pyscf 2.6.1__tar.gz → 2.6.2__tar.gz

{pyscf-2.6.1 → pyscf-2.6.2}/CHANGELOG

@@ -1,10 +1,16 @@
+PySCF 2.6.2 (2024-06-19)
+------------------------
+* Fixes
+  - Compatibility issues for NumPy 2.0 release.
+
+
 PySCF 2.6.1 (2024-06-17)
 ------------------------
 * Improved
   - Allow for custom options for opening h5py file.
   - Linear dependency threshold for density fitting auxiliary basis.
 * Fixes
-  - Compatibility issues due for NumPy 2.0 release.
+  - Compatibility issues due to NumPy 2.0 release.
 
 
 PySCF 2.6.0 (2024-06-01)

{pyscf-2.6.1 → pyscf-2.6.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyscf
-Version: 2.6.1
+Version: 2.6.2
 Summary: PySCF: Python-based Simulations of Chemistry Framework
 Author-email: Qiming Sun <osirpt.sun@gmail.com>
 Maintainer-email: Qiming Sun <osirpt.sun@gmail.com>
@@ -76,9 +76,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2024-06-17
+2024-06-19
 
-* [Stable release 2.6.1](https://github.com/pyscf/pyscf/releases/tag/v2.6.1)
+* [Stable release 2.6.2](https://github.com/pyscf/pyscf/releases/tag/v2.6.2)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

{pyscf-2.6.1 → pyscf-2.6.2}/README.md

@@ -7,9 +7,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2024-06-17
+2024-06-19
 
-* [Stable release 2.6.1](https://github.com/pyscf/pyscf/releases/tag/v2.6.1)
+* [Stable release 2.6.2](https://github.com/pyscf/pyscf/releases/tag/v2.6.2)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/__init__.py

@@ -35,7 +35,7 @@ to try out the package::
 
 '''
 
-__version__ = '2.6.1'
+__version__ = '2.6.2'
 
 import os
 import sys

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/cc/ccsd_lambda.py

@@ -364,7 +364,7 @@ def update_lambda(mycc, t1, t2, l1, l2, eris=None, imds=None):
     return l1new, l2new
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 
 if __name__ == '__main__':

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/cc/dfccsd.py

@@ -191,7 +191,7 @@ def _make_df_eris(cc, mo_coeff=None):
     return eris
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 if __name__ == '__main__':
     from pyscf import gto

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/cc/rccsd_lambda.py

@@ -69,7 +69,7 @@ def make_intermediates(mycc, t1, t2, eris):
     oooo = np.asarray(eris.oooo)
     woooo  = lib.einsum('icjl,kc->ikjl', ovoo, t1)
     woooo += lib.einsum('jcil,kc->iljk', ovoo, t1)
-    woooo += oooo.copy()
+    woooo += oooo
     woooo += lib.einsum('icjd,klcd->ikjl', ovov, tau)
 
     theta = t2*2 - t2.transpose(0,1,3,2)

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/cc/rccsd_slow.py

@@ -1047,7 +1047,7 @@ class _IMDS:
         raise NotImplementedError
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.asarray(a, order='C')
 
 
 if __name__ == '__main__':

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/ci/cisd.py

@@ -1141,7 +1141,7 @@ scf.hf.RHF.CISD = lib.class_as_method(RCISD)
 scf.rohf.ROHF.CISD = None
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 
 if __name__ == '__main__':

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/ci/ucisd.py

@@ -976,4 +976,4 @@ from pyscf import scf
 scf.uhf.UHF.CISD = lib.class_as_method(CISD)
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/dft/gen_grid.py

@@ -366,7 +366,7 @@ def arg_group_grids(mol, coords, box_size=GROUP_BOX_SIZE):
     box_ids[box_ids[:,2] > boxes[2], 2] = boxes[2]
     rev_idx, counts = numpy.unique(box_ids, axis=0, return_inverse=True,
                                    return_counts=True)[1:3]
-    return rev_idx.argsort(kind='stable')
+    return rev_idx.ravel().argsort(kind='stable')
 
 def _load_conf(mod, name, default):
     var = getattr(__config__, name, None)

