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Update dev branch #16

Merged
merged 170 commits into from
Jul 17, 2024
Merged

Update dev branch #16

merged 170 commits into from
Jul 17, 2024

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timbernat
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Description

Provide a brief description of the PR's purpose here.

Todos

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

  • TODO 1

Questions

  • Question1

Status

  • Ready to go

timbernat and others added 30 commits March 14, 2024 17:21
@timbernat
Merge pull request #10 from timbernat/dev
0579bad 
Feature merge into main
@timbernat
Merge pull request #11 from timbernat/dev
43d50f2 
Passes pdb_path to serialize_openmm_pdb kwarg to arg to avoid trippin…
@timbernat
This is a test commit to check that GitHub sync is working properly
76b1645
@timbernat
Initial commit with MolSSI Cookiecutter template
cdf2d5e
@timbernat
Deleted now-redundant internal .gitignore
d9352fe
@timbernat
Removed manual author/version dunders
9d29b2e
@timbernat
Merge pull request #12 from timbernat/cookiecutter
61cd652 
Cookiecutter functionality
@timbernat
Consolidated and renamed conda env requirements files
9be967a
@timbernat
Reinstated test_env.tml
17808bf
@timbernat
Removed unneccesary detail from canonical conda requirements YAML
89482da
@timbernat
Updated conda reqs
b418b5f
@timbernat
Update README.md
6340174
@timbernat
Update README.md
6a7fcba
@timbernat
Update README.md
adf5ad8
@timbernat
Added dirty install instructions to README
77a2d24
@timbernat
Added TOC graphic to static docs files
1f8557c
@timbernat
Added graphical abstract and links to publication
bae3858
@timbernat
Corrected typos and improved aesthetics
3a23a40
@timbernat
Added reaction name attr transfer in ReactionAssembler.assemble_rxn()
b8a360f
@timbernat
Merge remote-tracking branch 'refs/remotes/origin/main'
5ea3a4c
@timbernat
Added functions for labelling and unlabelling bond indices
e260b01
@timbernat
Changed IBIS passing to Polymerizationreactor.propagate() from class-…
54b0c94 
…based to instance-based (allows for custom init args)
@timbernat
Disabled Mol sanitization in IBIS.produce_fragments(), implemented un…
edf96d3 
…iquified version of ReseparateRGroups IBIS
@timbernat
Changed default PolymerizationReactor IBIS from ReseparateRGroups to …
a32a146 
…ReseparateRGroupsUnique
@timbernat
Fixed typos in README
305968c
@timbernat
Converted "textual" into module with dedicated submodules for specifi…
aad21e4 
…c functionality
@timbernat
Added module-wide references to ASCII character subsets
d2b9de0
@timbernat
Added function for identifying minimal repeating substrings of strings
8346ece
@timbernat
Added dedicated module for parsing and validating parenthetical delim…
534406d 
…iters
@timbernat
Implemented translation between monomer graphs and in-line strings (s…
49b67f7 
…implified SMILES-like format)
timbernat added 29 commits May 17, 2024 17:29
@timbernat
Switched integer type from unsigned to signed (i.e. np.uint64 -> np.i…
5c21eed 
…nt64) to support negative reals
@timbernat
Added dynamic Union registration for numpy float and int types
6dcacd1
@timbernat
Implemented the extended Euclidean algorithm, strengthened typing
3a93581
@timbernat
Updated section header
d9433f6
@timbernat
Removed "_numbers" suffix from Catalan and Bell number functions for …
e7a0485 
…consistency with module
@timbernat
Updated relative imports in polymers.monomers
60dbb6d
@timbernat
Updated relative imports in mdtools
444630b
@timbernat
Fixed Simulation state loading, with support for both State objects a…
3a68ea7 
…nd file-like inputs (or None)
@timbernat
Imported OpenFF Quantities, corrected typos
0e20595
@timbernat
Added molecular mass calculations methods for OpenFF Molecule and Top…
d4acf7b 
…ology objects
@timbernat
Deprecated RDKit conversion in packmol number density mass calculation
ac05347
@timbernat
Migrated product() from seuquences.py to iteration.py (incuding in de…
b52c09c 
…pendencies)
@timbernat
Expanded genutils.sequences into full module (with prior functionalit…
663669a 
…y moved into seqops.py submodule), updated dependencies
@timbernat
Updated seqops docstring, made core utils importable thru toplevel mo…
b2cf13f 
…dule
@timbernat
Added new genutils.bits package for bitwise operations
344a34a
@timbernat
Added sort_dict_by_keys() counterpart function to sort_dict_by_values()
3e6cc8e
@timbernat
Created new sequence similarity submodule which implements Levenshtei…
541b944 
…n distance-related functionality (among other things)
@timbernat
Migrated bin_ids_forming_sequence from sequences.seqops to new sequen…
0f7bb23 
…ces.choices, updating dependencies
@timbernat
Corrected typo in imports (containers -> collections)
beb26e7
@timbernat
Craeted new module for solving the generalized ransom note index enum…
7b40a9e 
…eration problem
@timbernat
Implemented representation class for manipulations on ordered sequenc…
d88aff4 
…es of symbol multisets
@timbernat
Implemented base solution interface and cartesian, recursive, and sta…
d337087 
…ck-based concrete solution algorithms
@timbernat
Implemented front-facing solver interface class
2e26fee
@timbernat
Wrote unit tests to ensure consistency between DISCERNMENT algorithm …
bcef779 
…implementations
@timbernat
Deprecated sequences.choices in favor of sequences.discernment, updat…
833358d 
…ed dependent co-modules
@timbernat
Made num_automorphisms() more secure by removing possibility of confl…
51777a8 
…icting "uniquify" kwargs values
@timbernat
Cleaned up naming on full_builtin() (now called "full_arr_builtin()")…
6a36c60 
… for clarity
@timbernat
Made valid_reactant_ordering() implementation more explicit (clearer …
1309ead 
…typing and variable names, more re-use of calculations)
@timbernat
Fixed relative imports from genutils and unitutils (remnants of move …
855faa5 
…into mdtools)
@timbernat timbernat merged commit 6eda90d into dev Jul 17, 2024
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@timbernat