Refactor documentation | PSM reader tutorial #306
+1,367
−942
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
mschwoer
approved these changes
Mar 19, 2025
|
|
||
|
|
||
| def test_read_psm(psm_example): | ||
| search_engine, data, expected_shape = psm_example |
There was a problem hiding this comment.
could add a one-line docstring descibing the intent of the test and a # when before df = psm_reader.import_file(copy(data)) to be able to quickly spot where the code under test is called
There was a problem hiding this comment.
Thanks! First time I learned about the given, when, then structure in unittests!
docs/nbs/psm_readers.ipynb
Outdated
There was a problem hiding this comment.
Thanks! Fixed the table formatting + changed the representation of the currently available readers.
added 5 commits
March 19, 2025 20:23
…m in pretty format
…actor-docs_psm-reader_I
Merged
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Refactor PSM reader tutorial. This PR restructures the PSM reader tutorial in background (Basic/Advanced), Code, Advanced examples. Comparison old/new attached
Tutorial
Theory
alphabaseworkflowCode
Tests
/tests/unit/psm_reader/test_psm_reader_provider.py)Edit: Just saw PR #305, but this PR seems to be complementary
Missing
Short example on implementing a custom reader. This is currently not easily possible as at the moment the
modification_mappinghas to be hard coded inalphabase.psm_reader.psm_reader_yaml(see new ticket)tutorial_new.pdf
tutorial_old.pdf