`1.9.1` "Could not collect", relative path config #160

CBroz1 · 2024-05-10T16:01:58Z

CBroz1
May 10, 2024

I'm able to build with 1.9.0, but building with 1.9.1 results in ...

> mkdocs build --clean --config-file ./docs/mkdocs.yml
INFO    -  Cleaning site directory
INFO    -  Building documentation to directory: /home/{path}/{package}/docs/site
ERROR   -  mkdocstrings: src.spyglass.settings could not be found
ERROR   -  Error reading page 'api/settings.md':
ERROR   -  Could not collect 'src.{package}.settings'

Aborted with a BuildError!

The verbose build log suggests it errors out on the first case

mkdocs build -v --clean --config-file ./docs/mkdocs.yml
DEBUG   -  Loading configuration file: <_io.BufferedReader name='./docs/mkdocs.yml'>
DEBUG   -  Loaded theme configuration for 'material' from
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates/mkdocs_theme.yml':
           {'language': 'en', 'direction': None, 'features': [], 'font': {'text': 'Roboto', 'code':
           'Roboto Mono'}, 'icon': None, 'favicon': 'assets/images/favicon.png', 'static_templates':
           ['404.html']}
DEBUG   -  Config value 'config_file_path' = './docs/mkdocs.yml'
DEBUG   -  Config value 'site_name' = 'Spyglass'
DEBUG   -  Config value 'nav' = [{'Home': 'index.md'}, {'Installation': 'installation.md'}, {'Tutorials':
           [{'Overview': 'notebooks/index.md'}, {'Intro': [{'Setup': 'notebooks/00_Setup.ipynb'}, {'Insert
           Data': 'notebooks/01_Insert_Data.ipynb'}, {'Data Sync': 'notebooks/02_Data_Sync.ipynb'},
           {'Merge Tables': 'notebooks/03_Merge_Tables.ipynb'}, {'Config Populate':
           'notebooks/04_PopulateConfigFile.ipynb'}, {'Export': 'notebooks/05_Export.ipynb'}]}, {'Spikes':
           [{'Spike Sorting V0': 'notebooks/10_Spike_SortingV0.ipynb'}, {'Spike Sorting V1':
           'notebooks/10_Spike_SortingV1.ipynb'}]}, {'Position': [{'Position Trodes':
           'notebooks/20_Position_Trodes.ipynb'}, {'DLC Models': 'notebooks/21_DLC.ipynb'}, {'Looping
           DLC': 'notebooks/22_DLC_Loop.ipynb'}, {'Linearization': 'notebooks/24_Linearization.ipynb'}]},
           {'LFP': [{'LFP': 'notebooks/30_LFP.ipynb'}, {'Theta': 'notebooks/31_Theta.ipynb'}, {'Ripple
           Detection': 'notebooks/32_Ripple_Detection.ipynb'}]}, {'Decoding': [{'Extracting Waveforms':
           'notebooks/40_Extracting_Clusterless_Waveform_Features.ipynb'}, {'Decoding Clusterless':
           'notebooks/41_Decoding_Clusterless.ipynb'}, {'Decoding Sorted Spikes':
           'notebooks/42_Decoding_SortedSpikes.ipynb'}]}, {'MUA Detection':
           'notebooks/50_MUA_Detection.ipynb'}]}, {'Miscellaneous': [{'Overview': 'misc/index.md'},
           {'FigURL': 'misc/figurl_views.md'}, {'Session Groups': 'misc/session_groups.md'}, {'Insert
           Data': 'misc/insert_data.md'}, {'Mixin': 'misc/mixin.md'}, {'Merge Tables':
           'misc/merge_tables.md'}, {'Database Management': 'misc/database_management.md'}, {'Export':
           'misc/export.md'}]}, {'API Reference': 'api/'}, {'How to Contribute': 'contribute.md'},
           {'Change Log': 'CHANGELOG.md'}, {'Copyright': 'LICENSE.md'}]
DEBUG   -  Config value 'pages' = None
DEBUG   -  Config value 'exclude_docs' = None
DEBUG   -  Config value 'draft_docs' = None
DEBUG   -  Config value 'not_in_nav' = None
DEBUG   -  Config value 'site_url' = 'https://lorenfranklab.github.io/spyglass/'
DEBUG   -  Config value 'site_description' = 'Spyglass Documentation'
DEBUG   -  Config value 'site_author' = 'CBroz1'
DEBUG   -  Config value 'theme' = Theme(name='material', dirs=['./docs/overrides',
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates',
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/mkdocs/templates'],
           static_templates={'sitemap.xml', '404.html'}, name='material', locale=Locale('en'),
           language='en', direction=None, features=['toc.follow', 'navigation.top', 'navigation.instant',
           'navigation.tracking', 'navigation.top', 'search.suggest', 'search.share', 'navigation.footer',
           'content.code.copy'], font={'text': 'Roboto', 'code': 'Roboto Mono'}, icon=None,
           favicon='images/Spyglass.svg', logo='images/FrankLab.png', palette=[{'media':
           '(prefers-color-scheme: light)', 'scheme': 'auto', 'toggle': {'icon': 'material/brightness-7',
           'name': 'Switch to dark mode'}}, {'media': '(prefers-color-scheme: slate)', 'scheme': 'slate',
           'toggle': {'icon': 'material/brightness-4', 'name': 'Switch to light mode'}}],
           disable_nav_previous_next=True, disable_nav_search=False, navigation_depth=2)
DEBUG   -  Config value 'docs_dir' = '/home/cb/wrk/spyglass/docs/src'
DEBUG   -  Config value 'site_dir' = '/home/cb/wrk/spyglass/docs/site'
DEBUG   -  Config value 'copyright' = 'Copyright (c) 2020-present Loren Frank'
DEBUG   -  Config value 'google_analytics' = None
DEBUG   -  Config value 'dev_addr' = _IpAddressValue(host='127.0.0.1', port=8000)
DEBUG   -  Config value 'use_directory_urls' = True
DEBUG   -  Config value 'repo_url' = 'https://github.com/LorenFrankLab/spyglass'
DEBUG   -  Config value 'repo_name' = 'GitHub'
DEBUG   -  Config value 'edit_uri_template' = None
DEBUG   -  Config value 'edit_uri' = 'blob/main/docs/src/'
DEBUG   -  Config value 'extra_css' = ['stylesheets/extra.css']
DEBUG   -  Config value 'extra_javascript' = []
DEBUG   -  Config value 'extra_templates' = []
