From d2447edc903d48180107962cc9827c387637e1ce Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 11:41:45 +0800
Subject: [PATCH 01/42] copy pyproject from 4073

---
 pyproject.toml | 28 +++++++++++-----------------
 1 file changed, 11 insertions(+), 17 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8805c438ae0..4e30b2c9612 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,40 +87,34 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-ase = ["ase>=3.23.0"]
-# tblite only support Python 3.12+ through conda-forge
-# https://github.com/tblite/tblite/issues/175
-tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
-vis = ["vtk>=6.0.0"]
 abinit = ["netcdf4>=1.7.1"]
-mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
-electronic_structure = ["fdint>=2.0.2"]
+ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
+electronic_structure = ["fdint>=2.0.2"]
+mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
+numba = ["numba>=0.55"]
+numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [
-    "ase>=3.23.0",
-    "beautifulsoup4",
+    "pymatgen[abinit,ase,mlp,tblite]",
+    "beautifulsoup4>=4.6.0",
     # BoltzTraP2 build fails on Windows GitHub runners
     "BoltzTraP2>=24.9.4 ; platform_system != 'Windows'",
     "chemview>=0.6",
-    "chgnet>=0.3.8",
     "f90nml>=1.1.2",
     "galore>=0.6.1",
     "h5py>=3.11.0",
     "jarvis-tools>=2020.7.14",
-    "matgl>=1.1.3",
     "matplotlib>=3.8",
-    "netCDF4>=1.6.5",
     "phonopy>=2.23",
     "seekpath>=2.0.1",
-    # tblite only support Python 3.12+ through conda-forge
-    # https://github.com/tblite/tblite/issues/175
     "hiphive>=1.3.1",
     "openbabel-wheel>=3.1.1.20",
-    "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
 ]
-numba = ["numba>=0.55"]
-numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
+# tblite only support Python 3.12+ through conda-forge
+# https://github.com/tblite/tblite/issues/175
+tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
+vis = ["vtk>=6.0.0"]
 
 [project.scripts]
 pmg = "pymatgen.cli.pmg:main"

From 1eb855b9074105034bd6b91cf837c4e5675e82d0 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 11:50:01 +0800
Subject: [PATCH 02/42] bump monty

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 4e30b2c9612..d5bf9cd6a3d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,7 @@ classifiers = [
 dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
-    "monty>=2024.7.29",
+    "monty>=2024.10.21",
     "networkx>=3",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",

From aae9f4ba262d547011b60991d73172c442f3dcce Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 13:50:26 +0800
Subject: [PATCH 03/42] recover networkx pin, and bump sympy

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index d5bf9cd6a3d..e662142aa3c 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,7 @@ dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
     "monty>=2024.10.21",
-    "networkx>=3",  # PR #4116
+    "networkx>=2.7",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",
@@ -69,7 +69,7 @@ dependencies = [
     # https://github.com/scipy/scipy/issues/21052
     "scipy>=1.14.1; platform_system == 'Windows'",
     "spglib>=2.5.0",
-    "sympy>=1.2",
+    "sympy>=1.3",  # PR #4116
     "tabulate>=0.9",
     "tqdm>=4.60",
     "uncertainties>=3.1.4",

From e08454eaa2c73a6c997c6a8c468109893405fdbb Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 14:29:38 +0800
Subject: [PATCH 04/42] pin monty to lower ver to see what is causing the
 failure

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index e662142aa3c..8c1d2e8dd90 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,7 @@ classifiers = [
 dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
-    "monty>=2024.10.21",
+    "monty==2024.7.30",  # DEBUG
     "networkx>=2.7",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",

From f8b572374a600e1608b052fb53d20cc74f34888c Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 14:50:46 +0800
Subject: [PATCH 05/42] revert all changes to pyproject but monty

---
 pyproject.toml | 34 ++++++++++++++++++++--------------
 1 file changed, 20 insertions(+), 14 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 8c1d2e8dd90..dd8e7f5dbf9 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,8 +56,8 @@ classifiers = [
 dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
-    "monty==2024.7.30",  # DEBUG
-    "networkx>=2.7",  # PR #4116
+    "monty==2024.10.21",  # DEBUG
+    "networkx>=3",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",
@@ -69,7 +69,7 @@ dependencies = [
     # https://github.com/scipy/scipy/issues/21052
     "scipy>=1.14.1; platform_system == 'Windows'",
     "spglib>=2.5.0",
-    "sympy>=1.3",  # PR #4116
+    "sympy>=1.2",
     "tabulate>=0.9",
     "tqdm>=4.60",
     "uncertainties>=3.1.4",
@@ -87,34 +87,40 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4>=1.7.1"]
 ase = ["ase>=3.23.0"]
+# tblite only support Python 3.12+ through conda-forge
+# https://github.com/tblite/tblite/issues/175
+tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
+vis = ["vtk>=6.0.0"]
+abinit = ["netcdf4>=1.7.1"]
+mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
+electronic_structure = ["fdint>=2.0.2"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
-electronic_structure = ["fdint>=2.0.2"]
-mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
-numba = ["numba>=0.55"]
-numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [
-    "pymatgen[abinit,ase,mlp,tblite]",
-    "beautifulsoup4>=4.6.0",
+    "ase>=3.23.0",
+    "beautifulsoup4",
     # BoltzTraP2 build fails on Windows GitHub runners
     "BoltzTraP2>=24.9.4 ; platform_system != 'Windows'",
     "chemview>=0.6",
+    "chgnet>=0.3.8",
     "f90nml>=1.1.2",
     "galore>=0.6.1",
     "h5py>=3.11.0",
     "jarvis-tools>=2020.7.14",
+    "matgl>=1.1.3",
     "matplotlib>=3.8",
+    "netCDF4>=1.6.5",
     "phonopy>=2.23",
     "seekpath>=2.0.1",
+    # tblite only support Python 3.12+ through conda-forge
+    # https://github.com/tblite/tblite/issues/175
     "hiphive>=1.3.1",
     "openbabel-wheel>=3.1.1.20",
+    "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
 ]
-# tblite only support Python 3.12+ through conda-forge
-# https://github.com/tblite/tblite/issues/175
-tblite = ["tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
-vis = ["vtk>=6.0.0"]
+numba = ["numba>=0.55"]
+numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 
 [project.scripts]
 pmg = "pymatgen.cli.pmg:main"

From 19484429fe1bd598e82e9ce63f2bd1c9f631b175 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 16:01:12 +0800
Subject: [PATCH 06/42] bump sympy

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index dd8e7f5dbf9..5bf4e07963f 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -56,7 +56,7 @@ classifiers = [
 dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
-    "monty==2024.10.21",  # DEBUG
+    "monty>=2024.10.21",
     "networkx>=3",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",
@@ -69,7 +69,7 @@ dependencies = [
     # https://github.com/scipy/scipy/issues/21052
     "scipy>=1.14.1; platform_system == 'Windows'",
     "spglib>=2.5.0",
-    "sympy>=1.2",
+    "sympy>=1.3",  # PR #4116
     "tabulate>=0.9",
     "tqdm>=4.60",
     "uncertainties>=3.1.4",

From 03df9b055459e90c7f1c077f058cba083775ecc6 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 16:15:19 +0800
Subject: [PATCH 07/42] sort and group optional deps

