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.

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

Link fixin #252

Merged
merged 8 commits into from
Feb 25, 2024
Merged

Link fixin #252

merged 8 commits into from
Feb 25, 2024

Conversation

poshul
Copy link
Collaborator

@poshul poshul commented Jan 14, 2022

Fixed a bunch of stale links, added files for future nase tutorial

@poshul poshul requested a review from jpfeuffer January 14, 2022 11:19
@poshul
Copy link
Collaborator Author

poshul commented Jan 14, 2022

Should I be worried about the failing build_test?

@jpfeuffer
Copy link
Contributor

It seems we did not have a working pyopenms build in 30? days, so there is not artifact anymore.

@sonarcloud
Copy link

sonarcloud bot commented Jan 20, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@timosachsenberg
Copy link
Contributor

there are autofixes available: https://github.com/OpenMS/pyopenms-extra/pull/252/checks?check_run_id=4879571790
does anyone know how trustworthy those are?

@sonarcloud
Copy link

sonarcloud bot commented Apr 29, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@timosachsenberg
Copy link
Contributor

If the links work like this I think we can move forward here

@poshul
Copy link
Collaborator Author

poshul commented Apr 29, 2022

Lint fails with ImportError: cannot import name 'soft_unicode' from 'markupsafe' (/usr/local/lib/python3.7/site-packages/markupsafe/__init__.py)

@jpfeuffer
Copy link
Contributor

This is an error in the action. See their GitHub repo. Should be a comment from me as well. There is a workaround using a fork from someone. But maybe the action was updated by now. Please check.

@jpfeuffer
Copy link
Contributor

jpfeuffer commented Apr 29, 2022

@timosachsenberg when fixing the API docs I saw quite some warnings like XYZ.rst never referenced anywhere. Including hyper score. Can you check this? Just build yourself locally and you will see.

Indeed I cannot find hyperscore except in the search.

@jpfeuffer
Copy link
Contributor

Unfortunately we have a lot of warning now from the API docs. We should check if we can filter them somehow.
Or do CI without building the API docs, which also takes a few minutes.

@timosachsenberg
Copy link
Contributor

Why are these not referenced? What is missing?

See the next section for a SimpleExample_ and a more AdvancedExample_ of a wrapped class with several functions.

See the next section for a `simple example <#Simple-Example>`_ and a more AdvancedExample_ of a wrapped class with several functions.
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

can we have the same style for both links?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

yup. fixed

@timosachsenberg
Copy link
Contributor

can you revive this so we can move it over the finish line?

docs/source/hyperscore.rst Outdated Show resolved Hide resolved
docs/source/hyperscore.rst Outdated Show resolved Hide resolved
docs/source/hyperscore.rst Outdated Show resolved Hide resolved
hscore = HyperScore()
fragment_mass_tolerance = 5.0
is_tol_in_ppm = True
result = hscore.compute(fragment_mass_tolerance, is_tol_in_ppm, spectrum_of_interest, thspec)
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

[blacken-docs] reported by reviewdog 🐶

Suggested change
result = hscore.compute(fragment_mass_tolerance, is_tol_in_ppm, spectrum_of_interest, thspec)
result = hscore.compute(
fragment_mass_tolerance, is_tol_in_ppm, spectrum_of_interest, thspec
)

docs/source/hyperscore.rst Outdated Show resolved Hide resolved
Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@poshul poshul merged commit ffe3ddb into master Feb 25, 2024
4 of 5 checks passed
@timosachsenberg
Copy link
Contributor

cool! thanks

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

3 participants