Merge pull request #268 from VlachosGroup/core_subpackage

initial efforts towards building a core-only package
VlachosGroup · Mar 1, 2024 · 05760b1 · 05760b1
2 parents be07183 + 78ced29
commit 05760b1
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Showing 9 changed files with 221 additions and 312 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -96,3 +96,14 @@ jobs:
           password: ${{ secrets.PYPI_API_TOKEN }}
           skip-existing: true
           verbose: true
+
+      - run: rm -rf dist
+      - name: Build a binary wheel and a source tarball for core package
+        run: |
+          CORE_ONLY=1 python -m build --sdist --wheel --outdir dist/ .
+      - name: Publish distribution 📦 to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}
+          skip-existing: true
+          verbose: true
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1 +1 @@
-global-include config.yaml *.png *.csv *.md requirements.txt
+global-include config.yaml *.png *.csv *.md requirements.txt requirements_core.txt
diff --git a/aimsim/__init__.py b/aimsim/__init__.py
@@ -1,6 +1,10 @@
 from . import ops
-from . import tasks
 from . import chemical_datastructures
 from . import utils
 
+try:
+    from . import tasks
+except ImportError:
+    pass  # aimsim_core does not include this
+
 __version__ = "2.1.3"
diff --git a/aimsim/ops/descriptor.py b/aimsim/ops/descriptor.py
@@ -1,4 +1,5 @@
 """This module contains methods to featurize molecules."""
+
 import numpy as np
 from rdkit.Chem import rdmolops
 from rdkit import Chem
@@ -10,13 +11,8 @@
 from rdkit.DataStructs import cDataStructs
 from aimsim.utils.ccbmlib_fingerprints import generate_fingerprints
 from padelpy import from_smiles
-from aimsim.utils.extras import requires_mordred
 from mhfp.encoder import MHFPEncoder
-
-try:
-    from mordred import Calculator, descriptors
-except ImportError:
-    NO_MORDRED = True
+from mordred import Calculator, descriptors
 
 
 from ..exceptions import (
@@ -59,10 +55,7 @@ def to_numpy(self):
 
         """
         if self.check_init() is False:
-            raise NotInitializedError(
-                "Descriptor value not generated. Use "
-                "make_fingerprint() to initialize it."
-            )
+            raise NotInitializedError("Descriptor value not generated. Use " "make_fingerprint() to initialize it.")
         if not hasattr(self, "numpy_"):
             self.numpy_ = np.zeros((0,), dtype=np.int8)
             DataStructs.ConvertToNumpyArray(self.rdkit_, self.numpy_)
@@ -82,15 +75,9 @@ def to_rdkit(self):
 
         """
         if self.check_init() is False:
-            raise NotInitializedError(
-                "Descriptor value not generated. Use "
-                "make_fingerprint() to initialize it."
-            )
+            raise NotInitializedError("Descriptor value not generated. Use " "make_fingerprint() to initialize it.")
         if not hasattr(self, "rdkit_"):
-            raise ValueError(
-                "Attempting to convert arbitrary numpy array "
-                "to rdkit bit vector is not supported"
-            )
+            raise ValueError("Attempting to convert arbitrary numpy array " "to rdkit bit vector is not supported")
         return self.rdkit_
 
     def check_init(self):
@@ -100,10 +87,7 @@ def check_init(self):
             (bool): True if object is initialized.
 
         """
-        return (
-            getattr(self, "numpy_", None) is not None
-            or getattr(self, "rdkit_", None) is not None
-        )
+        return getattr(self, "numpy_", None) is not None or getattr(self, "rdkit_", None) is not None
 
     def _set_morgan_fingerprint(self, molecule_graph, radius, n_bits, **kwargs):
         """Set the descriptor to a morgan fingerprint.
@@ -117,15 +101,11 @@ def _set_morgan_fingerprint(self, molecule_graph, radius, n_bits, **kwargs):
                 as count.
 
         """
-        self.rdkit_ = AllChem.GetMorganFingerprintAsBitVect(
-            molecule_graph, radius, nBits=n_bits, **kwargs
-        )
+        self.rdkit_ = AllChem.GetMorganFingerprintAsBitVect(molecule_graph, radius, nBits=n_bits, **kwargs)
         self.label_ = "morgan_fingerprint"
         self.params_ = {"radius": radius, "n_bits": n_bits}
 
-    def _set_rdkit_topological_fingerprint(
-        self, molecule_graph, min_path, max_path, **kwargs
-    ):
+    def _set_rdkit_topological_fingerprint(self, molecule_graph, min_path, max_path, **kwargs):
         """Set the descriptor to a topological fingerprint.
 
         Args:
@@ -147,9 +127,7 @@ def _set_rdkit_topological_fingerprint(
                 f"greater than the minimum path "
                 f"used for fingerprint."
             )
-        self.rdkit_ = rdmolops.RDKFingerprint(
-            molecule_graph, minPath=min_path, maxPath=max_path
-        )
+        self.rdkit_ = rdmolops.RDKFingerprint(molecule_graph, minPath=min_path, maxPath=max_path)
         self.label_ = "topological_fingerprint"
         self.params_ = {"min_path": min_path, "max_path": max_path}
 
@@ -167,11 +145,8 @@ def _set_padelpy_descriptor(self, molecule_graph, descriptor, **kwargs):
             self.numpy_ = np.array(all_desc[descriptor])
             self.label_ = descriptor
         except Exception as e:
-            raise RuntimeError(
-                f"Unable to retrieve PaDELPy Descriptor '{descriptor}'. Is it a valid descriptor?"
-            )
+            raise RuntimeError(f"Unable to retrieve PaDELPy Descriptor '{descriptor}'. Is it a valid descriptor?")
 