---
 pyproject.toml | 30 ++++++++++++------------------
 1 file changed, 12 insertions(+), 18 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 5bf4e07963f..27585144659 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,40 +87,34 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
+abinit = ["netcdf4>=1.6.5"]
 ase = ["ase>=3.23.0"]
-# tblite only support Python 3.12+ through conda-forge
-# https://github.com/tblite/tblite/issues/175
-tblite = ["tblite[ase]>=0.3.0; python_version<'3.12'"]
-vis = ["vtk>=6.0.0"]
-abinit = ["netcdf4>=1.7.1"]
-mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
-electronic_structure = ["fdint>=2.0.2"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
+electronic_structure = ["fdint>=2.0.2"]
+mlp = ["chgnet>=0.3.8", "matgl>=1.1.3"]
+numba = ["numba>=0.55"]
+numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
 optional = [
-    "ase>=3.23.0",
+    "pymatgen[abinit,ase,mlp,tblite]",
     "beautifulsoup4",
     # BoltzTraP2 build fails on Windows GitHub runners
     "BoltzTraP2>=24.9.4 ; platform_system != 'Windows'",
     "chemview>=0.6",
-    "chgnet>=0.3.8",
     "f90nml>=1.1.2",
     "galore>=0.6.1",
     "h5py>=3.11.0",
+    "hiphive>=1.3.1",
     "jarvis-tools>=2020.7.14",
-    "matgl>=1.1.3",
     "matplotlib>=3.8",
-    "netCDF4>=1.6.5",
+    "openbabel-wheel>=3.1.1.20",
     "phonopy>=2.23",
     "seekpath>=2.0.1",
-    # tblite only support Python 3.12+ through conda-forge
-    # https://github.com/tblite/tblite/issues/175
-    "hiphive>=1.3.1",
-    "openbabel-wheel>=3.1.1.20",
-    "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'",
 ]
-numba = ["numba>=0.55"]
-numpy-v1 = ["numpy>=1.25.0,<2"] # Test NP1 on Windows (quite buggy ATM)
+# tblite only support Python 3.12+ through conda-forge
+# https://github.com/tblite/tblite/issues/175
+tblite = [ "tblite[ase]>=0.3.0; platform_system=='Linux' and python_version<'3.12'"]
+vis = ["vtk>=6.0.0"]
 
 [project.scripts]
 pmg = "pymatgen.cli.pmg:main"

From 4492816667cab80c4be1a903f57b676377f812de Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 16:28:57 +0800
Subject: [PATCH 08/42] loose networkx pin for compatibility

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 27585144659..a55ade83109 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -57,7 +57,7 @@ dependencies = [
     "joblib>=1",
     "matplotlib>=3.8",
     "monty>=2024.10.21",
-    "networkx>=3",  # PR #4116
+    "networkx>=2.7",  # PR #4116
     "palettable>=3.3.3",
     "pandas>=2",
     "plotly>=4.5.0",

From a1231745dcb6ba572b02b351f400a8f90aae656c Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 18:29:39 +0800
Subject: [PATCH 09/42] lazy import sympy

---
 src/pymatgen/symmetry/settings.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/pymatgen/symmetry/settings.py b/src/pymatgen/symmetry/settings.py
index 3abd7f547f3..8dbecb534f3 100644
--- a/src/pymatgen/symmetry/settings.py
+++ b/src/pymatgen/symmetry/settings.py
@@ -7,8 +7,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from sympy import Matrix
-from sympy.parsing.sympy_parser import parse_expr
 
 from pymatgen.core.lattice import Lattice
 from pymatgen.core.operations import MagSymmOp, SymmOp
@@ -100,6 +98,10 @@ def parse_transformation_string(
         Returns:
             tuple[list[list[float]] | np.ndarray, list[float]]: transformation matrix & vector
         """
+        # Import sympy is expensive
+        from sympy import Matrix
+        from sympy.parsing.sympy_parser import parse_expr
+
         try:
             a, b, c = np.eye(3)
             b_change, o_shift = transformation_string.split(";")

From 968824429c69efff73638791dfcb62dde590fa04 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 18:31:48 +0800
Subject: [PATCH 10/42] lazy load scipy

---
 src/pymatgen/core/lattice.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/pymatgen/core/lattice.py b/src/pymatgen/core/lattice.py
index c98af8ca916..678ccd72f8c 100644
--- a/src/pymatgen/core/lattice.py
+++ b/src/pymatgen/core/lattice.py
@@ -16,7 +16,6 @@
 import numpy as np
 from monty.dev import deprecated
 from monty.json import MSONable
-from scipy.spatial import Voronoi
 
 from pymatgen.util.coord import pbc_shortest_vectors
 from pymatgen.util.due import Doi, due
@@ -1263,6 +1262,9 @@ def get_wigner_seitz_cell(self) -> list[list[np.ndarray]]:
             Wigner Seitz cell. For instance, a list of four coordinates will
             represent a square facet.
         """
+        # Import scipy is expensive
+        from scipy.spatial import Voronoi
+
         vec1, vec2, vec3 = self._matrix
 
         list_k_points = []

From 6e0a89c0d3a00f765d14583cd386b41957c37be8 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 18:40:33 +0800
Subject: [PATCH 11/42] Revert "lazy load scipy"

This reverts commit 968824429c69efff73638791dfcb62dde590fa04.
---
 src/pymatgen/core/lattice.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/pymatgen/core/lattice.py b/src/pymatgen/core/lattice.py
index 678ccd72f8c..c98af8ca916 100644
--- a/src/pymatgen/core/lattice.py
+++ b/src/pymatgen/core/lattice.py
@@ -16,6 +16,7 @@
 import numpy as np
 from monty.dev import deprecated
 from monty.json import MSONable
+from scipy.spatial import Voronoi
 
 from pymatgen.util.coord import pbc_shortest_vectors
 from pymatgen.util.due import Doi, due
@@ -1262,9 +1263,6 @@ def get_wigner_seitz_cell(self) -> list[list[np.ndarray]]:
             Wigner Seitz cell. For instance, a list of four coordinates will
             represent a square facet.
         """
-        # Import scipy is expensive
-        from scipy.spatial import Voronoi
-
         vec1, vec2, vec3 = self._matrix
 
         list_k_points = []

From 75e23b13b113f06e28bc6513a14485b0e0a0bb28 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 19:03:07 +0800
Subject: [PATCH 12/42] try netcdf4 install with delvewheel,
 https://github.com/materialsproject/pymatgen/pull/3894/commits/1dfc9e4f7bbddaf5d93fe9b09b425ca1be6a58f4

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a55ade83109..7d643300d63 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4>=1.6.5"]
+abinit = ["netcdf4>=1.7.1.post1", "delvewheel>=1.7.4"]  # DEBUG: #3894
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 4320868b19d6a6a21fdfcda029504d7a6f7b819b Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Tue, 22 Oct 2024 19:49:53 +0800
Subject: [PATCH 13/42] Revert "try netcdf4 install with delvewheel,
 https://github.com/materialsproject/pymatgen/pull/3894/commits/1dfc9e4f7bbddaf5d93fe9b09b425ca1be6a58f4"

This reverts commit 75e23b13b113f06e28bc6513a14485b0e0a0bb28.
---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 7d643300d63..a55ade83109 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4>=1.7.1.post1", "delvewheel>=1.7.4"]  # DEBUG: #3894
+abinit = ["netcdf4>=1.6.5"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 206ea5216e91f6883ba2efa17d5704024f9a8023 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 09:54:12 +0800
Subject: [PATCH 14/42] test netcdf4 1.7.1.post2, notice new release is out
 today

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index a55ade83109..3ddbbf1c915 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4>=1.6.5"]
+abinit = ["netcdf4==1.7.1.post2"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 25975dde6fd595e6f8e175f8bbb28a89bdb9fd4b Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 10:08:48 +0800
Subject: [PATCH 15/42] netcdf4 1.7.1.post2 doesn't work, try latest 1.7.2

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 3ddbbf1c915..812827c5bc7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4==1.7.1.post2"]
+abinit = ["netcdf4==1.7.2"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 762b85a33fa4abd1b0272836d75c8d3bfdd8f170 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 10:25:19 +0800
Subject: [PATCH 16/42] reset netcdf4 pin

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 812827c5bc7..f9edc4087ab 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,7 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4==1.7.2"]
+abinit = ["netcdf4==1.6.5"]  # PR4128: 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 038ce9af6daafdc8e46fa0277e9665866862562d Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 10:42:19 +0800
Subject: [PATCH 17/42] why <= doesn't work?

