bug: Failing docs build

[kenibrewer]

I just noticed that our docs build hasn't updated since 1.0.1. https://pycytominer.readthedocs.io/en/stable/

@d33bs You recently changed something about how we are authenticating with RTD right? Is this something that you can look into?

[d33bs]

Hi @kenibrewer, yes, happy to look into this!

[kenibrewer]

@d33bs I was working on #391 and put together a makefile command for the docs build. I got the following error message:

📚 Building documentation
Running Sphinx v7.1.2
building [mo]: targets for 0 po files that are out of date
writing output... 
building [html]: targets for 9 source files that are out of date
updating environment: [new config] 9 added, 0 changed, 0 removed
/workspaces/pycytominer/pycytominer/normalize.py:docstring of pycytominer.normalize.normalize:67: ERROR: Unexpected indentation.
/workspaces/pycytominer/pycytominer/normalize.py:docstring of pycytominer.normalize.normalize:75: WARNING: Block quote ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/normalize.py:docstring of pycytominer.normalize.normalize:80: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/normalize.py:docstring of pycytominer.normalize.normalize:81: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/normalize.py:docstring of pycytominer.normalize.normalize:89: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:49: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:50: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:52: ERROR: Unexpected indentation.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:57: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:58: WARNING: Block quote ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:59: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:60: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/consensus.py:docstring of pycytominer.consensus.consensus:68: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/cells.py:docstring of pycytominer.cyto_utils.cells.SingleCells:136: ERROR: Unexpected indentation.
/workspaces/pycytominer/pycytominer/cyto_utils/cells.py:docstring of pycytominer.cyto_utils.cells.SingleCells:139: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/cells.py:docstring of pycytominer.cyto_utils.cells.SingleCells:142: WARNING: Block quote ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:35: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:36: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:38: ERROR: Unexpected indentation.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:43: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:44: WARNING: Block quote ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:45: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:46: WARNING: Definition list ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:50: ERROR: Unexpected indentation.
/workspaces/pycytominer/pycytominer/cyto_utils/output.py:docstring of pycytominer.cyto_utils.output.output:55: WARNING: Block quote ends without a blank line; unexpected unindent.
/workspaces/pycytominer/pycytominer/cyto_utils/features.py:docstring of pycytominer.cyto_utils.features.drop_outlier_features:5: ERROR: Unknown target name: "cells".
/workspaces/pycytominer/pycytominer/cyto_utils/features.py:docstring of pycytominer.cyto_utils.features.drop_outlier_features:5: ERROR: Unknown target name: "nuclei".
/workspaces/pycytominer/pycytominer/cyto_utils/features.py:docstring of pycytominer.cyto_utils.features.drop_outlier_features:5: ERROR: Unknown target name: "cytoplasm".
/workspaces/pycytominer/pycytominer/cyto_utils/load.py:docstring of pycytominer.cyto_utils.load.load_platemap:5: ERROR: Unknown target name: "metadata".
/workspaces/pycytominer/pycytominer/cyto_utils/modz.py:docstring of pycytominer.cyto_utils.modz.modz:8: ERROR: Unknown target name: "cells".
/workspaces/pycytominer/pycytominer/cyto_utils/modz.py:docstring of pycytominer.cyto_utils.modz.modz:8: ERROR: Unknown target name: "nuclei".
/workspaces/pycytominer/pycytominer/cyto_utils/modz.py:docstring of pycytominer.cyto_utils.modz.modz:8: ERROR: Unknown target name: "cytoplasm".
/workspaces/pycytominer/pycytominer/operations/correlation_threshold.py:docstring of pycytominer.operations.correlation_threshold.correlation_threshold:5: ERROR: Unknown target name: "cells".
/workspaces/pycytominer/pycytominer/operations/correlation_threshold.py:docstring of pycytominer.operations.correlation_threshold.correlation_threshold:5: ERROR: Unknown target name: "nuclei".
/workspaces/pycytominer/pycytominer/operations/correlation_threshold.py:docstring of pycytominer.operations.correlation_threshold.correlation_threshold:5: ERROR: Unknown target name: "cytoplasm".
/workspaces/pycytominer/pycytominer/operations/get_na_columns.py:docstring of pycytominer.operations.get_na_columns.get_na_columns:5: ERROR: Unknown target name: "cells".
/workspaces/pycytominer/pycytominer/operations/get_na_columns.py:docstring of pycytominer.operations.get_na_columns.get_na_columns:5: ERROR: Unknown target name: "nuclei".
/workspaces/pycytominer/pycytominer/operations/get_na_columns.py:docstring of pycytominer.operations.get_na_columns.get_na_columns:5: ERROR: Unknown target name: "cytoplasm".
/workspaces/pycytominer/pycytominer/operations/variance_threshold.py:docstring of pycytominer.operations.variance_threshold.variance_threshold:5: ERROR: Unknown target name: "cells".
/workspaces/pycytominer/pycytominer/operations/variance_threshold.py:docstring of pycytominer.operations.variance_threshold.variance_threshold:5: ERROR: Unknown target name: "nuclei".
/workspaces/pycytominer/pycytominer/operations/variance_threshold.py:docstring of pycytominer.operations.variance_threshold.variance_threshold:5: ERROR: Unknown target name: "cytoplasm".

Notebook error:
PandocMissing in walkthroughs/single_cell_usage.ipynb:
Pandoc wasn't found.
Please check that pandoc is installed:
https://pandoc.org/installing.html
make: *** [Makefile:22: docs] Error 2

So it seems likely to me that some of our formatting and other changes broke the docs build process.

This means two thing in my mind.

1. We may want to add a docs build command as a ci check to make sure sure that off target changes don't break it again in the future.
2. We may wish to to add pydocstyle ruff lint checks to identify these issues at pre-commit time.

[kenibrewer]

@d33bs I've started working on the pydocstyle ruff lint checks. If it's alright with you, I'd like to re-assign this to myself.

[d33bs]

@kenibrewer , yes, apologies for my delay here, please feel free to reassign.