Add ptu support and modernize build process#212
Closed
tsbischof wants to merge 12 commits intoFCS-analysis:mainfrom
Closed
Add ptu support and modernize build process#212tsbischof wants to merge 12 commits intoFCS-analysis:mainfrom
tsbischof wants to merge 12 commits intoFCS-analysis:mainfrom
Conversation
A user requested the ability to load ptu (t2) files from a PicoQuant PicoHarp. The test suite covers HydraHarp (t2, t3) and PicoHarp (t2) but the code should be as general as the underlying ptufile package. In the process of setting this up I debugged a bit and made a few changes: * bump minimum Python version to 3.11 to support ptufile * migrated from setup.py to pyproject.toml (tested on Linux) * set up tox.ini for running the test suite * set up ruff, ty, and codespell placeholders for gradual linting (remove the exclusions as desired) * fix some stray numpy bugs (np.float_ deprecation) * remove distutils due to deprecation in Python 3.12 * do version generation through setuptools_scm * ensure the test suite fully passes for all versions supported
Collaborator
Author
|
Closes #84 |
There was only one function that required cython. I have replaced it with a pure numpy implementation that seems to perform equivalently and gets the same results for both random and test data. In tests/test_file_format.py:test_pt3_basic the behavior is the same as before (expected 2037 is actually 2037.5) but I have no insight as to why that happened in the first place. The correlation data (last two lines of that test) pass on my machine though. So all I can say is that no observable behavior has changed for loading pt3 or running dividAndConquer, not that the trace value is actually correct.
Collaborator
Author
|
Closes #204 |
Collaborator
Author
|
Closes #208 |
Collaborator
Author
|
I will close this and clean things up before sending for proper review, sorry for the noise |
This file contains hidden or 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
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
1 participant
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.
A user requested the ability to load ptu (t2) files from a PicoQuant PicoHarp. I added this support and the test suite covers HydraHarp (t2, t3) and PicoHarp (t2) but the code should be as general as the underlying ptufile package.
In the process of setting this up I debugged a bit and made a few changes:
So far I have only tested this on Linux since that is what I have available.
Regarding the shift from setup.py to pyproject.toml this mostly just arose when setting up tox for my own purposes. If you prefer to stick with the older version let me know and I can send a branch with that reverted.