modernise packaging, and better manage optional depencencies

pyproject.toml

@@ -0,0 +1,66 @@
+[build-system]
+requires = [
+    "setuptools",
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "qstack"
+#version = "0.0.0"
+dynamic = ["version"]
+description = "Stack of codes for dedicated pre- and post-processing tasks for Quantum Machine Learning"
+readme = "README.md"
+license = {file = "LICENSE"}
+
+authors = [
+    {name = "Alberto Fabrisio"},  # orcid = "0000-0002-4440-3149"
+    {name = "Ksenia Briling", email = "[email protected]"},  # orcid = "0000-0003-2250-9898"
+    {name = "Yannick Calvino", email = "[email protected]"},  # orcid = "0009-0008-9573-7772"
+    {name = "Liam Marsh", email = "[email protected]"},  # orcid = "0000-0002-7276-5673"
+]
+maintainers = [
+    {name = "Ksenia Briling", email = "[email protected]"},  # orcid = "0000-0003-2250-9898"
+    {name = "Yannick Calvino", email = "[email protected]"},  # orcid = "0009-0008-9573-7772"
+    {name = "Liam Marsh", email = "[email protected]"},  # orcid = "0000-0002-7276-5673"
+]
+
+classifiers = [
+    "Programming Language :: Python :: 3",
+    "Programming Language :: C",
+    "License :: OSI Approved :: MIT License",
+    "Development Status :: 3 - Alpha",
+    "Intended Audience :: Science/Research",
+    "Programming Language :: Python :: Implementation :: CPython",
+]
+
+requires-python = ">=3.9"
+dependencies = [
+    'numpy',
+    'scipy',
+    'pyscf',
+    'tqdm',
+    #'scikit-learn',
+    #'equistore-core @ git+https://github.com/lab-cosmo/equistore.git@e5b9dc365369ba2584ea01e9d6a4d648008aaab8#subdirectory=python/equistore-core',
+]
+
+[project.optional-dependencies]
+qml = ["ase"]
+regression = ["scikit-learn"]
+wigner = ["sympy"]
+gmol = ["cell2mol"]
+equio = ["equistore-core @ git+https://github.com/lab-cosmo/equistore.git@e5b9dc365369ba2584ea01e9d6a4d648008aaab8#subdirectory=python/equistore-core"]
+all = ["qstack[qml,regression,wigner,equio,gmol]"]
+
+#dev = ["tqdm"]  # those are deps for the tests
+
+[project.urls]
+Repository = "https://github.com/lcmd-epfl/Q-stack.git"
+"Bug Tracker" = "https://github.com/lcmd-epfl/Q-stack/issues"
+
+
+[tool.setuptools.packages.find]
+where = ["."]
+exclude = ["tests","examples"]
+namespaces = false
+[tool.setuptools.package-data]
+"*" = ['regression/lib/manh.c', 'spahm/rho/basis_opt/*.bas']

qstack/__init__.py

@@ -6,6 +6,13 @@
 from qstack import fields
 from qstack import basis_opt
 from qstack import spahm
-from qstack import regression
 from qstack import mathutils
 from qstack import orcaio
+
+try:
+    import sklearn
+except ImportError:
+    pass
+else:
+    from qstack import regression
+    del sklearn

qstack/compound.py

@@ -108,8 +108,18 @@ def gmol_to_mol(fin, basis="def2-svp"):
         pyscf Mole: pyscf Mole object.
     """
 
-    from cell2mol.tmcharge_common import Cell, atom, molecule, ligand, metal
-    from cell2mol.tmcharge_common import labels2formula
+    try:
+        from cell2mol.tmcharge_common import Cell, atom, molecule, ligand, metal
+        from cell2mol.tmcharge_common import labels2formula
+    except ImportError:
+            print("""
+
+ERROR: cannot import ĉell2mol. Have you installed qstack with the \gmol\" option?\n\n
+(for instance, with `pip install qstack[gmol] or `pip install qstack[all]``)
+
+""")
+    raise
+
 
     # Open and read the file
     if fin.endswith(".gmol"):

qstack/fields/decomposition.py

@@ -1,7 +1,7 @@
 import numpy as np
 import scipy
 from pyscf import scf
-import qstack
+from qstack import compound
 
 def decompose(mol, dm, auxbasis):
     """Fit molecular density onto an atom-centered basis. 
@@ -15,8 +15,8 @@ def decompose(mol, dm, auxbasis):
         A copy of the pyscf Mole object with the auxbasis basis in a pyscf Mole object, and a 1D numpy array containing the decomposition coefficients. 
     """
 
