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Merged
timbernat merged 31 commits into from
Feb 25, 2026
Merged

1.0.2 patches #53

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78dbcfd
Renamed ring piercing tests to make them visible on pytest collection
timbernat Dec 10, 2025
f77e922
Removed outdated DISCERNMENT solution data
timbernat Dec 10, 2025
6b2275c
Wrote test to catch RDKit stereo inversion bug (TODO: patch internally!)
timbernat Dec 10, 2025
f46bb03
Referenced chiral atom index, added TODO note for patch
timbernat Dec 10, 2025
32daca8
Added patch to detect and correct stereoinversion in RDKit's ComputeC…
timbernat Dec 10, 2025
dd98bd5
Updated tiling test to directly check call to tiler; verified fail be…
timbernat Dec 10, 2025
89a66f4
Delete LICENSE
timbernat Jan 9, 2026
8b2d619
Swapped MIT License for GPL v3
timbernat Jan 9, 2026
af9fc2a
Added autopolymerization detection convenience method to AnnotatedRea…
timbernat Jan 9, 2026
321e5d1
Added SetSerializer, fixed NDArraySerializer signature, specialized d…
timbernat Jan 9, 2026
854f947
Created placeholder test module for json serialization
timbernat Jan 9, 2026
4dc8230
Fixed *arg typehints, function singature indents
timbernat Jan 26, 2026
a9e8229
Fixed builder arg indent
timbernat Jan 26, 2026
8c57a0f
Merge branch 'main' into patches
timbernat Jan 27, 2026
86d477f
Fixed typehint errors in MonomerGroup methods
timbernat Jan 27, 2026
df08822
Wrote sequencing tests for build_linear_polymer()
timbernat Jan 28, 2026
13e6001
Corrected docstring + logs in build_linear_polymer()
timbernat Jan 29, 2026
67c3fcb
Cleaned up imports and class references
timbernat Jan 30, 2026
dfce7ab
Wrote extensive unit tests for JSONification
timbernat Jan 30, 2026
7192daf
Updated literal reqs for dev env
timbernat Jan 30, 2026
5b3d9aa
Fixed arg indents on openmmutils
timbernat Jan 30, 2026
0ea3b8d
Added support for custom sequence-to-repeat unit map
timbernat Jan 30, 2026
f89a8e8
Moved halogenated hydrocarbon fragments into monomers.fragments
timbernat Jan 30, 2026
fc51830
Added sequencing tests for new sequence_map arg
timbernat Jan 30, 2026
0299ad3
Improved error handling, restored test coverage
timbernat Jan 30, 2026
cbf2e1f
Revert "Swapped MIT License for GPL v3"
timbernat Feb 10, 2026
22a4f42
Revert "Delete LICENSE"
timbernat Feb 10, 2026
d3c1d6b
Converted assert --> np.assert_equal to handle array value equality c…
timbernat Feb 18, 2026
667c593
Tweaked typehints and arg indents
timbernat Feb 19, 2026
4562b01
Pinned setuptools versions to suppress pkg_resources error
timbernat Feb 19, 2026
a354e5d
Updated docs link to point to 'latest'
timbernat Feb 25, 2026
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -22,7 +22,7 @@ Includes functionality for:
* Much more!

## Documentation
Complete documentation for polymerist can be found on the [`polymerist` ReadTheDocs page](https://polymerist.readthedocs.io/en/docs/)
Complete documentation for polymerist can be found on the [`polymerist` ReadTheDocs page](https://polymerist.readthedocs.io/en/latest/)

## Examples
Examples of how to import and invoke the core features of `polymerist` can be found in the accompanying [polymerist_examples repository](https://github.com/timbernat/polymerist_examples).
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