---
 pyproject.toml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f9edc4087ab..b71e512ae9d 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -87,7 +87,8 @@ Issues = "https://github.com/materialsproject/pymatgen/issues"
 Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
-abinit = ["netcdf4==1.6.5"]  # PR4128: 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
+# PR4128: netcdf4 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
+abinit = ["netcdf4>=1.6.5,!=1.7.1.post1,!=1.7.1.post2"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]
@@ -107,7 +108,6 @@ optional = [
     "hiphive>=1.3.1",
     "jarvis-tools>=2020.7.14",
     "matplotlib>=3.8",
-    "openbabel-wheel>=3.1.1.20",
     "phonopy>=2.23",
     "seekpath>=2.0.1",
 ]

From 24fdcdcf7fa14be72b9abd3bcc3b1d3f01680956 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 11:05:00 +0800
Subject: [PATCH 18/42] add comment

---
 tests/io/abinit/test_netcdf.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tests/io/abinit/test_netcdf.py b/tests/io/abinit/test_netcdf.py
index 77c313c53c3..ddc0e95ec50 100644
--- a/tests/io/abinit/test_netcdf.py
+++ b/tests/io/abinit/test_netcdf.py
@@ -92,6 +92,8 @@ def test_read_fe(self):
                 ref_magmom_collinear = [-0.5069359730980665]
                 path = os.path.join(tmp_dir, "Fe_magmoms_collinear_GSR.nc")
 
+                # TODO: PR4128, EtsfReader would fail in Ubuntu CI with netCDF4 > 1.6.5
+                # Need someone with knowledge in netCDF4 to fix it
                 with EtsfReader(path) as data:
                     structure = data.read_structure()
                     assert structure.site_properties["magmom"] == ref_magmom_collinear

From 022b91ad370c6b96072d1a2dea1d2186205c6aec Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 16:11:18 +0800
Subject: [PATCH 19/42] exclude 1.7.2 as well (perhaps conditionally skip that
 test?)

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index b71e512ae9d..9f68a690cdd 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -88,7 +88,7 @@ Pypi = "https://pypi.org/project/pymatgen"
 
 [project.optional-dependencies]
 # PR4128: netcdf4 1.7.[0/1] yanked, 1.7.1.post[1/2]/1.7.2 cause CI error
-abinit = ["netcdf4>=1.6.5,!=1.7.1.post1,!=1.7.1.post2"]
+abinit = ["netcdf4>=1.6.5,!=1.7.1.post1,!=1.7.1.post2,!=1.7.2"]
 ase = ["ase>=3.23.0"]
 ci = ["pytest-cov>=4", "pytest-split>=0.8", "pytest>=8"]
 docs = ["invoke", "sphinx", "sphinx_markdown_builder", "sphinx_rtd_theme"]

From 3dd2cdfd74cd0a9a0444ce6dd8d7f990dbf147a6 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 23 Oct 2024 17:45:35 +0800
Subject: [PATCH 20/42] add place holder

---
 tests/performance_tests/test_import_time.py | 69 +++++++++++++++++++++
 1 file changed, 69 insertions(+)
 create mode 100644 tests/performance_tests/test_import_time.py

diff --git a/tests/performance_tests/test_import_time.py b/tests/performance_tests/test_import_time.py
new file mode 100644
index 00000000000..b08badec84c
--- /dev/null
+++ b/tests/performance_tests/test_import_time.py
@@ -0,0 +1,69 @@
+"""
+Test the import time of several important modules.
+"""
+
+from __future__ import annotations
+
+
+class TestCore:
+    def test_bonds(self):
+        pass
+
+    def test_composition(self):
+        pass
+
+    def test_interface(self):
+        pass
+
+    def test_ion(self):
+        pass
+
+    def test_lattice(self):
+        pass
+
+    def test_libxcfunc(self):
+        pass
+
+    def test_molecular_orbitals(self):
+        pass
+
+    def test_operations(self):
+        pass
+
+    def test_peridict_table(self):
+        pass
+
+    def test_settings(self):
+        pass
+
+    def test_sites(self):
+        pass
+
+    def test_spectrum(self):
+        pass
+
+    def test_structure(self):
+        pass
+
+    def test_surface(self):
+        pass
+
+    def test_tensors(self):
+        pass
+
+    def test_trajectory(self):
+        pass
+
+    def test_units(self):
+        pass
+
+    def test_xcfunc(self):
+        pass
+
+
+class TestIoVasp:
+    def test_inputs(self):
+        pass
+
+    def test_outputs(self):
+        pass

From 9b7f35adfffdac53a6596cafbfac8b660f3caa24 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 10:08:33 +0800
Subject: [PATCH 21/42] enhance comment

---
 src/pymatgen/symmetry/settings.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pymatgen/symmetry/settings.py b/src/pymatgen/symmetry/settings.py
index 5a914de3cfe..ae407b7a412 100644
--- a/src/pymatgen/symmetry/settings.py
+++ b/src/pymatgen/symmetry/settings.py
@@ -98,7 +98,7 @@ def parse_transformation_string(
         Returns:
             tuple[list[list[float]] | np.ndarray, list[float]]: transformation matrix & vector
         """
-        # Import sympy is expensive
+        # Import sympy is expensive (PR4128)
         from sympy import Matrix
         from sympy.parsing.sympy_parser import parse_expr
 

From 87267f4bc1255f136032c73aec66ed88b3034f98 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 10:08:46 +0800
Subject: [PATCH 22/42] add TODO tag

---
 tests/performance_tests/test_import_time.py | 15 ++++++---------
 1 file changed, 6 insertions(+), 9 deletions(-)

diff --git a/tests/performance_tests/test_import_time.py b/tests/performance_tests/test_import_time.py
index b08badec84c..2ddbb6e14e0 100644
--- a/tests/performance_tests/test_import_time.py
+++ b/tests/performance_tests/test_import_time.py
@@ -12,13 +12,13 @@ def test_bonds(self):
     def test_composition(self):
         pass
 
-    def test_interface(self):
+    def test_interface(self):  # TODO
         pass
 
     def test_ion(self):
         pass
 
-    def test_lattice(self):
+    def test_lattice(self):  # TODO
         pass
 
     def test_libxcfunc(self):
@@ -33,22 +33,19 @@ def test_operations(self):
     def test_peridict_table(self):
         pass
 
-    def test_settings(self):
-        pass
-
     def test_sites(self):
         pass
 
-    def test_spectrum(self):
+    def test_spectrum(self):  # TODO
         pass
 
-    def test_structure(self):
+    def test_structure(self):  # TODO
         pass
 
-    def test_surface(self):
+    def test_surface(self):  # TODO
         pass
 
-    def test_tensors(self):
+    def test_tensors(self):  # TODO
         pass
 
     def test_trajectory(self):

From 313d5530578f2ca2c8bd051d35f6deeaa5fc78c3 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 12:59:36 +0800
Subject: [PATCH 23/42] tweak placeholder

---
 tests/performance/test_performance.py       | 14 +++++
 tests/performance_tests/test_import_time.py | 66 ---------------------
 2 files changed, 14 insertions(+), 66 deletions(-)
 create mode 100644 tests/performance/test_performance.py
 delete mode 100644 tests/performance_tests/test_import_time.py

diff --git a/tests/performance/test_performance.py b/tests/performance/test_performance.py
new file mode 100644
index 00000000000..5a6acc4c221
--- /dev/null
+++ b/tests/performance/test_performance.py
@@ -0,0 +1,14 @@
+"""
+Test the import time of several important modules.
+
+TODO:
+    Test the runtime of several important modules.
+"""
+
+from __future__ import annotations
+
+
+class TestImportTime:
+    """
+    Test import time of important modules.
+    """
diff --git a/tests/performance_tests/test_import_time.py b/tests/performance_tests/test_import_time.py
deleted file mode 100644
index 2ddbb6e14e0..00000000000
--- a/tests/performance_tests/test_import_time.py
+++ /dev/null
@@ -1,66 +0,0 @@
-"""
-Test the import time of several important modules.
-"""
-
-from __future__ import annotations
-
-
-class TestCore:
-    def test_bonds(self):
-        pass
-
-    def test_composition(self):
-        pass
-
-    def test_interface(self):  # TODO
-        pass
-
-    def test_ion(self):
-        pass
-
-    def test_lattice(self):  # TODO
-        pass
-
-    def test_libxcfunc(self):
-        pass
-
-    def test_molecular_orbitals(self):
-        pass
-
-    def test_operations(self):
-        pass
-
-    def test_peridict_table(self):
-        pass
-
-    def test_sites(self):
-        pass
-
-    def test_spectrum(self):  # TODO
-        pass
-
-    def test_structure(self):  # TODO
-        pass
-
-    def test_surface(self):  # TODO
-        pass
-
-    def test_tensors(self):  # TODO
-        pass
-
-    def test_trajectory(self):
-        pass
-
-    def test_units(self):
-        pass
-
-    def test_xcfunc(self):
-        pass
-
-
-class TestIoVasp:
-    def test_inputs(self):
-        pass
-
-    def test_outputs(self):
-        pass

