Setup Python package information and build setup for 3.12 (#1)

.github/workflows/test.yml

@@ -0,0 +1,35 @@
+
+name: Test Python package
+
+on:
+  push:
+    branches:
+      - '**'
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  test:
+    name: Testing
+    runs-on: "ubuntu-latest"
+    defaults:
+      run:
+        shell: bash -l {0}
+    strategy:
+      matrix:
+        python-version: ['3.12']
+    steps:
+      - uses: actions/checkout@v2
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          activate-environment: dev
+          environment-file: ./environment_dev.yaml
+          python-version: ${{ matrix.python-version }}
+      - run: |
+          ls
+          pwd
+          which python
+          conda info
+      - run: pip install . -v
+      - run: make test python=python
+      # - run: make format python=python

.gitignore

@@ -1,3 +1,9 @@
+# repo specific
+./env
+*.sqlite3
+*.whl
+
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]

.pre-commit-config.yaml

@@ -21,7 +21,7 @@ repos:
         args: ['--maxkb=3000']
 
   - repo: https://github.com/myint/autoflake
-    rev: v1.4
+    rev: v2.2.0
     hooks:
       - id: autoflake
         name: Removes unused variables
@@ -54,7 +54,7 @@ repos:
         args: ["--line-length=99"]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
+    rev: 7.0.0
     hooks:
       - id: flake8
         name: Checks pep8 style
@@ -65,7 +65,8 @@ repos:
           # ignore long comments (E501), as long lines are formatted by black
           # ignore Whitespace before ':' (E203)
           # ignore Line break occurred before a binary operator (W503)
-          "--ignore=E501,E203,W503",
+          # ignore ambiguous variable name (E741)
+          "--ignore=E501,E203,W503,E741",
         ]
 
   - repo: https://github.com/pseewald/fprettify

Makefile

@@ -0,0 +1,57 @@
+python=./env/bin/python
+mamba=mamba
+pkg=qmllib
+pip=./env/bin/pip
+j=1
+
+.PHONY: build
+
+all: env setup
+
+env:
+	${mamba} env create -f ./environment_dev.yaml -p ./env --quiet
+	${pip} install -e .
+
+setup: ./.git/hooks/pre-commit
+
+./.git/hooks/pre-commit:
+	${python} -m pre_commit install
+
+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
+
+types:
+	${python} -m monkeytype run $(which pytest) ./tests/
+	${python} -m monkeytype list-modules | grep ${pkg} | parallel -j${j} "${python} -m monkeytype apply {}"
+
+cov:
+	${python} -m pytest -vrs --cov=${pkg} --cov-report html tests
+
+compile:
+	${python} _compile.py
+
+build:
+	@#${python} -m build .
+	# ${python} -m pip wheel --no-deps -v .
+	${python} -m pip wheel -v .
+	ls *.whl
+
+clean:
+	find ./src/ -type f \
+		-name "*.so" \
+		-name "*.pyc" \
+		-name ".pyo" \
+		-delete
+	rm -rf *.whl
+	rm -fr ./build/ ./__pycache__/
+
+clean-env:
+	rm -rf ./env/
+	rm ./.git/hooks/pre-commit

README.rst

@@ -23,7 +23,30 @@ This package is and should stay free-function design oriented.
 How to install
 ====
 
-    raise NotImplementedError
+A proper pip-package is on the way, for now
+
+    pip install git+https://github.com/qmlcode/qmllib
+
+or if you want a specific feature branch
+
+    pip install git+https://github.com/qmlcode/qmllib@feature_branch
+
+====
+How to start developing
+====
+
+Know a issue and want to get started developing?
+
+    git clone repo.url qmllib.git
+    cd qmllib.git
+    make # setup env
+    make compile # compile
+
+You know have a conda environment in `./env` and are ready to run
+
+    make test
+
+happy developing
 
 ====
 How to use
@@ -45,3 +68,11 @@ How to contribute
  * Create pull requests
  * Create discussions
 
+=====
+What TODO
+=====
+
+ * Setup ifort flags
+ * Setup based on FCC env variable or --global-option flags
+ * Find MKL from env (for example conda)
+ * Find what numpy has been linked too (lapack or mkl)