-    auxmol = qstack.compound.make_auxmol(mol, auxbasis)
-    S, eri2c, eri3c = qstack.fields.decomposition.get_integrals(mol, auxmol)
+    auxmol = compound.make_auxmol(mol, auxbasis)
+    S, eri2c, eri3c = get_integrals(mol, auxmol)
     c = get_coeff(dm, eri2c, eri3c)
     return auxmol, c
 

qstack/fields/excited.py

@@ -1,7 +1,8 @@
 import numpy as np
 import pyscf
 from pyscf import scf, tdscf
-from qstack import compound, fields
+from qstack import compound
+from qstack.fields import moments
 
 def get_cis(mf, nstates):
     """
@@ -26,7 +27,7 @@ def get_cis_tdm(td):
 
 def get_holepart(mol, x, coeff):
     """Computes the hole and particle density matrices (atomic orbital basis) of selected states.
-    
+
     Args:
         mol (pyscf Mole): pyscf Mole object.
         x (numpy ndarray): Response vector (nstates×occ×virt) normalized to 1.
@@ -71,11 +72,11 @@ def exciton_properties_c(mol, hole, part):
         part (numpy ndarray): Particle density matrix.
 
     Returns:
-        Three floats: the hole-particle distance, the hole size, and the particle size respectively. 
+        Three floats: the hole-particle distance, the hole size, and the particle size respectively.
     """
 
-    hole_N, hole_r, hole_r2 = fields.moments.r2_c(hole, mol)
-    part_N, part_r, part_r2 = fields.moments.r2_c(part, mol)
+    hole_N, hole_r, hole_r2 = moments.r2_c(hole, mol)
+    part_N, part_r, part_r2 = moments.r2_c(part, mol)
 
     dist = np.linalg.norm(hole_r-part_r)
     hole_extent = np.sqrt(hole_r2-hole_r@hole_r)
@@ -91,7 +92,7 @@ def exciton_properties_dm(mol, hole, part):
         part (numpy ndarray): Particle density matrix.
 
     Returns:
-        Three floats: the hole-particle distance, the hole size, and the particle size respectively. 
+        Three floats: the hole-particle distance, the hole size, and the particle size respectively.
     """
 
     with mol.with_common_orig((0,0,0)):

qstack/fields/moments.py

@@ -1,6 +1,6 @@
 import numpy as np
 import pyscf
-from qstack import compound, fields
+from qstack import compound
 
 def first(mol, rho):
     """ Computes the transition dipole moments.

qstack/mathutils/wigner.py

@@ -2,8 +2,8 @@
 
 import sys
 import sympy as sp
-from sympy import symbols, Symbol, simplify, expand, cancel, expand_trig, Ynm, Ynm_c, Matrix, poly, zeros
 from .xyz_integrals_sym import xyz as xyzint
+from sympy import symbols, Symbol, simplify, expand, cancel, expand_trig, Ynm, Ynm_c, Matrix, poly, zeros
 
 
 # variables

qstack/mathutils/xyz_integrals_sym.py

@@ -1,7 +1,17 @@
 #!/usr/bin/env python3
 
 import sys
-import sympy
+
+try:
+    import sympy
+except ImportError:
+    print("""
+
+ERROR: cannot import sympy. Have you installed qstack with the \"wigner\" option?\n\n
+(for instance, with `pip install qstack[wigner]` or `pip install qstack[all]`)
+
+""")
+    raise
 
 def xyz(n,m,k):
 # computes the integral of x^2k y^2n z^2m over a sphere

qstack/qml/__init__.py

@@ -1 +1,15 @@
-from qstack.qml import slatm
+try:
+    import ase
+except ImportError:
+    print("""
+
+ERROR: cannot import ase. Have you installed qstack with the \"qml\" option?\n\n
+(for instance, with `pip install qstack[qml]` or `pip install qstack[all]`)
+
+""")
+    raise
+else:
+    from . import b2r2
+    from . import slatm
+    del ase
+

qstack/regression/kernel_utils.py

@@ -1,6 +1,6 @@
 import numpy
 from types import SimpleNamespace
-import qstack
+from qstack.regression import __path__ as REGMODULE_PATH
 import argparse
 
 
@@ -120,7 +120,6 @@ def get_covariance(mol1, mol2, max_sizes, kernel , sigma=None):
     .. todo::
         Write the docstring
     """
-    from qstack.regression.kernel_utils import get_kernel
     species = sorted(max_sizes.keys())
     mol1_dict = mol_to_dict(mol1, species)
     mol2_dict = mol_to_dict(mol2, species)
@@ -213,7 +212,6 @@ def cdist(X, Y):
   numpy.exp(K, K)
   return K
 
-
 def my_kernel_c(akernel):
     """
 
