From 168470ab58bcd5df5c46282c4d137acd60d51bdb Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 16:33:33 -0500
Subject: [PATCH 01/27] better typing and fixed a minor bug for cubegen

---
 src/quemb/shared/helper.py | 21 +++++++++++++--------
 1 file changed, 13 insertions(+), 8 deletions(-)

diff --git a/src/quemb/shared/helper.py b/src/quemb/shared/helper.py
index 428a9a3e..f28621e6 100644
--- a/src/quemb/shared/helper.py
+++ b/src/quemb/shared/helper.py
@@ -1,5 +1,6 @@
+from collections.abc import Sequence
 from pathlib import Path
-from typing import Any, Callable, Optional, TypeVar
+from typing import Any, Callable, Optional, TypeVar, Dict
 
 from pyscf.tools.cubegen import orbital
 
@@ -71,26 +72,30 @@ def ncore_(z: int) -> int:
 
 
 def write_cube(
-    be_object: object, cube_file_path: PathLike, fragment_idx: Optional[list], **kwargs
+    be_object: molbe.BE,
+    cube_file_path: PathLike,
+    fragment_idx: Optional[Sequence[int]] = None,
+    cubegen_kwargs: Optional[Dict[str, Any]] = None,
 ) -> None:
     """Write cube files of embedding orbitals from a BE object.
 
     Parameters
     ----------
-    be_object : object
+    be_object
         BE object containing the fragments, each of which contains embedding orbitals.
-    cube_file_path : PathLike
+    cube_file_path
         Directory to write the cube files to.
-    fragment_idx : Optional[list]
+    fragment_idx
         Index of the fragments to write the cube files for.
         If None, write all fragments.
-    kwargs: Any
+    cubegen_kwargs
         Keyword arguments passed to cubegen.orbital.
     """
     cube_file_path = Path(cube_file_path)
+    cubegen_kwargs = cubegen_kwargs if cubegen_kwargs else {}
     if not isinstance(be_object, molbe.BE):
         raise NotImplementedError("Support for Periodic BE not implemented yet.")
-    if not fragment_idx:
+    if fragment_idx is None:
         fragment_idx = range(be_object.Nfrag)
     for idx in fragment_idx:
         for emb_orb_idx in range(be_object.Fobjs[idx].TA.shape[1]):
@@ -98,5 +103,5 @@ def write_cube(
                 be_object.mol,
                 cube_file_path / f"frag_{idx}_orb_{emb_orb_idx}.cube",
                 be_object.Fobjs[idx].TA[:, emb_orb_idx],
-                **kwargs,
+                **cubegen_kwargs,
             )

From 3e833ed00ddb605806268b813eb480395e2977a4 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 16:34:13 -0500
Subject: [PATCH 02/27] explicitly fail when `lo_method == "iao" and
 iao_val_core`

this automatically fixes a non-resolved import as well
---
 src/quemb/kbe/lo.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/quemb/kbe/lo.py b/src/quemb/kbe/lo.py
index 1a6914bb..488e45f1 100644
--- a/src/quemb/kbe/lo.py
+++ b/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

From 6309fcb6bc4206e565337c3ab36477c183eef391 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 16:38:18 -0500
Subject: [PATCH 03/27] kbe should use the molbe be_func and be_func_parallel

this fixes the last wrong import
---
 src/quemb/kbe/pbe.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/quemb/kbe/pbe.py b/src/quemb/kbe/pbe.py
index 39c5c8a5..221aed53 100644
--- a/src/quemb/kbe/pbe.py
+++ b/src/quemb/kbe/pbe.py
@@ -18,7 +18,6 @@
 from quemb.molbe.helper import get_eri, get_scfObj, get_veff
 from quemb.molbe.be_parallel import be_func_parallel
 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,

From c3a728081cf70f57fabb045475f240b7a9599c2d Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:23:46 -0500
Subject: [PATCH 04/27] fixed mypy of scratch manager

---
 src/quemb/shared/manage_scratch.py | 18 +++++++++++-------
 tests/scratch_manager_test.py      | 18 +++++++++---------
 2 files changed, 20 insertions(+), 16 deletions(-)

diff --git a/src/quemb/shared/manage_scratch.py b/src/quemb/shared/manage_scratch.py
index c7d214a4..e8db745b 100644
--- a/src/quemb/shared/manage_scratch.py
+++ b/src/quemb/shared/manage_scratch.py
@@ -5,7 +5,7 @@
 from shutil import rmtree
 from types import TracebackType
 
-from attr import define
+from attr import define, field
 from typing_extensions import Literal, Optional, TypeAlias, Union
 
 from quemb.shared.be_var import SCRATCH
@@ -13,6 +13,10 @@
 PathLike: TypeAlias = Union[str, os.PathLike]
 
