Enforce stricter checks (ruff, mypy, and pylint)

.githooks/pre-commit

@@ -19,15 +19,20 @@ if [ "`git diff --check --cached | wc -c`" -gt 0 ]; then
 fi
 
 
-if ! command -v ruff 2>&1 >/dev/null; then
+if ! command -v ruff >/dev/null 2>&1; then
     >&2 echo "Please install ruff via 'pip install ruff'."
     exit 1
 else
-    if ! ruff format --diff `git rev-parse --show-toplevel`; then
+    if ! ruff format --diff `git rev-parse --show-toplevel` >/dev/null 2>&1; then
         >&2 echo "There are problems with PEP8-compliance."
         >&2 echo 'You can check yourself by executing "ruff format --diff `git rev-parse --show-toplevel`"'
         exit 1
     fi
+    if ! ruff check `git rev-parse --show-toplevel` >/dev/null 2>&1; then
+        >&2 echo "There are problems in the code."
+        >&2 echo 'You can check yourself by executing "ruff check `git rev-parse --show-toplevel`"'
+        exit 1
+    fi
 fi
 
 

.github/workflows/build_docs.yml

@@ -18,10 +18,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up Python 3.9
+    - name: Set up Python 3.10
       uses: actions/setup-python@v5
       with:
-        python-version: "3.9"
+        python-version: "3.10"
         cache: 'pip'
     - name: Install dependencies
       run: |

.github/workflows/quemb_unittest.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.10"]
 
 
     steps:
@@ -48,7 +48,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --upgrade --upgrade-strategy eager ruff pylint mypy scipy-stubs
+        pip install -r tests/static_analysis_requirements.txt
         pip install .
 
 
@@ -58,9 +58,8 @@ jobs:
 
 
     - name: Static analysis with ruff
-      # for the moment we want to report always report success
       run: |
-        ruff check . || true
+        ruff check .
 
 
     - name: Static analysis with pylint
@@ -69,12 +68,12 @@ jobs:
       # TODO: if they add it to ruff as well https://github.com/astral-sh/ruff/issues/9103
       #   remove pylint.
       run: |
-        pylint --disable=all --enable=E0401,R0401,E0611 . || true    # for the moment we want to report always report success
+        pylint --disable=all --enable=E0401,R0401,E0611 .
 
 
     - name: Static analysis with mypy
       run: |
-        mypy tests/ example/ src/ || true    # for the moment we want to report always report success
+        mypy tests/ example/ src/
 
 
 
@@ -83,7 +82,7 @@ jobs:
     needs: analysis
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -106,14 +105,12 @@ jobs:
 
     - 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 -r tests/test_requirements.txt
         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

README.md

@@ -25,35 +25,32 @@ processors.
 
