Successfull setup of solvers

Makefile

@@ -1,22 +1,33 @@
-python=python
+python=./env/bin/python
 mamba=mamba
 pkg=qmllib
 pip=./env/bin/pip
 
-all: env
+all: env setup
 
 env:
 	${mamba} env create -f ./environment_dev.yaml -p ./env --quiet
 	${pip} install -e .
 
-setup:
-	pre-commit install
+setup: ./.git/hooks/pre-commit
+
+./.git/hooks/pre-commit:
+	${python} -m pre_commit install
 
 format:
-	pre-commit run --all-files
+	${python} pre_commit run --all-files
 
 test:
-	${python} -m pytest -rs tests
+	${python} -m pytest -rs ./tests/test_solvers.py
+
+types:
+	# ${python} -m monkeytype run $(which pytest) ./tests/test_solvers.py
+	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j1 "${python} -m monkeytype apply {}"
 
 cov:
 	${python} -m pytest -vrs --cov=${pkg} --cov-report html tests
+
+clean:
+	rm -rf ./env/
+	find ./src/ | grep -E "\(/__pycache__$$|\.pyc$$|\.pyo$$\)" | xargs rm -rf
+	rm ./.git/hooks/pre-commit

environment_dev.yaml

@@ -3,15 +3,13 @@ channels:
   - conda-forge
   - defaults
 dependencies:
+  - python==3.11
   - jupytext
   - monkeytype
   - numpy
-  - openbabel
   - pandas
   - pip
   - pre-commit
   - pytest
   - scikit-learn
   - scipy
-  - pip:
-     - pybel

pyproject.toml

@@ -9,7 +9,7 @@ authors = []
 requires-python = ">=3.10"
 
 [tool.setuptools.dynamic]
-version = {attr = "qmllib.__version__"}
+version = {attr = "qmllib.version.__version__"}
 
 [options.packages.find]
 where="src"

src/qmllib/__init__.py

@@ -1 +1 @@
-from qmllib.__version__ import VERSION as __version__
+from qmllib.version import __version__

src/qmllib/solvers/Makefile

@@ -0,0 +1,2 @@
+all:
+	f2py -L/usr/lib/ -lblas -llapack -c ./fsolvers.f90 -m fsolvers

src/qmllib/math/math.py → src/qmllib/solvers/__init__.py

@@ -1,4 +1,5 @@
 import numpy as np
+from numpy import ndarray
 
 from .fsolvers import (
     fbkf_invert,
@@ -12,7 +13,7 @@
 )
 
 
-def cho_invert(A):
+def cho_invert(A: ndarray) -> ndarray:
     """Returns the inverse of a positive definite matrix, using a Cholesky decomposition
     via calls to LAPACK dpotrf and dpotri in the F2PY module.
 
@@ -26,20 +27,20 @@ def cho_invert(A):
     if len(A.shape) != 2 or A.shape[0] != A.shape[1]:
         raise ValueError("expected square matrix")
 
-    I = np.asfortranarray(A)
+    matrix = np.asfortranarray(A)
 
-    fcho_invert(I)
+    fcho_invert(matrix)
 
     # Matrix to store the inverse
     i_lower = np.tril_indices_from(A)
 
     # Copy lower triangle to upper
-    I.T[i_lower] = I[i_lower]
+    matrix.T[i_lower] = matrix[i_lower]
 
-    return I
+    return matrix
 
 
-def cho_solve(A, y, l2reg=0.0, destructive=False):
+def cho_solve(A: ndarray, y: ndarray, l2reg: float = 0.0, destructive: bool = False) -> ndarray:
     """Solves the equation
 
         :math:`A x = y`
@@ -90,7 +91,7 @@ def cho_solve(A, y, l2reg=0.0, destructive=False):
     return x
 
 
-def bkf_invert(A):
+def bkf_invert(A: ndarray) -> ndarray:
     """Returns the inverse of a positive definite matrix, using a Bausch-Kauffman decomposition
     via calls to LAPACK dpotrf and dpotri in the F2PY module.
 
@@ -104,20 +105,20 @@ def bkf_invert(A):
     if len(A.shape) != 2 or A.shape[0] != A.shape[1]:
         raise ValueError("expected square matrix")
 
-    I = np.asfortranarray(A)
+    matrix = np.asfortranarray(A)
 
-    fbkf_invert(I)
+    fbkf_invert(matrix)
 
     # Matrix to store the inverse
     i_lower = np.tril_indices_from(A)
 
     # Copy lower triangle to upper
-    I.T[i_lower] = I[i_lower]
+    matrix.T[i_lower] = matrix[i_lower]
 
-    return I
+    return matrix
 
 
-def bkf_solve(A, y):
+def bkf_solve(A: ndarray, y: ndarray) -> ndarray:
     """Solves the equation
 
         :math:`A x = y`

src/qmllib/version.py

@@ -0,0 +1 @@
+__version__ = "1.0.0"

tests/test_math.py → tests/test_solvers.py

@@ -3,8 +3,7 @@
 
 import numpy as np
 
-import qmllib
-import qmllib.math
+from qmllib.solvers import bkf_invert, bkf_solve, cho_invert, cho_solve
 
 
 def test_cho_solve():
@@ -16,7 +15,7 @@ def test_cho_solve():
 
     A = deepcopy(A_ref)
     y = deepcopy(y_ref)
-    x_qml = qmllib.math.cho_solve(A, y)
+    x_qml = cho_solve(A, y)
 
     # Check arrays are unchanged
     assert np.allclose(y, y_ref)
@@ -36,7 +35,7 @@ def test_cho_invert():
     A_ref = np.loadtxt(test_dir + "/data/K_local_gaussian.txt")
 
     A = deepcopy(A_ref)
-    Ai_qml = qmllib.math.cho_invert(A)
+    Ai_qml = cho_invert(A)
 
     # Check A is unchanged
     assert np.allclose(A, A_ref)
@@ -55,7 +54,7 @@ def test_bkf_invert():
     A_ref = np.loadtxt(test_dir + "/data/K_local_gaussian.txt")
 
     A = deepcopy(A_ref)
-    Ai_qml = qmllib.math.bkf_invert(A)
+    Ai_qml = bkf_invert(A)
 
     # Check A is unchanged
     assert np.allclose(A, A_ref)
@@ -76,7 +75,7 @@ def test_bkf_solve():
 
     A = deepcopy(A_ref)
     y = deepcopy(y_ref)
-    x_qml = qmllib.math.bkf_solve(A, y)
+    x_qml = bkf_solve(A, y)
 
     # Check arrays are unchanged
     assert np.allclose(y, y_ref)