Rename project to "YAMMBS"

.github/workflows/ci.yaml

@@ -33,9 +33,9 @@ jobs:
 
     - name: Run tests
       run: |
-        pytest -v -n logical --durations=10 \
-          --cov=ibstore/ --cov-report=xml --cov-config=setup.cfg \
-          ibstore/
+        pytest -r fEx -n logical --durations=10 \
+          --cov=yammbs/ --cov-report=xml --cov-config=setup.cfg \
+          yammbs/
 
     - name: CodeCov
       uses: codecov/codecov-action@v3

README.md

@@ -1,13 +1,18 @@
-ib
-==
+YAMMBS
+======
+
+Yet Another Molecular Mechanics Benchmaring Suite (YAMMBS, pronounced like "yams") is a tool for
+benchmarking force fields.
+
+YAMMBS is currently developed for internal use at Open Force Field. It is not currently recommended for external use. No guarantees are made about the stability of the API or the accuracy of any results.
 
 # Getting started
 
 ## Installation
 
-Use the file `../devtools/conda-envs/dev.yaml` and also install `ibstore` with something like `python -m pip install -e .`.
+Use the file `./devtools/conda-envs/dev.yaml` and also install `yammbs` with something like `python -m pip install -e .`.
 
-## Data source
+## Data sources
 
 It is assumed that the input molecules are stored in a `openff-qcsubmit` model like `OptimizationResultCollection`.
 
@@ -18,7 +23,7 @@ See the file `run.py` for a start-to-finish example.
 Load a molecule dataset into the used representation:
 
 ```python
-from ibstore import MoleculeStore
+from yammbs import MoleculeStore
 
 store = MoleculeStore.from_qcsubmit_collection(
     collection=my_collection,
@@ -32,19 +37,18 @@ Run MM optimizations of all molecules using a particular force field
 store.optimize_mm(force_field="openff-2.1.0.offxml")
 ```
 
-Run DDE or RMSD analysis and save to disk:
+Run DDE (or RMSD, TFD, etc.) analyses and save to results disk:
 
 ```python
 ddes = store.get_dde(force_field="openff-2.1.0.offxml")
 ddes.to_csv(f"{force_field}-dde.csv")
-
-rmsds = store.get_rmsd(force_field="openff-2.1.0.offxml")
-rmsds.to_csv(f"{force_field}-rmsd.csv")
 ```
 
-Note that the pattern
+Note that the pattern in the script
 
 ```python
+from multiprocessing import freeze_support
+
 def main():
     # Your code here
 
@@ -54,6 +58,12 @@ if __name__ == "__main__":
 ```
 
 must be used for Python's `multiprocessing` module to behave well.
+
+### License
+
+YAMMBS is open-source software distrubuted under the MIT license (see LICENSE). It derives from
+other open-source work that may be distributed under other licenses (see LICENSE-3RD-PARTY).
+
 ### Copyright
 
 Copyright (c) 2022, Open Force Field Initiative

devtools/conda-envs/dev.yaml

@@ -1,9 +1,9 @@
-name: ib-dev
+name: yammbs-dev
 channels:
   - openeye
   - conda-forge
 dependencies:
-  - python =3.10
+  - python
 
   - openff-toolkit
   - openff-qcsubmit
@@ -27,4 +27,4 @@ dependencies:
   - pytest-timeout
 
   - pip:
-    - git+https://github.com/mattwthompson/de-forcefields.git@periodic-nonperiodic-methods
+    - git+https://github.com/jthorton/de-forcefields.git@eb99f5ea1347dc3fd079038a52a21554b9e44caf

run.py

@@ -6,7 +6,7 @@
 from matplotlib import pyplot
 from openff.qcsubmit.results import OptimizationResultCollection
 
-from ibstore._store import MoleculeStore
+from yammbs import MoleculeStore
 
 
 def main():
@@ -29,7 +29,7 @@ def main():
     else:
         store = MoleculeStore.from_qcsubmit_collection(
             OptimizationResultCollection.parse_file(
-                f"ibstore/_tests/data/01-processed-qm-{data}.json",
+                f"yammbs/_tests/data/01-processed-qm-{data}.json",
             ),
             database_name=f"{data}.sqlite",
         )

setup.cfg

@@ -1,5 +1,5 @@
 [metadata]
-name = ibstore
+name = yammbs
 version = 0.0.0
 description = Internal benchmarking storage tools
 long_description = file: README.md
@@ -26,10 +26,10 @@ exclude =
 
 [coverage:run]
 omit =
-    ibstore/_tests/*
+    yammbs/_tests/*
     versioneer.py
     setup.py
-    ibstore/_version.py
+    yammbs/_version.py
 
 [coverage:report]
 exclude_lines =
@@ -41,16 +41,16 @@ exclude_lines =
 max-line-length = 119
 ignore = E203
 per-file-ignores =
-    ibstore/__init__.py:F401
+    yammbs/__init__.py:F401
 