From fa17222a9ad12a3f5c25ca32fba96aff5c904f74 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 13:09:49 +0800
Subject: [PATCH 24/42] replace assert_allclose for scalar compare

---
 src/pymatgen/core/interface.py | 15 ++++++++++-----
 1 file changed, 10 insertions(+), 5 deletions(-)

diff --git a/src/pymatgen/core/interface.py b/src/pymatgen/core/interface.py
index 823d009849f..4bb1d76eec8 100644
--- a/src/pymatgen/core/interface.py
+++ b/src/pymatgen/core/interface.py
@@ -14,7 +14,6 @@
 
 import numpy as np
 from monty.fractions import lcm
-from numpy.testing import assert_allclose
 from scipy.cluster.hierarchy import fcluster, linkage
 from scipy.spatial.distance import squareform
 
@@ -2784,10 +2783,16 @@ def from_slabs(
             substrate_slab = substrate_slab.get_orthogonal_c_slab()
         if isinstance(film_slab, Slab):
             film_slab = film_slab.get_orthogonal_c_slab()
-        assert_allclose(film_slab.lattice.alpha, 90, 0.1)
-        assert_allclose(film_slab.lattice.beta, 90, 0.1)
-        assert_allclose(substrate_slab.lattice.alpha, 90, 0.1)
-        assert_allclose(substrate_slab.lattice.beta, 90, 0.1)
+
+        if not math.isclose(film_slab.lattice.alpha, 90, rel_tol=0.1) or not math.isclose(
+            film_slab.lattice.beta, 90, rel_tol=0.1
+        ):
+            raise ValueError("The lattice angles alpha or beta of the film slab are not approximately 90 degrees.")
+
+        if not math.isclose(substrate_slab.lattice.alpha, 90, rel_tol=0.1) or not math.isclose(
+            substrate_slab.lattice.beta, 90, rel_tol=0.1
+        ):
+            raise ValueError("The lattice angles alpha or beta of the substrate slab are not approximately 90 degrees.")
 
         # Ensure sub is right-handed
         # IE sub has surface facing "up"

From 74ec0c92208c8d455813f791fa3af2d74ecd2dc7 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 13:21:09 +0800
Subject: [PATCH 25/42] replace assert_allclose with isclose

---
 .../interfaces/coherent_interfaces.py         | 54 ++++++-------------
 src/pymatgen/io/vasp/outputs.py               |  5 +-
 2 files changed, 19 insertions(+), 40 deletions(-)

diff --git a/src/pymatgen/analysis/interfaces/coherent_interfaces.py b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
index cce7bb2f2e0..dca5c5b33b5 100644
--- a/src/pymatgen/analysis/interfaces/coherent_interfaces.py
+++ b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
@@ -2,11 +2,11 @@
 
 from __future__ import annotations
 
+import math
 from itertools import product
 from typing import TYPE_CHECKING
 
 import numpy as np
-from numpy.testing import assert_allclose
 from scipy.linalg import polar
 
 from pymatgen.analysis.elasticity.strain import Deformation
@@ -101,21 +101,15 @@ def _find_matches(self) -> None:
         for match in self.zsl_matches:
             xform = get_2d_transform(film_vectors, match.film_vectors)
             strain, _rot = polar(xform)
-            assert_allclose(
-                strain,
-                np.round(strain),
-                atol=1e-12,
-                err_msg="Film lattice vectors changed during ZSL match, check your ZSL Generator parameters",
-            )
+            if not np.isclose(strain, np.round(strain), atol=1e-12):
+                raise ValueError("Film lattice vectors changed during ZSL match, check your ZSL Generator parameters")
 
             xform = get_2d_transform(substrate_vectors, match.substrate_vectors)
             strain, _rot = polar(xform)
-            assert_allclose(
-                strain,
-                strain.astype(int),
-                atol=1e-12,
-                err_msg="Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters",
-            )
+            if not np.isclose(strain, strain.astype(int), atol=1e-12):
+                raise ValueError(
+                    "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters"
+                )
 
     def _find_terminations(self):
         """Find all terminations."""
@@ -226,18 +220,12 @@ def get_interfaces(
             ).astype(int)
             film_sl_slab = film_slab.copy()
             film_sl_slab.make_supercell(super_film_transform)
-            assert_allclose(
-                film_sl_slab.lattice.matrix[2],
-                film_slab.lattice.matrix[2],
-                atol=1e-08,
-                err_msg="2D transformation affected C-axis for Film transformation",
-            )
-            assert_allclose(
-                film_sl_slab.lattice.matrix[:2],
-                match.film_sl_vectors,
-                atol=1e-08,
-                err_msg="Transformation didn't make proper supercell for film",
-            )
+            if not math.isclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], abs_tol=1e-08):
+                raise ValueError(
+                    "2D transformation affected C-axis for Film transformation",
+                )
+            if not np.isclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08):
+                raise ValueError("Transformation didn't make proper supercell for film")
 
             # Build substrate superlattice
             super_sub_transform = np.round(
@@ -245,18 +233,10 @@ def get_interfaces(
             ).astype(int)
             sub_sl_slab = sub_slab.copy()
             sub_sl_slab.make_supercell(super_sub_transform)
-            assert_allclose(
-                sub_sl_slab.lattice.matrix[2],
-                sub_slab.lattice.matrix[2],
-                atol=1e-08,
-                err_msg="2D transformation affected C-axis for Film transformation",
-            )
-            assert_allclose(
-                sub_sl_slab.lattice.matrix[:2],
-                match.substrate_sl_vectors,
-                atol=1e-08,
-                err_msg="Transformation didn't make proper supercell for substrate",
-            )
+            if not math.isclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], abs_tol=1e-08):
+                raise ValueError("2D transformation affected C-axis for Film transformation")
+            if not np.isclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08):
+                raise ValueError("Transformation didn't make proper supercell for substrate")
 
             # Add extra info
             match_dict = match.as_dict()
diff --git a/src/pymatgen/io/vasp/outputs.py b/src/pymatgen/io/vasp/outputs.py
index 19bf4e46589..93e35b4a0f9 100644
--- a/src/pymatgen/io/vasp/outputs.py
+++ b/src/pymatgen/io/vasp/outputs.py
@@ -24,7 +24,6 @@
 from monty.json import MSONable, jsanitize
 from monty.os.path import zpath
 from monty.re import regrep
-from numpy.testing import assert_allclose
 from tqdm import tqdm
 
 from pymatgen.core import Composition, Element, Lattice, Structure
@@ -4978,8 +4977,8 @@ def __init__(
 
                     if i_spin == 0:
                         self.kpoints.append(kpoint)
-                    else:
-                        assert_allclose(self.kpoints[i_nk], kpoint)
+                    elif not np.allclose(self.kpoints[i_nk], kpoint, rtol=1e-7, atol=0):
+                        raise ValueError(f"kpoints of {i_nk=} mismatch")
 
                     if verbose:
                         print(f"kpoint {i_nk: 4} with {nplane: 5} plane waves at {kpoint}")

From df8e2ff5d5e346252a21a5206c59ebd4915501d5 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 13:36:59 +0800
Subject: [PATCH 26/42] fix is close