DEBUG   -  Config value 'markdown_extensions' = ['toc', 'tables', 'fenced_code', 'attr_list',
           'pymdownx.highlight', 'pymdownx.inlinehilite', 'pymdownx.snippets', 'pymdownx.superfences']
DEBUG   -  Config value 'mdx_configs' = {'toc': {'permalink': True}, 'pymdownx.highlight':
           {'anchor_linenums': True, 'line_spans': '__span', 'pygments_lang_class': True}}
DEBUG   -  Config value 'strict' = False
DEBUG   -  Config value 'remote_branch' = 'gh-pages'
DEBUG   -  Config value 'remote_name' = 'origin'
DEBUG   -  Config value 'extra' = {'generator': False, 'version': {'provider': 'mike'}, 'social':
           [{'icon': 'fontawesome/brands/github', 'link': 'https://github.com/LorenFrankLab/spyglass'},
           {'icon': 'fontawesome/brands/python', 'link': 'https://pypi.org/project/spyglass-neuro/'}]}
DEBUG   -  Config value 'plugins' = {'material/search': <material.plugins.search.plugin.SearchPlugin
           object at 0x7a9abd9efe20>, 'exclude': <mkdocs_exclude.plugin.Exclude object at 0x7a9abda04ca0>,
           'mike': <mike.mkdocs_plugin.MikePlugin object at 0x7a9abda04ee0>, 'mkdocstrings':
           <mkdocstrings.plugin.MkdocstringsPlugin object at 0x7a9abd544d90>, 'literate-nav':
           <mkdocs_literate_nav.plugin.LiterateNavPlugin object at 0x7a9abd544e80>, 'exclude-search':
           <mkdocs_exclude_search.plugin.ExcludeSearch object at 0x7a9abd458a30>, 'gen-files':
           <mkdocs_gen_files.plugin.GenFilesPlugin object at 0x7a9abd458520>}
DEBUG   -  Config value 'hooks' = {}
DEBUG   -  Config value 'watch' = []
DEBUG   -  Config value 'validation' = {'nav': {'omitted_files': 20, 'not_found': 30, 'absolute_links':
           20}, 'links': {'not_found': 30, 'absolute_links': 20, 'unrecognized_links': 20, 'anchors': 20}}
DEBUG   -  Running `startup` event from plugin 'material/search'
DEBUG   -  Running `config` event from plugin 'material/search'
DEBUG   -  Looking for translations for locale 'en'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/mkdocs/templates/locales'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates/locales'
DEBUG   -  No translations found here: './docs/overrides/locales'
DEBUG   -  Looking for translations for locale 'en'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/mkdocs/templates/locales'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates/locales'
DEBUG   -  No translations found here: './docs/overrides/locales'
DEBUG   -  Looking for translations for locale 'en'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/mkdocs/templates/locales'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates/locales'
DEBUG   -  No translations found here: './docs/overrides/locales'
DEBUG   -  Running `config` event from plugin 'mike'
DEBUG   -  Running `config` event from plugin 'mkdocstrings'
DEBUG   -  mkdocstrings: Adding extension to the list
DEBUG   -  mkdocstrings: Added a subdued autorefs instance <mkdocs_autorefs.plugin.AutorefsPlugin object
           at 0x7a9abd3f9b20>
DEBUG   -  Running `config` event from plugin 'autorefs'
DEBUG   -  mkdocs_autorefs: Adding AutorefsExtension to the list
INFO    -  Cleaning site directory
INFO    -  Building documentation to directory: /home/cb/wrk/spyglass/docs/site
DEBUG   -  Looking for translations for locale 'en'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/mkdocs/templates/locales'
DEBUG   -  No translations found here:
           '/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/material/templates/locales'
DEBUG   -  No translations found here: './docs/overrides/locales'
DEBUG   -  Running `files` event from plugin 'exclude'
DEBUG   -  Running `files` event from plugin 'mike'
DEBUG   -  Running `files` event from plugin 'gen-files'
DEBUG   -  Running `files` event from plugin 'literate-nav'
DEBUG   -  Navigation for 'api' based on 'api/navigation.md'.
DEBUG   -  Running `nav` event from plugin 'literate-nav'
DEBUG   -  Reading markdown pages.
DEBUG   -  Reading: index.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: CHANGELOG.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: LICENSE.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: contribute.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: installation.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: api/index.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: api/navigation.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  Running `page_content` event from plugin 'gen-files'
DEBUG   -  Running `page_content` event from plugin 'autorefs'
DEBUG   -  Reading: api/settings.md
DEBUG   -  Running `page_markdown` event from plugin 'autorefs'
DEBUG   -  mkdocstrings: Matched '::: src.spyglass.settings'
DEBUG   -  mkdocstrings: Using handler 'python'
DEBUG   -  mkdocstrings: Collecting data
DEBUG   -  griffe: Found src: loading
DEBUG   -  griffe: Loading path
           [PosixPath('/home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/src')]
DEBUG   -  griffe: Loading path
           /home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/src/datatjoint_linter/__init__.py
DEBUG   -  griffe: Loading path
           /home/cb/miniconda3/envs/spy/lib/python3.9/site-packages/src/datatjoint_linter/linter.py
DEBUG   -  griffe: Iteration 1 finished, 0 aliases resolved, still 0 to go
ERROR   -  mkdocstrings: src.spyglass.settings could not be found
ERROR   -  Error reading page 'api/settings.md':
ERROR   -  Could not collect 'src.spyglass.settings'

