From ede4ac8b91d40985638a842aa2941f8f990364c9 Mon Sep 17 00:00:00 2001
From: Liam Marsh <liam.marsh@epfl.ch>
Date: Wed, 12 Nov 2025 11:25:57 +0100
Subject: [PATCH 1/7] fix: rewire cell2mol dependency in requirements and
 pyproject

---
 pyproject.toml          |  2 +-
 requirements.py3.11.txt | 14 +++++++-------
 requirements.py3.13.txt |  2 +-
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index 577ac85a..ce5d6a53 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -53,7 +53,7 @@ equio-itself = ["metatensor-core >= 0.1.8, == 0.1.*"]
 equio = ["qstack[pyscf,equio-itself]"]
 spahm = ["qstack[pyscf]"]
 docs-build = ["sphinx", "sphinx-argparse", "sphinx-autobuild", "myst-parser", "furo"]
-all = ["qstack[pyscf,qml,regression,wigner,equio,gmol]"]
+all = ["qstack[pyscf,qml,regression,wigner,equio,gmol,cell2mol]"]
 
 [project.urls]
 Repository = "https://github.com/lcmd-epfl/Q-stack.git"
diff --git a/requirements.py3.11.txt b/requirements.py3.11.txt
index cf14f794..96276ae4 100644
--- a/requirements.py3.11.txt
+++ b/requirements.py3.11.txt
@@ -2,17 +2,17 @@ attrs==21.4.0
 certifi==2021.10.8
 h5py==3.11.0
 iniconfig==1.1.1
-packaging==21.3
+packaging==25.0
 pluggy==1.0.0
 py==1.11.0
-pyparsing==3.0.6
+pyparsing==3.2.5
 pyscf==2.5.0
 pytest==6.2.5
 numpy==2.3.*
-scipy==1.10
+scipy==1.16.3
 toml==0.10.2
-scikit-learn==1.5.0
-ase==3.22
+scikit-learn==1.7.2
+ase==3.26
 tqdm==4.66
-metatensor-core==0.1.8
-cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@22473bbf12a013467137a55a63c88fbbdc95baa2
+metatensor-core==0.1.17
+cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
diff --git a/requirements.py3.13.txt b/requirements.py3.13.txt
index 18459e4a..2e89926e 100644
--- a/requirements.py3.13.txt
+++ b/requirements.py3.13.txt
@@ -6,7 +6,7 @@ pyparsing==3.2.5
 pyscf==2.11.0
 pytest==8.4.2
 numpy==2.3.*
-scipy==1.16.2
+scipy==1.16.3
 scikit-learn==1.7.2
 ase==3.26
 tqdm==4.67

From ea2f6388815b9e7234e572c6ef8b6e84e96781c1 Mon Sep 17 00:00:00 2001
From: Liam Marsh <liam.marsh@epfl.ch>
Date: Wed, 19 Nov 2025 11:11:56 +0100
Subject: [PATCH 2/7] fix molden test for other versions of pyscf

Co-authored by: Liam Marsh <liam.marsh@epfl.ch>
Co-authored by: Ksenia Briling <ksenia.briling@epfl.ch>
---
 tests/test_molden.py | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/tests/test_molden.py b/tests/test_molden.py
index 8ea95543..01e0a478 100755
--- a/tests/test_molden.py
+++ b/tests/test_molden.py
@@ -2,7 +2,6 @@
 
 import os
 import tempfile
-import filecmp
 import numpy as np
 from qstack import compound
 from qstack.fields.density2file import coeffs_to_molden
@@ -14,7 +13,13 @@ def test_molden():
     c = np.load(path+'/data/H2O_dist.ccpvdz.ccpvdzjkfit.npy')
     tmpfile = tempfile.mktemp() + '.molden'
     coeffs_to_molden(auxmol, c, tmpfile)
-    assert (filecmp.cmp(path+'/data/H2O_dist.ccpvdz.ccpvdzjkfit.molden', tmpfile))
+    with open(tmpfile) as f:
+        output = f.readlines()
+        output = ''.join(output[0:1]+output[2:])
+    with open(path+'/data/H2O_dist.ccpvdz.ccpvdzjkfit.molden') as f:
+        output0 = f.readlines()
+        output0 = ''.join(output0[0:1]+output0[2:])
+    assert np.all(output==output0)
 
 
 if __name__ == '__main__':

