Formatting and changed tests to functional (#2)

* Fixed all test for new format
* Restructured utils functions

---------

Co-authored-by: Anders S. Christensen <andersbiceps@gmail.com>
Co-authored-by: Lars Andersen Bratholm <larsbratholm@gmail.com>

.pre-commit-config.yaml

@@ -1,3 +1,5 @@
+# TODO Added grep test for src; no print allowed, no assert allowed
+
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks

Makefile

@@ -21,11 +21,7 @@ format:
 	${python} -m pre_commit run --all-files
 
 test:
-	${python} -m pytest -rs \
-	./tests/test_kernels.py \
-	./tests/test_solvers.py \
-	./tests/test_distance.py \
-	./tests/test_slatm.py
+	${python} -m pytest -rs ./tests
 
 types:
 	${python} -m monkeytype run $(which pytest) ./tests/

README.rst

@@ -19,6 +19,11 @@ applications, but without the high-level abstraction, for example SKLearn.
 
 This package is and should stay free-function design oriented.
 
+Breaking changes from `qml`:
+
+ - FCHL representations callable interface to be consistent with other representations (e.i. atoms, coordinates)
+
+
 ====
 How to install
 ====

_compile.py

@@ -8,6 +8,7 @@
     "representations/frepresentations": ["frepresentations.f90"],
     "representations/facsf": ["facsf.f90"],
     "representations/fslatm": ["fslatm.f90"],
+    "representations/arad/farad_kernels": ["farad_kernels.f90"],
     "representations/fchl/ffchl_module": [
         "ffchl_module.f90",
         "ffchl_scalar_kernels.f90",
@@ -41,7 +42,9 @@ def find_flags(fcc: str):
     #                 "-Wno-maybe-uninitialized", "-Wno-unused-function", "-Wno-cpp"]
     # LINKER_FLAGS = ["-lgomp"]
 
-    flags = ["-L/usr/lib/", "-lblas", "-llapack"]
+    extra_flags = ["-lgomp", "-lpthread", "-lm", "-ldl"]
+
+    flags = ["-L/usr/lib/", "-lblas", "-llapack"] + extra_flags
 
     return flags
 

environment_dev.yaml

@@ -8,6 +8,7 @@ dependencies:
   - monkeytype
   - numpy
   - pandas
+  - pyarrow
   - pip
   - pre-commit
   - pytest

src/qmllib/kernels/__init__.py

@@ -1,3 +1,3 @@
-from .distance import *
-from .gradient_kernels import *
-from .kernels import *
+from qmllib.kernels.distance import *  # noqa:F403
+from qmllib.kernels.gradient_kernels import *  # noqa:F403
+from qmllib.kernels.kernels import *  # noqa:F403

src/qmllib/kernels/distance.py

@@ -77,7 +77,7 @@ def p_distance(A, B, p=2):
     The value of the keyword argument ``p =`` sets the norm order.
     E.g. ``p = 1.0`` and ``p = 2.0`` with yield the Manhattan and L2 distances, respectively.
 
-        .. math:: D_{ij} = \|A_i - B_j\|_p
+        .. math:: D_{ij} = \\|A_i - B_j\\|_p
 
     Where :math:`A_{i}` and :math:`B_{j}` are representation vectors.
     D is calculated using an OpenMP parallel Fortran routine.
@@ -104,13 +104,13 @@ def p_distance(A, B, p=2):
 
     D = np.empty((na, nb), order="F")
 
-    if type(p) == type(1):
+    if isinstance(p, int):
         if p == 2:
             fl2_distance(A, B, D)
         else:
             fp_distance_integer(A.T, B.T, D, p)
 
-    elif type(p) == type(1.0):
+    elif isinstance(p, float):
         if p.is_integer():
             p = int(p)
             if p == 2:

src/qmllib/kernels/gradient_kernels.py

@@ -1,7 +1,11 @@
-import ctypes
-
 import numpy as np
 
+from qmllib.utils.environment_manipulation import (
+    mkl_get_num_threads,
+    mkl_reset_num_threads,
+    mkl_set_num_threads,
+)
+
 from .fgradient_kernels import (
     fatomic_local_gradient_kernel,
     fatomic_local_kernel,
@@ -18,33 +22,6 @@
 )
 
 
-def mkl_set_num_threads(cores):
-
-    if cores is None:
-        return
-
-    try:
-        mkl_rt = ctypes.CDLL("libmkl_rt.so")
-        mkl_rt.mkl_set_num_threads(ctypes.byref(ctypes.c_int(cores)))
-
-    except:
-
-        pass
-
-
-def mkl_get_num_threads():
-
-    try:
-        mkl_rt = ctypes.CDLL("libmkl_rt.so")
-        mkl_num_threads = mkl_rt.mkl_get_max_threads()
-
-        return mkl_num_threads
-
-    except:
-
-        return None
-
-
 def get_global_kernel(X1, X2, Q1, Q2, SIGMA):
     """Calculates the Gaussian kernel matrix K with the local decomposition where :math:`K_{ij}`:
 
@@ -427,7 +404,10 @@ def get_atomic_local_gradient_kernel(X1, X2, dX2, Q1, Q2, SIGMA):
     )
 
     # Reset MKL_NUM_THREADS back to its original value
-    mkl_set_num_threads(original_mkl_threads)
+    if original_mkl_threads is not None:
+        mkl_set_num_threads(original_mkl_threads)
+    else:
+        mkl_reset_num_threads()
 
     return K
 

src/qmllib/representations/__init__.py

@@ -1 +1 @@
-from .representations import *
+from .representations import *  # noqa:F403

src/qmllib/representations/arad/__init__.py

@@ -0,0 +1,23 @@
+# MIT License
+#
+# Copyright (c) 2017 Anders S. Christensen and Felix A. Faber
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+from .arad import *