chore(all): PEP 639 compliance #2089

DimitriPapadopoulos · 2025-10-27T14:04:27Z

In all packages metadata, change licence (deprecated in PEP 639) to licence-files.

thomass-dev · 2025-10-27T14:36:10Z

The main reason we did it this way using hatch trigger, was because the build badly integrates the shared files in the build artifacts (in this case, the shared ../LICENSE and the shared ../README.md).

We need to check if your change properly integrates the said files into the build artifacts.

thomass-dev · 2025-10-27T14:46:56Z

As far as i can understand, dynamic license (files) and readme are not needed, because the respective files are not generated during the build process.

The properties licence and readme are currently dynamic because they are generated by the hatch hooks (which is the prelude of the build process) by reading the dedicated files from the root of the repository.

thomass-dev · 2025-10-27T15:22:38Z

With your PR, hatch==1.15.1 and hatchling==1.27.0, i can confirm my suspicions:

$ python -m build --sdist && tar -tvf dist/skore*.tar.gz | less +G

[...]
-rw-r--r-- 0/0            1069 2020-02-02 01:00 skore-0.0.0+unknown/../LICENSE
-rw-r--r-- 0/0            5746 2020-02-02 01:00 skore-0.0.0+unknown/../README.md

$ python -m build --wheel && unzip -l dist/skore*.whl | less +G

[...]
1069  2020-02-02 00:00   skore-0.0.0+unknown.dist-info/licenses/../LICENSE

which will lead to errors when installing the sdist:

ERROR: Invalid member in the tar file [...]/skore/skore/dist/skore-0.0.0+unknown.tar.gz: '../LICENSE' would be extracted to '/tmp/LICENSE', which is outside the destination

Also for the wheel, i don't think the METADATA are valid either: License-File: ../LICENSE.

DimitriPapadopoulos · 2025-10-27T17:45:29Z

The properties licence and readme are currently dynamic because they are generated by the hatch hooks (which is the prelude of the build process) by reading the dedicated files from the root of the repository.

Why do you need to generate these properties in the the hatch hooks?

DimitriPapadopoulos · 2025-10-27T17:51:52Z

I guess this could be a bug of the hatch implementation of PEP 639. Whatever the values of readme and license-files, the files should never end up outside of the sdist root directory or outside the wheel licenses directory.

I'll compare with setuptools and flint, and create a hatch issue if they behave differently. I'll check PEP 639 as well, although I doubt it gets into such details.

DimitriPapadopoulos · 2025-10-27T20:00:56Z

From Add license-files key in PEP 639:

Parent directory indicators (..) MUST NOT be used.

So I guess there is no way to point to files outside the directory containing pyproject.toml, hence the need for a hatch hook. OK, I'll keep the existing hooks and simply change license → license-files. How does this sound?

Update licensing metadata as described in PEP 639.

skore-hub-project/hatch/metadata.py

skore/pyproject.toml

thomass-dev

Please use cp instead of read/open/write to feed licence-files.

skore-hub-project/hatch/metadata.py

thomass-dev · 2025-10-28T13:49:44Z

Please use cp instead of read/open/write to feed licence-files.

Please commit this change without force-pushing. This will make the diff easier to review.

skore-hub-project/hatch/metadata.py

skore-local-project/hatch/metadata.py

Co-authored-by: Thomas S. <[email protected]>

DimitriPapadopoulos · 2025-10-28T14:15:41Z

Finally, should the classifiers from skore/pyproject.toml be copied to other pyproject.toml files?

skore/skore/pyproject.toml

Lines 11 to 28 in 2eefa98

    
           classifiers = [ 
        
             "Intended Audience :: Science/Research", 
        
             "Intended Audience :: Developers", 
        
             "License :: OSI Approved :: MIT License", 
        
             "Programming Language :: Python", 
        
             "Topic :: Software Development", 
        
             "Topic :: Scientific/Engineering", 
        
             "Development Status :: 3 - Alpha", 
        
             "Operating System :: Microsoft :: Windows", 
        
             "Operating System :: POSIX", 
        
             "Operating System :: Unix", 
        
             "Operating System :: MacOS", 
        
             "Programming Language :: Python :: 3", 
        
             "Programming Language :: Python :: 3.10", 
        
             "Programming Language :: Python :: 3.11", 
        
             "Programming Language :: Python :: 3.12", 
        
             "Programming Language :: Python :: 3.13", 
        
           ]

