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1.8.0#437

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mauvais2 merged 218 commits intomasterfrom
1.8.0
Apr 28, 2026
Merged

1.8.0#437
mauvais2 merged 218 commits intomasterfrom
1.8.0

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@mauvais2 mauvais2 commented Apr 28, 2026

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stewarthe6 and others added 30 commits January 21, 2025 10:10
@stewarthe6
New sklearn transformer wrapper
78b3c37
@stewarthe6
This should be an else if since it is an else if in the init and in u…
f35e3fb 
…ntransform
@stewarthe6
Remove UMAP transformer since it is deprecated
458e188
@stewarthe6
deleted large chunk of commented code
2479de0
@stewarthe6
Inserted Sklearn RobustScaler and PowerTransformer into the pipeline …
9e8dfce 
…and added tests
@stewarthe6
Fixed argument name. Changed from robustscaler_with_scaling to robust…
53d3f74 
…scaler_unit_variance
@stewarthe6
Updated test to use mordred_filtered features. Added arguments to def…
8feea36 
…ault true and default false lists
@stewarthe6
feature_transformer_type should be feature_transform_type
1eda346
@stewarthe6
unit_variance parameter must be a tuple
fd22692
@stewarthe6
Convert quartiles
28cd0e0
@stewarthe6
Updated rdkit to use AvgIpc for a numerically better behaved feature
77c8b26
@stewarthe6
set default for PowerTransformer method
2551e38
@stewarthe6
Merge branch '1.7.0' into feature_sklearn_transformer
225c00d
@stewarthe6
Update descriptor_sets_sources_by_descr_type.csv
fa3ea05 
Ipc should not be changed to AvgIpc like this because it would break all rdkit_raw models.
@stewarthe6
rdkit_scaled by heavy atom count is working
01b4c28
@stewarthe6
rdkit_raw has the Ipc feature which causes RobustTransformer to retur…
94326bc 
…n nans
@stewarthe6
Added SimpleImputer to help sort out nans in the dataset when used wi…
6e7805a 
…th RobustScaler and PowerTransformer. Updated documentation in related sections. Added functions to ModelFileReader to read out transformer specific parameters. Changed models that test RobustScaler and PowerTransformer to use RF to speed up the training
@stewarthe6
Set add_indicator to True so inverse transform works. Also cleaned up…
46fe7a1 
… unused imports
@stewarthe6
Merged in sklearn transformer branch. Added mordred_filtered_scaled f…
2592636 
…eatures
@stewarthe6
Added json needed for the delaney_panel test.
cdb6f98
@stewarthe6
default_true and default_false were being overwritten. Now calls set_…
da690e6 
…default function for all sklearn parameters
@stewarthe6
Merge branch 'feature_sklearn_transformer' into feat_scaled_rdkit_mor…
216e02b 
…dred
@stewarthe6
Refactor so we wrap sklearn Pipelines instead of transformers to make…
8634988 
… it more generalizeable. Fixed tests. Fixed bug where the imputer_strategy parameter was not used
@stewarthe6
Merge branch 'feature_sklearn_transformer' into feat_scaled_rdkit_mor…
c748d0a 
…dred
@stewarthe6
Updated rdkit_scaled and mordred_filtered_scaled. Added option to hav…
2969378 
…e log scale features
@stewarthe6
Updated input sanity check for SklearnPipeLineWrapper. Removed 'add_i…
e0af6a2 
…ndicator' flag because that changed the number of features and crashed.
@stewarthe6
Updated transformer test to expect NotImpelmentedError when untransfo…
8d98165 
…rming using SklearnPipelineWrapper
@stewarthe6
Merge branch '1.7.0' into feature_sklearn_transformer
35eb9e9
@stewarthe6
Merge branch 'feature_sklearn_transformer' into feat_scaled_rdkit_mor…
c3ae805 
…dred
@mauvais2
Create 1.8.0
0a9033a
mauvais2 and others added 22 commits April 22, 2026 08:26
@mauvais2
merged with 1.8.0
670999e
@mauvais2
merged with 1.8.0. add more info in pyproject.toml
2f94055
@mauvais2
fixed pyproject.tooml
99896ae
@mauvais2
put '>=3.10,<3.11' back to avoid rebuild of all lock files
23ae055
@mauvais2
include new params in the test
76a5318
@mauvais2
moved the atom logo file and reformatted to work for pypi
168e341
@mauvais2
updated readme, pyproject.toml
36f9fc3
@mauvais2
use relative path for the icon file for now. after push to master, ch…
c542f88 
…ange it to raw path for pypi to work.
@mauvais2
added new params for #434
78e47aa
@mauvais2
brought files from prep-1.8.0. restored the build.sh, install*.sh and…
338133e 
… updated related docs on building locally
@stewarthe6
Adding mordred features to speed up tests
8c2f997
@mauvais2
Merge pull request #435 from ATOMScience-org/fix_test_param_parse
935cdee 
added new params for #434
@mauvais2
updated README.md and makefile
da8e078
@mauvais2
updated publish.yml to manaul only
5424a48
@stewarthe6
Add installation instructions for atomsci-ampl
a4a7111 
Added instructions to install the latest release version from PyPI.
@mauvais2
1) updated readme. rearranged the toc 2) added generate_transformers …
95b3299 
…to docs
@mauvais2
Merge pull request #436 from ATOMScience-org/feat_MRP3_features
aae5e96 
MRP3 mordred features to speed up tests.
@mauvais2
changed the docker build to manual, added comments
5e46ed5
@mauvais2
fixed syntax
46a06fd
@mauvais2
cleaned up readme
0ee4334
@mauvais2
Merge pull request #429 from ATOMScience-org/uv-setup
cd3d1a1 
Standardizing Python project setup using uv
@mauvais2
updated readme shield version. chnage the logo to raw
570daa4
@mauvais2 mauvais2 self-assigned this Apr 28, 2026
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codecov Bot commented Apr 28, 2026 •
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Codecov Report

