Enable whole testsuite

.github/workflows/build_docs.yml

@@ -26,6 +26,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
+        pip install .
         pip install --upgrade --upgrade-strategy eager -r docs/requirements.txt
         echo ${{ github.workspace }} > $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/quemb.pth
     - name: Test building docs & Archive the results

.github/workflows/quemb_unittest.yml

@@ -27,33 +27,46 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
+    - name: Prepare pip
+      run: |
+        python -m pip install --upgrade pip
+
+
     - uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
         key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}-${{ hashFiles('dev-requirements.txt') }}
 
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install --upgrade --upgrade-strategy eager pytest
+        pip install --upgrade --upgrade-strategy eager pytest ruff
         if [ -f requirements.txt ]; then pip install --upgrade --upgrade-strategy eager -r requirements.txt; fi
+        pip install git+https://github.com/pyscf/dmrgscf
+        PYSCFHOME=$(pip show pyscf-dmrgscf | grep 'Location' | tr ' ' '\n' | tail -n 1)
+        wget https://raw.githubusercontent.com/pyscf/dmrgscf/master/pyscf/dmrgscf/settings.py.example
+        mv settings.py.example ${PYSCFHOME}/pyscf/dmrgscf/settings.py
+        pip install .
         echo ${{ github.workspace }} > $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/quemb.pth
 
+
+    - name: Check formatting
+      run: |
+        ruff format --diff || true    # for the moment we want to report always report success
+
+
+    - name: Static analysis
+      run: |
+        ruff check . || true    # for the moment we want to report always report success
+
+
     - name: Test with pytest
       run: |
         cd tests
-        pytest --doctest-modules --junitxml=junit/quemb-test-results_${{ matrix.python-version }}.xml
-      if: always()
+        QUEMB_SKIP_EXPENSIVE_TESTS=true pytest --doctest-modules --junitxml=junit/quemb-test-results_${{ matrix.python-version }}.xml
 
     - name: Upload pytest junit results
       uses: actions/upload-artifact@v4
       with:
         name: quemb-test-results_${{ matrix.python-version }}
-        path: tests/junit/quemb-test-results_${{ matrix.python-version }}.xml
-
-    #- name: Upload pytest html results
-    #  uses: actions/upload-artifact@v4
-    #  with:
-    #    name: quemb-tests-coverage_${{ matrix.python-version }}
-    #    path: tests/htmlcov
-    #  if: always()
+        path: tests/junit/quemb-test-results_${{ matrix.python-version }}.xml

.ruff.toml

@@ -0,0 +1,14 @@
+[lint]
+# see the rules [here](https://docs.astral.sh/ruff/rules/)
+select = ["E", "F", "I", "NPY", "ARG"]
+# select = ["E501"]
+ignore = [
+    "S101",
+        # https://docs.astral.sh/ruff/rules/assert/
+        # We want to use assert especially because it is disabled for
+        # optimized builds.
+    "E741",
+        # https://docs.astral.sh/ruff/rules/ambiguous-variable-name/
+        # Prevents the use of the characters 'l', 'O', or 'I' as variable names.
+        # Overly restrictive, in particular when implementing mathematical expressions.
+]

docs/requirements.txt

@@ -1,5 +1,2 @@
+# the additional (!) requirements for building the doc
 sphinx_rtd_theme
-numpy
-scipy
-h5py
-pyscf

example/kbe_polyacetylene.py

@@ -3,8 +3,9 @@
 # pyscf's periodic HF calculation
 
 import numpy
-from pyscf.pbc import gto, scf, df
-from kbe import fragpart, BE
+from pyscf.pbc import df, gto, scf
+
+from kbe import BE, fragpart
 
 kpt = [1, 1, 3]
 cell = gto.Cell()
@@ -49,7 +50,7 @@
 # Define fragment in the supercell
 kfrag = fragpart(be_type="be2", mol=cell, kpt=kpt, frozen_core=True)
 # Initialize BE
-mykbe = BE(kmf, fobj, kpts=kpts)
+mykbe = BE(kmf, kfrag, kpts=kpts)
 
 # Perform BE density matching
 mykbe.optimize(solver="CCSD")

example/molbe_dmrg_block2.py

@@ -2,9 +2,12 @@
 # `block2` is a DMRG and sparse tensor network library developed by the
 # Garnet-Chan group at Caltech: https://block2.readthedocs.io/en/latest/index.html
 
-import os, numpy, sys
+import os
+
 import matplotlib.pyplot as plt
-from pyscf import gto, scf, fci, cc
+import numpy
+from pyscf import cc, fci, gto, scf
+
 from molbe import BE, fragpart
 