 
+def _get_absolute_path(pathlike: PathLike) -> Path:
+    return Path(pathlike).resolve()
+
+
 @define(order=False)
 class WorkDir:
     """Manage a scratch area.
@@ -41,13 +45,13 @@ class WorkDir:
     without errors.
     """
 
-    path: Path
-    cleanup_at_end: bool
-
-    def __init__(self, scratch_area: PathLike, cleanup_at_end: bool = True) -> None:
-        self.path = Path(scratch_area).resolve()
-        self.cleanup_at_end = cleanup_at_end
+    path: Path = field(converter=_get_absolute_path)
+    cleanup_at_end: bool = True
 
+    # The __init__ is automatically created
+    # the values `self.path` and `self.cleanup_at_end` are already filled.
+    # we define the __attrs_post_init__ to create the directory
+    def __attrs_post_init__(self) -> None:
         self.path.mkdir(parents=True, exist_ok=True)
         if any(self.path.iterdir()):
             self.cleanup_at_end = False
diff --git a/tests/scratch_manager_test.py b/tests/scratch_manager_test.py
index 94add337..c971e82c 100644
--- a/tests/scratch_manager_test.py
+++ b/tests/scratch_manager_test.py
@@ -7,7 +7,7 @@
 from quemb.shared.manage_scratch import WorkDir
 
 
-def test_already_created():
+def test_already_created() -> None:
     my_tmp = Path(mkdtemp())
     assert my_tmp.exists()
 
@@ -20,7 +20,7 @@ def test_already_created():
         scratch.cleanup()
 
 
-def test_keep_upon_error():
+def test_keep_upon_error() -> None:
     my_tmp = Path(mkdtemp())
     assert my_tmp.exists()
 
@@ -34,7 +34,7 @@ def test_keep_upon_error():
     assert not my_tmp.exists()
 
 
-def test_already_created_non_empty():
+def test_already_created_non_empty() -> None:
     my_tmp = Path(mkdtemp())
 
     assert my_tmp.exists()
@@ -48,7 +48,7 @@ def test_already_created_non_empty():
     assert my_tmp.exists()
 
 
-def test_context_manager():
+def test_context_manager() -> None:
     my_tmp = Path(mkdtemp())
     assert my_tmp.exists()
 
@@ -58,7 +58,7 @@ def test_context_manager():
     assert not my_tmp.exists()
 
 
-def test_creation_user_defined():
+def test_creation_user_defined() -> None:
     test_dir = Path("./scratch_test")
     with WorkDir("./scratch_test") as scratch:
         assert test_dir.exists()
@@ -66,9 +66,9 @@ def test_creation_user_defined():
     assert not test_dir.exists()
 
 
-def test_creation_PID():
+def test_creation_PID() -> None:
     PID = os.getpid()
-    with WorkDir(scratch_area=Path("./scratch_root")) as scratch_root:
+    with WorkDir(path=Path("./scratch_root")) as scratch_root:
         tmp_root = scratch_root.path
         with WorkDir.from_environment(user_defined_root=tmp_root) as dir:
             assert dir.path == tmp_root / f"QuEmb_{PID}"
@@ -76,9 +76,9 @@ def test_creation_PID():
                 assert dir_2.path == tmp_root / f"QuEmb_{PID + 1}"
 
 
-def test_dunder_methods():
+def test_dunder_methods() -> None:
     "Test if we can use an instance of `WorkDir` as if it was a `Path`"
-    with WorkDir(scratch_area=Path("./scratch")) as scratch:
+    with WorkDir(path=Path("./scratch")) as scratch:
         with open(scratch / "test.txt", "w") as f:
             f.write("hello world")
 

From 9bf111f1d6b316e85da1f6b5da93484084045659 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:24:01 -0500
Subject: [PATCH 05/27] fixed molbe_io_fcidump_test

---
 tests/molbe_io_fcidump_test.py | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/tests/molbe_io_fcidump_test.py b/tests/molbe_io_fcidump_test.py
index 3845efe8..ede232d2 100644
--- a/tests/molbe_io_fcidump_test.py
+++ b/tests/molbe_io_fcidump_test.py
@@ -15,7 +15,7 @@
 from quemb.molbe.misc import be2fcidump, libint2pyscf
 
 
-def prepare_system():
+def prepare_system() -> BE:
     # Read in molecular integrals expressed in libint basis ordering
     # numpy.loadtxt takes care of the input under the hood
     mol, mf = libint2pyscf(
@@ -36,7 +36,7 @@ def prepare_system():
     return oct_be
 
 
-def verify_fcidump_writing(kind_of_MO: str):
+def verify_fcidump_writing(kind_of_MO: str) -> None:
     oct_be = prepare_system()
     tmp_dir = Path(mkdtemp())
     data_dir = Path("data/octane_FCIDUMPs/")
@@ -60,7 +60,7 @@ def verify_fcidump_writing(kind_of_MO: str):
     not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
     reason="This test is known to fail.",
 )
-def test_embedding():
+def test_embedding() -> None:
     verify_fcidump_writing("embedding")
 