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/grad/ccsd.py

@@ -416,7 +416,7 @@ def _load_block_tril(h5dat, row0, row1, nao, out=None):
     return out
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 class Gradients(rhf_grad.GradientsBase):
 

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/grad/uccsd.py

@@ -485,7 +485,7 @@ def _rdm2_mo2ao(mycc, d2, mo_coeff, fsave=None):
         return fsave
 
 def _cp(a):
-    return numpy.array(a, copy=False, order='C')
+    return numpy.asarray(a, order='C')
 
 class Gradients(ccsd_grad.Gradients):
     grad_elec = grad_elec

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/lib/diis.py

@@ -217,7 +217,7 @@ class DIIS:
         if nd < self.min_space:
             return x
 
-        dt = numpy.array(self.get_err_vec(self._head-1), copy=False)
+        dt = numpy.asarray(self.get_err_vec(self._head-1))
         if self._H is None:
             self._H = numpy.zeros((self.space+1,self.space+1), dt.dtype)
             self._H[0,1:] = self._H[1:,0] = 1

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/lib/linalg_helper.py

@@ -1477,15 +1477,12 @@ def _qr(xs, dot, lindep=1e-14):
     xs = (r.T).dot(qs)
     '''
     nvec = len(xs)
-    dtype = xs[0].dtype
-    qs = numpy.empty((nvec,xs[0].size), dtype=dtype)
-    rmat = numpy.empty((nvec,nvec), order='F', dtype=dtype)
+    xs = qs = numpy.array(xs, copy=True)
+    rmat = numpy.eye(nvec, order='F', dtype=xs.dtype)
 
     nv = 0
     for i in range(nvec):
-        xi = numpy.array(xs[i], copy=True)
-        rmat[:,nv] = 0
-        rmat[nv,nv] = 1
+        xi = xs[i]
         for j in range(nv):
             prod = dot(qs[j].conj(), xi)
             xi -= qs[j] * prod

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/lib/numpy_helper.py

@@ -1144,7 +1144,7 @@ class NPArrayWithTag(numpy.ndarray):
 
     # Whenever the contents of the array were modified (through ufunc), the tag
     # should be expired. Overwrite the output of ufunc to restore ndarray type.
-    def __array_wrap__(self, out, context=None):
+    def __array_wrap__(self, out, context=None, return_scalar=False):
         if out.ndim == 0:  # if ufunc returns a scalar
             return out[()]
         else:

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/mp/dfmp2.py

@@ -62,7 +62,7 @@ def kernel(mp, mo_energy=None, mo_coeff=None, eris=None, with_t2=WITH_T2,
     for i in range(nocc):
         buf = numpy.dot(Lov[:,i*nvir:(i+1)*nvir].T,
                         Lov).reshape(nvir,nocc,nvir)
-        gi = numpy.array(buf, copy=False)
+        gi = numpy.asarray(buf)
         gi = gi.reshape(nvir,nocc,nvir).transpose(1,0,2)
         t2i = gi/lib.direct_sum('jb+a->jba', eia, eia[i])
         edi = numpy.einsum('jab,jab', t2i, gi) * 2

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/cc/eom_kccsd_uhf.py

@@ -1238,7 +1238,7 @@ if __name__ == '__main__':
     r1, r2 = eom_kgccsd.spin2spatial_ip_doublet(spin_r1_ip, spin_r2_ip, kconserv, kshift, orbspin)
     vector = myeom.amplitudes_to_vector(r1, r2, kshift)
     vector = myeom.matvec(vector, kshift=kshift, imds=imds)
-    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, nkpts, (nmoa, nmob), (nocca, noccb))
+    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, 0, nkpts, (nmoa, nmob), (nocca, noccb))
     Hr1a, Hr1b = Hr1
     Hr2aaa, Hr2baa, Hr2abb, Hr2bbb = Hr2
     print('ip Hr1a',   abs(lib.fp(Hr1a)   - (-0.34462696543560045-1.6104596956729178j)))
@@ -1263,7 +1263,7 @@ if __name__ == '__main__':
 
