Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

ReadTheDocs build failure on LORIS API symlinks #6209

Closed
johnsaigle opened this issue Mar 31, 2020 · 2 comments · Fixed by #6667
Closed

ReadTheDocs build failure on LORIS API symlinks #6209

johnsaigle opened this issue Mar 31, 2020 · 2 comments · Fixed by #6667
Assignees
@laemtl
Labels
Category: Bug PR or issue that aims to report or fix a bug Category: Documentation PR or issue that aims to improve the documentation (test plans, wiki, comments...)

Comments

@johnsaigle
Copy link
Contributor

Describe the bug
ReadTheDocs is failing because it's unable to resolve the following symlinks:

docs/wiki/99\ -\ Developers/LORIS-REST-API-0.0.2.md
docs/wiki/99\ -\ Developers/LORIS-REST-API-0.0.3-dev.md

These were added in #6151

What did you expect to happen?
ReadTheDocs and mkdocs should resolve the symlinks and render the documentation.

We may need to modify these to include relative path characters as RTD is served from docs/ rather than the LORIS root.

Additional context
ReadTheDocs build error:

INFO    -  Cleaning site directory 
INFO    -  Building documentation to directory: /home/docs/checkouts/readthedocs.org/user_builds/acesloris/checkouts/latest/_build/html 
INFO    -  The following pages exist in the docs directory, but are not included in the "nav" configuration:
  - React.README.md
  - SQLModelingStandard.md
  - deprecated_wiki/About-superuser.md
  - deprecated_wiki/CentOS-Imaging-installation-transcript.md
  - deprecated_wiki/Code-Customization.md
  - deprecated_wiki/Developer's-Instrument-Guide.md
  - deprecated_wiki/Getting-the-Release.md
  - deprecated_wiki/Guide-to-Loris-React-components.md
  - deprecated_wiki/How-to-Code-an-Instrument.md
  - deprecated_wiki/How-to-make-a-LORIS-module.md
  - deprecated_wiki/Installing-Loris-in-Brief.md
  - deprecated_wiki/Instrument-Groups.md
  - deprecated_wiki/Instrument-Insertion.md
  - deprecated_wiki/Instrument-Scoring.md
  - deprecated_wiki/Instrument-Scripts.md
  - deprecated_wiki/Instrument-Testing-and-Troubleshooting.md
  - deprecated_wiki/LORIS-Dictionary.md
  - deprecated_wiki/LORIS-Form.md
  - deprecated_wiki/LORIS-Module-Testing.md
  - deprecated_wiki/LORIS-Modules.md
  - deprecated_wiki/LORIS-scripts-in-the-tools--directory.md
  - deprecated_wiki/Notification-system.md
  - deprecated_wiki/Open-LORIS.md
  - deprecated_wiki/Other-Imaging-Scripts.md
  - deprecated_wiki/Reloading-MRI-data-for-mislabelled-session.md
  - deprecated_wiki/Updating-your-LORIS.md
  - deprecated_wiki/Upgrading-Loris.md
  - deprecated_wiki/Using-Google-reCAPTCHA.md
  - deprecated_wiki/Working-with-React.md
  - deprecated_wiki/XIN-Rules.md
  - deprecated_wiki/About/About.md
  - deprecated_wiki/Setup/Setup.md
  - deprecated_wiki/Setup/Initial Setup/Backups/Backups.md
  - deprecated_wiki/Setup/Initial Setup/Behavioural Database/Behavioural-Database.md
  - deprecated_wiki/Setup/Initial Setup/Data Querying Tool/Data-Querying-Tool.md
  - deprecated_wiki/Setup/Initial Setup/Enable Mail Server/Enable-mail-server.md
  - deprecated_wiki/Setup/Initial Setup/Imaging Database/Imaging-Database.md
  - deprecated_wiki/Setup/Initial Setup/Install Script/Install-Script.md
  - deprecated_wiki/Setup/Initial Setup/LORIS Modules/Candidate Information Page/Candidate-Information-Page.md
  - deprecated_wiki/Setup/Initial Setup/LORIS Modules/Candidate Parameters/Candidate-Parameters.md
  - deprecated_wiki/Technical/Code-Review-Checklist.md
  - deprecated_wiki/Technical/Developer-Workshop-2015-02-13.md
  - deprecated_wiki/Technical/Developer-Workshops.md
  - deprecated_wiki/Technical/Technical.md
  - wiki/00 - SERVER INSTALL AND CONFIGURATION/README.md
  - wiki/00 - SERVER INSTALL AND CONFIGURATION/01 - LORIS Install/README.md
  - wiki/00 - SERVER INSTALL AND CONFIGURATION/01 - LORIS Install/Macintosh/README.md
  - wiki/01 - STUDY PARAMETERS SETUP/README.md
  - wiki/01 - STUDY PARAMETERS SETUP/01 - Study Variables/README.md
  - wiki/01 - STUDY PARAMETERS SETUP/01 - Study Variables/01 - Identifiers.md
  - wiki/_ARCHIVE/README.md
  - wiki/_DELETED/README.md
  - wiki/_DELETED/API.md
  - wiki/_DELETED/Install-Script-for-16.X.md
  - wiki/_DELETED/Installing-Loris-(After-Installing-Prerequisites).md
