trevorgokey / besmarts Goto Github PK
View Code? Open in Web Editor NEWA toolkit for data-driven force field design based on binary-encoded SMARTS
Home Page: https://besmarts.readthedocs.io
License: MIT License
A toolkit for data-driven force field design based on binary-encoded SMARTS
Home Page: https://besmarts.readthedocs.io
License: MIT License
Hi @trevorgokey , I'm using the issue tracker here to point out what I have found from my review openjournals/joss-reviews#6653 .
Installation instructions in the README of the repository work fine, but the installation instructions in the Readthedocs does not work. There are currently no [PyPI packages] (https://pypi.org/search/?q=besmarts) related to your packages.
I've ran the tests using pytest
and they all 'pass'. However, I recommend that in line 34 of test_branch_split.py
,
test
to something that does not have test in its name as this causes pytest to assume that it is a function to be tested. You can see the output of running pytest in the expandable section below.
pytest -v
============================= test session starts =============================
platform win32 -- Python 3.12.3, pytest-8.1.1, pluggy-1.5.0 -- C:\Users\AntObi\anaconda3\envs\besmarts\python.exe
cachedir: .pytest_cache
rootdir: C:\Users\AntObi\OneDrive - Imperial College London\Postdoc\joss_reviews\besmarts-git
plugins: anyio-4.3.0
collecting ... collected 24 items
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_and PASSED [ 4%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_equal PASSED [ 8%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_in PASSED [ 12%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_not PASSED [ 16%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_not_in PASSED [ 20%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_or PASSED [ 25%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bitwise_xor PASSED [ 29%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_bool_set PASSED [ 33%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_int_set PASSED [ 37%]
besmarts-core/python/tests/test_arrays.py::test_bitvec::test_bitvec_on_off PASSED [ 41%]
besmarts-core/python/tests/test_arrays.py::test_intvec::test_intvec_indexing PASSED [ 45%]
besmarts-core/python/tests/test_branch_split.py::test_branch_split::test_atom_branch_one PASSED [ 50%]
besmarts-core/python/tests/test_branch_split.py::test_branch_split::test_atom_branch_two PASSED [ 54%]
besmarts-core/python/tests/test_branch_split.py::test ERROR [ 58%]
besmarts-core/python/tests/test_extender.py::test_extender::test_extender PASSED [ 62%]
besmarts-core/python/tests/test_import.py::test_import::test_import_assign PASSED [ 66%]
besmarts-core/python/tests/test_import.py::test_import::test_import_cluster PASSED [ 70%]
besmarts-core/python/tests/test_import.py::test_import::test_import_codecs PASSED [ 75%]
besmarts-core/python/tests/test_import.py::test_import::test_import_core PASSED [ 79%]
besmarts-core/python/tests/test_import.py::test_import::test_import_mechanics PASSED [ 83%]
besmarts-core/python/tests/test_intvec.py::test_intvec::test_intvec PASSED [ 87%]
besmarts-core/python/tests/test_io.py::test_io::test_io PASSED [ 91%]
besmarts-core/python/tests/test_mapping.py::test_mapping::test_mapping PASSED [ 95%]
besmarts-core/python/tests/test_match.py::test_match::test_match PASSED [100%]
=================================== ERRORS ====================================
___________________________ ERROR at setup of test ____________________________
file C:\Users\AntObi\OneDrive - Imperial College London\Postdoc\joss_reviews\besmarts-git\besmarts-core\python\tests\test_branch_split.py, line 34
def test(self, smiles, branches, depth):
E fixture 'self' not found
> available fixtures: anyio_backend, anyio_backend_name, anyio_backend_options, cache, capfd, capfdbinary, caplog, capsys, capsysbinary, doctest_namespace, monkeypatch, pytestconfig, record_property, record_testsuite_property, record_xml_attribute, recwarn, tmp_path, tmp_path_factory, tmpdir, tmpdir_factory
> use 'pytest --fixtures [testpath]' for help on them.
C:\Users\AntObi\OneDrive - Imperial College London\Postdoc\joss_reviews\besmarts-git\besmarts-core\python\tests\test_branch_split.py:34
=========================== short test summary info ===========================
ERROR besmarts-core/python/tests/test_branch_split.py::test
========================= 23 passed, 1 error in 1.10s =========================
My configuration for running these examples was as follows:
File | Runs ? | Notes |
---|---|---|
bond_union.py |
Yes | propane.bg isn't on the joss-manuscript branch, but it is on the main branch. |
forcefield_fit.py |
No | Requires installation of besmarts-scipy . Fails* |
matching.py |
Yes | |
smarts_cluster_bond_lengths.py |
Yes | |
smarts_split.py |
Yes | |
smiles_io.py |
Yes |
* forcefield_fit.py
and besmarts-scipy/python/examples/optimize_positions.py
fail despite besmarts-scipy
being installed with the following error:
Traceback (most recent call last):
File "/home/anthony/besmarts-git/besmarts-core/python/examples/forcefield_fit.py", line 27, in <module>
from besmarts.mechanics import optimizers_scipy
ImportError: cannot import name 'optimizers_scipy' from 'besmarts.mechanics' (unknown location)
In the documentation I have found areas in which the examples do not work.
from besmarts.codecs import native
does not work:ImportError: cannot import name 'native' from 'besmarts.codecs' (unknown location)
print(indices)
for indices in graphs.graph_impropers(g):
print(indices)```
* `print(geometry.bond(idx[::-1]))` fails: `TypeError: 'int' object is not subscriptable`
* The following lines do not work:
```for struct in graphs.graph_to_structure_dihedrals(g):
print(gcd.smarts_encode(struct))
for struct in graphs.graph_to_structure_impropers(g):
print(gcd.smarts_encode(struct))
In the SMILES/SMARTS binary operations section, there appears to be syntax errors with lines ending in colons (:) such as A, B = graphs.graph_to_structure_atoms(g)[:2]:
In the following code block, the variable bonds
is used but is never defined, and structure_mapper
does not appear to be a function in the mapper
module from a search of the codebase:
from besmarts.codecs.codec_rdkit import graph_codec_rdkit
from besmarts.core import graphs
from besmarts.core import mapper
from besmarts.core import configs
g = 'CCC=O'
g = gcd.smiles_decode(g)
atoms = graphs.graph_to_structure_atoms(g):
min_depth = 2
max_depth = 2
hydrogen = True
config = configs.smarts_extender_config(min_depth, max_depth, hydrogen)
modified = mapper.mapper_smarts_extend(config, bonds)
domain = atoms[0]
T = mapper.structure_mapper(domain)
for atom in atoms:
T.add(atom)
C = mapper.mapper_union(T)
besmarts.splitter
does not exist, so the first example cannot be run on this pagesmiles_assignment_str
is not imported prior to its useTypeError: cluster_means() missing 1 required positional argument: 'sag'
besmarts.resolve
is not a module. I cannot run this example.From a brief scan of the codebase, many of the classes and the functions require documentation to make it easy for an external user to make good use of the modules available in this package.
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