---
 .../analysis/interfaces/coherent_interfaces.py      | 13 ++++++-------
 1 file changed, 6 insertions(+), 7 deletions(-)

diff --git a/src/pymatgen/analysis/interfaces/coherent_interfaces.py b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
index dca5c5b33b5..0a0633e273a 100644
--- a/src/pymatgen/analysis/interfaces/coherent_interfaces.py
+++ b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
@@ -2,7 +2,6 @@
 
 from __future__ import annotations
 
-import math
 from itertools import product
 from typing import TYPE_CHECKING
 
@@ -101,12 +100,12 @@ def _find_matches(self) -> None:
         for match in self.zsl_matches:
             xform = get_2d_transform(film_vectors, match.film_vectors)
             strain, _rot = polar(xform)
-            if not np.isclose(strain, np.round(strain), atol=1e-12):
+            if not np.allclose(strain, np.round(strain), atol=1e-12):
                 raise ValueError("Film lattice vectors changed during ZSL match, check your ZSL Generator parameters")
 
             xform = get_2d_transform(substrate_vectors, match.substrate_vectors)
             strain, _rot = polar(xform)
-            if not np.isclose(strain, strain.astype(int), atol=1e-12):
+            if not np.allclose(strain, strain.astype(int), atol=1e-12):
                 raise ValueError(
                     "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters"
                 )
@@ -220,11 +219,11 @@ def get_interfaces(
             ).astype(int)
             film_sl_slab = film_slab.copy()
             film_sl_slab.make_supercell(super_film_transform)
-            if not math.isclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], abs_tol=1e-08):
+            if not np.allclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], atol=1e-08):
                 raise ValueError(
                     "2D transformation affected C-axis for Film transformation",
                 )
-            if not np.isclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08):
+            if not np.allclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08):
                 raise ValueError("Transformation didn't make proper supercell for film")
 
             # Build substrate superlattice
@@ -233,9 +232,9 @@ def get_interfaces(
             ).astype(int)
             sub_sl_slab = sub_slab.copy()
             sub_sl_slab.make_supercell(super_sub_transform)
-            if not math.isclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], abs_tol=1e-08):
+            if not np.allclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], atol=1e-08):
                 raise ValueError("2D transformation affected C-axis for Film transformation")
-            if not np.isclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08):
+            if not np.allclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08):
                 raise ValueError("Transformation didn't make proper supercell for substrate")
 
             # Add extra info

From 2778e2841b24da042e546e1fcc20e0d53fd3a6d1 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 13:43:34 +0800
Subject: [PATCH 27/42] use np.allclose over np.all(np.isclose())

---
 src/pymatgen/core/operations.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/pymatgen/core/operations.py b/src/pymatgen/core/operations.py
index d395c2c3d3b..5c6ea895a12 100644
--- a/src/pymatgen/core/operations.py
+++ b/src/pymatgen/core/operations.py
@@ -449,7 +449,7 @@ def as_xyz_str(self) -> str:
         Only works for integer rotation matrices.
         """
         # Check for invalid rotation matrix
-        if not np.all(np.isclose(self.rotation_matrix, np.round(self.rotation_matrix))):
+        if not np.allclose(self.rotation_matrix, np.round(self.rotation_matrix)):
             warnings.warn("Rotation matrix should be integer")
 
         return transformation_to_string(

From 8952c4a0bc101a6ba706a32cde21ca3f9a1d8fad Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 14:10:20 +0800
Subject: [PATCH 28/42] lazy import AseAtomsAdaptor

---
 src/pymatgen/core/trajectory.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/src/pymatgen/core/trajectory.py b/src/pymatgen/core/trajectory.py
index 06a58f77a3c..a7bc74ac2d6 100644
--- a/src/pymatgen/core/trajectory.py
+++ b/src/pymatgen/core/trajectory.py
@@ -15,7 +15,6 @@
 from monty.json import MSONable
 
 from pymatgen.core.structure import Composition, DummySpecies, Element, Lattice, Molecule, Species, Structure
-from pymatgen.io.ase import AseAtomsAdaptor
 
 if TYPE_CHECKING:
     from collections.abc import Iterator
@@ -580,9 +579,12 @@ def from_file(cls, filename: str | Path, constant_lattice: bool = True, **kwargs
             try:
                 from ase.io.trajectory import Trajectory as AseTrajectory
 
+                from pymatgen.io.ase import AseAtomsAdaptor
+
                 ase_traj = AseTrajectory(filename)
                 # Periodic boundary conditions should be the same for all frames so just check the first
                 pbc = ase_traj[0].pbc
+
                 if any(pbc):
                     structures = [AseAtomsAdaptor.get_structure(atoms) for atoms in ase_traj]
                 else:

From c37ba45421977dab0e284fce581fbcd1f9358440 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 14:10:30 +0800
Subject: [PATCH 29/42] guard type check import

---
 src/pymatgen/core/__init__.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/pymatgen/core/__init__.py b/src/pymatgen/core/__init__.py
index 840b16e9b69..ad56b0f72b7 100644
--- a/src/pymatgen/core/__init__.py
+++ b/src/pymatgen/core/__init__.py
@@ -5,7 +5,7 @@
 import os
 import warnings
 from importlib.metadata import PackageNotFoundError, version
-from typing import Any
+from typing import TYPE_CHECKING
 
 from ruamel.yaml import YAML
 
@@ -17,6 +17,9 @@
 from pymatgen.core.structure import IMolecule, IStructure, Molecule, PeriodicNeighbor, SiteCollection, Structure
 from pymatgen.core.units import ArrayWithUnit, FloatWithUnit, Unit
 
+if TYPE_CHECKING:
+    from typing import Any
+
 __author__ = "Pymatgen Development Team"
 __email__ = "pymatgen@googlegroups.com"
 __maintainer__ = "Shyue Ping Ong, Matthew Horton, Janosh Riebesell"

From 1674a960ee1174bf2e40f78cc839390520a57313 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 14:26:47 +0800
Subject: [PATCH 30/42] lazy import matplotlib

---
 src/pymatgen/analysis/adsorption.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/pymatgen/analysis/adsorption.py b/src/pymatgen/analysis/adsorption.py
index 3e953ec00e7..fcb96a935e8 100644
--- a/src/pymatgen/analysis/adsorption.py
+++ b/src/pymatgen/analysis/adsorption.py
@@ -9,8 +9,6 @@
 from typing import TYPE_CHECKING
 
 import numpy as np
-from matplotlib import patches
-from matplotlib.path import Path
 from monty.serialization import loadfn
 from scipy.spatial import Delaunay
 
@@ -664,6 +662,10 @@ def plot_slab(
         decay (float): how the alpha-value decays along the z-axis
         inverse (bool): invert z axis to plot opposite surface
     """
+    # Expensive import (PR4128)
+    from matplotlib import patches
+    from matplotlib.path import Path
+
     orig_slab = slab.copy()
     slab = reorient_z(slab)
     orig_cell = slab.lattice.matrix.copy()

From 8ac0c7f4b8eb7a36fb735bad6b74824bf0adc4d7 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 16:34:52 +0800
Subject: [PATCH 31/42] toggle reference generation

---
 tests/performance/test_import_time.py | 112 ++++++++++++++++++++++++++
 tests/performance/test_performance.py |  14 ----
 2 files changed, 112 insertions(+), 14 deletions(-)
 create mode 100644 tests/performance/test_import_time.py
 delete mode 100644 tests/performance/test_performance.py