  - wiki/_DELETED/LORIS database schema.md
  - wiki/_DELETED/LORIS-Setup-Schematic.md
  - wiki/_DELETED/Request-Accounts-module.md
  - wiki/_DELETED/_Footer.md
  - wiki/_DELETED/_Sidebar.md
  - wiki/_DELETED/Community/Community.md
  - wiki/_DELETED/Community/Development.md
  - wiki/_DELETED/Community/Documentation.md
  - wiki/_DELETED/Community/Get-in-Touch.md
  - wiki/_DELETED/Resources/Instrument Coding Guide/Instrument-Coding-Guide.md
  - wiki/_DELETED/Resources/Ubuntu Upgrading/Upgrading-from-Ubuntu-12.04-to-14.04.md 
WARNING -  Documentation file 'CodingStandards.md' contains a link to 'wiki/99%20-%20Developers/Automated%20Testing.md' which is not found in the documentation files. 
WARNING -  Documentation file 'deprecated_wiki/Setup/Initial Setup/Install Script/Install-Script.md' contains a link to 'deprecated_wiki/Setup/Initial Setup/Install Script/Install-Script-for-16.X' which is not found in the documentation files. 
WARNING -  Documentation file 'wiki/00 - SERVER INSTALL AND CONFIGURATION/01 - LORIS Install/CentOS/README.md' contains a link to '../README.md' which is not found in the documentation files. 
WARNING -  Documentation file 'wiki/00 - SERVER INSTALL AND CONFIGURATION/01 - LORIS Install/CentOS/README.md' contains a link to '../README.md' which is not found in the documentation files. 
WARNING -  Documentation file 'wiki/01 - STUDY PARAMETERS SETUP/01 - Study Variables/03 - Sites.md' contains a link to 'wiki/01 - STUDY PARAMETERS SETUP/01 - Study Variables/SQL Dictionary.md' which is not found in the documentation files. 
WARNING -  Documentation file 'wiki/99 - Developers/Automated Testing.md' contains a link to '../test/UnitTestGuide.md' which is not found in the documentation files. 
ERROR   -  File not found: wiki/99 - Developers/LORIS-REST-API-0.0.2.md 
ERROR   -  Error reading page 'wiki/99 - Developers/LORIS-REST-API-0.0.2.md': [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/acesloris/checkouts/latest/docs/wiki/99 - Developers/LORIS-REST-API-0.0.2.md' 
Traceback (most recent call last):
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/runpy.py", line 193, in _run_module_as_main
    "__main__", mod_spec)
  File "/home/docs/.pyenv/versions/3.7.3/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/mkdocs/__main__.py", line 202, in <module>
    cli()
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/click/core.py", line 829, in __call__
    return self.main(*args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/click/core.py", line 782, in main
    rv = self.invoke(ctx)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/click/core.py", line 1259, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/click/core.py", line 1066, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/click/core.py", line 610, in invoke
    return callback(*args, **kwargs)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/mkdocs/__main__.py", line 163, in build_command
    ), dirty=not clean)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/mkdocs/commands/build.py", line 274, in build
    _populate_page(file.page, config, files, dirty)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/mkdocs/commands/build.py", line 170, in _populate_page
    page.read_source(config)
  File "/home/docs/checkouts/readthedocs.org/user_builds/acesloris/envs/latest/lib/python3.7/site-packages/mkdocs/structure/pages.py", line 129, in read_source
    with io.open(self.file.abs_src_path, 'r', encoding='utf-8-sig', errors='strict') as f:
FileNotFoundError: [Errno 2] No such file or directory: '/home/docs/checkouts/readthedocs.org/user_builds/acesloris/checkouts/latest/docs/wiki/99 - Developers/LORIS-REST-API-0.0.2.md'
@johnsaigle johnsaigle added Category: Bug PR or issue that aims to report or fix a bug Category: Documentation PR or issue that aims to improve the documentation (test plans, wiki, comments...) labels Mar 31, 2020
This was referenced Apr 6, 2020
Closed
Closed
This was referenced Apr 6, 2020
Closed
Closed
@christinerogers
Copy link
Contributor

cc @AlexandraLivadas @laemtl for examples of symlinks in the docs

@johnsaigle
Copy link
Contributor Author

examples of symlinks in the docs

specifically that they don't work!

