAPI] Rendering Data... [ 50%] aiproteomics.modelgen.test_prosit_to_onnx
[AutoAPI] Rendering Data... [ 56%] aiproteomics.modelgen.prosit1.layers
[AutoAPI] Rendering Data... [ 62%] aiproteomics.modelgen.prosit1
[AutoAPI] Rendering Data... [ 68%] aiproteomics.modelgen.prosit1.losses
[AutoAPI] Rendering Data... [ 75%] aiproteomics.modelgen.prosit1.sanitize
[AutoAPI] Rendering Data... [ 81%] aiproteomics.modelgen.prosit1.constants
[AutoAPI] Rendering Data... [ 87%] aiproteomics.frag
[AutoAPI] Rendering Data... [ 93%] aiproteomics.frag.models
[AutoAPI] Rendering Data... [100%] aiproteomics.frag.models.transformer_frag

[autosummary] generating autosummary for: autoapi/aiproteomics/frag/index.rst, autoapi/aiproteomics/frag/models/index.rst, autoapi/aiproteomics/frag/models/transformer_frag/index.rst, autoapi/aiproteomics/index.rst, autoapi/aiproteomics/modelgen/index.rst, autoapi/aiproteomics/modelgen/prosit1/constants/index.rst, autoapi/aiproteomics/modelgen/prosit1/index.rst, autoapi/aiproteomics/modelgen/prosit1/layers/index.rst, autoapi/aiproteomics/modelgen/prosit1/losses/index.rst, autoapi/aiproteomics/modelgen/prosit1/sanitize/index.rst, autoapi/aiproteomics/modelgen/prosit1_gen/index.rst, autoapi/aiproteomics/modelgen/save_model/index.rst, autoapi/aiproteomics/modelgen/test_prosit_to_onnx/index.rst, autoapi/aiproteomics/rt/index.rst, autoapi/aiproteomics/rt/models/index.rst, autoapi/aiproteomics/rt/models/transformer_rt/index.rst, autoapi/index.rst, index.rst
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], 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=None, 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 [doctest]: targets for 18 source files that are out of date
updating environment: 0 added, 17 changed, 0 removed
reading sources... [  5%] autoapi/aiproteomics/frag/index
reading sources... [ 11%] autoapi/aiproteomics/frag/models/index
reading sources... [ 17%] autoapi/aiproteomics/frag/models/transformer_frag/index
reading sources... [ 23%] autoapi/aiproteomics/index
reading sources... [ 29%] autoapi/aiproteomics/modelgen/index
reading sources... [ 35%] autoapi/aiproteomics/modelgen/prosit1/constants/index
reading sources... [ 41%] autoapi/aiproteomics/modelgen/prosit1/index
reading sources... [ 47%] autoapi/aiproteomics/modelgen/prosit1/layers/index
reading sources... [ 52%] autoapi/aiproteomics/modelgen/prosit1/losses/index
reading sources... [ 58%] autoapi/aiproteomics/modelgen/prosit1/sanitize/index
reading sources... [ 64%] autoapi/aiproteomics/modelgen/prosit1_gen/index
reading sources... [ 70%] autoapi/aiproteomics/modelgen/save_model/index
reading sources... [ 76%] autoapi/aiproteomics/modelgen/test_prosit_to_onnx/index
reading sources... [ 82%] autoapi/aiproteomics/rt/index
reading sources... [ 88%] autoapi/aiproteomics/rt/models/index
reading sources... [ 94%] autoapi/aiproteomics/rt/models/transformer_rt/index
reading sources... [100%] autoapi/index
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:109: ERROR: Unexpected indentation.

/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:143: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:124: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:125: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:148: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline interpreted text or phrase reference start-string without end-string.
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/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:146: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:198: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:220: ERROR: Unexpected indentation.
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/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:32: WARNING: Block quote ends without a blank line; unexpected unindent.
looking for now-outdated files... none found
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/index.rst: WARNING: document isn't included in any toctree
pickling environment... done
checking consistency... done
running tests...

Doctest summary
===============
    0 tests
    0 failures in tests
    0 failures in setup code
    0 failures in cleanup code
build succeeded, 26 warnings.

