Setup repository for pypi package management (#4)

* Creating pip package setup

* Updated documentation

* Reconfigure package

* Set python based on sys

MANIFEST.in

@@ -0,0 +1,3 @@
+include *.py
+recursive-include src/qmllib *.f90
+global-exclude *~ *.py[cod] *.so

Makefile

@@ -11,7 +11,8 @@ all: env setup
 
 env:
 	${mamba} env create -f ./environment_dev.yaml -p ./env --quiet
-	${pip} install -e .
+	${python} -m pre_commit install
+	${python} -m pip install -e .
 
 setup: ./.git/hooks/pre-commit
 
@@ -35,19 +36,21 @@ compile:
 	${python} _compile.py
 
 build:
-	@#${python} -m build .
-	# ${python} -m pip wheel --no-deps -v .
-	${python} -m pip wheel -v .
-	ls *.whl
+	${python} -m build --sdist --skip-dependency-check  .
+	@# ${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 ./src/*.egg-info/
 	rm -rf *.whl
-	rm -fr ./build/ ./__pycache__/
+	rm -rf ./build/ ./__pycache__/
+	rm -rf ./dist/
 
 clean-env:
 	rm -rf ./env/

README.rst

@@ -9,75 +9,79 @@ building blocks to carry out efficient and accurate machine learning. As such,
 the goal is to provide usable and efficient implementations of concepts such as
 representations and kernels.
 
-====
+==============
 QML or QMLLib?
-====
+==============
 
 ``qmllib`` represents the core library functionality derived from the original
 QML package, providing a powerful toolkit for quantum machine learning
 applications, but without the high-level abstraction, for example SKLearn.
 
 This package is and should stay free-function design oriented.
 
-Breaking changes from `qml`:
+Breaking changes from ``qml``:
 
- - FCHL representations callable interface to be consistent with other representations (e.i. atoms, coordinates)
+* FCHL representations callable interface to be consistent with other representations (e.i. atoms, coordinates)
 
 
-====
+==============
 How to install
-====
+==============
 
 A proper pip-package is on the way, for now
 
+.. code-block:: bash
+
     pip install git+https://github.com/qmlcode/qmllib
 
 or if you want a specific feature branch
 
+.. code-block:: bash
+
     pip install git+https://github.com/qmlcode/qmllib@feature_branch
 
-====
-How to start developing
-====
+=================
+How to contribute
+=================
 
 Know a issue and want to get started developing?
 
+.. code-block:: bash
+
     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
 
+.. code-block:: bash
+
     make test
 
 happy developing
 
-====
+==========
 How to use
-====
+==========
+
+.. code-block:: python
 
     raise NotImplementedError
 
-====
+===========
 How to cite
-====
+===========
 
-    raise NotImplementedError
+.. code-block:: python
 
-=====
-How to contribute
-=====
-
- * Raise issues
- * Create pull requests
- * Create discussions
+    raise NotImplementedError
 
-=====
+=========
 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)
+* 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

@@ -2,6 +2,7 @@
 
 import os
 import subprocess
+import sys
 from pathlib import Path
 
 f90_modules = {
@@ -69,11 +70,13 @@ def main():
     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)]
+        cmd = (
+            [sys.executable, "-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)

environment_dev.yaml

@@ -8,12 +8,14 @@ dependencies:
   - monkeytype
   - numpy
   - pandas
-  - pyarrow
   - pip
   - pre-commit
+  - pyarrow
   - pytest
   - scikit-learn
   - scipy
   # build
+  - build
   - meson
   - ninja
+  - twine

pyproject.toml

@@ -6,7 +6,23 @@ build-backend = "setuptools.build_meta"
 name = "qmllib"
 dynamic = ["version"]
 authors = []
-requires-python = ">=3.12"
+requires-python = ">=3.8"
+readme="README.rst"
+description="Python/Fortran toolkit for representation of molecules and solids for machine learning of properties of molecules and solids."
+classifiers = [
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python",
+    "Topic :: Scientific/Engineering :: Artificial Intelligence",
+    "Topic :: Scientific/Engineering :: Chemistry",
+]
+keywords = ["qml", "quantum chemistry", "machine learning"]
+dependencies=["numpy", "scipy"]
+
+[project.urls]
+Homepage = "https://qmlcode.org"
 
 [options.packages.find]
 where="src"
@@ -20,6 +36,5 @@ version = {attr = "qmllib.version.__version__"}
 [tool.setuptools.package-data]
 "*" = ['*.so']
 
-
 # [tool.black]
 # line-length = 120

setup.py

@@ -1,14 +1,26 @@
-import sys
-from pathlib import Path
-
 from setuptools import setup
 
 try:
     import _compile
 except ImportError:
+    import sys
+    from pathlib import Path
+
     sys.path.append(str(Path(__file__).resolve().parent))
     import _compile
 
 if __name__ == "__main__":
     _compile.main()
-    setup()
+    setup(
+        description="Python/Fortran toolkit for representation of molecules and solids for machine learning of properties of molecules and solids.",
+        classifiers=[
+            "Intended Audience :: Developers",
+            "Intended Audience :: Science/Research",
+            "License :: OSI Approved :: MIT License",
+            "Programming Language :: Python :: 3",
+            "Programming Language :: Python",
+            "Topic :: Scientific/Engineering :: Artificial Intelligence",
+            "Topic :: Scientific/Engineering :: Chemistry",
+        ],
+        keywords=["qml", "quantum chemistry", "machine learning"],
+    )

src/qmllib/version.py

@@ -1 +1 @@
-__version__ = "1.0.0"
+__version__ = "1.0.1"