More generally, how about striving to make the pyproject.toml files identical, for example tool.ruff.lint.select?

thomass-dev · 2025-10-28T14:17:17Z

This is not necessary, because the only visible/searchable package we want is skore/.

skore-local-project/hatch/metadata.py

github-actions · 2025-10-28T14:23:29Z

Coverage Report for skore/

File	Stmts	Miss	Cover	Missing
skore/src/skore
__init__.py	23	0	100%
_config.py	31	0	100%
exceptions.py	4	4	0%	4, 15, 19, 23
skore/src/skore/_sklearn
__init__.py	6	0	100%
_base.py	198	14	92%	45, 58, 127, 130, 183, 186–187, 189–192, 225, 228–229
find_ml_task.py	61	0	100%
types.py	27	1	96%	28
skore/src/skore/_sklearn/_comparison
__init__.py	7	0	100%
feature_importance_accessor.py	39	2	94%	90, 109
metrics_accessor.py	178	3	98%	173, 253, 1215
report.py	107	0	100%
utils.py	54	0	100%
skore/src/skore/_sklearn/_cross_validation
__init__.py	9	0	100%
data_accessor.py	45	3	93%	134, 137, 140
feature_importance_accessor.py	24	0	100%
metrics_accessor.py	182	1	99%	244
report.py	135	1	99%	487
skore/src/skore/_sklearn/_estimator
__init__.py	9	0	100%
data_accessor.py	66	1	98%	82
feature_importance_accessor.py	141	2	98%	223–224
metrics_accessor.py	356	8	97%	200, 202, 209, 300, 369, 373, 388, 423
report.py	167	2	98%	448–449
skore/src/skore/_sklearn/_plot
__init__.py	3	0	100%
base.py	102	7	93%	61–62, 200, 224–226, 230
utils.py	77	0	100%
skore/src/skore/_sklearn/_plot/data
__init__.py	2	0	100%
table_report.py	185	1	99%	706
skore/src/skore/_sklearn/_plot/metrics
__init__.py	6	0	100%
confusion_matrix.py	70	4	94%	92, 100, 122, 230
feature_importance_display.py	67	21	68%	88, 121–122, 124, 142–146, 148–155, 158–160, 162
metrics_summary_display.py	8	0	100%
precision_recall_curve.py	281	5	98%	455, 555, 559, 619, 751
prediction_error.py	227	5	97%	179, 186, 422, 505, 705
roc_curve.py	294	8	97%	387, 510, 515, 616, 621, 625, 694, 834
skore/src/skore/_sklearn/train_test_split
__init__.py	0	0	100%
train_test_split.py	58	0	100%
skore/src/skore/_sklearn/train_test_split/warning
__init__.py	8	0	100%
high_class_imbalance_too_few_examples_warning.py	19	1	94%	83
high_class_imbalance_warning.py	20	0	100%
random_state_unset_warning.py	10	0	100%
shuffle_true_warning.py	9	0	100%
stratify_is_set_warning.py	10	0	100%
time_based_column_warning.py	21	0	100%
train_test_split_warning.py	3	0	100%
skore/src/skore/_utils
__init__.py	6	2	66%	8, 13
_accessor.py	90	3	96%	34, 146, 190
_environment.py	27	0	100%
_fixes.py	8	0	100%
_index.py	5	0	100%
_logger.py	22	4	81%	15–17, 19
_measure_time.py	10	0	100%
_parallel.py	38	3	92%	23, 33, 124
_patch.py	13	5	61%	21, 23–24, 35, 37
_progress_bar.py	46	0	100%
_repr_html.py	8	0	100%
_show_versions.py	38	0	100%
_testing.py	55	0	100%
skore/src/skore/project
__init__.py	2	0	100%
project.py	48	0	100%
summary.py	75	1	98%	120
widget.py	189	0	100%
TOTAL	4029	112	97%