From 878797d9e2bef443868e6e3328b877d514b3e091 Mon Sep 17 00:00:00 2001
From: Ksenia <ksenia.briling@epfl.ch>
Date: Wed, 19 Nov 2025 16:18:22 +0100
Subject: [PATCH 3/7] Add dev options

---
 pyproject.toml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index ce5d6a53..f59adca8 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -52,8 +52,10 @@ cell2mol = ["qstack[pyscf,cell2mol-itself]"]
 equio-itself = ["metatensor-core >= 0.1.8, == 0.1.*"]
 equio = ["qstack[pyscf,equio-itself]"]
 spahm = ["qstack[pyscf]"]
-docs-build = ["sphinx", "sphinx-argparse", "sphinx-autobuild", "myst-parser", "furo"]
 all = ["qstack[pyscf,qml,regression,wigner,equio,gmol,cell2mol]"]
+docs-build = ["sphinx", "sphinx-argparse", "sphinx-autobuild", "myst-parser", "furo"]
+lint = ["ruff"]
+dev = ["qstack[all,docs-build,lint]"]
 
 [project.urls]
 Repository = "https://github.com/lcmd-epfl/Q-stack.git"

From 15e9147c5d93a8b71232c1f86a61b65ddaa6c862 Mon Sep 17 00:00:00 2001
From: Liam Marsh <liam.marsh@epfl.ch>
Date: Wed, 19 Nov 2025 12:36:16 +0100
Subject: [PATCH 4/7] fix: setup.py when no access to gitdir

---
 setup.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup.py b/setup.py
index 0d090ec4..20e5c56a 100644
--- a/setup.py
+++ b/setup.py
@@ -19,6 +19,8 @@ def get_git_version_hash():
     except OSError:
         return VERSION + "+unknown"
     version = p.communicate()[0]
+    if not version.strip():
+        return VERSION + "+unknown"
     print(version)
     return VERSION+'+'+version.strip().decode()
 

From 9a9e40106e655f9b821b436ba6183448ec8ffa71 Mon Sep 17 00:00:00 2001
From: Liam Marsh <liam.marsh@epfl.ch>
Date: Thu, 20 Nov 2025 11:30:57 +0100
Subject: [PATCH 5/7] fix: blind replacement of vulnerable dependencies

---
 requirements.py3.11.txt | 3 +--
 requirements.py3.9.txt  | 5 ++---
 2 files changed, 3 insertions(+), 5 deletions(-)

diff --git a/requirements.py3.11.txt b/requirements.py3.11.txt
index 96276ae4..b91ce11d 100644
--- a/requirements.py3.11.txt
+++ b/requirements.py3.11.txt
@@ -1,5 +1,4 @@
 attrs==21.4.0
-certifi==2021.10.8
 h5py==3.11.0
 iniconfig==1.1.1
 packaging==25.0
@@ -13,6 +12,6 @@ scipy==1.16.3
 toml==0.10.2
 scikit-learn==1.7.2
 ase==3.26
-tqdm==4.66
+tqdm==4.67
 metatensor-core==0.1.17
 cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@40b3237
diff --git a/requirements.py3.9.txt b/requirements.py3.9.txt
index 7e0f3719..50ac614b 100644
--- a/requirements.py3.9.txt
+++ b/requirements.py3.9.txt
@@ -1,5 +1,4 @@
 attrs==21.4.0
-certifi==2021.10.8
 h5py==3.6.0
 iniconfig==1.1.1
 packaging==21.3
@@ -11,8 +10,8 @@ pytest==6.2.5
 numpy===1.22.3
 scipy==1.10
 toml==0.10.2
-scikit-learn==0.24.2
+scikit-learn==1.6.1
 ase==3.22
-tqdm==4.66
+tqdm==4.67
 metatensor-core==0.1.8
 cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@22473bbf12a013467137a55a63c88fbbdc95baa2

From 45875ac7edca67f26504d879c7cecbe200b984f8 Mon Sep 17 00:00:00 2001
From: Ksenia <briling@mail.ru>
Date: Wed, 3 Dec 2025 15:46:26 +0100
Subject: [PATCH 6/7] Fix later versions compatibility