Testing of doctests in the sources finished, look at the results in _build/doctest/output.txt.
Running Sphinx v5.3.0
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loading pickled environment... done
[AutoAPI] Reading files... [  6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
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[AutoAPI] Reading files... [ 18%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/rt/models/transformer_rt.py
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[AutoAPI] Rendering Data... [  6%] aiproteomics
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[autosummary] generating autosummary for: autoapi/aiproteomics/frag/index.rst, autoapi/aiproteomics/frag/models/index.rst, autoapi/aiproteomics/frag/models/transformer_frag/index.rst, autoapi/aiproteomics/index.rst, autoapi/aiproteomics/modelgen/index.rst, autoapi/aiproteomics/modelgen/prosit1/constants/index.rst, autoapi/aiproteomics/modelgen/prosit1/index.rst, autoapi/aiproteomics/modelgen/prosit1/layers/index.rst, autoapi/aiproteomics/modelgen/prosit1/losses/index.rst, autoapi/aiproteomics/modelgen/prosit1/sanitize/index.rst, autoapi/aiproteomics/modelgen/prosit1_gen/index.rst, autoapi/aiproteomics/modelgen/save_model/index.rst, autoapi/aiproteomics/modelgen/test_prosit_to_onnx/index.rst, autoapi/aiproteomics/rt/index.rst, autoapi/aiproteomics/rt/models/index.rst, autoapi/aiproteomics/rt/models/transformer_rt/index.rst, autoapi/index.rst, index.rst
myst v0.18.1: MdParserConfig(commonmark_only=False, gfm_only=False, enable_extensions=[], 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=None, 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 18 source files that are out of date
updating environment: 0 added, 17 changed, 0 removed
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reading sources... [ 76%] autoapi/aiproteomics/modelgen/test_prosit_to_onnx/index
reading sources... [ 82%] autoapi/aiproteomics/rt/index
reading sources... [ 88%] autoapi/aiproteomics/rt/models/index
reading sources... [ 94%] autoapi/aiproteomics/rt/models/transformer_rt/index
reading sources... [100%] autoapi/index
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:109: ERROR: Unexpected indentation.

/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:94: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:112: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:143: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:124: WARNING: Definition list ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:125: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:148: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:140: WARNING: Inline interpreted text or phrase reference start-string without end-string.
looking for now-outdated files... none found
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:146: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:146: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:163: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:170: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:198: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline literal start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:192: WARNING: Inline interpreted text or phrase reference start-string without end-string.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:220: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:262: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:13: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:282: ERROR: Unexpected indentation.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/aiproteomics/modelgen/prosit1/layers/index.rst:32: WARNING: Block quote ends without a blank line; unexpected unindent.
/home/runner/work/aiproteomics/aiproteomics/docs/autoapi/index.rst: WARNING: document isn't included in any toctree
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writing output... [ 94%] autoapi/index
writing output... [100%] index

generating indices... genindex py-modindex done
highlighting module code... [ 11%] aiproteomics.frag.models.transformer_frag
highlighting module code... [ 22%] aiproteomics.modelgen.prosit1.constants
highlighting module code... [ 33%] aiproteomics.modelgen.prosit1.layers

Exception occurred:
  File "/opt/hostedtoolcache/Python/3.9.15/x64/lib/python3.9/site-packages/sphinx/ext/viewcode.py", line 268, in collect_pages
    lines[start])
IndexError: list index out of range
The full traceback has been saved in /tmp/sphinx-err-jzw0sts9.log, if you want to report the issue to the developers.
Please also report this if it was a user error, so that a better error message can be provided next time.
A bug report can be filed in the tracker at <https://github.com/sphinx-doc/sphinx/issues>. Thanks!
make: *** [Makefile:20: html] Error 2
Error: Process completed with exit code 2.

How to Reproduce

The command was make coverage doctest html. run in the docs/ directory of our repo: https://github.com/aiproteomics/aiproteomics

It is possible to cause this with make html

Environment Information

text Platform: darwin; (macOS-10.16-x86_64-i386-64bit) Python version: 3.9.15 (main, Nov 24 2022, 08:29:02) [Clang 14.0.6 ]) Python implementation: CPython Sphinx version: 5.3.0 Docutils version: 0.17.1 Jinja2 version: 3.1.2

Sphinx extensions

No response

Additional context

No response
@raar1 raar1 mentioned this issue Dec 5, 2022
Closed
@DaniBodor DaniBodor mentioned this issue Dec 5, 2022
Closed
@AA-Turner AA-Turner added this to the some future version milestone Apr 29, 2023
@n-dusan
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n-dusan commented Aug 2, 2023 •
edited
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I'm experiencing the same issue. Do we know why this is happening and how can I resolve?

@jjacekk
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jjacekk commented Aug 7, 2023 •
edited
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I have the same issue. It is observed after pydantic migration (from 1.10.2 to 2.1.1).

Instalation of autodoc-pydantic sphinx extension helps for me.

@Stausssi
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Running into the same issue myself.
I've managed to mitigate the issue by fixing Sphinx to version 7.2.6. The issue appears since 7.3.0, but confusingly this only happens in one of the projects inside the organization. All other doc build succeed, even with Sphinx 7.3.7

@picnixz
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picnixz commented Apr 23, 2024

Could you pinpoint the exact commit please?

@Stausssi
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Stausssi commented Apr 23, 2024 •
edited
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Unfortunately I can't, but it must be one of the commits between version 7.2.6 and 7.3.0.