 
@@ -68,7 +68,7 @@ def test_embedding():
     not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
     reason="This test is known to fail.",
 )
-def test_fragment_mo():
+def test_fragment_mo() -> None:
     verify_fcidump_writing("fragment_mo")
 
 

From 3645ae1fc66765eed52ad499f0a4086047befe5c Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:35:34 -0500
Subject: [PATCH 06/27] improved mypy testing

---
 example/__init__.py       | 3 +++
 mypy.ini                  | 8 ++------
 tests/__init__.py         | 3 +++
 tests/chem_dm_kBE_test.py | 6 +++---
 4 files changed, 11 insertions(+), 9 deletions(-)
 create mode 100644 example/__init__.py
 create mode 100644 tests/__init__.py

diff --git a/example/__init__.py b/example/__init__.py
new file mode 100644
index 00000000..c4216c09
--- /dev/null
+++ b/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.
diff --git a/mypy.ini b/mypy.ini
index dbb78019..01100bb4 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -3,16 +3,12 @@
     disallow_untyped_defs = True
     check_untyped_defs = True
 
-[mypy-quemb.molbe.*]
+[mypy-quemb.molbe.*,quemb.kbe.*,quemb.shared.external.*]
     disallow_untyped_defs = False
     check_untyped_defs = False
 
 
-[mypy-quemb.kbe.*]
-    disallow_untyped_defs = False
-    check_untyped_defs = False
-
-[mypy-quemb.shared.external.*]
+[mypy-tests.*,example.*]
     disallow_untyped_defs = False
     check_untyped_defs = False
 
diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 00000000..c4216c09
--- /dev/null
+++ b/tests/__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.
diff --git a/tests/chem_dm_kBE_test.py b/tests/chem_dm_kBE_test.py
index 076ae4c0..dff2ceea 100644
--- a/tests/chem_dm_kBE_test.py
+++ b/tests/chem_dm_kBE_test.py
@@ -21,7 +21,7 @@
 
 class Test_kBE_Full(unittest.TestCase):
     @unittest.skipIf(libdmet is None, "Module `libdmet` not imported correctly.")
-    def test_kc2_sto3g_be1_chempot(self):
+    def test_kc2_sto3g_be1_chempot(self) -> None:
         kpt = [1, 1, 1]
         cell = gto.Cell()
 
@@ -46,7 +46,7 @@ def test_kc2_sto3g_be1_chempot(self):
             cell, kpt, "be1", "C2 (kBE1)", "autogen", -74.64695833012868, only_chem=True
         )
 
-    def test_kc4_sto3g_be2_density(self):
+    def test_kc4_sto3g_be2_density(self) -> None:
         kpt = [1, 1, 1]
         cell = gto.Cell()
 
@@ -87,7 +87,7 @@ def periodic_test(
         target,
         delta=1e-4,
         only_chem=True,
-    ):
+    ) -> None:
         kpts = cell.make_kpts(kpt, wrap_around=True)
         mydf = df.GDF(cell, kpts)
         mydf.build()

From 8d74c81b42e0abeedbd8590dd2fe03b8de8576ab Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:37:52 -0500
Subject: [PATCH 07/27] fixed a wrong import

---
 example/molbe_io_fcidump.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/example/molbe_io_fcidump.py b/example/molbe_io_fcidump.py
index 3c774d54..239f3897 100644
--- a/example/molbe_io_fcidump.py
+++ b/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
 

From a8f687f313ef319a374443bb181fd19a0355b321 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:41:15 -0500
Subject: [PATCH 08/27] more explicit blacklist for tests

---
 mypy.ini | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/mypy.ini b/mypy.ini
index 01100bb4..6c9c788d 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -7,8 +7,12 @@
     disallow_untyped_defs = False
     check_untyped_defs = False
 
+# blacklist tests
+[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_octane_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-tests.*,example.*]
+[mypy-example.*]
     disallow_untyped_defs = False
     check_untyped_defs = False
 

From ca5d1119c19ec1d07003539df7165e15956f40cb Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Tue, 10 Dec 2024 17:43:09 -0500
Subject: [PATCH 09/27] enable the test for mypy

---
 .github/workflows/quemb_unittest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 17964874..ea193b96 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -74,7 +74,7 @@ jobs:
 
     - 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/
 
 
 