❌ Patch coverage is 83.40249% with 240 lines in your changes missing coverage. Please review.

Files with missing lines Patch % Lines
atomsci/ddm/pipeline/compare_models.py 55.31% 63 Missing ⚠️
atomsci/ddm/pipeline/model_wrapper.py 79.90% 41 Missing ⚠️
atomsci/ddm/pipeline/perf_data.py 87.54% 34 Missing ⚠️
atomsci/ddm/pipeline/model_datasets.py 81.81% 20 Missing ⚠️
atomsci/ddm/pipeline/perf_plots.py 83.96% 17 Missing ⚠️
atomsci/ddm/pipeline/model_pipeline.py 81.39% 16 Missing ⚠️
atomsci/ddm/pipeline/GeneticAlgorithm.py 78.12% 7 Missing ⚠️
atomsci/ddm/pipeline/featurization.py 93.91% 7 Missing ⚠️
atomsci/ddm/pipeline/splitting.py 79.31% 6 Missing ⚠️
atomsci/ddm/pipeline/MultitaskScaffoldSplit.py 95.76% 5 Missing ⚠️
... and 9 more 
@@            Coverage Diff            @@
##             master     #437   +/-   ##
=========================================
  Coverage          ?   52.90%           
=========================================
  Files             ?       38           
  Lines             ?    12205           
  Branches          ?        0           
=========================================
  Hits              ?     6457           
  Misses            ?     5748           
  Partials          ?        0
Flag Coverage Δ
unittests 52.90% <83.40%> (?)

Flags with carried forward coverage won't be shown. Click here to find out more.

Files with missing lines Coverage Δ
atomsci/ddm/__init__.py 100.00% <100.00%> (ø)
atomsci/ddm/pipeline/predict_from_model.py 80.00% <100.00%> (ø)
atomsci/ddm/utils/checksum_utils.py 87.87% <ø> (ø)
atomsci/ddm/utils/compare_splits_plots.py 92.92% <ø> (ø)
atomsci/ddm/utils/curate_data.py 56.52% <ø> (ø)
atomsci/ddm/utils/datastore_functions.py 5.89% <ø> (ø)
atomsci/ddm/utils/file_utils.py 91.66% <ø> (ø)
atomsci/ddm/utils/generate_transformers.py 100.00% <ø> (ø)
atomsci/ddm/utils/hyperparam_search_wrapper.py 30.31% <ø> (ø)
atomsci/ddm/utils/llnl_utils.py 36.36% <ø> (ø)
... and 26 more
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@mauvais2 mauvais2 merged commit e77c696 into master Apr 28, 2026
14 checks passed
@mauvais2 mauvais2 deleted the 1.8.0 branch April 28, 2026 21:44
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@stewarthe6 stewarthe6 stewarthe6 approved these changes

@mcloughlin2 mcloughlin2 Awaiting requested review from mcloughlin2

@paulsonak paulsonak Awaiting requested review from paulsonak

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@mauvais2 @stewarthe6 @ATOMconsortium @mcloughlin2 @paulsonak