     vector = myeom.amplitudes_to_vector(r1, r2, kshift)
     vector = myeom.matvec(vector, kshift=kshift, imds=imds)
-    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, nkpts, (nmoa, nmob), (nocca, noccb))
+    Hr1, Hr2 = myeom.vector_to_amplitudes(vector, 0, nkpts, (nmoa, nmob), (nocca, noccb))
     Hr1a, Hr1b = Hr1
     Hr2aaa, Hr2aba, Hr2bab, Hr2bbb = Hr2
 

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/cc/kccsd_rhf_ksymm.py

@@ -326,6 +326,7 @@ def add_vvvv_(cc, Ht2, t1, t2, eris):
         get_Wvvvv = lambda ka, kb, kc: _Wvvvv[ka, kb, kc]
 
     kakb, igroup = np.unique(kqrts.kqrts_ibz[:,2:], axis=0, return_inverse=True)
+    igroup = igroup.ravel()
     for i in range(np.amax(igroup) + 1):
         ka, kb = kakb[i]
         idx = np.where(igroup==i)[0]

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/dft/multigrid/multigrid.py

@@ -294,8 +294,8 @@ def eval_rho(cell, dm, shls_slice=None, hermi=0, xctype='LDA', kpts=None,
                 dm_i = dm_i.real
             has_imag = dm_i.dtype == numpy.complex128
             if has_imag:
-                dmR = numpy.array(dm_i.real, order='C')
-                dmI = numpy.array(dm_i.imag, order='C')
+                dmR = numpy.asarray(dm_i.real, order='C')
+                dmI = numpy.asarray(dm_i.imag, order='C')
             else:
                 # make a copy because the dm may be overwritten in the
                 # NUMINT_rho_drv inplace

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/mp/kmp2_ksymm.py

@@ -54,6 +54,7 @@ def kernel(mp, mo_energy, mo_coeff, verbose=logger.NOTE, with_t2=WITH_T2):
 
     kijab, weight, k4_bz2ibz = kd.make_k4_ibz(sym='s2')
     _, igroup = np.unique(kijab[:,:2], axis=0, return_index=True)
+    igroup = igroup.ravel()
     igroup = list(igroup) + [len(kijab)]
 
     emp2_ss = emp2_os = 0.

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/mpicc/kccsd_rhf.py

@@ -3276,4 +3276,4 @@ class _IMDS:
         self.WvvvoR1  = self.fint2['WvvvoR1' ]
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.array(a, order='C')

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/mpicc/kintermediates_rhf.py

@@ -187,7 +187,7 @@ def cc_Woooo(cc,t1,t2,eris,feri2=None):
             for iterkl, kl in enumerate(ranges1):
                 for iterki, ki in enumerate(ranges2):
                     kj = kconserv[kk,ki,kl]
-                    oooo_tmp[iterkk,iterkl,iterki] = np.array(eris.oooo[kk,kl,ki],copy=True)
+                    oooo_tmp[iterkk,iterkl,iterki] = np.array(eris.oooo[kk,kl,ki], copy=True)
                     oooo_tmp[iterkk,iterkl,iterki] += einsum('klic,jc->klij',eris.ooov[kk,kl,ki],t1[kj])
                     oooo_tmp[iterkk,iterkl,iterki] += einsum('klcj,ic->klij',eris.ooov[kl,kk,kj].transpose(1,0,3,2),t1[ki])
 