From 06296dc7bbc0738bc622c56e79c4a9a9a95b619e Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 09:54:24 -0500
Subject: [PATCH 10/27] moved write_cube to shared.io

this fixes a circular import of molbe.BE
molbe.BE depends on shared/helper, so we cannot import it in
shared/helper.py
---
 src/quemb/shared/helper.py | 49 ++++----------------------------------
 src/quemb/shared/io.py     | 45 ++++++++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 44 deletions(-)
 create mode 100644 src/quemb/shared/io.py

diff --git a/src/quemb/shared/helper.py b/src/quemb/shared/helper.py
index f28621e6..4b7618fc 100644
--- a/src/quemb/shared/helper.py
+++ b/src/quemb/shared/helper.py
@@ -1,14 +1,11 @@
-from collections.abc import Sequence
-from pathlib import Path
-from typing import Any, Callable, Optional, TypeVar, Dict
-
-from pyscf.tools.cubegen import orbital
-
-from quemb import molbe
-from quemb.shared.manage_scratch import PathLike
+from typing import Any, Callable, Dict, Optional, TypeAlias, TypeVar
 
 Function = TypeVar("Function", bound=Callable)
 
+# A dictionary that is used to pass keyword arguments via unpacking
+# to the next function
+KwargDict: TypeAlias = Dict[str, Any]
+
 
 # Note that we have once Callable and once Function.
 # This is **intentional**.
@@ -69,39 +66,3 @@ def ncore_(z: int) -> int:
     else:
         raise ValueError("Ncore not computed in helper.ncore(), add it yourself!")
     return nc
-
-
-def write_cube(
-    be_object: molbe.BE,
-    cube_file_path: PathLike,
-    fragment_idx: Optional[Sequence[int]] = None,
-    cubegen_kwargs: Optional[Dict[str, Any]] = None,
-) -> None:
-    """Write cube files of embedding orbitals from a BE object.
-
-    Parameters
-    ----------
-    be_object
-        BE object containing the fragments, each of which contains embedding orbitals.
-    cube_file_path
-        Directory to write the cube files to.
-    fragment_idx
-        Index of the fragments to write the cube files for.
-        If None, write all fragments.
-    cubegen_kwargs
-        Keyword arguments passed to cubegen.orbital.
-    """
-    cube_file_path = Path(cube_file_path)
-    cubegen_kwargs = cubegen_kwargs if cubegen_kwargs else {}
-    if not isinstance(be_object, molbe.BE):
-        raise NotImplementedError("Support for Periodic BE not implemented yet.")
-    if fragment_idx is None:
-        fragment_idx = range(be_object.Nfrag)
-    for idx in fragment_idx:
-        for emb_orb_idx in range(be_object.Fobjs[idx].TA.shape[1]):
-            orbital(
-                be_object.mol,
-                cube_file_path / f"frag_{idx}_orb_{emb_orb_idx}.cube",
-                be_object.Fobjs[idx].TA[:, emb_orb_idx],
-                **cubegen_kwargs,
-            )
diff --git a/src/quemb/shared/io.py b/src/quemb/shared/io.py
new file mode 100644
index 00000000..79c9a0a1
--- /dev/null
+++ b/src/quemb/shared/io.py
@@ -0,0 +1,45 @@
+from collections.abc import Sequence
+from pathlib import Path
+from typing import Optional
+
+from pyscf.tools.cubegen import orbital
+
+from quemb import molbe
+from quemb.shared.helper import KwargDict
+from quemb.shared.manage_scratch import PathLike
+
+
+def write_cube(
+    be_object: molbe.BE,
+    cube_file_path: PathLike,
+    fragment_idx: Optional[Sequence[int]] = None,
+    cubegen_kwargs: Optional[KwargDict] = None,
+) -> None:
+    """Write cube files of embedding orbitals from a BE object.
+
+    Parameters
+    ----------
+    be_object
+        BE object containing the fragments, each of which contains embedding orbitals.
+    cube_file_path
+        Directory to write the cube files to.
+    fragment_idx
+        Index of the fragments to write the cube files for.
+        If None, write all fragments.
+    cubegen_kwargs
+        Keyword arguments passed to cubegen.orbital.
+    """
+    cube_file_path = Path(cube_file_path)
+    cubegen_kwargs = cubegen_kwargs if cubegen_kwargs else {}
+    if not isinstance(be_object, molbe.BE):
+        raise NotImplementedError("Support for Periodic BE not implemented yet.")
+    if fragment_idx is None:
+        fragment_idx = range(be_object.Nfrag)
+    for idx in fragment_idx:
+        for emb_orb_idx in range(be_object.Fobjs[idx].TA.shape[1]):
+            orbital(
+                be_object.mol,
+                cube_file_path / f"frag_{idx}_orb_{emb_orb_idx}.cube",
+                be_object.Fobjs[idx].TA[:, emb_orb_idx],
+                **cubegen_kwargs,
+            )

From 5b9c13eaabdf8ed57f009152f6943b8714d29983 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 09:56:06 -0500
Subject: [PATCH 11/27] fixed import in test

---
 tests/molbe_octane_test.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/molbe_octane_test.py b/tests/molbe_octane_test.py
index d60c1842..408e5cbe 100644
--- a/tests/molbe_octane_test.py
+++ b/tests/molbe_octane_test.py
@@ -9,7 +9,7 @@
 from pyscf import cc, gto, scf
 
 from quemb.molbe import BE, fragpart
-from quemb.shared.helper import write_cube
+from quemb.shared.io import write_cube
 