 ### Prerequisites
 
-- Python 3.6 or higher
+- Python `>=3.10`
 - PySCF library
 - Numpy
 - Scipy
-- libDMET (required for periodic BE)
-- [Wannier90](https://github.com/wannier-developers/wannier90)<sup>&&</sup> (to use Wannier functions)
-
-<sup>&&</sup>Wannier90 code is interfaced via [libDMET](https://github.com/gkclab/libdmet_preview) in QuEmb</sub>
-
-### Steps
-
-1. Clone the repository:
-   ```bash
-   git clone https://github.com/oimeitei/quemb.git
-   cd quemb
-
-2. Install QuEmb using one of the following approaches:
-    ```bash
-    pip install .
-    ```
-    or simply add `path/to/quemd` to `PYTHONPATH`
-    ```bash
-    export PYTHONPATH=/path/to/quemb:$PYTHONPATH
-    ```
-
-    For conda (or virtual environment) installations, after creating your environment, specify the path to mol-be source as a path file, as in:
-    ```bash
-    echo path/to/quemb > $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/quemb.pth
-    ```
+- [libDMET](https://github.com/gkclab/libdmet_preview) (required for periodic BE)
+- [Wannier90](https://github.com/wannier-developers/wannier90)<sup>##</sup> (to use Wannier functions)
+
+<sup>##</sup> `Wannier90` code is optional and only necessary to use Wannier functions in periodic code. </sub>
+
+The required dependencies, with the exception of the optional `Wannier90`,
+are automatically installed by `pip`.
+
+### Installation
+
+One can just `pip install` directly from the Github repository:
+```bash
+pip install git+https://https://github.com/troyvvgroup/quemb
+```
+
+Alternatively one can manually clone and install as in:
+```bash
+git clone https://https://github.com/troyvvgroup/quemb
+cd quemb
+pip install .
+```
+
 
 
 ## Basic Usage

docs/requirements.txt

@@ -1,3 +1,4 @@
 # the additional (!) requirements for building the doc
+# the dependencies of `quemb` itself are given in the setup.py
 sphinx_rtd_theme
 sphinx_autodoc_typehints

docs/source/index.rst

@@ -36,3 +36,8 @@ References
    optimize
    solvers
    misc
+
+
+
+.. role:: bash(code)
+   :language: bash

docs/source/install.rst

@@ -4,39 +4,34 @@ Installation
 Prerequisites
 -------------
 
- * Python 3.6 or higher
+ * Python >=10 or higher
  * PySCF library
  * Numpy
  * Scipy
- * libDMET :sup:`##` (required for periodic BE)
- * `Wannier90 <https://github.com/wannier-developers/wannier90>`_ :sup:`&&` (to use Wannier functions)
+ * `libDMET <https://github.com/gkclab/libdmet_preview>`__ (required for periodic BE)
+ * `Wannier90 <https://github.com/wannier-developers/wannier90>`_ :sup:`##`
 
-| :sup:`##` The modified version of `libDMET <https://github.com/gkclab/libdmet_preview>`_ available at `here <https://github.com/oimeitei/libdmet_preview>`_ is recommended to run periodic BE using QuEmb.
-| :sup:`&&` Wannier90 code is interfaced via `libDMET <https://github.com/gkclab/libdmet_preview>`_ in QuEmb
+| :sup:`##` :code:`Wannier90` code is optional and only necessary to use Wannier functions in periodic code.
 
+The required dependencies, with the exception of the optional :code:`Wannier90`,
+are automatically installed by :bash:`pip`.
 
-Obtain the source code
-----------------------
-Clone the Github repository::
 
-  git clone https://github.com/oimeitei/quemb.git
+Installation
+-------------
+
+One can just :bash:`pip install` directly from the Github repository
 
-pip install
------------
+.. code-block:: bash
 
-::
+  pip install git+https://https://github.com/troyvvgroup/quemb
 
-  pip install .
 
-Add to ``PYTHONPATH``
----------------------
-Simply add ``path/to/quemb`` to ``PYTHONPATH``
-::
 
-   export PYTHONPATH=/path/to/quemb:$PYTHONPATH
+Alternatively one can manually clone and install as in
 
-Conda or virtual environment
-----------------------------
-For conda (or virtual environment) installations, after creating your environment, specify the path to mol-be source as a path file, as in::
+.. code-block:: bash
 
-  echo path/to/quemb > $(python -c "from distutils.sysconfig import get_python_lib; print(get_python_lib())")/quemb.pth
+  git clone https://https://github.com/troyvvgroup/quemb
+  cd quemb
+  pip install .

example/__init__.py

@@ -0,0 +1,3 @@
+# the __init__.py file only exists so that we can
+# have more fine-grained control over which file we want to test how
+# in mypy.

example/molbe_io_fcidump.py

@@ -1,8 +1,9 @@
 # Illustrates how fcidump file containing fragment hamiltonian
 # can be generated using be2fcidump
 
-from quemb.molbe import BE, be_var, fragpart
+from quemb.molbe import BE, fragpart
 from quemb.molbe.misc import be2fcidump, libint2pyscf
+from quemb.shared import be_var
 
 be_var.PRINT_LEVEL = 3
 

mypy.ini

@@ -3,16 +3,26 @@
     disallow_untyped_defs = True
     check_untyped_defs = True
 
-[mypy-quemb.molbe.*]
+
+# explicitly blacklist files, this means we can easily add in stricter type checks
+# by removing them from the blacklist
+[mypy-quemb.molbe.ube,quemb.molbe.be_parallel,quemb.molbe.autofrag,quemb.molbe.eri_onthefly,quemb.molbe.fragment,quemb.molbe.helper,quemb.molbe.lchain,quemb.molbe.lo,quemb.molbe.mbe,quemb.molbe.misc,quemb.molbe._opt,quemb.molbe.pfrag,quemb.molbe.solver]