@@ -233,7 +233,7 @@ def cc_Wvvvv(cc,t1,t2,eris,feri2=None):
             for kc in ranges1:
                 for kb in range(ka+1):
                     kd = kconserv[ka,kc,kb]
-                    vvvv_tmp = np.array(eris.vvvv[ka,kb,kc],copy=True)
+                    vvvv_tmp = np.array(eris.vvvv[ka,kb,kc], copy=True)
                     vvvv_tmp += einsum('akcd,kb->abcd',eris.ovvv[kb,ka,kd].transpose(1,0,3,2),-t1[kb])
                     vvvv_tmp += einsum('kbcd,ka->abcd',eris.ovvv[ka,kb,kc],-t1[ka])
                     Wvvvv[ka,kb,kc] = vvvv_tmp
@@ -336,7 +336,7 @@ def cc_Wvovo(cc,t1,t2,eris,feri2=None):
             for iterkk, kk in enumerate(ranges1):
                 for iterkc, kc in enumerate(ranges2):
                     ki = kconserv[ka,kc,kk]
-                    vovo_tmp[iterka,iterkk,iterkc] = np.array(eris.ovov[kk,ka,ki]).transpose(1,0,3,2)
+                    vovo_tmp[iterka,iterkk,iterkc] = np.asarray(eris.ovov[kk,ka,ki]).transpose(1,0,3,2)
                     vovo_tmp[iterka,iterkk,iterkc] -= einsum('lkci,la->akci',eris.ooov[kk,ka,ki].transpose(1,0,3,2),t1[ka])
                     vovo_tmp[iterka,iterkk,iterkc] += einsum('akcd,id->akci',eris.ovvv[kk,ka,ki].transpose(1,0,3,2),t1[ki])
                     # Beginning of change
@@ -391,7 +391,7 @@ def cc_Wovov(cc,t1,t2,eris,feri2=None):
             for iterka, ka in enumerate(ranges1):
                 for iterki, ki in enumerate(ranges2):
                     kc = kconserv[kk,ki,ka]
-                    ovov_tmp[iterkk,iterka,iterki] = np.array(eris.ovov[kk,ka,ki],copy=True)
+                    ovov_tmp[iterkk,iterka,iterki] = np.asarray(eris.ovov[kk,ka,ki])
                     ovov_tmp[iterkk,iterka,iterki] -= einsum('lkci,la->kaic',eris.ooov[kk,ka,ki].transpose(1,0,3,2),t1[ka])
                     ovov_tmp[iterkk,iterka,iterki] += einsum('akcd,id->kaic',eris.ovvv[kk,ka,ki].transpose(1,0,3,2),t1[ki])
                     # Beginning of change
@@ -1308,7 +1308,7 @@ def Wovoo(cc,t1,t2,eris,fint=None):
                 for iterki,ki in enumerate(ranges2):
                     kj = kconserv[kk,ki,kb]
 
-                    ovoo_tmp[iterkk,iterkb,iterki] = np.array(eris.ovoo[kk,kb,ki],copy=True)
+                    ovoo_tmp[iterkk,iterkb,iterki] = np.asarray(eris.ovoo[kk,kb,ki])
                     ovoo_tmp[iterkk,iterkb,iterki] += einsum('kbid,jd->kbij',WW1ovov_kbi[iterkk,iterkb,iterki], t1[kj])
                     ovoo_tmp[iterkk,iterkb,iterki] += einsum('klij,lb->kbij', WWoooo_kbi[iterkk,iterkb,iterki],-t1[kb])
                     #ovoo_tmp[iterkk,iterkb,iterki] += einsum('kbcj,ic->kbij',WW1ovvo_kbi[iterkk,iterkb,iterki],t1[ki])
@@ -1550,4 +1550,4 @@ def WvoovR1(cc,t1,t2,eris,fint=None):
     return Wkaci
 
 def _cp(a):
-    return np.array(a, copy=False, order='C')
+    return np.array(a, order='C')

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/pbc/symm/group.py

@@ -300,7 +300,7 @@ class FiniteGroup(ABC):
                 The indices to reconstruct `conjugacy_mask` from `classes`.
         '''
         _, idx = np.unique(self.conjugacy_mask, axis=0, return_index=True)
-        representatives = np.sort(idx)
+        representatives = np.sort(idx.ravel())
         classes = self.conjugacy_mask[representatives]
         inverse = -np.ones((self.order), dtype=int)
         diff = (self.conjugacy_mask[None,:,:]==classes[:,None,:]).all(axis=-1)

