Add more checks

.github/workflows/quemb_unittest.yml

@@ -13,11 +13,12 @@ permissions:
   contents: read
 
 jobs:
-  build:
+  analysis:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.12"]
+
 
     steps:
     - uses: actions/checkout@v4
@@ -31,7 +32,6 @@ jobs:
       run: |
         python -m pip install --upgrade pip
 
-
     - uses: actions/cache@v4
       with:
         path: ${{ env.pythonLocation }}
@@ -40,31 +40,79 @@ jobs:
 
     - name: Install dependencies
       run: |
-        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 --upgrade --upgrade-strategy eager ruff pylint mypy scipy-stubs
         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
 
 
-    - name: Static analysis
+    - name: Static analysis with ruff
       run: |
         ruff check . || true    # for the moment we want to report always report success
 
 
+    - name: Static analysis with pylint
+      run: |
+        # ruff does nearly everything that we want from pylint
+        # except for detecting unresolved imports
+        # TODO: if they add it to ruff as well https://github.com/astral-sh/ruff/issues/9103
+        #   remove pylint.
+        pylint --disable=all --enable=E0401,R0401,E0611 . || true    # for the moment we want to report always report success
+
+
+    - name: Static analysis with mypy
+      run: |
+        mypy tests/ example/ src/ || true    # for the moment we want to report always report success
+
+
+
+  build:
+    runs-on: ubuntu-latest
+    needs: analysis
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v4
+
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v5
+      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') }}-${{ hashFiles('dev-requirements.txt') }}
+
+
+    - name: Install dependencies
+      run: |
+        pip install --upgrade --upgrade-strategy eager pytest
+        if [ -f requirements.txt ]; then pip install --upgrade --upgrade-strategy eager -r requirements.txt; fi
+        pip install git+https://github.com/pyscf/dmrgscf
+        PYSCFHOME=$(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 }} > $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/quemb.pth
+
+
     - name: Test with pytest
       run: |
         cd tests
         QUEMB_SKIP_EXPENSIVE_TESTS=true pytest --doctest-modules --junitxml=junit/quemb-test-results_${{ matrix.python-version }}.xml
 
+
     - name: Upload pytest junit results
       uses: actions/upload-artifact@v4
       with:

.gitignore

@@ -165,3 +165,6 @@ cython_debug/
 # pyscf files
 eri_file.h5
 
+
+# vim swap files
+.*.swp

.ruff.toml

@@ -1,6 +1,6 @@
 [lint]
 # see the rules [here](https://docs.astral.sh/ruff/rules/)
-select = ["E", "F", "I", "NPY", "ARG"]
+select = ["E", "F", "I", "NPY", "ARG", "PL"]
 ignore = [
     "S101",
         # https://docs.astral.sh/ruff/rules/assert/
@@ -10,5 +10,9 @@ ignore = [
         # 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.
+    "PLR",
+        # https://docs.astral.sh/ruff/rules/#refactor-r
+        # while these warnings are nice for a fresh codebase,
+        # they are too many to fix now and not important enough
 ]
 preview = true

mypy.ini

@@ -0,0 +1,17 @@
+[mypy]
+    no_implicit_optional = True
+
+# TODO: whenever the following packages have stubs available,
+#   stop ignoring them.
+
+[mypy-pyscf.*]
+    ignore_missing_imports = True
+
+[mypy-libdmet.*]
+    ignore_missing_imports = True
+
+[mypy-setuptools.*]
+    ignore_missing_imports = True
+
+[mypy-h5py.*]
+    ignore_missing_imports = True

setup.py

@@ -23,6 +23,6 @@
         "scipy>=1.7.0",
         "pyscf>=2.0.0",
         "matplotlib",
-        "libdmet @ git+https://github.com/mcocdawc/libdmet_preview.git@add_fixes_for_BE",
+        "libdmet @ git+https://github.com/gkclab/libdmet_preview.git",
     ],
 )

src/kbe/autofrag.py

@@ -471,7 +471,7 @@ def autogen(
             sys.exit()
         # kmesh lkpt ends
 
-    ## starts here
+    # starts here
     normlist = []
     for i in coord:
         normlist.append(numpy.linalg.norm(i))
@@ -572,7 +572,7 @@ def autogen(
         # part of l,r,d,u,m,t but are in the
         # unit cell that is their k is 1
         # for example, klsts[i] = 1
-        ## WARNING !!!
+        # WARNING !!!
         # For systems like Graphene, BN, SiC, hexagonal 2D sheets,
         # BE4 can give wrong fragmentations
         # the following code adds in redundant atoms

src/molbe/be_parallel.py

@@ -132,6 +132,7 @@ def run_solver(
         efci, civec = mc_.kernel()
         rdm1_tmp = mc_.make_rdm1(civec, mc_.norb, mc_.nelec)
     elif solver == "HCI":
+        # pylint: disable-next=E0611
         from pyscf import hci  # noqa: PLC0415  # hci is an optional module
 
         nao, nmo = mf_.mo_coeff.shape
@@ -158,6 +159,7 @@ def run_solver(
         rdm2s = rdm2aa + rdm2ab + rdm2ab.transpose(2, 3, 0, 1) + rdm2bb
 
     elif solver == "SHCI":
+        # pylint: disable-next=E0401,E0611
         from pyscf.shciscf import shci  # noqa: PLC0415    # shci is an optional module
 