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
new file mode 100644
index 00000000000..49adb49cddd
--- /dev/null
+++ b/tests/performance/test_import_time.py
@@ -0,0 +1,112 @@
+"""
+Test the import time of several important modules.
+"""
+# ruff: noqa: T201 (check for print statement)
+
+from __future__ import annotations
+
+import json
+import os
+import subprocess
+import time
+from typing import TYPE_CHECKING
+
+import pytest
+
+if TYPE_CHECKING:
+    from typing import Literal
+
+# Toggle this to generate reference import times
+GEN_REF_TIME = True
+
+MODULES_TO_TEST = (
+    "from pymatgen.core.bonds import CovalentBond",
+    "from pymatgen.core.composition import Composition",
+    "from pymatgen.core.interface import Interface",
+    "from pymatgen.core.ion import Ion",
+    "from pymatgen.core.lattice import Lattice",
+    "from pymatgen.core.libxcfunc import LibxcFunc",
+    "from pymatgen.core.molecular_orbitals import MolecularOrbitals",
+    "from pymatgen.core.operations import SymmOp",
+    "from pymatgen.core.periodic_table import Element",
+    "from pymatgen.core.sites import Site",
+    "from pymatgen.core.spectrum import Spectrum",
+    "from pymatgen.core.structure import Structure",
+    "from pymatgen.core.surface import Slab",
+    "from pymatgen.core.tensors import Tensor",
+    "from pymatgen.core.trajectory import Trajectory",
+    "from pymatgen.core.units import Unit",
+    "from pymatgen.core.xcfunc import XcFunc",
+)
+
+# Get runner OS and reference file
+RUNNER_OS: Literal["linux", "windows", "macos"] = os.getenv("RUNNER_OS", "").lower()  # type: ignore[assignment]
+assert RUNNER_OS in {"linux", "windows", "macos"}
+REF_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), f"import_time_{RUNNER_OS}.json")
+
+
+@pytest.mark.skipif(not GEN_REF_TIME, reason="Set GEN_REF_TIME to generate reference import time.")
+def test_get_ref_import_time() -> None:
+    """A dummy test that would always fail, used to generate copyable reference time."""
+    import_times = {
+        module_import_cmd: _measure_import_time_in_ms(module_import_cmd) for module_import_cmd in MODULES_TO_TEST
+    }
+
+    # Print a copyable JSON format for easy reference updating
+    print("\nCopyable import time JSON:")
+    print(json.dumps(import_times, indent=4))
+
+    pytest.fail("Reference import times generated. Copy from output to update JSON file.")
+
+
+@pytest.mark.skipif(GEN_REF_TIME, reason="Generating reference import time.")
+def test_import_time(grace_percent: float = 0.20, hard_percent: float = 0.50) -> None:
+    """Test the import time of core modules to avoid performance regression.
+
+    Args:
+        grace_percent (float): Maximum allowed percentage increase in import time
+            before a warning is raised.
+        hard_percent (float): Maximum allowed percentage increase in import time
+            before the test fails.
+    """
+    try:
+        with open(REF_FILE, encoding="utf-8") as file:
+            ref_import_times = json.load(file)
+    except FileNotFoundError:
+        pytest.fail(f"Reference file {REF_FILE} not found. Please generate it.")
+
+    for module_import_cmd, ref_time in ref_import_times.items():
+        current_time = _measure_import_time_in_ms(module_import_cmd)
+
+        # Calculate thresholds for grace and hard limits
+        grace_threshold = ref_time * (1 + grace_percent)
+        hard_threshold = ref_time * (1 + hard_percent)
+
+        if current_time > grace_threshold:
+            if current_time > hard_threshold:
+                pytest.fail(f"{module_import_cmd} import too slow! {hard_threshold=:.2f} ms")
+            else:
+                pytest.warns(
+                    UserWarning,
+                    f"{module_import_cmd} import slightly slower than reference: {grace_threshold=:.2f} ms",
+                )
+
+
+def _measure_import_time_in_ms(module_import_cmd: str, count: int = 3) -> float:
+    """Measure import time of a module in milliseconds across several runs.
+
+    Args:
+        module_import_cmd (str): The module import command.
+        count (int): Number of runs to average.
+
+    Returns:
+        float: Import time in milliseconds.
+    """
+    total_time = 0.0
+
+    for _ in range(count):
+        start_time = time.perf_counter()
+        subprocess.run(["python", "-c", f"{module_import_cmd}"], check=True)
+        total_time += time.perf_counter() - start_time
+
+    return (total_time / count) * 1000
diff --git a/tests/performance/test_performance.py b/tests/performance/test_performance.py
deleted file mode 100644
index 5a6acc4c221..00000000000
--- a/tests/performance/test_performance.py
+++ /dev/null
@@ -1,14 +0,0 @@
-"""
-Test the import time of several important modules.
-
-TODO:
-    Test the runtime of several important modules.
-"""
-
-from __future__ import annotations
-
-
-class TestImportTime:
-    """
-    Test import time of important modules.
-    """

From 2f7f99322a9a191c779a5704e2507e39a14c9633 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 16:54:02 +0800
Subject: [PATCH 32/42] update import time records

---
 .../files/performance/import_time_linux.json  | 19 +++++++++++++
 .../files/performance/import_time_macos.json  | 19 +++++++++++++
 .../performance/import_time_windows.json      | 19 +++++++++++++
 tests/performance/test_import_time.py         | 28 +++++++++++--------
 4 files changed, 73 insertions(+), 12 deletions(-)
 create mode 100644 tests/files/performance/import_time_linux.json
 create mode 100644 tests/files/performance/import_time_macos.json
 create mode 100644 tests/files/performance/import_time_windows.json

diff --git a/tests/files/performance/import_time_linux.json b/tests/files/performance/import_time_linux.json
new file mode 100644
index 00000000000..3492c93a840
--- /dev/null
+++ b/tests/files/performance/import_time_linux.json
@@ -0,0 +1,19 @@
+{
+    "from pymatgen.core.bonds import CovalentBond": 289.5851116666108,
+    "from pymatgen.core.composition import Composition": 292.8479909999548,
+    "from pymatgen.core.interface import Interface": 969.5693099999593,
+    "from pymatgen.core.ion import Ion": 291.07530133334575,
+    "from pymatgen.core.lattice import Lattice": 288.8340153333881,
+    "from pymatgen.core.libxcfunc import LibxcFunc": 293.4184753333587,
+    "from pymatgen.core.molecular_orbitals import MolecularOrbitals": 294.19796566658835,
+    "from pymatgen.core.operations import SymmOp": 296.4627546666634,
+    "from pymatgen.core.periodic_table import Element": 295.95872066662804,
+    "from pymatgen.core.sites import Site": 292.66485499999817,
+    "from pymatgen.core.spectrum import Spectrum": 486.72776566669046,
+    "from pymatgen.core.structure import Structure": 291.01618733333606,
+    "from pymatgen.core.surface import Slab": 301.90875833329756,
+    "from pymatgen.core.tensors import Tensor": 304.27744800003137,
+    "from pymatgen.core.trajectory import Trajectory": 300.45536066666045,
+    "from pymatgen.core.units import Unit": 305.4779056666348,
+    "from pymatgen.core.xcfunc import XcFunc": 309.1085626666275
+}
\ No newline at end of file
diff --git a/tests/files/performance/import_time_macos.json b/tests/files/performance/import_time_macos.json
new file mode 100644
index 00000000000..9ac1e63fc9d
--- /dev/null
+++ b/tests/files/performance/import_time_macos.json
@@ -0,0 +1,19 @@
+{
+    "from pymatgen.core.bonds import CovalentBond": 321.8502360000457,
+    "from pymatgen.core.composition import Composition": 292.35445800009074,
+    "from pymatgen.core.interface import Interface": 855.005861000033,
+    "from pymatgen.core.ion import Ion": 240.8930970000256,
+    "from pymatgen.core.lattice import Lattice": 329.09868066659936,
+    "from pymatgen.core.libxcfunc import LibxcFunc": 306.6966386666839,
+    "from pymatgen.core.molecular_orbitals import MolecularOrbitals": 281.78087466661356,
+    "from pymatgen.core.operations import SymmOp": 299.9741943333447,
+    "from pymatgen.core.periodic_table import Element": 293.6565829999533,
+    "from pymatgen.core.sites import Site": 280.3443330000543,
+    "from pymatgen.core.spectrum import Spectrum": 459.20266666666976,
+    "from pymatgen.core.structure import Structure": 265.4675833332476,
+    "from pymatgen.core.surface import Slab": 306.0919996667053,
+    "from pymatgen.core.tensors import Tensor": 310.54281933325,
+    "from pymatgen.core.trajectory import Trajectory": 335.25658333329983,
+    "from pymatgen.core.units import Unit": 294.03472200003006,
+    "from pymatgen.core.xcfunc import XcFunc": 309.3993196666058
+}
\ No newline at end of file
diff --git a/tests/files/performance/import_time_windows.json b/tests/files/performance/import_time_windows.json
new file mode 100644
index 00000000000..270b73a9d65
--- /dev/null
+++ b/tests/files/performance/import_time_windows.json
@@ -0,0 +1,19 @@
+{
+    "from pymatgen.core.bonds import CovalentBond": 443.7560000000455,
+    "from pymatgen.core.composition import Composition": 441.06553333335796,
+    "from pymatgen.core.interface import Interface": 1828.751033333295,
+    "from pymatgen.core.ion import Ion": 443.58053333333675,
+    "from pymatgen.core.lattice import Lattice": 445.729999999988,
+    "from pymatgen.core.libxcfunc import LibxcFunc": 459.24773333338936,
+    "from pymatgen.core.molecular_orbitals import MolecularOrbitals": 440.4825999999957,
+    "from pymatgen.core.operations import SymmOp": 440.62226666665083,
+    "from pymatgen.core.periodic_table import Element": 441.64050000002436,
+    "from pymatgen.core.sites import Site": 442.1802333333744,
+    "from pymatgen.core.spectrum import Spectrum": 737.3025000000174,
+    "from pymatgen.core.structure import Structure": 445.0546333332568,
+    "from pymatgen.core.surface import Slab": 463.0683333333157,
+    "from pymatgen.core.tensors import Tensor": 463.5761666666743,
+    "from pymatgen.core.trajectory import Trajectory": 443.9995333333779,
+    "from pymatgen.core.units import Unit": 446.352766666602,
+    "from pymatgen.core.xcfunc import XcFunc": 469.42599999996065
+}
\ No newline at end of file
diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index 49adb49cddd..d969ec50288 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -1,7 +1,9 @@
 """
 Test the import time of several important modules.
+
+NOTE:
+    - Toggle the "GEN_REF_TIME" to generate reference import time.
 """
-# ruff: noqa: T201 (check for print statement)
 
