diff options
| author | Vedran Miletić | 2025-02-13 08:06:23 +0100 |
|---|---|---|
| committer | Vedran Miletić | 2025-02-13 08:06:23 +0100 |
| commit | 1b7b5a80e88bc249da8bc0429c697c1bc8598511 (patch) | |
| tree | 81d75a7e8fe3a34ba7a597fa9cfd1248ce09f939 | |
| parent | 6d211aab10188ee274472d2312e5f123d527e150 (diff) | |
| download | aur-1b7b5a80e88bc249da8bc0429c697c1bc8598511.tar.gz | |
Added NumPy 2.0 compatibility patch
| -rw-r--r-- | .SRCINFO | 4 | ||||
| -rw-r--r-- | 0003-NumPy-2-compatibility.patch | 129 | ||||
| -rw-r--r-- | PKGBUILD | 7 |
3 files changed, 137 insertions, 3 deletions
@@ -1,7 +1,7 @@ pkgbase = ambertools pkgdesc = Biomolecular simulation package (tools only) pkgver = 24.00 - pkgrel = 3 + pkgrel = 4 url = http://ambermd.org/ arch = x86_64 license = GPL-3.0-or-later AND LGPL-3.0-or-later AND BSD-3-Clause AND MIT @@ -28,10 +28,12 @@ pkgbase = ambertools source = https://ambermd.org/downloads/AmberTools24_rc5.tar.bz2 source = 0001-Allow-using-newer-CUDA.patch source = 0002-Use-cxx14-for-Boost.patch + source = 0003-NumPy-2-compatibility.patch source = 50-ambertools.conf sha256sums = 52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f sha256sums = e5da8dd8bc22a98142e36dcf336d8d008378070b4aa4389d8aa75a25a2041f9a sha256sums = 216de362c73dce1b214be2c12f8f31913f83bb22863ae15311dc3336c70b2bd8 + sha256sums = 4104d0dc4c381930c100b11a198bb1b16c89d1f6b5071e4e6be542d2f1492e8e sha256sums = 38835459f9710fc33bf2a96f4dfa26aef08d21754aec2e297032c214c4e781ef pkgname = ambertools diff --git a/0003-NumPy-2-compatibility.patch b/0003-NumPy-2-compatibility.patch new file mode 100644 index 000000000000..f7b626951c63 --- /dev/null +++ b/0003-NumPy-2-compatibility.patch @@ -0,0 +1,129 @@ +--- a/AmberTools/src/parmed/parmed/amber/_amberparm.py ++++ b/AmberTools/src/parmed/parmed/amber/_amberparm.py +@@ -2147,7 +2147,7 @@ class AmberParm(AmberFormat, Structure): + box[4] = box[4].value_in_unit(u.degrees) + if u.is_quantity(box[5]): + box[5] = box[5].value_in_unit(u.degrees) +- box = np.array(box, dtype=np.float64, copy=False, subok=True).reshape((-1, 6)) ++ box = np.asanyarray(box, dtype=np.float64).reshape((-1, 6)) + + # We are adding a box for the first time, so make sure we add some flags + if self._box is None: +@@ -2373,7 +2373,7 @@ class Rst7(object): + @property + def velocities(self): + """ Atomic velocities in units of angstroms/picoseconds """ +- return np.array(self.vels, copy=False).reshape(self.natom, 3) ++ return np.asarray(self.vels).reshape(self.natom, 3) + + @property + def box_vectors(self): +--- a/AmberTools/src/parmed/parmed/amber/asciicrd.py ++++ b/AmberTools/src/parmed/parmed/amber/asciicrd.py +@@ -317,7 +317,7 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile): + def coordinates(self, stuff): + if self._status == 'old': + raise RuntimeError('Cannot set coordinates on an old restart') +- stuff = np.array(stuff, copy=False).ravel() ++ stuff = np.asarray(stuff).ravel() + if self.natom > 0 and len(stuff) != 3 * self.natom: + raise ValueError(f'Got {len(stuff)} coordinates for {self.natom} atoms') + if self._coords_written: +@@ -351,7 +351,7 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile): + def velocities(self, stuff): + if self._status == 'old': + raise RuntimeError('Cannot set velocities on an old restart') +- stuff = np.array(stuff, copy=False).ravel() ++ stuff = np.asarray(stuff).ravel() + if not self._coords_written: + raise RuntimeError('Coordinates must be set before velocities') + if self._cell_lengths_written or self._cell_angles_written: +@@ -413,7 +413,7 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile): + raise RuntimeError('Can only write cell lengths once') + if len(stuff) != 3: + raise ValueError('Expected 3 numbers for cell lengths') +- self._cell_lengths = np.array(stuff, copy=False) ++ self._cell_lengths = np.asarray(stuff) + self._file.write('%12.7f%12.7f%12.7f' % (stuff[0], stuff[1], stuff[2])) + self._cell_lengths_written = True + +@@ -429,7 +429,7 @@ class AmberAsciiRestart(_AmberAsciiCoordinateFile): + raise RuntimeError('Can only write cell angles once') + if len(stuff) != 