matscipy: Add version 1.3.0

docs/packages/matscipy.yaml

@@ -16,3 +16,4 @@ versions:
   - filename: matscipy-1.2.0-cp314-cp314-manylinux_2_34_riscv64.manylinux_2_39_riscv64.whl
     sha256: edec7c83ef02d487442a94a3b4ad5f2f180d4f98ae927c6628eb0b54e2b6a8da
     requires-python: '>=3.9.0'
+- version: 1.3.0

patches/matscipy/1.3.0/0001-eam-io-index-1-element-arrays-before-int-float.patch

@@ -0,0 +1,33 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Thu, 01 Oct 2026 00:00:00 +0000
+Subject: [PATCH] eam/io: index 1-element arrays before int()/float()
+
+write_eam's "eam" (DYNAMO funcfl) branch calls int(atomic_numbers) and
+float(atomic_masses)/float(lattice_parameters) directly on the
+EAMParameters fields, which read_eam builds as 1-element numpy arrays
+(np.array((int(words[0]),), dtype=int), etc.), not scalars - the
+function's own "# FIXME: atomic numbers etc are now arrays, and not
+scalars" comment already says as much. NumPy 2.x turned the implicit
+conversion of a non-0-d array into a hard TypeError: "only
+0-dimensional arrays can be converted to Python scalars", so
+test_eam_io.py::test_eam_read_write's round-trip through this branch
+fails outright. Indexing [0] before the int()/float() calls is what
+the FIXME already describes as the fix; upstream made the same change
+in 255201ab (released in 1.3.0).
+
+Upstream-Status: Backport [https://github.com/libAtoms/matscipy/commit/255201aba4d827bb97dead8964c80e7276161603]
+
+Signed-off-by: Ludovic Henry <git@ludovic.dev>
+---
+--- a/matscipy/calculators/eam/io.py
++++ b/matscipy/calculators/eam/io.py
+@@ -548,7 +548,7 @@
+         # parameters unpacked
+         # FIXME: atomic numbers etc are now arrays, and not scalars
+         crystal_structures_str = ' '.join(s for s in crystal_structures)
+-        atline = f"{int(atomic_numbers)} {float(atomic_masses)}  {float(lattice_parameters)} {crystal_structures_str}"
++        atline = f"{int(atomic_numbers[0])} {float(atomic_masses[0])}  {float(lattice_parameters[0])} {crystal_structures_str}"
+         parameterline = f'{int(Nrho)}\t{float(drho):.16e}\t{int(Nr)}\t{float(dr):.16e}\t{float(cutoff):.10e}'
+         potheader = f"# EAM potential from : # {source} \n {atline} \n {parameterline}"
+         # --- Writing new EAM alloy pot file --- #

patches/matscipy/1.3.0/0002-cauchy_born-drop-removed-sqrtm-disp-keyword.patch

@@ -0,0 +1,38 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Thu, 01 Oct 2026 00:00:00 +0000
+Subject: [PATCH] cauchy_born: drop the removed sqrtm(disp=) keyword
+
+SciPy 1.18 removed the deprecated disp= keyword of scipy.linalg.sqrtm,
+so CubicCauchyBorn's two sqrtm(Usqr, disp=True) calls raise
+"TypeError: sqrtm() got an unexpected keyword argument 'disp'" and all
+nine test_cauchy_born_corrector.py::TestPredictCauchyBornShifts tests
+fail. disp=True was the default, so sqrtm(Usqr) is unchanged on older
+SciPy. Upstream made the same change in 75f077ff (released in 1.3.0).
+
+Upstream-Status: Backport [https://github.com/libAtoms/matscipy/commit/75f077ff7de629fc65814b760d6ebd225b630d64]
+
+Signed-off-by: Ludovic Henry <git@ludovic.dev>
+---
+diff --git a/matscipy/cauchy_born.py b/matscipy/cauchy_born.py
+index c84a2534..ad973424 100644
+--- a/matscipy/cauchy_born.py
++++ b/matscipy/cauchy_born.py
+@@ -268,7 +268,7 @@ class CubicCauchyBorn:
+             # get U^2
+             Usqr = 2 * E + np.eye(3)
+             # square root matrix to get U
+-            U = sqrtm(Usqr, disp=True)
++            U = sqrtm(Usqr)
+
+             # this is just the symmetric stretch tensor, exactly what we need.
+             x = U
+@@ -1330,7 +1330,7 @@ class CubicCauchyBorn:
+         # get U^2
+         Usqr = 2 * E + np.eye(3)
+         # square root matrix
+-        U = sqrtm(Usqr, disp=True)
++        U = sqrtm(Usqr)
+
+         # this is just the symmetric stretch tensor, exactly what we need.
+         x = U

patches/matscipy/1.3.0/0003-molecules-lammpsdata-replace-ndarray-resize-for-py314.patch

