fix: parse and clean archive badges and markdown links to URL #243

banesullivan · 2024-12-15T06:02:44Z

This will parse markdown links/badges to consistently capture a URLs from the archive and JOSS DOI fields.

Note that this adds https://github.com/papis/python-doi as a dependency

The solution I landed on here is to always coerce the link to a single URL since this is what the review templates expect here:

https://github.com/pyOpenSci/pyopensci.github.io/blob/d0b561cc493f6e4691f171b4460b0f7d4793267a/_includes/package-grid.html#L42

Since this now validates the DOI links, I needed to use a real/valid DOI for the test data so I used PyVista's DOI for these 😄

I also noticed that some review issues had the JOSS archive key as JOSS DOI and others have it as JOSS. The changes here account for that and ensure data are normalized to JOSS

To see the specific tasks where the Asana app for GitHub is being used, see below:
- https://app.asana.com/0/0/1209011748769325

codecov · 2024-12-15T06:04:24Z

Codecov Report

Attention: Patch coverage is 82.50000% with 7 lines in your changes missing coverage. Please review.

Project coverage is 75.25%. Comparing base (b6179f3) to head (2b9db98).

Files with missing lines	Patch %	Lines
src/pyosmeta/utils_clean.py	78.57%	3 Missing and 3 partials ⚠️
src/pyosmeta/models/base.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #243      +/-   ##
==========================================
+ Coverage   74.06%   75.25%   +1.18%     
==========================================
  Files          10       10              
  Lines         671      699      +28     
  Branches       82       89       +7     
==========================================
+ Hits          497      526      +29     
+ Misses        166      162       -4     
- Partials        8       11       +3

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

lwasser · 2024-12-19T19:12:15Z

hey @banesullivan i'll leave some more specific feedback here but it looks like

this is erroring on a review (bibat) which means there is an outlier format in archive that isn't being handled as we would like it to be handled.

update-reviews
/Users/leahawasser/Documents/GitHub/pyos/pyosMeta/src/pyosmeta/parse_issues.py:489: UserWarning: ## Community Partnerships not found in the list
  warnings.warn(f"{section_str} not found in the list")
Error in review at url: https://api.github.com/repos/pyOpenSci/software-submission/issues/83
Traceback (most recent call last):

  File "/Users/leahawasser/Documents/GitHub/pyos/pyosMeta/src/pyosmeta/parse_issues.py", line 310, in parse_issues
    review = self.parse_issue(issue)

  File "/Users/leahawasser/Documents/GitHub/pyos/pyosMeta/src/pyosmeta/parse_issues.py", line 284, in parse_issue
    return ReviewModel(**model)

  File "/Users/leahawasser/mambaforge/envs/pyosmeta/lib/python3.10/site-packages/pydantic/main.py", line 214, in __init__
    validated_self = self.__pydantic_validator__.validate_python(data, self_instance=self)

pydantic_core._pydantic_core.ValidationError: 1 validation error for ReviewModel
joss
  Value error, Invalid archive URL:  [type=value_error, input_value='', input_type=str]
    For further information visit https://errors.pydantic.dev/2.10/v/value_error

--------------------
http://www.sunpy.org 'http://' replacing w 'https://'
http://sourmash.readthedocs.io/en/latest/ 'http://' replacing w 'https://'
http://movingpandas.org 'http://' replacing w 'https://'

When running it locally is that it hangs. I suspect it's slower because adding python-doi means we are parsing and checking urls / DOIs for each package. For now, we might consider adding more output so a user knows it's doing something. Maybe the package name it's processing in the terminal would be good to print out? I almost thought it was broken, and then I saw it was just processing but slower than it was previously.

lwasser · 2024-12-19T19:30:55Z

I'm also noticing some inconsistency in JOSS:

for joss / sleplet, there is a link to the paper.
issue_link: pyOpenSci/software-submission#149
joss: https://joss.theoj.org/papers/10.21105/joss.05221

For nbcompare, there is a link to the DOI, which resolves to the paper!
issue_link: pyOpenSci/software-submission#146
joss: https://doi.org/10.21105/joss.06490

Both will work! My question is, should we be consistent in how we save the doi and always link to the doi rather than the paper in terms of the data we store in our "database," aka YML file?

the archive value is inconsistent, too, but I think it's OK as is. Especially because sometimes it's a GitHub link and others it's Zenodo, and sometimes the Zenodo link is to the "latest" rather than the actual archive VERSION that we approved. So let's not worry about archive and focus on JOSS DOI as it hopefully isn't a huge amount of work. if it is, we are ok as is and we can open an issue about a future iteration that cleans it up just a bit more.

