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Polymerist omnibus improvements #37

Merged
merged 204 commits into from
Dec 18, 2024
Merged

Polymerist omnibus improvements #37

merged 204 commits into from
Dec 18, 2024

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timbernat
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Description

Bulk PR containing many quality-of-life improvements and API-breaking changes

Todos

Notable points that this PR has either accomplished or will accomplish.

Status

  • Pass tests
  • Create 1.0.0 GitHub tag
  • Build and upload docs to ReadTheDocs
  • Compile list of pip-installable dependencies

timbernat and others added 30 commits July 16, 2024 18:49
@timbernat
Merge pull request #16 from timbernat/main
6eda90d 
Update dev branch
@timbernat
Created new genutils.attrs submodule for inspecting attributes
cbba4c3
@timbernat
Moved compiled_simple_gettable_attrs() from genutils.importutils to g…
a38b3da 
…enutils.attrs; updated dependent imports
@timbernat
Added return type annotations to class decorators
83054f6
@timbernat
Wrote decorator which dynamically registers abstract class attributes
3fa94c7
@timbernat
Fixed bug where class attribute was not actually being set in registe…
357fb91 
…r_abstract_class_attrs
@timbernat
Created new genutils submodule for generic tree-related functionality
23c94ef
@timbernat
Added option to filter (via "stop" Callable) in compile_tree()
30df13a
@timbernat
Broke treetools into component submodules
edd5e93
@timbernat
Moved filter typehints to their own dedicated module
7338e7f
@timbernat
Added option to filter down node attributes when copying nodes/trees
aa30f4e
@timbernat
Renamed compiled_simple_getable_attrs() to compile_argfree_getable_at…
c46bf5c 
…trs() to make intent clearer
@timbernat
Added option to filter attributes when copying a Node or tree
d0af3d3
@timbernat
Added explicit "ALWAYS_TRUE" and "ALWAYS_FALSE" filters to cover alte…
dd03eef 
…rnate use-cases
@timbernat
Merge branch 'main' into feature-trees (adds unit test setup)
914f31e
@timbernat
Merge pull request #22 from timbernat/main
74af987 
Updates to GitHub CI setup
@timbernat
Merge branch 'main' into feature-trees
cdbe8cf
@timbernat
Merge branch 'main' into feature-trees
f011f5b
@timbernat
Merge branch 'main' into feature-trees
5473e04
@timbernat
Merge branch 'main' into dev
d4a4214
@timbernat
Created new genutils.attrs submodule for inspecting attributes
de46645
@timbernat
Moved compiled_simple_gettable_attrs() from genutils.importutils to g…
9ffbbdd 
…enutils.attrs; updated dependent imports
@timbernat
Added return type annotations to class decorators
b72dfbd
@timbernat
Wrote decorator which dynamically registers abstract class attributes
b3ec0e4
@timbernat
Fixed bug where class attribute was not actually being set in registe…
0099373 
…r_abstract_class_attrs
@timbernat
Created new genutils submodule for generic tree-related functionality
05fd391
@timbernat
Added option to filter (via "stop" Callable) in compile_tree()
bde603c
@timbernat
Broke treetools into component submodules
4311da4
@timbernat
Moved filter typehints to their own dedicated module
c2205ed
@timbernat
Added option to filter down node attributes when copying nodes/trees
0c32bca
timbernat and others added 23 commits December 9, 2024 20:01
@timbernat
Added bug note for validation skipping when accessing monomer attribu…
10b8b8c 
…tes directly
@timbernat
Added test for degenerate eng group autoassignment (i.e. when NO term…
30642dc 
…inal monomers are present)
@timbernat
Attempted (unsuccessfully) to get __hash__ working for MonomerGroup
bda08d8
@timbernat
Wrote unit tests for linear polymer builder
32f8d53
@timbernat
Fixed indent on openff_topology_to_openmm() arguments
4e31488
@timbernat
Removed deprecated local TKREGS import
051d128
@timbernat
Moved unitsys outside of omminter to resolve circular import
e0cdfc5
@timbernat
Moved sample monomer fragment sets from unit tests to polymerist proper
f416a32
@timbernat
Corrected typo in end group autogen warning
a770906
@timbernat
Fixed indent on serialize_openmm_pdb() arguments
c991c17
@timbernat
Fixed accidental duplication of 3-functional TMC monomer fragment
040a718
@timbernat
Added new subpackage for molecule file I/O
bbd1b85
@timbernat
Froze SerialAtomLabeller dataclass to avoid unintentional label forma…
34d1a7b 
…t mutation
@timbernat
Switched PDB atom labelled to dependency-injection based model
d9afdc4
@timbernat
Renamed "chain" to "polymer" where it occurs to avoid confusion with …
668c3f9 
…the related-but-distinct OpenMM notion of a Chain
@timbernat
Added placeholder unit tests for newly-created molfiles subpackage
a5cc442
@timbernat
Added residue info injection into mbmol_to_openmm_pdb (PDB outputs ar…
4d128e3 
…e now totally consistent with RDKit PDB output)
@timbernat
Renamed "atom_label_size" to "atom_label_length" for clarity
f1f8039
@timbernat
Renamed once more to atom_label_width
370dc3a
@timbernat
Fixed non-attribute value in atom_label_width Exception message
c61f16a
@timbernat
Added string type check for atom element symbols
e40600e
@timbernat
Wrote unit tests for molfiles.pdb.SerialAtomLabeller
5c282d7
@timbernat
Merge pull request #34 from timbernat/DOP-hotfix
ce9e052 
Polymer builder overhaul
@timbernat timbernat self-assigned this Dec 12, 2024
@timbernat timbernat added enhancement New feature or request external dependency Refactors based on relationship to an outside package api breaking Will change how codes invoking a part of polymerist will be written priority:high Immediate attention required, breaks most or all package-level functionality labels Dec 12, 2024
@timbernat timbernat changed the title Polymerist 1.0.0 fixes Polymerist omnibus improvements Dec 18, 2024
@timbernat timbernat merged commit 84a530d into main Dec 18, 2024
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api breaking Will change how codes invoking a part of polymerist will be written enhancement New feature or request external dependency Refactors based on relationship to an outside package priority:high Immediate attention required, breaks most or all package-level functionality
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