sphinx
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Published
20 hours ago •
sphinx-doc
sphinx-doc
viewcode.py gives "list index out of range"
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.
/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.
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Doctest summary
===============
0 tests
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build succeeded, 26 warnings.
Testing of doctests in the sources finished, look at the results in _build/doctest/output.txt.
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[AutoAPI] Reading files... [ 6%] /home/runner/work/aiproteomics/aiproteomics/aiproteomics/__init__.py
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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')
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generating indices... genindex py-modindex done
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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