 [isort]
 profile = black
 
 [versioneer]
 VCS = git
 style = pep440
-versionfile_source = ibstore/_version.py
-versionfile_build = ibstore/_version.py
+versionfile_source = yammbs/_version.py
+versionfile_build = yammbs/_version.py
 tag_prefix = 'v'
 
 [mypy]

ibstore/__init__.py → yammbs/__init__.py

@@ -1,5 +1,5 @@
-from ibstore._store import MoleculeStore
-from ibstore._version import get_versions
+from yammbs._store import MoleculeStore
+from yammbs._version import get_versions
 
 __all__ = ("MoleculeStore",)
 

ibstore/_db.py → yammbs/_db.py

@@ -4,7 +4,7 @@
 from sqlalchemy import Column, Float, ForeignKey, Integer, PickleType, String
 from sqlalchemy.orm import declarative_base, relationship
 
-from ibstore.models import MMConformerRecord, QMConformerRecord
+from yammbs.models import MMConformerRecord, QMConformerRecord
 
 DBBase = declarative_base()
 

ibstore/_minimize.py → yammbs/_minimize.py

@@ -12,8 +12,8 @@
 from pydantic.v1 import Field
 from tqdm import tqdm
 
-from ibstore._base.array import Array
-from ibstore._base.base import ImmutableModel
+from yammbs._base.array import Array
+from yammbs._base.base import ImmutableModel
 
 _AVAILABLE_FORCE_FIELDS = get_available_force_fields()
 
@@ -135,15 +135,15 @@ def _run_openmm(
     )
 
     if input.force_field.startswith("gaff"):
-        from ibstore._forcefields import _gaff
+        from yammbs._forcefields import _gaff
 
         system = _gaff(
             molecule=molecule,
             force_field_name=input.force_field,
         )
 
     elif input.force_field.startswith("espaloma"):
-        from ibstore._forcefields import _espaloma
+        from yammbs._forcefields import _espaloma
 
         system = _espaloma(
             molecule=molecule,

ibstore/_molecule.py → yammbs/_molecule.py

@@ -3,7 +3,7 @@
 
 from openff.toolkit import Molecule
 
-from ibstore._base.array import Array
+from yammbs._base.array import Array
 
 if TYPE_CHECKING:
     from geometric.molecule import Molecule as GeometricMolecule

ibstore/_session.py → yammbs/_session.py

@@ -2,7 +2,7 @@
 from collections import defaultdict
 from typing import TYPE_CHECKING, Dict, List, NamedTuple, Optional
 
-from ibstore._db import (
+from yammbs._db import (
     DB_VERSION,
     DBGeneralProvenance,
     DBInformation,
@@ -15,7 +15,7 @@
 if TYPE_CHECKING:
     from sqlalchemy.orm import Session
 
-    from ibstore.models import MMConformerRecord, MoleculeRecord, QMConformerRecord
+    from yammbs.models import MMConformerRecord, MoleculeRecord, QMConformerRecord
 
 
 class DBQueryResult(NamedTuple):

ibstore/_store.py → yammbs/_store.py

@@ -10,15 +10,15 @@
 from sqlalchemy import create_engine
 from sqlalchemy.orm import Session, sessionmaker
 
-from ibstore._db import (
+from yammbs._db import (
     DBBase,
     DBMMConformerRecord,
     DBMoleculeRecord,
     DBQMConformerRecord,
 )
-from ibstore._session import DBSessionManager
-from ibstore._types import Pathlike
-from ibstore.analysis import (
+from yammbs._session import DBSessionManager
+from yammbs._types import Pathlike
+from yammbs.analysis import (
     DDE,
     ICRMSD,
     RMSD,
@@ -31,9 +31,9 @@
     get_rmsd,
     get_tfd,
 )
-from ibstore.cached_result import CachedResultCollection
-from ibstore.exceptions import DatabaseExistsError
-from ibstore.models import MMConformerRecord, MoleculeRecord, QMConformerRecord
+from yammbs.cached_result import CachedResultCollection
+from yammbs.exceptions import DatabaseExistsError
+from yammbs.models import MMConformerRecord, MoleculeRecord, QMConformerRecord
 
 LOGGER = logging.getLogger(__name__)
 
@@ -482,7 +482,7 @@ def optimize_mm(
         n_processes: int = 2,
         chunksize=32,
     ):
-        from ibstore._minimize import _minimize_blob
+        from yammbs._minimize import _minimize_blob
 
         inchi_keys = self.get_inchi_keys()
 

ibstore/_tests/conftest.py → yammbs/_tests/conftest.py

@@ -15,8 +15,8 @@
 from openff.toolkit import Molecule
 from openff.utilities.utilities import get_data_file_path
 