 # We'll consider the dissociation curve for a 1D chain of 8 H-atoms:
@@ -54,7 +57,7 @@
     # Next, run BE-DMRG with default parameters and maxM=100.
     mybe.oneshot(
         solver="block2",  # or 'DMRG', 'DMRGSCF', 'DMRGCI'
-        scratch=scratch,  # Scratch dir for fragment DMRG
+        scratch_dir=scratch,  # Scratch dir for fragment DMRG
         maxM=100,  # Max fragment bond dimension
         force_cleanup=True,  # Remove all fragment DMRG tmpfiles
     )

example/molbe_h8_chemical_potential.py

@@ -1,7 +1,8 @@
 # Illustrates a simple molecular BE calculation with chemical
 # potential matching
 
-from pyscf import gto, scf, fci
+from pyscf import fci, gto, scf
+
 from molbe import BE, fragpart
 
 # PySCF HF generated mol & mf (molecular desciption & HF object)

example/molbe_h8_density_matching.py

@@ -1,7 +1,8 @@
 # Illustrates a simple molecular BE calculation with BE
 # density matching between edge & centers of fragments.
 
-from pyscf import gto, scf, fci
+from pyscf import fci, gto, scf
+
 from molbe import BE, fragpart
 
 # PySCF HF generated mol & mf (molecular desciption & HF object)
@@ -31,18 +32,6 @@
 
 # Perform BE calculations with different fragment schemes:
 
-# Define BE1 fragments
-fobj = fragpart(be_type="be1", mol=mol)
-# Initialize BE
-mybe = BE(mf, fobj)
-# Density matching in BE
-mybe.optimize(solver="FCI")
-
-# Compute BE error
-be_ecorr = mybe.ebe_tot - mybe.ebe_hf
-err_ = (fci_ecorr - be_ecorr) * 100.0 / fci_ecorr
-print(f"*** BE1 Correlation Energy Error (%) : {err_:>8.4f} %")
-
 # Define BE2 fragments
 fobj = fragpart(be_type="be2", mol=mol)
 mybe = BE(mf, fobj)

example/molbe_hexene_oneshot_uccsd.py

@@ -1,11 +1,10 @@
 # Illustrates a one-shot BE UCCSD calculation from UHF reference
 # for hexene anion
 
-import numpy
 
 from pyscf import gto, scf
-from molbe import fragpart, UBE, be_var
-import sys
+
+from molbe import UBE, fragpart
 
 # Set up scratch directory settings
 # be_var.SCRATCH='{scratch location}'

example/molbe_io_fcidump.py

@@ -1,11 +1,8 @@
 # Illustrates how fcidump file containing fragment hamiltonian
 # can be generated using be2fcidump
 
-from pyscf import gto, scf
-from molbe import BE
-from molbe import fragpart
-from molbe.misc import *
-from molbe import be_var
+from molbe import BE, be_var, fragpart
+from molbe.misc import be2fcidump, libint2pyscf
 
 be_var.PRINT_LEVEL = 3
 

example/molbe_octane.py

@@ -1,7 +1,8 @@
 # Illustrates parallelized BE computation on octane
 
-from pyscf import gto, scf, cc
-from molbe import fragpart, BE
+from pyscf import cc, gto, scf
+
+from molbe import BE, fragpart
 
 # Perform pyscf HF calculation to get mol & mf objects
 mol = gto.M(

example/molbe_octane_get_rdms.py

@@ -1,7 +1,8 @@
 # Illustrates parallelized BE computation on octane
 
 from pyscf import gto, scf
-from molbe import fragpart, BE
+
+from molbe import BE, fragpart
 
 # Perform pyscf HF calculation to get mol & mf objects
 mol = gto.M(

example/molbe_oneshot_rbe_hcore.py

@@ -5,9 +5,9 @@
 # PySCF formats
 
 import numpy
-from pyscf import gto, scf, qmmm
+from pyscf import gto, qmmm, scf
+
 from molbe.misc import be2puffin
-from molbe import be_var
 
 # variables for scratch handling
 # pbe_var.SCRATCH = '{}'

example/molbe_oneshot_rbe_qmmm-fromchk.py

@@ -2,10 +2,7 @@
 # using the be2puffin functionality, starting from a checkfile.
 # Returns BE CCSD energy for the system
 
-import numpy
-from pyscf import gto, scf, qmmm
 from molbe.misc import be2puffin
-from molbe import be_var
 
 # variables for scratch handling
 # pbe_var.SCRATCH = '{}'

example/molbe_oneshot_ube_qmmm.py

@@ -2,9 +2,7 @@
 # using the be2puffin functionality.
 # Returns UBE UCCSD energy for the system
 
-import numpy
 from molbe.misc import be2puffin
-from molbe import be_var
 
 # variables for scratch handling
 # pbe_var.SCRATCH = '{}'

example/molbe_ppp.py

@@ -1,7 +1,8 @@
 # Perform BE calculation with 6-31g basis set
 
 from pyscf import gto, scf
-from molbe import fragpart, BE
+
+from molbe import BE, fragpart
 