@@ -0,0 +1,88 @@
+From 0000000000000000000000000000000000000000 Mon Sep 17 00:00:00 2001
+From: Ludovic Henry <git@ludovic.dev>
+Date: Thu, 01 Oct 2026 00:00:00 +0000
+Subject: [PATCH] molecules, io/lammpsdata: replace ndarray.resize for Python 3.14
+
+From NumPy 2.4 on, ndarray.resize(refcheck=True) on Python >= 3.14 uses
+PyUnstable_Object_IsUniquelyReferenced, which an attribute-held array
+never satisfies, so Molecules.__init__ and LAMMPSData's setter/reader
+raise "ValueError: cannot resize an array that may be referenced by
+another object" on cp314 only (test_newmb.py, test_neighbours.py,
+test_io.py collection errors, test_manybody_molecules.py setup errors).
+Upstream replaced every such resize with a fresh np.empty of the same
+dtype in libAtoms/matscipy#312 (commits 1b006eb4 and 3a1ec1dc, released
+in 1.3.0); this is those two hunks unchanged.
+
+Upstream-Status: Backport [https://github.com/libAtoms/matscipy/pull/312]
+
+Signed-off-by: Ludovic Henry <git@ludovic.dev>
+---
+diff --git a/matscipy/io/lammpsdata.py b/matscipy/io/lammpsdata.py
+index 4525a786..e7200f0a 100644
+--- a/matscipy/io/lammpsdata.py
++++ b/matscipy/io/lammpsdata.py
+@@ -193,10 +193,15 @@ class LAMMPSData:
+         """Set data component."""
+         if name in self._type_names:
+             name = self._type_names[name]
+-            self.__data[name].resize(len(value))
++            old = self.__data[name]
++            new_arr = np.empty(len(value), dtype=self._dtypes[name])
++            n = min(len(old), len(value))
++            if n > 0:
++                new_arr[:n] = old[:n]
++            self.__data[name] = new_arr
+             self.__data[name]['type'] = value
+         elif name in self._data_names:
+-            self.__data[name].resize(len(value))
++            self.__data[name] = np.empty(len(value), dtype=self._dtypes[name])
+             data = self.__data[name]
+             try:
+                 data[data.dtype.names[-1]] = np.array(value)
+@@ -309,16 +314,15 @@ class LAMMPSData:
+         for linum, line in enumerate(fd):
+             if 'Masses' in line:
+                 ntypes = type_counts['atom types']
+-                self['masses'].resize(ntypes)
+-                self['masses'][:] = \
++                self.__data['masses'] = \
+                     np.genfromtxt(fd, skip_header=1,
+-                                  max_rows=ntypes, usecols=(1,))
++                                  max_rows=ntypes, usecols=(1,), dtype=self._dtypes['masses'])
+
+             else:
+                 for label in self._data_names:
+                     if self.__headers[label] in line:
+                         nlines = data_counts[label]
+-                        self[label].resize(nlines)
++                        self.__data[label] = np.empty(nlines, dtype=self._dtypes[label])
+                         dtype = self[label].dtype
+
+                         raw_dtype = np.dtype([('num', np.int32)] + [
+diff --git a/matscipy/molecules.py b/matscipy/molecules.py
+index 4657da62..d9a88996 100644
+--- a/matscipy/molecules.py
++++ b/matscipy/molecules.py
+@@ -72,19 +72,19 @@ class Molecules:
+             self.__dict__[data] = np.array([], dtype=dtype)
+
+         if bonds_connectivity is not None:
+-            self.bonds.resize(len(bonds_connectivity))
++            self.bonds = np.empty(len(bonds_connectivity), dtype=self._dtypes["bonds"])
+             self.bonds["atoms"][:] = bonds_connectivity
+             self.bonds["type"][:] = bonds_types \
+                 if bonds_types is not None else default_type
+
+         if angles_connectivity is not None:
+-            self.angles.resize(len(angles_connectivity))
++            self.angles = np.empty(len(angles_connectivity), dtype=self._dtypes["angles"])
+             self.angles["atoms"][:] = angles_connectivity
+             self.angles["type"][:] = angles_types \
+                 if angles_types is not None else default_type
+
+         if dihedrals_connectivity is not None:
+-            self.dihedrals.resize(len(dihedrals_connectivity))
++            self.dihedrals = np.empty(len(dihedrals_connectivity), dtype=self._dtypes["dihedrals"])
+             self.dihedrals["atoms"][:] = dihedrals_connectivity
+             self.dihedrals["type"][:] = dihedrals_types \
+                 if dihedrals_types is not None else default_type