The besmarts from trevorgokey

[JOSS REVIEW] Comments

Hi @trevorgokey , I'm using the issue tracker here to point out what I have found from my review openjournals/joss-reviews#6653 .

Installation

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.

Testing

I've ran the tests using pytest and they all 'pass'. However, I recommend that in line 34 of test_branch_split.py,

besmarts/besmarts-core/python/tests/test_branch_split.py

Line 34 in 02a8c4c

def test(self, smiles, branches, depth):

you rename the function 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.

Test output from running `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 =========================

Examples

besmarts-core/python/examples/

My configuration for running these examples was as follows:

OS: CentOS
Python: 3.12
Packages installed: besmarts-core, besmarts-rdkit

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)

Usage - RTD

In the documentation I have found areas in which the examples do not work.

Graphs

from besmarts.codecs import native does not work:
ImportError: cannot import name 'native' from 'besmarts.codecs' (unknown location)
These lines do not work:

     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)

Labelling

Currently contains no example usage

Splitting

besmarts.splitter does not exist, so the first example cannot be run on this page

Clustering

smiles_assignment_str is not imported prior to its use
Running the second example on this page leads to the following error: TypeError: cluster_means() missing 1 required positional argument: 'sag'

Datasets

besmarts.resolve is not a module. I cannot run this example.

Documentation

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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Test output from running pytest -v

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Test output from running `pytest -v`