This was referenced May 19, 2020
Closed
Closed
@laemtl laemtl self-assigned this May 26, 2020
@laemtl laemtl mentioned this issue Jun 3, 2020
Merged
driusan pushed a commit that referenced this issue Aug 6, 2020
@laemtl
[ReadTheDocs] Structure and template fixes (#6667)
05f4d16 
Fixes merge conflicts in the wiki (99 - Developers should not exists).
Fixes several errors including some which prevents the Loris ReadTheDocs to compile
(last compiled version is 4 months old now).

Demo: https://loris-dev.readthedocs.io/en/latest

Docs is now part of the breadcrumb. I can probably find a way to remove it if that's undesirable.
Symlinks are problematic (and as pointed here, not really useful) as we need (for now) to use relative links across all the documentation to avoid broken links.

    Resolves #6209
    Resolves #6329
    Resolves #6545
    Resolves #6622
    Resolves #6623
    Resolves #6737
    Resolves #6736
spell00 pushed a commit to spell00/Loris that referenced this issue Aug 13, 2020
@laemtl @spell00
[ReadTheDocs] Structure and template fixes (aces#6667)
05f68ac 
Fixes merge conflicts in the wiki (99 - Developers should not exists).
Fixes several errors including some which prevents the Loris ReadTheDocs to compile
(last compiled version is 4 months old now).

Demo: https://loris-dev.readthedocs.io/en/latest

Docs is now part of the breadcrumb. I can probably find a way to remove it if that's undesirable.
Symlinks are problematic (and as pointed here, not really useful) as we need (for now) to use relative links across all the documentation to avoid broken links.

    Resolves aces#6209
    Resolves aces#6329
    Resolves aces#6545
    Resolves aces#6622
    Resolves aces#6623
    Resolves aces#6737
    Resolves aces#6736
AlexandraLivadas pushed a commit to AlexandraLivadas/Loris that referenced this issue Jun 15, 2021
@laemtl @AlexandraLivadas
[ReadTheDocs] Structure and template fixes (aces#6667)
7fc1bd0 
Fixes merge conflicts in the wiki (99 - Developers should not exists).
Fixes several errors including some which prevents the Loris ReadTheDocs to compile
(last compiled version is 4 months old now).

Demo: https://loris-dev.readthedocs.io/en/latest

Docs is now part of the breadcrumb. I can probably find a way to remove it if that's undesirable.
Symlinks are problematic (and as pointed here, not really useful) as we need (for now) to use relative links across all the documentation to avoid broken links.

    Resolves aces#6209
    Resolves aces#6329
    Resolves aces#6545
    Resolves aces#6622
    Resolves aces#6623
    Resolves aces#6737
    Resolves aces#6736
AlexandraLivadas pushed a commit to AlexandraLivadas/Loris that referenced this issue Jun 29, 2021
@laemtl @AlexandraLivadas
[ReadTheDocs] Structure and template fixes (aces#6667)
9a16067 
Fixes merge conflicts in the wiki (99 - Developers should not exists).
Fixes several errors including some which prevents the Loris ReadTheDocs to compile
(last compiled version is 4 months old now).

Demo: https://loris-dev.readthedocs.io/en/latest

Docs is now part of the breadcrumb. I can probably find a way to remove it if that's undesirable.
Symlinks are problematic (and as pointed here, not really useful) as we need (for now) to use relative links across all the documentation to avoid broken links.

    Resolves aces#6209
    Resolves aces#6329
    Resolves aces#6545
    Resolves aces#6622
    Resolves aces#6623
    Resolves aces#6737
    Resolves aces#6736
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Assignees

@laemtl laemtl

Labels
Category: Bug PR or issue that aims to report or fix a bug Category: Documentation PR or issue that aims to improve the documentation (test plans, wiki, comments...)
Projects
None yet
Milestone
No milestone
3 participants
@christinerogers @johnsaigle @laemtl