-from ibstore._store import MoleculeStore
-from ibstore.cached_result import CachedResultCollection
+from yammbs import MoleculeStore
+from yammbs.cached_result import CachedResultCollection
 
 
 @pytest.fixture()
@@ -54,14 +54,14 @@ def ligand():
 @pytest.fixture()
 def small_collection() -> OptimizationResultCollection:
     return OptimizationResultCollection.parse_file(
-        get_data_file_path("_tests/data/01-processed-qm-ch.json", "ibstore"),
+        get_data_file_path("_tests/data/01-processed-qm-ch.json", "yammbs"),
     )
 
 
 @pytest.fixture()
 def small_cache() -> CachedResultCollection:
     return CachedResultCollection.from_json(
-        get_data_file_path("_tests/data/tiny-opt.json", "ibstore"),
+        get_data_file_path("_tests/data/tiny-opt.json", "yammbs"),
     )
 
 
@@ -71,7 +71,7 @@ def small_store(tmp_path) -> MoleculeStore:
     # This file manually generated from data/01-processed-qm-ch.json
     source_path = get_data_file_path(
         "_tests/data/ch.sqlite",
-        package_name="ibstore",
+        package_name="yammbs",
     )
 
     dest_path = (tmp_path / "ch.sqlite").as_posix()
@@ -88,7 +88,7 @@ def tiny_cache() -> CachedResultCollection:
     return CachedResultCollection.from_json(
         get_data_file_path(
             "_tests/data/tiny-opt.json",
-            package_name="ibstore",
+            package_name="yammbs",
         ),
     )
 

ibstore/_tests/data/README.md → yammbs/_tests/data/README.md

@@ -2,13 +2,13 @@
 
 This file is built by calling this code
 
-``` python
+```python
 import logging
 
 import click
 from openff.qcsubmit.results import OptimizationResultCollection
 
-from ibstore.cached_result import CachedResultCollection
+from yammbs.cached_result import CachedResultCollection
 
 logging.getLogger("openff").setLevel(logging.ERROR)
 

ibstore/_tests/unit_tests/test_analysis.py → yammbs/_tests/unit_tests/test_analysis.py

@@ -2,7 +2,7 @@
 import pytest
 from openff.toolkit import Molecule
 
-from ibstore.analysis import get_internal_coordinate_rmsds
+from yammbs.analysis import get_internal_coordinate_rmsds
 
 
 class TestInternalCoordinateRMSD:

yammbs/_tests/unit_tests/test_cached_result.py

@@ -0,0 +1,18 @@
+import numpy
+
+from yammbs.cached_result import CachedResultCollection
+
+
+def test_json_roundtrip(tmp_path, small_cache):
+    """Test that we can round-trip a `CachedResultCollection` through JSON."""
+    with open(tmp_path / ".json", "w") as f:
+        f.write(small_cache.to_json())
+
+    new_cache = CachedResultCollection.from_json(tmp_path / ".json")
+
+    for old, new in zip(small_cache.inner, new_cache.inner):
+        assert old.mapped_smiles == new.mapped_smiles
+        assert old.inchi_key == new.inchi_key
+        assert old.qc_record_id == new.qc_record_id
+        assert old.qc_record_final_energy == new.qc_record_final_energy
+        assert numpy.allclose(old.coordinates, new.coordinates)

ibstore/_tests/unit_tests/test_forcefields.py → yammbs/_tests/unit_tests/test_forcefields.py

@@ -2,7 +2,7 @@
 import pytest
 from openff.toolkit import Molecule
 
-from ibstore._forcefields import _espaloma, _gaff, _smirnoff
+from yammbs._forcefields import _espaloma, _gaff, _smirnoff
 
 
 @pytest.fixture()

ibstore/_tests/unit_tests/test_minimize.py → yammbs/_tests/unit_tests/test_minimize.py

@@ -3,9 +3,9 @@
 from openff.toolkit import ForceField, Molecule
 from openff.units import unit
 
-from ibstore._minimize import MinimizationInput, _run_openmm
-from ibstore._store import MoleculeStore
-from ibstore.cached_result import CachedResultCollection
+from yammbs import MoleculeStore
+from yammbs._minimize import MinimizationInput, _run_openmm
+from yammbs.cached_result import CachedResultCollection
 
 
 @pytest.fixture()
@@ -93,7 +93,7 @@ def test_plugin_loadable(ethane):
 @pytest.mark.timeout(1)
 def test_cached_force_fields_load_quickly():
     """Test that cached force fields are loaded quickly."""
-    from ibstore._minimize import _lazy_load_force_field
+    from yammbs._minimize import _lazy_load_force_field
 
     # timeout includes the time it takes to load it the first time, but that should be << 1 second
     [_lazy_load_force_field("openff-1.0.0") for _ in range(1000)]