         nao, nmo = mf_.mo_coeff.shape
@@ -176,9 +178,8 @@ def run_solver(
         rdm1_tmp, rdm2s = mch.fcisolver.make_rdm12(0, nmo, nelec)
 
     elif solver == "SCI":
-        from pyscf import (  # noqa: PLC0415  # cornell_shci is an optional module
-            cornell_shci,
-        )
+        # pylint: disable-next=E0611
+        from pyscf import cornell_shci  # noqa: PLC0415  # optional module
 
         nao, nmo = mf_.mo_coeff.shape
         nelec = (nocc, nocc)

src/molbe/external/optqn.py

@@ -333,7 +333,7 @@ def get_atbe_Jblock_frag(fobj, res_func):
             for k_ in range(len(edge)):
                 if j_ > k_:
                     continue
-                ## response w.r.t matching pot
+                # response w.r.t matching pot
                 # edges
                 tmpje_ = []
 
@@ -366,7 +366,7 @@ def get_atbe_Jblock_frag(fobj, res_func):
 
                 Jc.append(tmpjc_)
 
-                ## response w.r.t. chem pot
+                # response w.r.t. chem pot
                 # edge
                 xe.append(dP_mu[edge[j_], edge[k_]])
                 cout += 1

src/molbe/pfrag.py

@@ -323,7 +323,7 @@ def set_udim(self, cout):
         return cout
 
     def energy(self, rdm2s, eri=None, print_fragE=False):
-        ## This function uses old energy expression and will be removed
+        # This function uses old energy expression and will be removed
         rdm2s = numpy.einsum(
             "ijkl,pi,qj,rk,sl->pqrs",
             0.5 * rdm2s,

src/molbe/solver.py

@@ -139,6 +139,7 @@ def be_func(
             rdm1_tmp = mc.make_rdm1(civec, mc.norb, mc.nelec)
 
         elif solver == "HCI":
+            # pylint: disable-next=E0611
             from pyscf import hci  # noqa: PLC0415    # optional module
 
             nao, nmo = fobj._mf.mo_coeff.shape
@@ -172,6 +173,7 @@ def be_func(
             rdm2s = rdm2aa + rdm2ab + rdm2ab.transpose(2, 3, 0, 1) + rdm2bb
 
         elif solver == "SHCI":
+            # pylint: disable-next=E0611,E0401
             from pyscf.shciscf import shci  # noqa: PLC0415    # shci is optional
 
             if scratch_dir is None and be_var.CREATE_SCRATCH_DIR:
@@ -203,6 +205,7 @@ def be_func(
             rdm1_tmp, rdm2s = mch.fcisolver.make_rdm12(0, nmo, nelec)
 
         elif solver == "SCI":
+            # pylint: disable-next=E0611
             from pyscf import cornell_shci  # noqa: PLC0415  # optional module
 
             nao, nmo = fobj._mf.mo_coeff.shape
@@ -685,16 +688,11 @@ def solve_ccsd(
     try:
         cc__.verbose = verbose
         cc__.kernel(eris=eris)
-    except:
+    except Exception as e:
         print(flush=True)
-        print(
-            "Exception in CCSD -> applying level_shift=0.2, diis_space=25", flush=True
-        )
+        print("Exception in CCSD, play with different CC options.", flush=True)
         print(flush=True)
-        cc__.verbose = 4
-        cc__.diis_space = 25
-        cc__.level_shift = 0.2
-        cc__.kernel(eris=eris)
+        raise e
 
     # Extract the CCSD amplitudes
     t1 = cc__.t1
@@ -782,6 +780,7 @@ def solve_block2(mf: object, nocc: int, frag_scratch: str = None, **solver_kwarg
 
 
     """
+    # pylint: disable-next=E0611
     from pyscf import dmrgscf  # noqa: PLC0415   # optional module
 
     use_cumulant = solver_kwargs.pop("use_cumulant", True)
@@ -813,7 +812,7 @@ def solve_block2(mf: object, nocc: int, frag_scratch: str = None, **solver_kwarg
 
     mc = mcscf.CASCI(mf, norb, nelec)
     mc.fcisolver = dmrgscf.DMRGCI(mf.mol)
-    ###Sweep scheduling
+    # Sweep scheduling
     mc.fcisolver.scheduleSweeps = schedule_kwargs.pop(
         "scheduleSweeps",
         [
@@ -844,7 +843,7 @@ def solve_block2(mf: object, nocc: int, frag_scratch: str = None, **solver_kwarg
         "scheduleNoises",
         [max_noise, max_noise, max_noise / 10, max_noise / 100, max_noise / 100, 0.0],
     )
-    ###Other DMRG parameters
+    # Other DMRG parameters
     mc.fcisolver.threads = int(os.environ.get("OMP_NUM_THREADS", 8))
     mc.fcisolver.twodot_to_onedot = int(twodot_to_onedot)
     mc.fcisolver.maxIter = int(max_iter)
@@ -857,7 +856,7 @@ def solve_block2(mf: object, nocc: int, frag_scratch: str = None, **solver_kwarg
     mc.kernel(orbs)
     rdm1, rdm2 = dmrgscf.DMRGCI.make_rdm12(mc.fcisolver, root, norb, nelec)
 
-    ###Subtract off non-cumulant contribution to correlated 2RDM.
+    # Subtract off non-cumulant contribution to correlated 2RDM.
     if use_cumulant:
         hf_dm = numpy.zeros_like(rdm1)
         hf_dm[numpy.diag_indices(nocc)] += 2.0