3: + raise ValueError('Expected 3 numbers for cell angles') +- self._cell_angles = np.array(stuff, copy=False) ++ self._cell_angles = np.asarray(stuff) + self._file.write('%12.7f%12.7f%12.7f\n' % (stuff[0],stuff[1],stuff[2])) + self._cell_angles_written = True + +--- a/AmberTools/src/parmed/parmed/amber/netcdffiles.py ++++ b/AmberTools/src/parmed/parmed/amber/netcdffiles.py +@@ -241,7 +241,7 @@ class NetCDFRestart(metaclass=FileFormatType): + + @coordinates.setter + def coordinates(self, stuff): +- stuff = np.array(stuff, copy=False).reshape((self.atom, 3)) ++ stuff = np.asarray(stuff).reshape((self.atom, 3)) + self._ncfile.variables['coordinates'][:] = stuff + self.flush() + +--- a/AmberTools/src/parmed/parmed/formats/pdb.py ++++ b/AmberTools/src/parmed/parmed/formats/pdb.py +@@ -971,7 +971,7 @@ class PDBFile(metaclass=FileFormatType): + symm_line = "REMARK 290 SMTRY" + fmt % tuple(arr_list) + dest.write(symm_line) + if coordinates is not None: +- coords = np.array(coordinates, copy=False, subok=True) ++ coords = np.asanyarray(coordinates) + try: + coords = coords.reshape((-1, len(struct.atoms), 3)) + except ValueError: +@@ -1646,7 +1646,7 @@ class CIFFile(metaclass=FileFormatType): + sym.append([struct.space_group]) + cont.append(sym) + if coordinates is not None: +- coords = np.array(coordinates, copy=False, subok=True) ++ coords = np.asanyarray(coordinates) + try: + coords = coords.reshape((-1, len(struct.atoms), 3)) + except ValueError: +--- a/AmberTools/src/parmed/parmed/formats/pqr.py ++++ b/AmberTools/src/parmed/parmed/formats/pqr.py +@@ -257,7 +257,7 @@ class PQRFile(metaclass=FileFormatType): + struct.box[0], struct.box[1], struct.box[2], struct.box[3], + struct.box[4], struct.box[5])) + if coordinates is not None: +- coords = np.array(coordinates, copy=False, subok=True) ++ coords = np.asanyarray(coordinates) + try: + coords = coords.reshape((-1, len(struct.atoms), 3)) + except ValueError: +--- a/AmberTools/src/parmed/parmed/structure.py ++++ b/AmberTools/src/parmed/parmed/structure.py +@@ -1796,7 +1796,7 @@ class Structure: + if u.is_quantity(value): + value = value.value_in_unit(u.angstroms) + value = list(value) +- coords = np.array(value, dtype=np.float64, copy=False, subok=True) ++ coords = np.asanyarray(value, dtype=np.float64) + coords = coords.reshape((-1, len(self.atoms), 3)) + if len(coords) > 0: + for a, xyz in zip(self.atoms, coords[0]): +@@ -1877,7 +1877,7 @@ class Structure: + box = value + else: + box = _strip_box_units(list(value)) +- box = np.array(box, dtype=np.float64, copy=False, subok=True) ++ box = np.asanyarray(box, dtype=np.float64) + if box.shape != (6,): + if len(box.shape) != 2 or box.shape[-1] != 6: + raise ValueError('Box information must be 6 floats') +@@ -1944,7 +1944,7 @@ class Structure: + except AttributeError: + pass + else: +- value = np.array(value, copy=False).reshape( ++ value = np.asarray(value).reshape( + (-1, len(self.atoms), 3)) + for atom, xyz in zip(self.atoms, value[0]): + atom.vx, atom.vy, atom.vz = xyz @@ -6,8 +6,8 @@ _majorver=24 _archivever="24_rc5" pkgname=ambertools -pkgver=24.00 -pkgrel=3 +pkgver=24.08 +pkgrel=1 pkgdesc="Biomolecular simulation package (tools only)" url="http://ambermd.org/" license=('GPL-3.0-or-later AND LGPL-3.0-or-later AND BSD-3-Clause AND MIT') @@ -24,10 +24,12 @@ options=(!buildflags) source=("https://ambermd.org/downloads/AmberTools${_archivever}.tar.bz2" "0001-Allow-using-newer-CUDA.patch" "0002-Use-cxx14-for-Boost.patch" + "0003-NumPy-2-compatibility.patch" "50-ambertools.conf") sha256sums=('52fb4fb3370a89b7ce738a2dc3e513c2fc1943fde4b4381846d9e75cc48d840f' 'e5da8dd8bc22a98142e36dcf336d8d008378070b4aa4389d8aa75a25a2041f9a' '216de362c73dce1b214be2c12f8f31913f83bb22863ae15311dc3336c70b2bd8' + '4104d0dc4c381930c100b11a198bb1b16c89d1f6b5071e4e6be542d2f1492e8e' '38835459f9710fc33bf2a96f4dfa26aef08d21754aec2e297032c214c4e781ef') prepare() { @@ -49,6 +51,7 @@ build() { patch -p1 -i ${srcdir}/0001-Allow-using-newer-CUDA.patch patch -p1 -i ${srcdir}/0002-Use-cxx14-for-Boost.patch + patch -p1 -i ${srcdir}/0003-NumPy-2-compatibility.patch mkdir -p build cd build |