 # TODO: actually add meaningful tests for energies etc.
 #   At the moment the test fails already for technical reasons.

From 85400498209db5f87d420274510111246b6b7baf Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 13:36:06 -0500
Subject: [PATCH 12/27] bumped up python versions

---
 .github/workflows/build_docs.yml     | 4 ++--
 .github/workflows/quemb_unittest.yml | 4 ++--
 README.md                            | 2 +-
 setup.py                             | 2 +-
 4 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/.github/workflows/build_docs.yml b/.github/workflows/build_docs.yml
index c9702419..c1fdc582 100644
--- a/.github/workflows/build_docs.yml
+++ b/.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: |
diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index ea193b96..a138b3f9 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.12"]
+        python-version: ["3.13"]
 
 
     steps:
@@ -83,7 +83,7 @@ jobs:
     needs: analysis
     strategy:
       matrix:
-        python-version: ["3.9", "3.12"]
+        python-version: ["3.10", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
diff --git a/README.md b/README.md
index 5908b31c..078d031a 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,7 @@ processors.
 
 ### Prerequisites
 
-- Python 3.6 or higher
+- Python `>=3.10`
 - PySCF library
 - Numpy
 - Scipy
diff --git a/setup.py b/setup.py
index f35132ad..ed548467 100644
--- a/setup.py
+++ b/setup.py
@@ -17,7 +17,7 @@
     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",

From fbbcef8773731b486ad538cd75ca07a8ef2f69cf Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 14:33:05 -0500
Subject: [PATCH 13/27] changed quemb unittest to install pytest earlier

---
 .github/workflows/quemb_unittest.yml | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index a138b3f9..5baa1f61 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -48,7 +48,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --upgrade --upgrade-strategy eager ruff pylint mypy scipy-stubs
+        pip install --upgrade --upgrade-strategy eager ruff pylint mypy scipy-stubs pytest
         pip install .
 
 
@@ -106,8 +106,6 @@ 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 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

From 1cfdd0bc023aeb6c09cedb0bf02550c3dbc61c2b Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 14:37:33 -0500
Subject: [PATCH 14/27] actually also install pytest for test :-D

---
 .github/workflows/quemb_unittest.yml | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 5baa1f61..1010d06f 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -106,6 +106,7 @@ jobs:
 
     - name: Install dependencies
       run: |
+        pip install pytest
         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

From fce077b29b73d4eb3f653d14f30d11320e3eba4d Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 17:40:15 -0500
Subject: [PATCH 15/27] fixed typing issues in tests

---
 mypy.ini                   |  8 ++++----
 tests/molbe_octane_test.py | 15 +++++++--------
 2 files changed, 11 insertions(+), 12 deletions(-)

diff --git a/mypy.ini b/mypy.ini
index 6c9c788d..a7f34214 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -7,12 +7,12 @@
     disallow_untyped_defs = False
     check_untyped_defs = False
 
-# blacklist tests
-[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_octane_test,tests.molbe_oneshot_rbe_hcore_test,tests.molbe_oneshot_rbe_qmmm-fromchk_test,tests.ube-oneshot_test]
+# explicitly blacklist tests
+[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.*]
+[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 +29,4 @@
     ignore_missing_imports = True
 
 [mypy-h5py.*]
-    ignore_missing_imports = True
+    ignore_missing_imports = True
\ No newline at end of file
diff --git a/tests/molbe_octane_test.py b/tests/molbe_octane_test.py
index 408e5cbe..3a01b7ce 100644
--- a/tests/molbe_octane_test.py
+++ b/tests/molbe_octane_test.py
@@ -3,6 +3,7 @@
 
 import os
 import tempfile
+from typing import Tuple
 
 import numpy as np
 import pytest
@@ -19,7 +20,7 @@
     not os.getenv("QUEMB_DO_KNOWN_TO_FAIL_TESTS") == "true",
     reason="This test is known to fail.",
 )
-def test_octane_molbe():
+def test_octane_molbe() -> None:
     # Prepare octane molecule
     mol, mf = prepare_octane()
 
@@ -45,7 +46,7 @@ def test_octane_molbe():
     print(f"*** BE2 Correlation Energy Error (%) : {err_:>8.4f} %")
 