-    @requires_mordred
     def _set_mordred_descriptor(self, molecule_graph, descriptor, **kwargs):
         """Set the value of numpy_ to the descriptor as indicated by descriptor.
 
@@ -192,7 +167,7 @@ def _set_mordred_descriptor(self, molecule_graph, descriptor, **kwargs):
         except KeyError:
             raise MordredCalculatorError(
                 """Mordred descriptor calculator unable to calculate descriptor \"{}\",
-                ensure correct name is used (https://mordred-descriptor.github.io/documentation/master/descriptors.html).""".format(
+                ensure correct name is used (https://jacksonburns.github.io/mordred-community/descriptors.html).""".format(
                     descriptor
                 )
             )
@@ -286,9 +261,7 @@ def _set_minhash_fingerprint(self, molecule_graph, **kwargs):
         self.label_ = "minhash_fingerprint"
         self.params_ = kwargs
 
-    def make_fingerprint(
-        self, molecule_graph, fingerprint_type, fingerprint_params=None
-    ):
+    def make_fingerprint(self, molecule_graph, fingerprint_type, fingerprint_params=None):
         """Make fingerprint of a molecule based on a graph representation.
         Set the state of the descriptor to this fingerprint.
 
@@ -316,15 +289,11 @@ def make_fingerprint(
                 "kekulize": True,
             }
             minhash_params.update(fingerprint_params)
-            self._set_minhash_fingerprint(
-                molecule_graph=molecule_graph, **minhash_params
-            )
+            self._set_minhash_fingerprint(molecule_graph=molecule_graph, **minhash_params)
         elif fingerprint_type == "topological_fingerprint":
             topological_params = {"min_path": 1, "max_path": 7}
             topological_params.update(fingerprint_params)
-            self._set_rdkit_topological_fingerprint(
-                molecule_graph=molecule_graph, **topological_params
-            )
+            self._set_rdkit_topological_fingerprint(molecule_graph=molecule_graph, **topological_params)
         elif fingerprint_type == "daylight_fingerprint":
             daylight_params = {
                 "minPath": 1,
@@ -336,25 +305,19 @@ def make_fingerprint(
                 "minSize": 64,
             }
             daylight_params.update(fingerprint_params)
-            self._set_daylight_fingerprint(
-                molecule_graph=molecule_graph, **daylight_params
-            )
+            self._set_daylight_fingerprint(molecule_graph=molecule_graph, **daylight_params)
         elif fingerprint_type == "maccs_keys":
             maccs_params = {}
             maccs_params.update(fingerprint_params)
             self._set_maccs_keys(molecule_graph=molecule_graph, **maccs_params)
         elif fingerprint_type == "atom-pair_fingerprint":
             atom_pair_fp_params = {}
             atom_pair_fp_params.update(fingerprint_params)
-            self._set_atom_pair_fingerprint(
-                molecule_graph=molecule_graph, **atom_pair_fp_params
-            )
+            self._set_atom_pair_fingerprint(molecule_graph=molecule_graph, **atom_pair_fp_params)
         elif fingerprint_type == "torsion_fingerprint":
             torsion_params = {}
             torsion_params.update(fingerprint_params)
-            self._set_torsion_fingerprint(
-                molecule_graph=molecule_graph, **torsion_params
-            )
+            self._set_torsion_fingerprint(molecule_graph=molecule_graph, **torsion_params)
         elif fingerprint_type.split(":")[0] == "mordred":
             mordred_params = {}
             self._set_mordred_descriptor(
@@ -418,18 +381,11 @@ def get_folded_fprint(self, fold_to_length):
             raise ValueError("Can only fold fingerprints")
         fingerprint = self.to_numpy()
         if len(fingerprint) < fold_to_length:
-            raise InvalidConfigurationError(
-                f"Cannot fold fingerprint of "
-                f"length {len(fingerprint)}to a "
-                f"higher length {fold_to_length}"
-            )
+            raise InvalidConfigurationError(f"Cannot fold fingerprint of " f"length {len(fingerprint)}to a " f"higher length {fold_to_length}")
         n_folds = np.log2(len(fingerprint) / fold_to_length)
         if n_folds - int(n_folds) > 0.0:
             raise InvalidConfigurationError(
-                f"Fingerprint length "
-                f"{len(fingerprint)} not "
-                f"a 2-multiple of required "
-                f"folded length {fold_to_length}"
+                f"Fingerprint length " f"{len(fingerprint)} not " f"a 2-multiple of required " f"folded length {fold_to_length}"
             )
         for _ in range(int(n_folds)):
             mid_point = int(len(fingerprint) / 2)
@@ -484,9 +440,7 @@ def fold_to_equal_length(fingerprint1, fingerprint2):
                 fprint2_arr,
             )
         else:
-            return fprint1_arr, fingerprint2.get_folded_fprint(
-                fold_to_length=len(fprint1_arr)
-            )
+            return fprint1_arr, fingerprint2.get_folded_fprint(fold_to_length=len(fprint1_arr))
 
     @staticmethod
     def get_supported_fprints():

diff --git a/aimsim/utils/extras.py b/aimsim/utils/extras.py
Original file line number	Diff line number	Diff line change
		@@ -1 +1 @@
		global-include config.yaml .png .csv *.md requirements.txt
		global-include config.yaml .png .csv *.md requirements.txt requirements_core.txt