What confuses me, is that it only affects one of the projects, even tho they use a central Sphinx conf.py with only slight modifications (not affecting viewcode). I will try to dig deeper later

Update: Managed to get the sphinx-err.log:

# Platform:         linux; (Linux-6.5.0-1018-azure-x86_64-with-glibc2.35)
# Sphinx version:   7.3.7
# Python version:   3.12.3 (CPython)
# Docutils version: 0.20.1
# Jinja2 version:   3.1.3
# Pygments version: 2.17.2

# Last messages:
#   highlighting module code... [ 71%]
#   src.ecu_fota.simulation.state
#   
#   highlighting module code... [ 79%]
#   src.ecu_fota.util
#   
#   highlighting module code... [ 86%]
#   src.mdm_config.util
#   
#   Needs successfully exported

# Loaded extensions:
#   sphinx.ext.mathjax (7.3.7)
#   alabaster (0.7.16)
#   sphinxcontrib.applehelp (1.0.8)
#   sphinxcontrib.devhelp (1.0.6)
#   sphinxcontrib.htmlhelp (2.0.5)
#   sphinxcontrib.serializinghtml (1.1.10)
#   sphinxcontrib.qthelp (1.0.7)
#   myst_parser (3.0.0)
#   sphinx.ext.autodoc.preserve_defaults (7.3.7)
#   sphinx.ext.autodoc.type_comment (7.3.7)
#   sphinx.ext.autodoc.typehints (7.3.7)
#   sphinx.ext.autodoc (7.3.7)
#   sphinx.ext.autosectionlabel (7.3.7)
#   sphinx.ext.extlinks (7.3.7)
#   sphinx.ext.intersphinx (7.3.7)
#   sphinx.ext.napoleon (7.3.7)
#   sphinx.ext.todo (7.3.7)
#   sphinx.ext.viewcode (7.3.7)
#   sphinx.ext.autosummary (7.3.7)
#   sphinx.ext.graphviz (7.3.7)
#   sphinx.ext.inheritance_diagram (7.3.7)
#   autoapi.extension (unknown version)
#   sphinx_data_viewer (0.1.4)
#   sphinxcontrib.jquery (4.1)
#   sphinx_needs (2.0.0)
#   sphinx_toolbox.assets (3.5.0)
#   sphinx_toolbox.tweaks.tabsize (3.5.0)
#   sphinx_toolbox.code (3.5.0)
#   sphinx_toolbox.collapse (3.5.0)
#   sphinx_toolbox.formatting (3.5.0)
#   sphinx_toolbox.github (3.5.0)
#   sphinx_toolbox.sidebar_links (3.5.0)
#   sphinxcontrib.mermaid (7.3.7)
#   sphinxcontrib.plantuml (unknown version)
#   sphinxcontrib.test_reports (1.0.2)
#   sphinxcontrib.httpdomain (unknown version)
#   sphinx_rtd_theme (unknown version)

# Traceback:
Traceback (most recent call last):
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/cmd/build.py", line 337, in build_main
    app.build(args.force_all, args.filenames)
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/application.py", line 351, in build
    self.builder.build_update()
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 293, in build_update
    self.build(to_build,
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/builders/__init__.py", line 365, in build
    self.finish()
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/builders/html/__init__.py", line 676, in finish
    self.finish_tasks.add_task(self.gen_pages_from_extensions)
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/util/parallel.py", line 41, in add_task
    res = task_func()
          ^^^^^^^^^^^
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/builders/html/__init__.py", line 696, in gen_pages_from_extensions
    for pagename, context, template in pagelist:
  File "/opt/hostedtoolcache/Python/3.12.3/x64/lib/python3.12/site-packages/sphinx/ext/viewcode.py", line 290, in collect_pages
    + lines[start])
      ~~~~~^^^^^^^
IndexError: list index out of range

@BrandonLiang
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Running into the same issue myself. I've managed to mitigate the issue by fixing Sphinx to version 7.2.6. The issue appears since 7.3.0, but confusingly this only happens in one of the projects inside the organization. All other doc build succeed, even with Sphinx 7.3.7

@Stausssi I tried this and got Theme error: UndefinedError("'style' is undefined") error, see readthedocs/readthedocs.org#10279

@BrandonLiang
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BrandonLiang commented Jul 9, 2024 •
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I have the same issue. It is observed after pydantic migration (from 1.10.2 to 2.1.1).

Instalation of autodoc-pydantic sphinx extension helps for me.

@jjacekk which version of autodoc_pydantic are you using? I have 2.1.0 and it's still failing with list index out of range

@jjacekk
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jjacekk commented Jul 10, 2024

@BrandonLiang Some of my packages:
autodoc-pydantic 2.0.1
pydantic 2.5.2
pydantic_core 2.14.5
pydantic-settings 2.0.2
Sphinx 5.2.3
sphinx-autoapi 2.1.1
sphinx-data-viewer 0.1.2
sphinx-rtd-theme 1.0.0
sphinxcontrib-applehelp 1.0.2
sphinxcontrib-devhelp 1.0.2
sphinxcontrib-htmlhelp 2.0.0
sphinxcontrib-jquery 4.1
sphinxcontrib-jsmath 1.0.1
sphinxcontrib-needs 0.7.9
sphinxcontrib-plantuml 0.24
sphinxcontrib-programoutput 0.17
sphinxcontrib-qthelp 1.0.3
sphinxcontrib-serializinghtml 1.1.5
sphinxcontrib-xlsxtable 1.0.0

@AA-Turner
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AA-Turner commented Jul 10, 2024 •
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@jjacekk / @BrandonLiang what build command are you using? Can you link to the documentation it is for?

A

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@raar1 @AA-Turner @picnixz @BrandonLiang @Stausssi @n-dusan @jjacekk