---
 pyproject.toml                 | 4 ++--
 qstack/__init__.py             | 7 -------
 qstack/fields/decomposition.py | 8 ++++----
 3 files changed, 6 insertions(+), 13 deletions(-)

diff --git a/pyproject.toml b/pyproject.toml
index f59adca8..9bf2a6e7 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -37,13 +37,13 @@ classifiers = [
 # note: maximal versions are just the latest versions to exist when compatibility checks were made, later versions may also work
 requires-python = ">=3.9"
 dependencies = [
-    'numpy >= 1.22.3, < 2.4',
+    'numpy >= 1.26.1, < 2.4',
     'scipy >= 1.1.0, < 1.17',
     'tqdm >= 4.66',
 ]
 
 [project.optional-dependencies]
-pyscf = ['pyscf >= 2.0.1, < 2.12']
+pyscf = ['pyscf >= 2.1.0, < 2.12']
 qml = ['ase >= 3.22, < 3.27']
 regression = ["scikit-learn >= 0.24.2, < 1.8"]
 wigner = ["sympy >= 1.5, < 1.15"]
diff --git a/qstack/__init__.py b/qstack/__init__.py
index dec7a3c4..1c16edc3 100644
--- a/qstack/__init__.py
+++ b/qstack/__init__.py
@@ -1,12 +1,5 @@
 """Q-stack."""
 
 from qstack import tools
-#from qstack import compound  # needs pyscf
 from qstack import constants
 from qstack import mathutils
-#from qstack import fields  # needs scipy, pyscf
-#from qstack import basis_opt  # needs pyscf, scipy
-#from qstack import spahm  # requires pyscf
-#from qstack import orcaio  # requires pyscf
-#from qstack import qml  # requires ase
-#from qstack import regression  # requires sklearn (scikit-learn  as pip calls it)
diff --git a/qstack/fields/decomposition.py b/qstack/fields/decomposition.py
index 91ba4b2a..40363a26 100644
--- a/qstack/fields/decomposition.py
+++ b/qstack/fields/decomposition.py
@@ -2,7 +2,7 @@
 
 import numpy as np
 import scipy
-from pyscf import scf
+from pyscf import scf, gto
 from qstack import compound
 from . import moments
 
@@ -59,10 +59,10 @@ def get_self_repulsion(mol_or_mf, dm):
     Returns:
         float: Self-repulsion energy (a.u).
     """
-    try:
-        j, _k = mol_or_mf.get_jk()
-    except AttributeError:
+    if isinstance(mol_or_mf, gto.mole.Mole):
         j, _k = scf.hf.get_jk(mol_or_mf, dm)
+    else:
+        j, _k = mol_or_mf.get_jk()
     return np.einsum('ij,ij', j, dm)
 
 

From 4072f8248abbd5606c512ca7b5a9888135bb819d Mon Sep 17 00:00:00 2001
From: Ksenia <briling@mail.ru>
Date: Wed, 3 Dec 2025 15:57:54 +0100
Subject: [PATCH 7/7] Adapt for python 3.9

---
 qstack/__init__.py                 | 12 ++++++++++++
 qstack/regression/local_kernels.py |  4 ++--
 qstack/reorder.py                  |  2 +-
 qstack/spahm/rho/utils.py          |  4 ++--
 qstack/tools.py                    | 20 +++++++++++++++++---
 requirements.py3.9.txt             |  5 ++---
 6 files changed, 36 insertions(+), 11 deletions(-)

diff --git a/qstack/__init__.py b/qstack/__init__.py
index 1c16edc3..e23b113f 100644
--- a/qstack/__init__.py
+++ b/qstack/__init__.py
@@ -1,5 +1,17 @@
 """Q-stack."""
 
+import sys
+import warnings
+import builtins
 from qstack import tools
 from qstack import constants
 from qstack import mathutils
+
+
+if sys.version_info[1]<10:
+    warnings.warn('Redefining built-in function zip for compatibility', stacklevel=1)
+    _zip = builtins.zip
+    def zip_override(*iterables, strict=False):
+        """Override built-in zip for python<3.10 to ignore `strict` argument."""
+        return _zip(*iterables)
+    builtins.zip = zip_override
diff --git a/qstack/regression/local_kernels.py b/qstack/regression/local_kernels.py
index c17b7158..759a466f 100644
--- a/qstack/regression/local_kernels.py
+++ b/qstack/regression/local_kernels.py
@@ -11,10 +11,10 @@
 import ctypes
 import sysconfig
 import warnings
-import itertools
 import numpy as np
 import sklearn.metrics.pairwise as _SKLEARN_PAIRWISE
 from qstack.regression import __path__ as REGMODULE_PATH
+from qstack.tools import pairwise
 