So, the takeaways here are:

the one issue that is erroring - let's fix that (comment above)
let's fill in tests and use pytest.raises match= for those try/except blocks
let's make the JOSS doi consistent!
let's make sure there is some information in the terminal when it's processing reviews so a user running it knows it's not stalled. A simple fix would be to write out the package name being processed. And to write out when it's failing on a doi URL (potentially?). I'll leave that up to you.

Thank you so much. This looks really great!! 🚀 If you'd like, we could merge this as is today, and you could work on the comments above in another pr. that would allow us to update the website tomorrow.

if you'd like to complete all of the work in this pr, say the word, and we can hold off until January to get things merged.

lwasser

oops. it looks like i left blocks of feedbak but not the line by line comments. i'm just making sure those are visible now.

lwasser · 2024-12-18T21:27:45Z

src/pyosmeta/utils_clean.py

@@ -7,6 +7,8 @@
 from datetime import datetime
 from typing import Any

+import doi


Since we've added a new dep, we should make sure that it is noted in the changelog and also document why we added it.

lwasser · 2024-12-19T19:13:15Z

CHANGELOG.md

@@ -4,6 +4,8 @@

 ## [Unreleased]

+* Fix: Parse archive and JOSS links to handle markdown links and validate DOI links are valid (@banesullivan)
+
 [v1.4] - 2024-11-22


Suggested change

[v1.4] - 2024-11-22

## [v1.4] - 2024-11-22

let's fix my mistake in the changelog :)

lwasser · 2024-12-19T19:14:02Z

CHANGELOG.md

@@ -4,6 +4,8 @@

 ## [Unreleased]

+* Fix: Parse archive and JOSS links to handle markdown links and validate DOI links are valid (@banesullivan)


Suggested change

* Fix: Parse archive and JOSS links to handle markdown links and validate DOI links are valid (@banesullivan)

* Fix: Parse archive and JOSS links to handle markdown links and validate DOI links are valid. Added python-doi as a dependency (@banesullivan)

i don't know how you handle a add and fix in one line but i think it's good to note that change here.

lwasser · 2024-12-19T19:17:25Z

src/pyosmeta/utils_clean.py

+    This utility will attempt to parse the DOI link from the various formats
+    that are commonly present in review metadata. This utility will handle:
+
+    * Markdown links in the format `[label](URL)`, e.g., `[my archive](https://doi.org/10.1234/zenodo.12345678)`


it looks like the issue that failed when i ran it locally using a zenodo badge

pyOpenSci/software-submission#83

honestly, I may have updated and added that (it is possible). But it would be good to parse a markdown badge url too.

let me know if you don't see that error but i saw it running locally.

lwasser · 2024-12-19T19:18:32Z

src/pyosmeta/utils_clean.py

+            archive = archive.replace("http://", "https://")
+        # Validate that the URL resolves
+        if not check_url(archive):
+            raise ValueError(f"Invalid archive URL: {archive}")


I think we want to use pytest.raises ValueError // match= to hit these missing lines in our coverage.

lwasser · 2025-01-07T21:13:07Z

hey @banesullivan i'm checking in on this pr. we are running into the issue that every pr on the website fails CI because of the dois! i think we have two options.

we can merge this almost as is and push a new release if it fixes things, then the website will atleast be green.
you can work on the tests and other smaller items in a separate pr.

The above approach is great if you are busy during this first full week back!!
Alternatively, we can leave this open for a bit longer and fix things here.

Please let me know what you prefer!

feat: parse and clean archive badges and markdown links to URL

3187744

banesullivan changed the title ~~feat: parse and clean archive badges and markdown links to URL~~ fix: parse and clean archive badges and markdown links to URL Dec 19, 2024

banesullivan added 8 commits December 18, 2024 23:51

Improve docs, reuse URL checker, improve test data

aa53640

coverage

dc3d627

Test with JOSS DOI

09c276b

cleanup

053f12d

Add changelog

7dce691

attribution in changelog

9e051cc

Better testing and normalize the JOSS field

cea651c

Correct changelog

2b9db98

lwasser requested changes Jan 7, 2025

View reviewed changes

lwasser mentioned this pull request Jan 8, 2025

fix: force create joss cross ref badge pyOpenSci/pyopensci.github.io#524

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fix: parse and clean archive badges and markdown links to URL #243

fix: parse and clean archive badges and markdown links to URL #243

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lwasser commented Jan 7, 2025

		@@ -4,6 +4,8 @@

		## [Unreleased]

		* Fix: Parse archive and JOSS links to handle markdown links and validate DOI links are valid (@banesullivan)

fix: parse and clean archive badges and markdown links to URL #243

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fix: parse and clean archive badges and markdown links to URL #243

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