Aborted with a BuildError!

I see in the release notes for 1.9.1, some mention of handling relative imports differently, but I don't use relative imports in the settings.py file where this is failing. Any suggestions for getting more verbose output from mkdocstrings?

StackOverflow seems to be out of date on this, with posts about much older versions. Not where to start to turn this into a MRE for a bug report. If it helps, this is the repo I'm working on

Answered by pawamoy

May 10, 2024

If you added ../src to the paths setting, now try removing src. from the autodoc instructions :::, i.e. ::: your.pkg instead of ::: src.your.pkg.

View full answer

pawamoy · 2024-05-10T16:42:43Z

pawamoy
May 10, 2024
Maintainer

Hello, yes since 1.9.1 mkdocstrings-python does not try to find packages using relative paths, as it caused issues for others and was never officially supported (we specify objects dotted-path, not file paths after :::).

See https://mkdocstrings.github.io/python/usage/#finding-modules to learn how to properly configure the Python handler for it to find your sources :)

0 replies

CBroz1 · 2024-05-10T18:11:37Z

CBroz1
May 10, 2024
Author

Thanks for the link! I've tried configuring my mkdocs.yml with the paths setting following example 4, but I'm still getting the same issue.

To clarify - this is about mkdocstrings finding the module. Relative paths within my module shouldn't impact the process, yeah?

Thanks again!

2 replies

pawamoy May 10, 2024
Maintainer

If you added ../src to the paths setting, now try removing src. from the autodoc instructions :::, i.e. ::: your.pkg instead of ::: src.your.pkg.

Answer selected by CBroz1

CBroz1 May 10, 2024
Author

That did it! Thanks!

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

`1.9.1` "Could not collect", relative path config #160

{{title}}

{{editor}}'s edit

{{editor}}'s edit

Replies: 2 comments 2 replies

{{title}}

{{title}}

{{title}}

{{title}}

Select a reply

1.9.1 "Could not collect", relative path config #160

CBroz1 May 10, 2024

Replies: 2 comments · 2 replies

pawamoy May 10, 2024 Maintainer

CBroz1 May 10, 2024 Author

pawamoy May 10, 2024 Maintainer

CBroz1 May 10, 2024 Author

`1.9.1` "Could not collect", relative path config #160

CBroz1
May 10, 2024

Replies: 2 comments 2 replies

pawamoy
May 10, 2024
Maintainer

CBroz1
May 10, 2024
Author

pawamoy May 10, 2024
Maintainer

CBroz1 May 10, 2024
Author