 from __future__ import annotations
 
@@ -9,17 +11,20 @@
 import os
 import subprocess
 import time
+import warnings
 from typing import TYPE_CHECKING
 
 import pytest
 
+from pymatgen.util.testing import TEST_FILES_DIR
+
 if TYPE_CHECKING:
     from typing import Literal
 
-# Toggle this to generate reference import times
-GEN_REF_TIME = True
+# NOTE: Toggle this to generate reference import time
+GEN_REF_TIME: bool = False
 
-MODULES_TO_TEST = (
+MODULES_TO_TEST: tuple[str, ...] = (
     "from pymatgen.core.bonds import CovalentBond",
     "from pymatgen.core.composition import Composition",
     "from pymatgen.core.interface import Interface",
@@ -42,7 +47,8 @@
 # Get runner OS and reference file
 RUNNER_OS: Literal["linux", "windows", "macos"] = os.getenv("RUNNER_OS", "").lower()  # type: ignore[assignment]
 assert RUNNER_OS in {"linux", "windows", "macos"}
-REF_FILE = os.path.join(os.path.dirname(os.path.abspath(__file__)), f"import_time_{RUNNER_OS}.json")
+
+REF_FILE: str = f"{TEST_FILES_DIR}/performance/import_time_{RUNNER_OS}.json"
 
 
 @pytest.mark.skipif(not GEN_REF_TIME, reason="Set GEN_REF_TIME to generate reference import time.")
@@ -69,11 +75,9 @@ def test_import_time(grace_percent: float = 0.20, hard_percent: float = 0.50) ->
         hard_percent (float): Maximum allowed percentage increase in import time
             before the test fails.
     """
-    try:
-        with open(REF_FILE, encoding="utf-8") as file:
-            ref_import_times = json.load(file)
-    except FileNotFoundError:
-        pytest.fail(f"Reference file {REF_FILE} not found. Please generate it.")
+
+    with open(REF_FILE, encoding="utf-8") as file:
+        ref_import_times = json.load(file)
 
     for module_import_cmd, ref_time in ref_import_times.items():
         current_time = _measure_import_time_in_ms(module_import_cmd)
@@ -86,9 +90,9 @@ def test_import_time(grace_percent: float = 0.20, hard_percent: float = 0.50) ->
             if current_time > hard_threshold:
                 pytest.fail(f"{module_import_cmd} import too slow! {hard_threshold=:.2f} ms")
             else:
-                pytest.warns(
-                    UserWarning,
+                warnings.warn(
                     f"{module_import_cmd} import slightly slower than reference: {grace_threshold=:.2f} ms",
+                    stacklevel=2,
                 )
 
 

From abf5f8ba7a983018c089b7cd3e9dca11b536d3c3 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 16:59:04 +0800
Subject: [PATCH 33/42] skip in not CI env

---
 tests/performance/test_import_time.py | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index d969ec50288..03ce60ef5f7 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -21,6 +21,9 @@
 if TYPE_CHECKING:
     from typing import Literal
 
+if not os.getenv("CI"):
+    pytest.skip("ref time only comparable in CI runner", allow_module_level=True)
+
 # NOTE: Toggle this to generate reference import time
 GEN_REF_TIME: bool = False
 

From de4dc3b30fdb1d2b96850ef0d7fc19de1ad1876b Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:10:24 +0800
Subject: [PATCH 34/42] include current time in err msg

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

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index 03ce60ef5f7..c33381fbf48 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -91,7 +91,7 @@ def test_import_time(grace_percent: float = 0.20, hard_percent: float = 0.50) ->
 
         if current_time > grace_threshold:
             if current_time > hard_threshold:
-                pytest.fail(f"{module_import_cmd} import too slow! {hard_threshold=:.2f} ms")
+                pytest.fail(f"{module_import_cmd} import too slow at {current_time:.2f} ms! {hard_threshold=:.2f} ms")
             else:
                 warnings.warn(
                     f"{module_import_cmd} import slightly slower than reference: {grace_threshold=:.2f} ms",

From 8f5c2ac56183619ee794249a6a6d2b69225b14c1 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:16:30 +0800
Subject: [PATCH 35/42] loose hard threshold to 100%, as it appear macos runner
 is prone to fluctuation

---
 tests/performance/test_import_time.py | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index c33381fbf48..66b790fba08 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -3,6 +3,13 @@
 
 NOTE:
     - Toggle the "GEN_REF_TIME" to generate reference import time.
+
+Last update: 2024-10-26
+
+Runner specs:
+Linux:   4 CPU
+Windows: 4 CPU
+macOS:   3 CPU (M1)
 """
 
 from __future__ import annotations
@@ -69,7 +76,7 @@ def test_get_ref_import_time() -> None:
 
 
 @pytest.mark.skipif(GEN_REF_TIME, reason="Generating reference import time.")
-def test_import_time(grace_percent: float = 0.20, hard_percent: float = 0.50) -> None:
+def test_import_time(grace_percent: float = 0.5, hard_percent: float = 1.0) -> None:
     """Test the import time of core modules to avoid performance regression.
 