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/scf/dhf.py

@@ -624,9 +624,9 @@ employing the updated GWH rule from doi:10.1021/ja00480a005.''')
         if mol is None: mol = self.mol
         if dm is None: dm = self.make_rdm1()
         if self.direct_scf:
-            ddm = numpy.array(dm, copy=False) - numpy.array(dm_last, copy=False)
+            ddm = numpy.array(dm) - numpy.array(dm_last)
             vj, vk = self.get_jk(mol, ddm, hermi=hermi)
-            return numpy.array(vhf_last, copy=False) + vj - vk
+            return numpy.array(vhf_last) + vj - vk
         else:
             vj, vk = self.get_jk(mol, dm, hermi=hermi)
             return vj - vk

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf/x2c/x2c.py

@@ -546,9 +546,9 @@ class SCF(hf.SCF):
         if mol is None: mol = self.mol
         if dm is None: dm = self.make_rdm1()
         if self.direct_scf:
-            ddm = numpy.array(dm, copy=False) - numpy.array(dm_last, copy=False)
+            ddm = numpy.array(dm) - numpy.array(dm_last)
             vj, vk = self.get_jk(mol, ddm, hermi=hermi)
-            return numpy.array(vhf_last, copy=False) + vj - vk
+            return numpy.array(vhf_last) + vj - vk
         else:
             vj, vk = self.get_jk(mol, dm, hermi=hermi)
             return vj - vk

{pyscf-2.6.1 → pyscf-2.6.2}/pyscf.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: pyscf
-Version: 2.6.1
+Version: 2.6.2
 Summary: PySCF: Python-based Simulations of Chemistry Framework
 Author-email: Qiming Sun <osirpt.sun@gmail.com>
 Maintainer-email: Qiming Sun <osirpt.sun@gmail.com>
@@ -76,9 +76,9 @@ Python-based Simulations of Chemistry Framework
 [![Build Status](https://github.com/pyscf/pyscf/workflows/CI/badge.svg)](https://github.com/pyscf/pyscf/actions?query=workflow%3ACI)
 [![codecov](https://codecov.io/gh/pyscf/pyscf/branch/master/graph/badge.svg)](https://codecov.io/gh/pyscf/pyscf)
 
-2024-06-17
+2024-06-19
 
-* [Stable release 2.6.1](https://github.com/pyscf/pyscf/releases/tag/v2.6.1)
+* [Stable release 2.6.2](https://github.com/pyscf/pyscf/releases/tag/v2.6.2)
 * [Changelog](../master/CHANGELOG)
 * [Documentation](http://www.pyscf.org)
 * [Installation](#installation)

{pyscf-2.6.1 → pyscf-2.6.2}/setup.py

@@ -83,13 +83,27 @@ class CMakeBuildPy(build_py):
 
 # build_py will produce plat_name = 'any'. Patch the bdist_wheel to change the
 # platform tag because the C extensions are platform dependent.
+# For setuptools<70
 from wheel.bdist_wheel import bdist_wheel
-initialize_options = bdist_wheel.initialize_options
+initialize_options_1 = bdist_wheel.initialize_options
 def initialize_with_default_plat_name(self):
-    initialize_options(self)
+    initialize_options_1(self)
     self.plat_name = get_platform()
+    self.plat_name_supplied = True
 bdist_wheel.initialize_options = initialize_with_default_plat_name
 
+# For setuptools>=70
+try:
+    from setuptools.command.bdist_wheel import bdist_wheel
+    initialize_options_2 = bdist_wheel.initialize_options
+    def initialize_with_default_plat_name(self):
+        initialize_options_2(self)
+        self.plat_name = get_platform()
+        self.plat_name_supplied = True
+    bdist_wheel.initialize_options = initialize_with_default_plat_name
+except ImportError:
+    pass
+
 # scipy bugs
 # https://github.com/scipy/scipy/issues/12533
 _scipy_version = 'scipy!=1.5.0,!=1.5.1'