 
-def test_cubegen():
+def test_cubegen() -> None:
     # Prepare octane molecule
     mol, mf = prepare_octane()
     # Build fragments
@@ -55,23 +56,21 @@ def test_cubegen():
     mybe.optimize(solver="CCSD", nproc=1, ompnum=1)
     # Write cube file to a temporary location
     with tempfile.TemporaryDirectory() as tmpdir:
-        write_cube(mybe, tmpdir, fragment_idx=[3], resolution=5)
+        write_cube(mybe, tmpdir, fragment_idx=[3], cubegen_kwargs=dict(resolution=5))
         with open(os.path.join(tmpdir, "frag_3_orb_2.cube"), "r") as f:
-            cube_content = f.read()
             cube_content = np.fromstring(
-                "".join(cube_content.split("\n")[2:]), sep=" ", dtype=float
+                "".join(f.read().split("\n")[2:]), sep=" ", dtype=float
             )
         with open("data/octane_frag_3_orb_2.cube", "r") as f:
-            reference_content = f.read()
             reference_content = np.fromstring(
-                "".join(reference_content.split("\n")[2:]), sep=" ", dtype=float
+                "".join(f.read().split("\n")[2:]), sep=" ", dtype=float
             )
         assert np.isclose(
             cube_content, reference_content
         ).all(), "Cube file content does not match reference content."
 
 
-def prepare_octane():
+def prepare_octane() -> Tuple[gto.Mole, scf.hf.RHF]:
     mol = gto.M(
         atom="""
     C   0.4419364699  -0.6201930287   0.0000000000

From 9eccd2797bae2c84ce6d94ab07a29a7cbbb8cd05 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 17:47:36 -0500
Subject: [PATCH 16/27] do explicit blacklist in mypy.ini

---
 mypy.ini | 14 ++++++++++++--
 1 file changed, 12 insertions(+), 2 deletions(-)

diff --git a/mypy.ini b/mypy.ini
index a7f34214..5ad72749 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -3,11 +3,21 @@
     disallow_untyped_defs = True
     check_untyped_defs = True
 
-[mypy-quemb.molbe.*,quemb.kbe.*,quemb.shared.external.*]
+
+# 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.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
 
-# explicitly blacklist tests
 [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

From 64d696e7647835d0481888176fbb7a065b022211 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Wed, 11 Dec 2024 18:16:38 -0500
Subject: [PATCH 17/27] refactored kbe update_heff

---
 src/quemb/kbe/pfrag.py   | 41 +++++++++++++---------------------------
 src/quemb/molbe/pfrag.py |  4 +---
 2 files changed, 14 insertions(+), 31 deletions(-)

diff --git a/src/quemb/kbe/pfrag.py b/src/quemb/kbe/pfrag.py
index 7fb2d87f..381e4dcc 100644
--- a/src/quemb/kbe/pfrag.py
+++ b/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:
diff --git a/src/quemb/molbe/pfrag.py b/src/quemb/molbe/pfrag.py
index fe62368a..62c19de0 100644
--- a/src/quemb/molbe/pfrag.py
+++ b/src/quemb/molbe/pfrag.py
@@ -268,9 +268,7 @@ def scf(
         mf_ = None
 
     def update_heff(self, u, cout=None, only_chem=False):
-        """
-        Update the effective Hamiltonian for the fragment.
-        """
+        """Update the effective Hamiltonian for the fragment."""
         heff_ = numpy.zeros_like(self.h1)
 
         if cout is None:

From b8a67820a3a657249b867eda40fa2f2d8932d0df Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Thu, 12 Dec 2024 12:46:58 -0500
Subject: [PATCH 18/27] updated doc and removed some unnecessary commands

- everythying uses `pip install .` now
- take out some not-anymore-needed conda specific installation commands
- take out PYTHONPATH fiddling
---
 .github/workflows/quemb_unittest.yml |  1 -
 README.md                            | 47 +++++++++++++---------------
 docs/source/index.rst                |  5 +++
 docs/source/install.rst              | 39 ++++++++++-------------
 4 files changed, 44 insertions(+), 48 deletions(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 1010d06f..53213adc 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -112,7 +112,6 @@ jobs:
         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
diff --git a/README.md b/README.md
index 078d031a..d553cde1 100644
--- a/README.md
+++ b/README.md
@@ -29,31 +29,28 @@ processors.
 - 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
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 9222d94f..30d6edfa 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -36,3 +36,8 @@ References
    optimize
    solvers
    misc
+
+
+
+.. role:: bash(code)
+   :language: bash
\ No newline at end of file
diff --git a/docs/source/install.rst b/docs/source/install.rst
index 2542ec68..7e8e2a35 100644
--- a/docs/source/install.rst
+++ b/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:`##` 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 .
\ No newline at end of file

From 0769f9acd65eb10bde41388889a41d4d3c4fe0d5 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Thu, 12 Dec 2024 13:16:51 -0500
Subject: [PATCH 19/27] enforce checks for `ruff check` and `pylint`

pylint only checks E0401,R0401,E0611 because the actually require
importing python code which `ruff` does not do
---
 .github/workflows/quemb_unittest.yml | 4 ++--
 docs/source/install.rst              | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 53213adc..bc30d1a8 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -60,7 +60,7 @@ 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
@@ -69,7 +69,7 @@ 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 .    # for the moment we want to report always report success
 
 
     - name: Static analysis with mypy
diff --git a/docs/source/install.rst b/docs/source/install.rst
index 7e8e2a35..50102d69 100644
--- a/docs/source/install.rst
+++ b/docs/source/install.rst
@@ -11,7 +11,7 @@ Prerequisites
  * `libDMET <https://github.com/gkclab/libdmet_preview>`__ (required for periodic BE)
  * `Wannier90 <https://github.com/wannier-developers/wannier90>`_ :sup:`##`
 
-| :sup:`##` Wannier90 code is optional and only necessary to use Wannier functions in periodic code.
+| :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`.