 
 RAM_BATCHING_SIZE = 1024**3 * 5  # 5GiB
@@ -66,7 +66,7 @@ def compute_distance_matrix(R1, R2):
     else:
         dists = np.zeros((batch_size, *R2.shape), dtype=dtype)
         batch_limits = np.minimum(np.arange(0, R1.shape[0]+batch_size, step=batch_size), R1.shape[0])
-        for batch_start, batch_end in itertools.pairwise(batch_limits):
+        for batch_start, batch_end in pairwise(batch_limits):
             dists_view = dists[:batch_end-batch_start]
             R1_view = R1[batch_start:batch_end, None, ...]
             np.subtract(R1_view, R2[None,:], out=dists_view)
diff --git a/qstack/reorder.py b/qstack/reorder.py
index 5c50ba75..f270a7e4 100644
--- a/qstack/reorder.py
+++ b/qstack/reorder.py
@@ -51,7 +51,7 @@ def _orca2gpr_idx(l_slices, m):
         idx[s] = np.concatenate((idx[s][::-2], idx[s][1::2]))
     signs = np.ones_like(idx)
     signs[np.where(np.abs(m)>=3)] = -1  # in pyscf order
-    signs[idx] = signs  # in orca order
+    signs[idx] = np.copy(signs)  # in orca order. copy for numpy < 2
     return idx, signs
 
 
diff --git a/qstack/spahm/rho/utils.py b/qstack/spahm/rho/utils.py
index b0e7c9bb..c87c2c5e 100644
--- a/qstack/spahm/rho/utils.py
+++ b/qstack/spahm/rho/utils.py
@@ -52,8 +52,8 @@ def chsp_converter(chsp):
     if fname is None:
         return np.full(n, None, dtype=object)
     if os.path.isfile(fname):
-        chsp = np.loadtxt(fname, dtype=object, converters=chsp_converter, encoding=None)
-        if len(chsp)!=n:
+        chsp = np.loadtxt(fname, dtype=object, converters={0: chsp_converter}, encoding=None)
+        if chsp.shape != (n,):
             raise RuntimeError(f'Wrong length of the file {fname}')
     else:
         raise RuntimeError(f"{fname} can not be found")
diff --git a/qstack/tools.py b/qstack/tools.py
index 11e30bd9..74df4800 100644
--- a/qstack/tools.py
+++ b/qstack/tools.py
@@ -4,11 +4,25 @@
 """
 
 import os
+import sys
 import time
 import resource
 import argparse
-import itertools
 import numpy as np
+from itertools import accumulate
+if sys.version_info[1]>=10:
+    from itertools import pairwise
+else:
+    def pairwise(iterable):
+        """Implement itertools.pairwise for python<3.10.
+
+        Taken from https://docs.python.org/3/library/itertools.html#itertools.pairwise
+        """
+        iterator = iter(iterable)
+        a = next(iterator, None)
+        for b in iterator:
+            yield a, b
+            a = b
 
 
 def unix_time_decorator(func):
@@ -115,8 +129,8 @@ def slice_generator(iterable, inc=lambda x: x, i0=0):
         tuple: (element, slice) pairs for each element in the iterable.
     """
     func = func=lambda total, elem: total+inc(elem)
-    starts = itertools.accumulate(iterable, func=func, initial=i0)
-    starts_ends = itertools.pairwise(starts)
+    starts = accumulate(iterable, func=func, initial=i0)
+    starts_ends = pairwise(starts)
     for elem, (start, end) in zip(iterable, starts_ends, strict=True):
         yield elem, np.s_[start:end]
 
diff --git a/requirements.py3.9.txt b/requirements.py3.9.txt
index 50ac614b..d38561ab 100644
--- a/requirements.py3.9.txt
+++ b/requirements.py3.9.txt
@@ -5,13 +5,12 @@ packaging==21.3
 pluggy==1.0.0
 py==1.11.0
 pyparsing==3.0.6
-pyscf==2.0.1
+pyscf>=2.1
 pytest==6.2.5
-numpy===1.22.3
+numpy>=1.26.1
 scipy==1.10
 toml==0.10.2
 scikit-learn==1.6.1
 ase==3.22
 tqdm==4.67
 metatensor-core==0.1.8
-cell2mol @ git+https://github.com/lcmd-epfl/cell2mol.git@22473bbf12a013467137a55a63c88fbbdc95baa2