@@ -225,9 +223,9 @@ def my_kernel_c(akernel):
     array_2d_double = numpy.ctypeslib.ndpointer(dtype=numpy.float64, ndim=2, flags='CONTIGUOUS')
     def kernel_func_c(X, Y, gamma):
         try:
-            manh = ctypes.cdll.LoadLibrary(qstack.regression.__path__[0]+"/lib/manh.so")
+            manh = ctypes.cdll.LoadLibrary(REGMODULE_PATH[0]+"/lib/manh.so")
         except:
-            manh = ctypes.cdll.LoadLibrary(qstack.regression.__path__[0]+"/lib/manh"+sysconfig.get_config_var('EXT_SUFFIX'))
+            manh = ctypes.cdll.LoadLibrary(REGMODULE_PATH[0]+"/lib/manh"+sysconfig.get_config_var('EXT_SUFFIX'))
         if akernel == 'myLfast':
             kfunc = manh.manh
         elif akernel == 'myG':

qstack/regression/regression.py

@@ -2,7 +2,18 @@
 
 import numpy as np
 import scipy
-from sklearn.model_selection import train_test_split
+
+try:
+    from sklearn.model_selection import train_test_split
+except ImportError:
+    print("""
+
+ERROR: cannot import scikit-learn. Have you installed qstack with the \"regression\" option?\n\n
+(for instance, with `pip install qstack[regression] or `pip install qstack[all]``)
+
+""")
+    raise
+
 from qstack.regression.kernel_utils import get_kernel, defaults, ParseKwargs
 from qstack.tools import correct_num_threads
 from qstack.mathutils.fps import do_fps

qstack/spahm/rho/rep_completion.py

@@ -6,7 +6,7 @@
 from os.path import join, isfile, isdir
 import numpy as np
 import pyscf
-from  qstack import compound, spahm
+from  qstack import compound
 import qstack.tools as tls
 from . import utils, dmb_rep_atom as dmba, dmb_rep_bond as dmbb
 

requirements.txt

@@ -5,13 +5,15 @@ iniconfig==1.1.1
 packaging==21.3
 pluggy==1.0.0
 py==1.11.0
+#cython==0.29.24
 pyparsing==3.0.6
 pyscf==2.0.1
 pytest==6.2.5
 numpy===1.22.3
 scipy==1.10
 toml==0.10.2
 scikit-learn==0.24.2
+#scikit-learn==1.0.2
 ase==3.22
 tqdm==4.66
 equistore-core @ git+https://github.com/lab-cosmo/equistore.git@e5b9dc365369ba2584ea01e9d6a4d648008aaab8#subdirectory=python/equistore-core

setup.py

@@ -33,29 +33,14 @@ def check_for_openmp():
     return not result
 
 
-def get_requirements():
-    fname = f"{os.path.dirname(os.path.realpath(__file__))}/requirements.txt"
-    with open(fname) as f:
-        install_requires = f.read().splitlines()
-    return install_requires
-
-
 if __name__ == '__main__':
     openmp_enabled = check_for_openmp()
 
     setup(
-        name='qstack',
         version=get_git_version_hash(),
-        description='Stack of codes for dedicated pre- and post-processing tasks for Quantum Machine Learning',
-        url='https://github.com/lcmd-epfl/Q-stack',
-        python_requires='==3.9.*',
-        install_requires=get_requirements(),
-        packages=setuptools.find_packages(exclude=['tests', 'examples']),
         ext_modules=[Extension('qstack.regression.lib.manh',
                                ['qstack/regression/lib/manh.c'],
                                extra_compile_args=['-fopenmp', '-std=gnu11'] if openmp_enabled else ['-std=gnu11'],
                                extra_link_args=['-lgomp'] if openmp_enabled else [])
                     ],
-        include_package_data=True,
-        package_data={'': ['regression/lib/manh.c', 'spahm/rho/basis_opt/*.bas']},
     )

tests/test_otpd.py

@@ -1,6 +1,7 @@
 #!/usr/bin/env python3
 
 import os
+import numpy as np
 from qstack import compound, fields
 
 def test_hf_otpd():
@@ -9,7 +10,7 @@ def test_hf_otpd():
     mol = compound.xyz_to_mol(path+'/data/H2O.xyz', 'def2svp', charge=0, spin=0)
     dm = fields.dm.get_converged_dm(mol, xc="pbe")
     otpd, grid = fields.hf_otpd.hf_otpd(mol, dm, return_all=True)
-    assert(abs(otpd @ grid.weights-20.190382555868)<1e-10)
+    assert np.allclose(otpd @ grid.weights, 20.190382555868)
 
 
 if __name__ == '__main__':