From 133e01c950721ea1aae2548c2dc9e0625e11a25d Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Thu, 12 Dec 2024 13:19:04 -0500
Subject: [PATCH 20/27] fixed comments in build yaml files

---
 .github/workflows/quemb_unittest.yml | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index bc30d1a8..1e183d5a 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -58,7 +58,6 @@ jobs:
 
 
     - name: Static analysis with ruff
-      # for the moment we want to report always report success
       run: |
         ruff check .
 
@@ -69,7 +68,7 @@ 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 .    # for the moment we want to report always report success
+        pylint --disable=all --enable=E0401,R0401,E0611 .
 
 
     - name: Static analysis with mypy

From d2b9d5041e74d93f97425916d48400b6a5260c35 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Thu, 12 Dec 2024 14:07:48 -0500
Subject: [PATCH 21/27] made mypy testing even more beautiful

---
 src/quemb/shared/manage_scratch.py | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/src/quemb/shared/manage_scratch.py b/src/quemb/shared/manage_scratch.py
index e8db745b..dfd8313c 100644
--- a/src/quemb/shared/manage_scratch.py
+++ b/src/quemb/shared/manage_scratch.py
@@ -4,16 +4,16 @@
 from pathlib import Path
 from shutil import rmtree
 from types import TracebackType
+from typing import Annotated, Final, Literal, Optional, TypeAlias
 
 from attr import define, field
-from typing_extensions import Literal, Optional, TypeAlias, Union
 
 from quemb.shared.be_var import SCRATCH
 
-PathLike: TypeAlias = Union[str, os.PathLike]
+PathLike: TypeAlias = str | os.PathLike
 
 
-def _get_absolute_path(pathlike: PathLike) -> Path:
+def _to_abs_path(pathlike: PathLike) -> Path:
     return Path(pathlike).resolve()
 
 
@@ -21,9 +21,10 @@ def _get_absolute_path(pathlike: PathLike) -> Path:
 class WorkDir:
     """Manage a scratch area.
 
-    Upon initialisation of the object the `path` is created,
+    Upon initialisation of the object the workdir `path` is created,
     if it does not exist yet.
     If it already exists, it is ensured, that it is empty.
+    Internally the `path` will be stored as absolute.
 
     If `do_cleanup` is true, then the scratch area is deleted,
     when if `self.cleanup` is called.
@@ -45,8 +46,8 @@ class WorkDir:
     without errors.
     """
 
-    path: Path = field(converter=_get_absolute_path)
-    cleanup_at_end: bool = True
+    path: Final[Annotated[Path, "An absolute path"]] = field(converter=_to_abs_path)
+    cleanup_at_end: Final[bool] = True
 
     # The __init__ is automatically created
     # the values `self.path` and `self.cleanup_at_end` are already filled.
@@ -54,7 +55,6 @@ class WorkDir:
     def __attrs_post_init__(self) -> None:
         self.path.mkdir(parents=True, exist_ok=True)
         if any(self.path.iterdir()):
-            self.cleanup_at_end = False
             raise ValueError("scratch_area has to be empty.")
 
     def __enter__(self) -> WorkDir:

From 2f55fba47b881698e46e93b7fe35cc46e1790f03 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Thu, 12 Dec 2024 14:32:53 -0500
Subject: [PATCH 22/27] fixed small type error in os.environ.get

---
 src/quemb/molbe/solver.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/quemb/molbe/solver.py b/src/quemb/molbe/solver.py
index 19fdea54..ae2794fd 100644
--- a/src/quemb/molbe/solver.py
+++ b/src/quemb/molbe/solver.py
@@ -816,7 +816,7 @@ def solve_block2(mf, nocc, frag_scratch, **solver_kwargs):
         [max_noise, max_noise, max_noise / 10, max_noise / 100, max_noise / 100, 0.0],
     )
     # Other DMRG parameters
-    mc.fcisolver.threads = int(os.environ.get("OMP_NUM_THREADS", 8))
+    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)
     mc.fcisolver.block_extra_keyword = list(block_extra_keyword)

From 03048d14a389fe86b7fd384c7683d459de6babdd Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Fri, 13 Dec 2024 10:15:54 -0500
Subject: [PATCH 23/27] fixed unsorted imports