 # Perform pyscf HF calculation to get mol & mf objects
 mol = gto.M(

requirements.txt

@@ -1,8 +1,4 @@
 pyscf==2.6.2
 pytest==8.3.2
-# TODO this temporarily points to mcocdawc/libdmet_preview.
-# as soon as this PR: https://github.com/gkclab/libdmet_preview/pull/21
-# is merged, let it point to the original libdmet
-# https://github.com/gkclab/libdmet_preview
-libdmet @ git+https://github.com/mcocdawc/libdmet_preview.git@add_fixes_for_BE
+libdmet @ git+https://github.com/gkclab/libdmet_preview.git
 matplotlib

setup.py

@@ -1,8 +1,8 @@
-from setuptools import setup, find_packages
-
 # Read the contents of your README file
 from pathlib import Path
 
+from setuptools import find_packages, setup
+
 this_directory = Path(__file__).parent
 long_description = (this_directory / "README.md").read_text()
 
@@ -14,17 +14,14 @@
     long_description_content_type="text/markdown",
     url="https://github.com/oimeitei/quemb",
     license="Apache 2.0",
-    packages=find_packages(),
+    packages=find_packages("src"),
+    package_dir={"": "src"},
     python_requires=">=3.7",
     install_requires=[
         "numpy>=1.22.0",
         "scipy>=1.7.0",
         "pyscf>=2.0.0",
         "matplotlib",
-        # TODO this temporarily points to mcocdawc/libdmet_preview.
-        # as soon as this PR: https://github.com/gkclab/libdmet_preview/pull/21
-        # is merged, let it point to the original libdmet
-        # https://github.com/gkclab/libdmet_preview
         "libdmet @ git+https://github.com/mcocdawc/libdmet_preview.git@add_fixes_for_BE",
     ],
 )

kbe/autofrag.py → src/kbe/autofrag.py

@@ -1,9 +1,10 @@
 # Author(s): Oinam Romesh Meitei
 
 import sys
+
 import numpy
+
 from molbe.helper import get_core
-from itertools import compress
 
 
 def warn_large_fragment():
@@ -103,13 +104,13 @@ def sidefunc(
         for lmin1 in unit2[numpy.where(unit1 == Idx)[0]]:
             for jdx, j in enumerate(coord):
                 if (
-                    not jdx in unit1
-                    and not jdx in unit2
+                    jdx not in unit1
+                    and jdx not in unit2
                     and not cell.atom_pure_symbol(jdx) == "H"
                 ):
                     dist = numpy.linalg.norm(coord[lmin1] - j)
                     if dist <= bond:
-                        if not jdx in sub_list:  # avoid repeated occurence
+                        if jdx not in sub_list:  # avoid repeated occurence
                             main_list.append(jdx)
                             sub_list.append(jdx)
                             close_be3.append(jdx)
@@ -119,8 +120,8 @@ def sidefunc(
                                     if kdx == jdx:
                                         continue
                                     if (
-                                        not kdx in unit1
-                                        and not kdx in unit2
+                                        kdx not in unit1
+                                        and kdx not in unit2
                                         and not cell.atom_pure_symbol(kdx) == "H"
                                     ):
                                         dist = numpy.linalg.norm(coord[jdx] - k)
@@ -165,10 +166,10 @@ def surround(
             NK=NK,
             rlist=rlist,
         )
-        sublist = [tmpi for tmpi in sublist_ if not tmpi in rlist]
+        sublist = [tmpi for tmpi in sublist_ if tmpi not in rlist]
         sublist = []
         for tmpi in sublist_:
-            if not tmpi in rlist:
+            if tmpi not in rlist:
                 for tmp_jdx, tmpj in enumerate(ext_list):
                     if tmpj == tmpi and klist[tmp_jdx] == NK:
                         break
@@ -311,6 +312,7 @@ def autogen(
         Weights for each fragment. Each entry contains a weight and a list of LO indices.
     """
     from pyscf import lib
+
     from .misc import sgeom
 
     if not float(unitcell).is_integer():
@@ -1311,9 +1313,9 @@ def autogen(
                 and dist in inter_layer_dict[idx][1]
                 and jdx in inter_layer_dict[idx][0]
                 and dist < perpend_dist * ang2bohr
-                and not jdx in pedg
+                and jdx not in pedg
             ):
-                if not jdx in clist_check:
+                if jdx not in clist_check:
                     flist.append(jdx)
                     pedg.append(jdx)
                 if dist > bond:
@@ -1732,7 +1734,7 @@ def autogen(
                                 and kdx in inter_layer_dict[jdx][0]
                                 and dist < perpend_dist * ang2bohr
                             ):
-                                if not kdx in pedg and not kdx in clist_check:
+                                if kdx not in pedg and kdx not in clist_check:
                                     flist.append(kdx)
                                     pedg.append(kdx)
                                 if be_type == "be4":
@@ -1937,7 +1939,7 @@ def autogen(
                     )
         w.close()
 
-    if not valence_basis is None:
+    if valence_basis is not None:
         pao = True
     else:
         pao = False