updates - restructure

.github/workflows/ci.yml

@@ -0,0 +1,34 @@
+name:CI
+
+on:
+  push:
+  pull_request:
+
+jobs:
+  run-tests:
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+          python-version:
+            - "3.11"
+
+    name: Test
+    runs-on: ${{matrix.os}}
+
+    steps:
+      - name: checkout
+        uses: actions/checkout@v3
+
+      - name: setup
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{matrix.python-version}}
+
+      - name: install deps
+        run: |
+          python -m pip install --upgrade pip
+          pip install -r requirements.txt
+      
+      - name: run tests
+        run: pytest

pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+requires = ["setuptools>=42.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tools.pytest.ini_options]
+adopts = '--cov=complexes'
+testpaths = [
+    "tests"
+]
+
+[mypy]
+mypy_path = "src"
+check_untyped_defs = false
+disallow_any_generics = false
+ignore_missing_imports = true
+show_error_codes = true
+ignore_errors = true

requirements.txt

@@ -13,27 +13,33 @@ beautifulsoup4==4.12.3
 biopandas==0.5.1.dev0
 biopython==1.83
 bioservices==1.11.2
+black==24.3.0
 bleach==6.1.0
 botorch==0.10.0
+cachetools==5.3.3
 cattrs==23.2.3
 certifi==2024.2.2
 cffi==1.16.0
+chardet==5.2.0
 charset-normalizer==3.3.2
 click==8.1.7
 colorama==0.4.6
 colorlog==6.8.2
 comm==0.2.2
 contourpy==1.2.0
+coverage==7.4.4
 cycler==0.12.1
 debugpy==1.8.1
 decorator==5.1.1
 deepdiff==6.7.1
 defusedxml==0.7.1
 dill==0.3.8
+distlib==0.3.8
 easydev==0.13.1
 executing==2.0.1
 fastjsonschema==2.19.1
 filelock==3.13.1
+flake8==7.0.0
 fonttools==4.50.0
 fqdn==1.5.1
 fsspec==2024.3.1
@@ -42,13 +48,13 @@ gevent==24.2.1
 gmsh==4.12.2
 gmsh_interop==2021.1.1
 gpytorch==1.11
-graphein==1.7.6
 greenlet==3.0.3
 grequests==0.7.0
 h11==0.14.0
 httpcore==1.0.4
 httpx==0.27.0
 idna==3.6
+iniconfig==2.0.0
 ipykernel==6.29.3
 ipython==8.22.2
 isoduration==20.11.0
@@ -82,6 +88,7 @@ markdown-it-py==3.0.0
 MarkupSafe==2.1.5
 matplotlib==3.8.3
 matplotlib-inline==0.1.6
+mccabe==0.7.0
 mdurl==0.1.2
 meshio==5.3.5
 MeshPy==2022.1.3
@@ -92,6 +99,7 @@ mmtf-python==1.1.3
 mpmath==1.3.0
 msgpack==1.0.8
 multipledispatch==1.0.0
+mypy==1.9.0
 mypy-extensions==1.0.0
 nbclient==0.10.0
 nbconvert==7.16.3
@@ -112,20 +120,26 @@ pexpect==4.9.0
 pillow==10.2.0
 platformdirs==4.2.0
 plotly==5.20.0
+pluggy==1.4.0
 prometheus_client==0.20.0
 prompt-toolkit==3.0.43
 psutil==5.9.8
 ptyprocess==0.7.0
 pure-eval==0.2.2
 pybind11==2.11.1
+pycodestyle==2.11.1
 pycparser==2.21
 pydantic==1.10.14
+pyflakes==3.2.0
 Pygments==2.17.2
 pygmsh==7.1.17
 pyparsing==3.1.2
+pyproject-api==1.6.1
 pyquaternion==0.9.9
 pyro-api==0.1.2
 pyro-ppl==1.9.0
+pytest==8.1.1
+pytest-cov==5.0.0
 python-dateutil==2.9.0.post0
 python-json-logger==2.0.7
 pytools==2024.1.1
@@ -168,6 +182,7 @@ tzdata==2024.1
 uri-template==1.3.0
 url-normalize==1.4.3
 urllib3==2.2.1
+virtualenv==20.25.1
 wcwidth==0.2.13
 webcolors==1.13
 webencodings==0.5.1

setup.cfg

@@ -0,0 +1,25 @@
+[metadata]
+name = complexes
+description = atomistic system modeling
+author = Rahul Khorana
+license = MIT
+license_file = LICENSE
+platforms = unix, linux, osx
+classifiers = 
+    Programming Language :: Python :: 3.11
+
+[options]
+packages = 
+    complexes
+install_requires = 
+    requests >= 2
+python_requires = >= 3.11
+package_dir = src
+zip_safe = no
+
+[flake8]
+max-line-length = 160
+
+[mypy]
+ignore_missing_imports = True
+ignore_errors = True

setup.py

@@ -0,0 +1,4 @@
+from setuptools import setup
+
+if __name__ == "__main__":
+    setup()

src/atomic_complex.py → src/complexes/atomic_complex.py

@@ -1,8 +1,8 @@
 import jax
 import numpy as np
 from typing import List, Tuple
-from building_blocks import Electron, Proton, Neutron
-from general_utils import GeneralComplexUtils
+from complexes.building_blocks import Electron, Proton, Neutron
+from complexes.general_utils import GeneralComplexUtils
 
 
 seed = np.random.randint(0, 10 * 3)
@@ -143,7 +143,7 @@ def general_build_complex(
         self.build_electrons()
         assert isinstance(using_distances, bool)
         K = np.asarray([])
-        while self.AP:
+        while self.AP and self.P > 0:
             p = self.AP.pop()
             p = np.asarray(p, dtype=np.float32)
             res = gcu.get_nsphere_and_sampled_boundary(
@@ -154,7 +154,7 @@ def general_build_complex(
             gluing_map = gcu.nuclear_force_map(boundary, boundary, K)
             K = gcu.topological_disjoint_union(gluing_map, K, n_sphere)
 
-        while self.AN:
+        while self.AN and self.N > 0:
             n = self.AN.pop()
             n = np.asarray(n, dtype=np.float32)
             res = gcu.get_nsphere_and_sampled_boundary(
@@ -165,11 +165,14 @@ def general_build_complex(
             gluing_map = gcu.nuclear_force_map(boundary, boundary, K)
             K = gcu.topological_disjoint_union(gluing_map, K, n_sphere)
 
-        while self.AE:
+        while self.AE and self.E > 0:
             e, we = self.AE.pop()
             if using_distances and hasattr(update_distances, "__call__"):
                 update_distances(self.DE, we, e)
-            ec = np.array([e[0] for _ in range(len(n[0]))])
+            try:
+                ec = np.array([e[0] for _ in range(len(n[0]))])
+            except Exception:
+                ec = np.array([e[0] for _ in range(self.P + self.E)])
             res = gcu.get_nsphere_and_sampled_boundary(
                 radius=2.8 * fm, center=ec, sample=10000, eps=1e-19
             )
@@ -190,14 +193,14 @@ def sanity_test(kind, *args):
     if kind == "general":
         try:
             ac.general_build_complex()
-            print(f"success ✅")
-        except:
+            print("success ✅")
+        except Exception:
             print("failed ❌")
     else:
         try:
             ac.fast_build_complex()
-            print(f"success ✅")
-        except:
+            print("success ✅")
+        except Exception:
             print("failed ❌")
 
 

src/build_atom_lookup.py → src/complexes/build_atom_lookup.py

@@ -3,7 +3,7 @@
 import dill
 import numpy as np
 from collections import defaultdict
-from atomic_complex import AtomComplex
+from complexes.atomic_complex import AtomComplex
 
 
 class BuildAtoms:
@@ -46,7 +46,7 @@ def sanity(self):
             assert isinstance(table["Bk"], tuple)
             assert isinstance(table["Bk"][0], np.ndarray)
             print("Success ✅")
-        except:
+        except Exception:
             print("Failed ❌")
 
 

src/core_utils.py → src/complexes/core_utils.py

@@ -1,7 +1,5 @@
 import re
-import jax
 import numpy as np
-import jax.numpy as jnp
 from typing import Tuple
 from collections import defaultdict
 

src/general_utils.py → src/complexes/general_utils.py

@@ -5,7 +5,7 @@
 from typing import List, Tuple
 from collections import defaultdict
 from microstructpy.geometry.n_sphere import NSphere
-from core_utils import GluingMap
+from complexes.core_utils import GluingMap
 
 
 class GeneralComplexUtils:
@@ -48,7 +48,7 @@ def centered_2_norm(self, X: np.array, center: np.array) -> np.float32:
 
     def get_nsphere_and_sampled_boundary(
         self, radius: np.float32, center: np.ndarray, sample: int, eps: np.float32
-    ) -> List[list, np.ndarray]:
+    ) -> Tuple[list, np.ndarray]:
         representation = NSphere(r=radius, center=center)
         nsphere = representation.approximate()
         dim = center.shape[0]
@@ -80,8 +80,8 @@ def compute_norm(mat: np.ndarray) -> jnp.float32:
                 remain = dim - len(boundary)
                 if remain == dim:
                     limits = representation.limits
-                    for l in limits[0]:
-                        boundary.append(l)
+                    for lim in limits[0]:
+                        boundary.append(lim)
                     rem = dim - len(boundary)
                     for _ in range(rem):
                         eps = np.random.randint(0, 10 * 2) * 1e-19

src/polyatomic_complex.py → src/complexes/polyatomic_complex.py

@@ -4,8 +4,8 @@
 import numpy as np
 import jax.numpy as jnp
 from typing import List, Tuple
-from core_utils import GluingMap, ElectronField
-from building_blocks import Electron
+from complexes.core_utils import GluingMap, ElectronField
+from complexes.building_blocks import Electron
 
 
 class PolyAtomComplex:
@@ -102,8 +102,8 @@ def dir_sum(a: np.ndarray, b: np.ndarray) -> np.ndarray:
             return dsum
 
         while A:
-            I = A.pop(0)
-            num_elec, k, _, df, de = I
+            data = A.pop(0)
+            num_elec, k, _, df, de = data
             if len(C) == 0:
                 C = k
             phi = GluingMap(C, k, target=C).construct_map()
@@ -127,14 +127,14 @@ def sanity_test(atom_list, kind):
     if kind == "general":
         try:
             pac.general_build_complex()
-            print(f"success ✅")
-        except:
+            print("success ✅")
+        except Exception:
             print("failed ❌")
     else:
         try:
             pac.fast_build_complex()
-            print(f"success ✅")
-        except:
+            print("success ✅")
+        except Exception:
             print("failed ❌")
 
 

src/process_esol.py → src/complexes/process_esol.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from rdkit import Chem
 from collections import defaultdict
-from polyatomic_complex import PolyAtomComplex
+from complexes.polyatomic_complex import PolyAtomComplex
 
 
 class ProcessESOL:
@@ -65,8 +65,8 @@ def smiles_to_atoms(self, smile: str) -> list:
         for k in atom_counts:
             cleaned = regex.sub(" ", k).split(" ")
             res = []
-            for l in cleaned:
-                r = l.strip()
+            for ch in cleaned:
+                r = ch.strip()
                 if r != "" and " " not in r:
                     res.append(r)
             atoms_list += res

src/process_freesolv.py → src/complexes/process_freesolv.py

@@ -4,7 +4,7 @@
 import pandas as pd
 from rdkit import Chem
 from collections import defaultdict
-from polyatomic_complex import PolyAtomComplex
+from complexes.polyatomic_complex import PolyAtomComplex
 
 
 class ProcessFreeSolv:
@@ -65,8 +65,8 @@ def smiles_to_atoms(self, smile: str) -> list:
         for k in atom_counts:
             cleaned = regex.sub(" ", k).split(" ")
             res = []
-            for l in cleaned:
-                r = l.strip()
+            for ch in cleaned:
+                r = ch.strip()
                 if r != "" and " " not in r:
                     res.append(r)
             atoms_list += res