---
 src/quemb/kbe/pbe.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/quemb/kbe/pbe.py b/src/quemb/kbe/pbe.py
index 221aed53..be617cab 100644
--- a/src/quemb/kbe/pbe.py
+++ b/src/quemb/kbe/pbe.py
@@ -15,8 +15,8 @@
 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 (

From 7ff5b354438daef458678d16d68409e3f923417b Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Fri, 13 Dec 2024 10:20:41 -0500
Subject: [PATCH 24/27] enable ruff check and redirect stderr in pre-commit
 hook

---
 .githooks/pre-commit | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.githooks/pre-commit b/.githooks/pre-commit
index 24ddcf39..1d72c2b1 100755
--- a/.githooks/pre-commit
+++ b/.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
 
 

From b799cceaea730da4ab358048f57ed75014b9ab7a Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Fri, 13 Dec 2024 10:33:06 -0500
Subject: [PATCH 25/27] do the mypy testing with 3.10

---
 .github/workflows/quemb_unittest.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 1e183d5a..7788fb0d 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.13"]
+        python-version: ["3.10"]
 
 
     steps:

From 5f2f57335d130e884aa12fd2a0ab87e83e27791d Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Fri, 13 Dec 2024 10:41:40 -0500
Subject: [PATCH 26/27] separated requirements clearly out

---
 .github/workflows/quemb_unittest.yml   | 4 ++--
 docs/requirements.txt                  | 1 +
 requirements.txt                       | 6 ------
 setup.py                               | 1 -
 tests/static_analysis_requirements.txt | 7 +++++++
 tests/test_requirements.txt            | 3 +++
 6 files changed, 13 insertions(+), 9 deletions(-)
 delete mode 100644 requirements.txt
 create mode 100644 tests/static_analysis_requirements.txt
 create mode 100644 tests/test_requirements.txt

diff --git a/.github/workflows/quemb_unittest.yml b/.github/workflows/quemb_unittest.yml
index 7788fb0d..1c902766 100644
--- a/.github/workflows/quemb_unittest.yml
+++ b/.github/workflows/quemb_unittest.yml
@@ -48,7 +48,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install --upgrade --upgrade-strategy eager ruff pylint mypy scipy-stubs pytest
+        pip install -r tests/static_analysis_requirements.txt
         pip install .
 
 
@@ -105,7 +105,7 @@ jobs:
 
     - name: Install dependencies
       run: |
-        pip install pytest
+        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
diff --git a/docs/requirements.txt b/docs/requirements.txt
index 144ce731..681d165c 100644
--- a/docs/requirements.txt
+++ b/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
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 49fd1fa5..00000000
--- a/requirements.txt
+++ /dev/null
@@ -1,6 +0,0 @@
-pyscf==2.6.2
-pytest==8.3.2
-libdmet @ git+https://github.com/gkclab/libdmet_preview.git
-matplotlib
-attrs
-typing_extensions
diff --git a/setup.py b/setup.py
index ed548467..6f8e8ffa 100644
--- a/setup.py
+++ b/setup.py
@@ -25,6 +25,5 @@
         "matplotlib",
         "libdmet @ git+https://github.com/gkclab/libdmet_preview.git",
         "attrs",
-        "typing_extensions",
     ],
 )
diff --git a/tests/static_analysis_requirements.txt b/tests/static_analysis_requirements.txt
new file mode 100644
index 00000000..e62e20cb
--- /dev/null
+++ b/tests/static_analysis_requirements.txt
@@ -0,0 +1,7 @@
+# the additional (!) requirements for performing static analysis of the code
+# the dependencies of `quemb` itself are given in the setup.py
+ruff
+pylint
+mypy
+scipy-stubs
+pytest
\ No newline at end of file
diff --git a/tests/test_requirements.txt b/tests/test_requirements.txt
new file mode 100644
index 00000000..2562dc10
--- /dev/null
+++ b/tests/test_requirements.txt
@@ -0,0 +1,3 @@
+# the additional (!) requirements for testing the code
+# the dependencies of `quemb` itself are given in the setup.py
+pytest
\ No newline at end of file

From 6140dbe13c6934f4e1a1d0ce6555f1562e5752c7 Mon Sep 17 00:00:00 2001
From: Oskar Weser <oskar.weser@gmail.com>
Date: Fri, 13 Dec 2024 12:30:12 -0500
Subject: [PATCH 27/27] deleted superfluos return

---
 src/quemb/kbe/pfrag.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/quemb/kbe/pfrag.py b/src/quemb/kbe/pfrag.py
index 381e4dcc..ca5f9d90 100644
--- a/src/quemb/kbe/pfrag.py
+++ b/src/quemb/kbe/pfrag.py
@@ -369,7 +369,6 @@ def update_heff(
 
         if only_chem:
             self.heff = heff_
-            return
         else:
             for idx, i in enumerate(self.edge_idx):
                 for j in range(len(i)):