Tests	Skipped	Failures	Errors	Time
1079	5 💤	0 ❌	0 🔥	4m 18s ⏱️

github-actions · 2025-10-28T14:23:30Z

Coverage Report for skore-hub-project/

File	Stmts	Miss	Cover	Missing
skore-hub-project/src/skore_hub_project
__init__.py	22	1	95%	39
protocol.py	31	0	100%
skore-hub-project/src/skore_hub_project/artifact
__init__.py	0	0	100%
artifact.py	23	0	100%
serializer.py	26	0	100%
upload.py	36	4	88%	175, 177–178, 180
skore-hub-project/src/skore_hub_project/artifact/media
__init__.py	5	0	100%
data.py	22	0	100%
feature_importance.py	44	1	97%	50
media.py	10	0	100%
model.py	9	0	100%
performance.py	44	0	100%
skore-hub-project/src/skore_hub_project/artifact/pickle
__init__.py	2	0	100%
pickle.py	24	0	100%
skore-hub-project/src/skore_hub_project/authentication
__init__.py	0	0	100%
login.py	66	0	100%
logout.py	4	0	100%
token.py	24	0	100%
uri.py	18	0	100%
skore-hub-project/src/skore_hub_project/client
__init__.py	0	0	100%
client.py	60	0	100%
skore-hub-project/src/skore_hub_project/metric
__init__.py	10	0	100%
accuracy.py	35	0	100%
brier_score.py	35	0	100%
log_loss.py	35	0	100%
metric.py	49	1	97%	25
precision.py	61	0	100%
r2.py	35	0	100%
recall.py	63	0	100%
rmse.py	35	0	100%
roc_auc.py	35	0	100%
timing.py	90	4	95%	52–53, 115–116
skore-hub-project/src/skore_hub_project/project
__init__.py	0	0	100%
project.py	102	3	97%	204, 308, 338
skore-hub-project/src/skore_hub_project/report
__init__.py	3	0	100%
cross_validation_report.py	64	1	98%	204
estimator_report.py	12	0	100%
report.py	52	0	100%
TOTAL	1186	15	98%

Tests	Skipped	Failures	Errors	Time
139	0 💤	0 ❌	0 🔥	1m 16s ⏱️

github-actions · 2025-10-28T14:23:33Z

Coverage Report for skore-local-project/

File	Stmts	Miss	Cover	Missing
skore-local-project/src/skore_local_project
__init__.py	5	0	100%
metadata.py	87	4	95%	26, 38, 150–151
project.py	102	1	99%	244
storage.py	40	2	95%	45, 187
TOTAL	234	7	97%

Tests	Skipped	Failures	Errors	Time
24	0 💤	0 ❌	0 🔥	5.747s ⏱️

github-actions · 2025-10-28T14:32:52Z

Documentation preview @ 5a0b241

skore-hub-project/hatch/metadata.py

DimitriPapadopoulos · 2025-10-28T15:20:10Z

This is not necessary, because the only visible/searchable package we want is skore/.

Makes sense, I would nevertheless suggest:

keeping tool.ruff.lint.select identical
adding some links such as project.urls.Homepage and project.urls.Repository to all packages

Co-authored-by: Thomas S. <[email protected]>

thomass-dev

Fine. Thank you for fixing this deprecation.

DimitriPapadopoulos marked this pull request as draft October 27, 2025 14:04

DimitriPapadopoulos force-pushed the PEP639 branch 2 times, most recently from b7a7aa8 to 7b0108a Compare October 27, 2025 14:13

thomass-dev self-requested a review October 27, 2025 14:26

chore: PEP 639 compliance

bc104a1

Update licensing metadata as described in PEP 639.

DimitriPapadopoulos force-pushed the PEP639 branch from 7b0108a to bc104a1 Compare October 27, 2025 20:49

DimitriPapadopoulos marked this pull request as ready for review October 27, 2025 21:00

DimitriPapadopoulos commented Oct 27, 2025

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Co-authored-by: Thomas S. <[email protected]>

DimitriPapadopoulos force-pushed the PEP639 branch from f0b6f6c to 5a0b241 Compare October 28, 2025 14:07

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thomass-dev merged commit 01dac69 into probabl-ai:main Oct 28, 2025
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DimitriPapadopoulos deleted the PEP639 branch October 28, 2025 19:26

chore(all): PEP 639 compliance #2089

chore(all): PEP 639 compliance #2089

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