     Args:

From 4849da01d75db6ba8a3e1901d17e097a1e5e8002 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:25:10 +0800
Subject: [PATCH 36/42] update type

---
 src/pymatgen/core/__init__.py         | 1 +
 tests/performance/test_import_time.py | 6 +++---
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/src/pymatgen/core/__init__.py b/src/pymatgen/core/__init__.py
index ad56b0f72b7..68343cac523 100644
--- a/src/pymatgen/core/__init__.py
+++ b/src/pymatgen/core/__init__.py
@@ -24,6 +24,7 @@
 __email__ = "pymatgen@googlegroups.com"
 __maintainer__ = "Shyue Ping Ong, Matthew Horton, Janosh Riebesell"
 __maintainer_email__ = "shyuep@gmail.com"
+
 try:
     __version__ = version("pymatgen")
 except PackageNotFoundError:  # pragma: no cover
diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index 66b790fba08..444a821e6fd 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -64,7 +64,7 @@
 @pytest.mark.skipif(not GEN_REF_TIME, reason="Set GEN_REF_TIME to generate reference import time.")
 def test_get_ref_import_time() -> None:
     """A dummy test that would always fail, used to generate copyable reference time."""
-    import_times = {
+    import_times: dict[str, float] = {
         module_import_cmd: _measure_import_time_in_ms(module_import_cmd) for module_import_cmd in MODULES_TO_TEST
     }
 
@@ -87,10 +87,10 @@ def test_import_time(grace_percent: float = 0.5, hard_percent: float = 1.0) -> N
     """
 
     with open(REF_FILE, encoding="utf-8") as file:
-        ref_import_times = json.load(file)
+        ref_import_times: dict[str, float] = json.load(file)
 
     for module_import_cmd, ref_time in ref_import_times.items():
-        current_time = _measure_import_time_in_ms(module_import_cmd)
+        current_time: float = _measure_import_time_in_ms(module_import_cmd)
 
         # Calculate thresholds for grace and hard limits
         grace_threshold = ref_time * (1 + grace_percent)

From aceb5b5b3a78a2a682035c2409e485b4b5b370e0 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:29:31 +0800
Subject: [PATCH 37/42] skip test for macos

---
 tests/performance/test_import_time.py | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index 444a821e6fd..c8ba6472a90 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -58,6 +58,10 @@
 RUNNER_OS: Literal["linux", "windows", "macos"] = os.getenv("RUNNER_OS", "").lower()  # type: ignore[assignment]
 assert RUNNER_OS in {"linux", "windows", "macos"}
 
+# Skip test on macOS due to inconsistent import time results
+if RUNNER_OS == "macos":
+    pytest.skip("Import time measurements are unstable on macOS", allow_module_level=True)
+
 REF_FILE: str = f"{TEST_FILES_DIR}/performance/import_time_{RUNNER_OS}.json"
 
 

From eb51fee96879fa6959d91378654a6b9441343a4f Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:32:12 +0800
Subject: [PATCH 38/42] add PR tag for easy tracing

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

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index c8ba6472a90..66255dc1ffa 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -4,7 +4,7 @@
 NOTE:
     - Toggle the "GEN_REF_TIME" to generate reference import time.
 
-Last update: 2024-10-26
+Last update: 2024-10-26 (PR 4128)
 
 Runner specs:
 Linux:   4 CPU

From c64ecaedd2561c4adeac00f91a6a9611a8825776 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Sat, 26 Oct 2024 17:38:15 +0800
Subject: [PATCH 39/42] use perf_counter_ns for precision

---
 tests/performance/test_import_time.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/tests/performance/test_import_time.py b/tests/performance/test_import_time.py
index 66255dc1ffa..9c9f9d5daf1 100644
--- a/tests/performance/test_import_time.py
+++ b/tests/performance/test_import_time.py
@@ -123,8 +123,8 @@ def _measure_import_time_in_ms(module_import_cmd: str, count: int = 3) -> float:
     total_time = 0.0
 
     for _ in range(count):
-        start_time = time.perf_counter()
+        start_time = time.perf_counter_ns()
         subprocess.run(["python", "-c", f"{module_import_cmd}"], check=True)
-        total_time += time.perf_counter() - start_time
+        total_time += time.perf_counter_ns() - start_time
 
-    return (total_time / count) * 1000
+    return (total_time / count) / 1e6

From 9c3d1865e632783519eb11d2009ad3d44e7041ec Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 30 Oct 2024 14:19:18 +0800
Subject: [PATCH 40/42] bump torch timeout all the way to 5 min

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

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index fb481f6270b..e37e27d6826 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -82,7 +82,7 @@ jobs:
           # TODO1 (use uv over pip) uv install torch is flaky, track #3826
           # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
           # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
-          pip install torch==2.2.1
+          pip install --timeout=300 torch==2.2.1
 
           uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 

From 9ea93eba75b7c72578a941ad96a88c6f1cb44950 Mon Sep 17 00:00:00 2001
From: "Haoyu (Daniel)" <yanghaoyu97@outlook.com>
Date: Wed, 30 Oct 2024 14:32:53 +0800
Subject: [PATCH 41/42] Revert "bump torch timeout all the way to 5 min"

This reverts commit 9c3d1865e632783519eb11d2009ad3d44e7041ec.
---
 .github/workflows/test.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index e37e27d6826..fb481f6270b 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -82,7 +82,7 @@ jobs:
           # TODO1 (use uv over pip) uv install torch is flaky, track #3826
           # TODO2 (pin torch version): DGL library (matgl) doesn't support torch > 2.2.1,
           # see: https://discuss.dgl.ai/t/filenotfounderror-cannot-find-dgl-c-graphbolt-library/4302
-          pip install --timeout=300 torch==2.2.1
+          pip install torch==2.2.1
 
           uv pip install --editable '.[${{ matrix.config.extras }}]' --resolution=${{ matrix.config.resolution }}
 

From b0013611e222c514c36ede7cfb846de6440e36ed Mon Sep 17 00:00:00 2001
From: Haoyu Yang <yanghaoyu97@outlook.com>
Date: Wed, 30 Oct 2024 18:44:19 +0800
Subject: [PATCH 42/42] migrate missing allclose relative tolerance

---
 .../analysis/interfaces/coherent_interfaces.py       | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/pymatgen/analysis/interfaces/coherent_interfaces.py b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
index 0a0633e273a..bc24592075a 100644
--- a/src/pymatgen/analysis/interfaces/coherent_interfaces.py
+++ b/src/pymatgen/analysis/interfaces/coherent_interfaces.py
@@ -100,12 +100,12 @@ def _find_matches(self) -> None:
         for match in self.zsl_matches:
             xform = get_2d_transform(film_vectors, match.film_vectors)
             strain, _rot = polar(xform)
-            if not np.allclose(strain, np.round(strain), atol=1e-12):
+            if not np.allclose(strain, np.round(strain), rtol=1e-7, atol=1e-12):
                 raise ValueError("Film lattice vectors changed during ZSL match, check your ZSL Generator parameters")
 
             xform = get_2d_transform(substrate_vectors, match.substrate_vectors)
             strain, _rot = polar(xform)
-            if not np.allclose(strain, strain.astype(int), atol=1e-12):
+            if not np.allclose(strain, strain.astype(int), rtol=1e-7, atol=1e-12):
                 raise ValueError(
                     "Substrate lattice vectors changed during ZSL match, check your ZSL Generator parameters"
                 )
@@ -219,11 +219,11 @@ def get_interfaces(
             ).astype(int)
             film_sl_slab = film_slab.copy()
             film_sl_slab.make_supercell(super_film_transform)
-            if not np.allclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], atol=1e-08):
+            if not np.allclose(film_sl_slab.lattice.matrix[2], film_slab.lattice.matrix[2], rtol=1e-7, atol=1e-08):
                 raise ValueError(
                     "2D transformation affected C-axis for Film transformation",
                 )
-            if not np.allclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, atol=1e-08):
+            if not np.allclose(film_sl_slab.lattice.matrix[:2], match.film_sl_vectors, rtol=1e-7, atol=1e-08):
                 raise ValueError("Transformation didn't make proper supercell for film")
 
             # Build substrate superlattice
@@ -232,9 +232,9 @@ def get_interfaces(
             ).astype(int)
             sub_sl_slab = sub_slab.copy()
             sub_sl_slab.make_supercell(super_sub_transform)
-            if not np.allclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], atol=1e-08):
+            if not np.allclose(sub_sl_slab.lattice.matrix[2], sub_slab.lattice.matrix[2], rtol=1e-7, atol=1e-08):
                 raise ValueError("2D transformation affected C-axis for Film transformation")
-            if not np.allclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, atol=1e-08):
+            if not np.allclose(sub_sl_slab.lattice.matrix[:2], match.substrate_sl_vectors, rtol=1e-7, atol=1e-08):
                 raise ValueError("Transformation didn't make proper supercell for substrate")
 
             # Add extra info