_compile.py

@@ -0,0 +1,89 @@
+""" Compile script for Fortran """
+
+import os
+import subprocess
+from pathlib import Path
+
+f90_modules = {
+    "representations/frepresentations": ["frepresentations.f90"],
+    "representations/facsf": ["facsf.f90"],
+    "representations/fslatm": ["fslatm.f90"],
+    "representations/fchl/ffchl_module": [
+        "ffchl_module.f90",
+        "ffchl_scalar_kernels.f90",
+        "ffchl_kernel_types.f90",
+        "ffchl_kernels.f90",
+        "ffchl_electric_field_kernels.f90",
+        "ffchl_force_kernels.f90",
+    ],
+    "solvers/fsolvers": ["fsolvers.f90"],
+    "kernels/fdistance": ["fdistance.f90"],
+    "kernels/fkernels": ["fkernels.f90", "fkpca.f90"],
+    "kernels/fgradient_kernels": ["fgradient_kernels.f90"],
+}
+
+
+def find_mkl():
+
+    return
+
+
+def find_flags(fcc: str):
+    """Find compiler flags"""
+
+    # 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"]
+
+    flags = ["-L/usr/lib/", "-lblas", "-llapack"]
+
+    return flags
+
+
+def find_fcc():
+    """Find the fortran compiler. Either gnu or intel"""
+
+    # fcc = "ifort"
+    fcc = "gfortran"
+
+    return fcc
+
+
+def main():
+    """Compile f90 in src/qmllib"""
+
+    fcc = find_fcc()
+    flags = find_flags(fcc)
+
+    os.environ["FCC"] = fcc
+
+    for module_name, module_sources in f90_modules.items():
+
+        path = Path(module_name)
+
+        parent = path.parent
+        stem = path.stem
+        cwd = Path("src/qmllib") / parent
+        cmd = ["python", "-m", "numpy.f2py", "-c"] + flags + module_sources + ["-m", str(stem)]
+        print(cwd, " ".join(cmd))
+
+        proc = subprocess.run(cmd, cwd=cwd, capture_output=True, text=True)
+        stdout = proc.stdout
+        stderr = proc.stderr
+        exitcode = proc.returncode
+
+        if exitcode > 0:
+            print(stdout)
+            print()
+            print(stderr)
+            exit(exitcode)
+
+
+if __name__ == "__main__":
+    main()

environment_dev.yaml

@@ -0,0 +1,18 @@
+name: qmllib_dev
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - python==3.12
+  - jupytext
+  - monkeytype
+  - numpy
+  - pandas
+  - pip
+  - pre-commit
+  - pytest
+  - scikit-learn
+  - scipy
+  # build
+  - meson
+  - ninja

pyproject.toml

@@ -0,0 +1,25 @@
+[build-system]
+requires = ["setuptools", "numpy", "meson", "ninja"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qmllib"
+dynamic = ["version"]
+authors = []
+requires-python = ">=3.12"
+
+[options.packages.find]
+where="src"
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.dynamic]
+version = {attr = "qmllib.version.__version__"}
+
+[tool.setuptools.package-data]
+"*" = ['*.so']
+
+
+# [tool.black]
+# line-length = 120

pyrightconfig.json

@@ -0,0 +1,8 @@
+{
+  "include": [
+    "src"
+  ],
+  "exclude": [
+    "env"
+  ]
+}

pytest.ini

@@ -0,0 +1,4 @@
+[pytest]
+log_cli_level = DEBUG
+log_cli_format = %(asctime)s [%(levelname)8s] %(message)s (%(filename)s:%(lineno)s)
+log_cli_date_format=%Y-%m-%d %H:%M:%S

setup.py

@@ -0,0 +1,14 @@
+import sys
+from pathlib import Path
+
+from setuptools import setup
+
+try:
+    import _compile
+except ImportError:
+    sys.path.append(str(Path(__file__).resolve().parent))
+    import _compile
+
+if __name__ == "__main__":
+    _compile.main()
+    setup()

src/qmllib/__init__.py

@@ -0,0 +1 @@
+from qmllib.version import __version__