     disallow_untyped_defs = False
     check_untyped_defs = False
 
+[mypy-quemb.kbe.autofrag,quemb.kbe.chain,quemb.kbe.fragment,quemb.kbe.helper,quemb.kbe.__init__,quemb.kbe.lo_k,quemb.kbe.lo,quemb.kbe.misc,quemb.kbe.pbe,quemb.kbe.pfrag,quemb.kbe.solver]
+    disallow_untyped_defs = False
+    check_untyped_defs = False
 
-[mypy-quemb.kbe.*]
+[mypy-quemb.shared.external.ccsd_rdm,quemb.shared.external.cphf_utils,quemb.shared.external.cpmp2_utils,quemb.shared.external.__init__,quemb.shared.external.jac_utils,quemb.shared.external.lo_helper,quemb.shared.external.optqn,quemb.shared.external.uccsd_eri,quemb.shared.external.unrestricted_utils]
     disallow_untyped_defs = False
     check_untyped_defs = False
 
-[mypy-quemb.shared.external.*]
+[mypy-tests.chem_dm_kBE_test,tests.chempot_molBE_test,tests.dm_molBE_test,tests.dmrg_molBE_test,tests.eri_onthefly_test,tests.hf-in-hf_BE_test,tests.kbe_polyacetylene_test,tests.molbe_h8_test,tests.molbe_io_fcidump_test,tests.molbe_octane_get_rdms_test,tests.molbe_oneshot_rbe_hcore_test,tests.molbe_oneshot_rbe_qmmm-fromchk_test,tests.ube-oneshot_test]
+    disallow_untyped_defs = False
+    check_untyped_defs = False
+
+[mypy-example.kbe_polyacetylene,example.molbe_dmrg_block2,example.molbe_h8_chemical_potential,example.molbe_h8_density_matching,example.molbe_hexene_oneshot_uccsd,example.molbe_io_fcidump,example.molbe_octane_get_rdms,example.molbe_octane,example.molbe_oneshot_rbe_hcore,example.molbe_oneshot_rbe_qmmm-fromchk,example.molbe_oneshot_ube_qmmm,example.molbe_ppp]
     disallow_untyped_defs = False
     check_untyped_defs = False
 
@@ -29,4 +39,4 @@
     ignore_missing_imports = True
 
 [mypy-h5py.*]
-    ignore_missing_imports = True
+    ignore_missing_imports = True

setup.py

@@ -17,14 +17,13 @@
     license="Apache 2.0",
     packages=find_packages("src"),
     package_dir={"": "src"},
-    python_requires=">=3.7",
+    python_requires=">=3.10",
     install_requires=[
         "numpy>=1.22.0",
         "scipy>=1.7.0",
         "pyscf>=2.0.0",
         "matplotlib",
         "libdmet @ git+https://github.com/gkclab/libdmet_preview.git",
         "attrs",
-        "typing_extensions",
     ],
 )

src/quemb/kbe/lo.py

@@ -55,7 +55,7 @@ def localize(
             Whether to perform Wannier localization in the IAO space
         """
         if lo_method == "iao" and iao_val_core:
-            raise NotImplementedError("This does not work. Contact Developers.")
+            raise NotImplementedError("iao_val_core and lo_method='iao' not supported.")
 
         if lo_method == "lowdin":
             # Lowdin orthogonalization with k-points

src/quemb/kbe/pbe.py

@@ -15,10 +15,9 @@
 from quemb.kbe.misc import print_energy, storePBE
 from quemb.kbe.pfrag import Frags
 from quemb.molbe._opt import BEOPT
-from quemb.molbe.helper import get_eri, get_scfObj, get_veff
 from quemb.molbe.be_parallel import be_func_parallel
+from quemb.molbe.helper import get_eri, get_scfObj, get_veff
 from quemb.molbe.solver import be_func
-
 from quemb.shared import be_var
 from quemb.shared.external.optqn import (
     get_be_error_jacobian as _ext_get_be_error_jacobian,

src/quemb/kbe/pfrag.py

@@ -353,49 +353,34 @@ def update_heff(
         self,
         u,
         cout=None,
-        return_heff=False,
-        no_chempot=False,
+        do_chempot=True,
         only_chem=False,
     ):
         """Update the effective Hamiltonian for the fragment."""
-
         heff_ = numpy.zeros_like(self.h1)
 
         if cout is None:
             cout = self.udim
 
-        if not no_chempot:
+        if do_chempot:
             for i, fi in enumerate(self.fsites):
                 if not any(i in sublist for sublist in self.edge_idx):
                     heff_[i, i] -= u[-1]
 
         if only_chem:
             self.heff = heff_
-            if return_heff:
-                if cout is None:
-                    return heff_
-                else:
-                    return (cout, heff_)
-            return cout
-
-        for idx, i in enumerate(self.edge_idx):
-            for j in range(len(i)):
-                for k in range(len(i)):
-                    if j > k:
-                        continue
-
-                    heff_[i[j], i[k]] = u[cout]
-                    heff_[i[k], i[j]] = u[cout]
-
-                    cout += 1
+            return
+        else:
+            for idx, i in enumerate(self.edge_idx):
+                for j in range(len(i)):
+                    for k in range(len(i)):
+                        if j > k:
+                            continue
+                        heff_[i[j], i[k]] = u[cout]
+                        heff_[i[k], i[j]] = u[cout]
+                        cout += 1
 
-        self.heff = heff_
-        if return_heff:
-            if cout is None:
-                return heff_
-            else:
-                return (cout, heff_)
-        return cout
+            self.heff = heff_
 
     def set_udim(self, cout):
         for i in self.edge_idx: