Compiled with numpy 2.0

.pre-commit-config.yaml

@@ -3,7 +3,7 @@
 repos:
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v5.0.0
     hooks:
       - id: trailing-whitespace
         exclude: ^tests/resources/
@@ -23,7 +23,7 @@ repos:
         args: ['--maxkb=3000']
 
   - repo: https://github.com/myint/autoflake
-    rev: v2.2.0
+    rev: v2.3.1
     hooks:
       - id: autoflake
         name: Removes unused variables
@@ -48,15 +48,15 @@ repos:
         ]
 
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 24.10.0
     hooks:
       - id: black
         name: Fixes formatting
         language_version: python3
         args: ["--line-length=99"]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 7.0.0
+    rev: 7.1.1
     hooks:
       - id: flake8
         name: Checks pep8 style
@@ -71,7 +71,7 @@ repos:
           "--ignore=E501,E203,W503,E741",
         ]
 
-  - repo: https://github.com/pseewald/fprettify
+  - repo: https://github.com/fortran-lang/fprettify
     rev: v0.3.7
     hooks:
       - id: fprettify

Makefile

@@ -31,7 +31,7 @@ test:
 
 types:
 	${python} -m monkeytype run $$(which ${pytest}) ./tests
-	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j${j} "${python} -m monkeytype apply {}"
+	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j${j} "${python} -m monkeytype apply {} > /dev/null && echo {}"
 
 cov:
 	${python} -m pytest -vrs --cov=${pkg} --cov-report html tests

README.rst

@@ -23,11 +23,18 @@ Breaking changes from ``qml``:
 
 * FCHL representations callable interface to be consistent with other representations (e.i. atoms, coordinates)
 
-
 ==============
 How to install
 ==============
 
+You need a fortran compiler and math library. Default is `gfortran` and `openblas`.
+
+
+.. code-block:: bash
+
+    sudo apt install libopenblas-dev gcc
+
+
 A proper pip-package is on the way, for now
 
 .. code-block:: bash

_compile.py

@@ -5,67 +5,85 @@
 import sys
 from pathlib import Path
 
+import numpy as np
+
 f90_modules = {
     "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",
         "ffchl_kernel_types.f90",
+        "ffchl_module.f90",
+        "ffchl_module_ef.f90",
         "ffchl_kernels.f90",
-        "ffchl_electric_field_kernels.f90",
+        "ffchl_scalar_kernels.f90",
+        "ffchl_kernels_ef.f90",
         "ffchl_force_kernels.f90",
     ],
     "solvers/fsolvers": ["fsolvers.f90"],
     "kernels/fdistance": ["fdistance.f90"],
-    "kernels/fkernels": ["fkernels.f90", "fkpca.f90"],
+    "kernels/fkernels": [
+        "fkernels.f90",
+        "fkpca.f90",
+        "fkwasserstein.f90",
+    ],
     "kernels/fgradient_kernels": ["fgradient_kernels.f90"],
+    "utils/fsettings": ["fsettings.f90"],
 }
 
 
 def find_mkl():
-
-    return
+    raise NotImplementedError()
 
 
-def find_flags(fcc: str):
+def find_env() -> dict[str, str]:
     """Find compiler flags"""
 
+    # TODO Find ifort flags, choose from FCC
     # TODO Find math lib
     # TODO Find os
 
-    # -lgomp", "-lpthread", "-lm", "-ldl
-    # ["-L${MKLROOT}/lib/intel64", "-lmkl_rt"]
-
-    # COMPILER_FLAGS = ["-O3", "-fopenmp", "-m64", "-march=native", "-fPIC",
-    #                 "-Wno-maybe-uninitialized", "-Wno-unused-function", "-Wno-cpp"]
-    # LINKER_FLAGS = ["-lgomp"]
+    COMPILER_FLAGS = [
+        "-O3",
+        "-fopenmp",
+        "-m64",
+        "-march=native",
+        "-fPIC",
+        "-Wno-maybe-uninitialized",
+        "-Wno-unused-function",
+        "-Wno-cpp",
+    ]
 
     extra_flags = ["-lgomp", "-lpthread", "-lm", "-ldl"]
+    math_flags = ["-L/usr/lib/", "-lblas", "-llapack"]
 
-    flags = ["-L/usr/lib/", "-lblas", "-llapack"] + extra_flags
-
-    return flags
-
-
-def find_fcc():
-    """Find the fortran compiler. Either gnu or intel"""
-
-    # fcc = "ifort"
+    fflags = [] + COMPILER_FLAGS
+    ldflags = [] + extra_flags + math_flags
     fcc = "gfortran"
 
-    return fcc
+    env = {"FFLAGS": " ".join(fflags), "LDFLAGS": " ".join(ldflags), "FCC": fcc}
+
+    return env
 
 
 def main():
     """Compile f90 in src/qmllib"""
 
-    fcc = find_fcc()
-    flags = find_flags(fcc)
+    print(f"Using numpy {np.__version__}")
+
+    # Find and set Fortran compiler, compiler flags and linker flags
+    env = find_env()
+    for key, value in env.items():
+        print(f"export {key}='{value}'")
+        os.environ[key] = value
+
+    f2py = [sys.executable, "-m", "numpy.f2py"]
 
-    os.environ["FCC"] = fcc
+    meson_flags = [
+        "--backend",
+        "meson",
+    ]
 
     for module_name, module_sources in f90_modules.items():
 
@@ -74,9 +92,7 @@ def main():
         stem = path.stem
 
         cwd = Path("src/qmllib") / parent
-        cmd = (
-            [sys.executable, "-m", "numpy.f2py", "-c"] + flags + module_sources + ["-m", str(stem)]
-        )
+        cmd = f2py + ["-c"] + module_sources + ["-m", str(stem)] + meson_flags
         print(cwd, " ".join(cmd))
 
         proc = subprocess.run(cmd, cwd=cwd, capture_output=True, text=True)
@@ -85,9 +101,9 @@ def main():
         exitcode = proc.returncode
 
         if exitcode > 0:
-            print(stdout)
-            print()
             print(stderr)
+            print()
+            print(stdout)
             exit(exitcode)
 
 

environment_dev.yaml

@@ -4,19 +4,22 @@ channels:
   - defaults
 dependencies:
   - python==3.12
-  - jupytext
-  - monkeytype
-  - numpy<2.0.0
-  - pandas
   - pip
-  - pre-commit
-  - pyarrow
-  - pytest
-  - scikit-learn
-  - scipy
-  # build
-  - build
-  - meson
-  - ninja
-  # publish
-  - twine
+  - pip:
+    - jupytext
+    - monkeytype
+    - numpy<2.0.0
+    - pandas
+    - pandas
+    - pip
+    - pre-commit
+    - pyarrow
+    - pytest
+    - scikit-learn
+    - scipy
+    # build
+    - build
+    - meson
+    - ninja
+    # publish
+    - twine