Merge pull request #1655 from jamesmkrieger/remove_numpy_alias_types

remove np alias types

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10"]
+        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
 
     steps:
     - uses: actions/checkout@v2
@@ -29,7 +29,7 @@ jobs:
         if [[ ${{ matrix.python-version }} != "2.7" ]]; then conda config --add channels conda-forge; fi
         conda create --yes -n test python=${{ matrix.python-version }}
         source activate test
-        conda install --yes numpy scipy nose pyparsing requests
+        conda install --yes numpy scipy nose requests
         if [[ ${{ matrix.python-version }} == "2.7" ]]; then conda install --yes unittest2; else conda install --yes pdbfixer; fi
         pip install mmtf-python scikit-learn
         pip install .

PKG-INFO

@@ -92,7 +92,7 @@ Classifier: Programming Language :: Python :: 3
 Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
 Classifier: Topic :: Scientific/Engineering :: Chemistry
 Requires: numpy (>=1.10)
-Requires: pyparsing
+Requires: pyparsing (<=3.1.1)
 Requires: biopython
 Requires: scipy
-Provides: prody (2.1.2)
+Provides: prody

prody/compounds/pdbligands.py

@@ -158,9 +158,9 @@ def fetchPDBLigand(cci, filename=None):
     resnums = np.ones(n_atoms, dtype=ATOMIC_FIELDS['charge'].dtype)
 
     alternate_atomnames = np.zeros(n_atoms, dtype=ATOMIC_FIELDS['name'].dtype)
-    leaving_atom_flags = np.zeros(n_atoms, np.bool)
-    aromatic_flags = np.zeros(n_atoms, np.bool)
-    stereo_configs = np.zeros(n_atoms, np.bool)
+    leaving_atom_flags = np.zeros(n_atoms, bool)
+    aromatic_flags = np.zeros(n_atoms, bool)
+    stereo_configs = np.zeros(n_atoms, bool)
     ordinals = np.zeros(n_atoms, int)
 
     name2index = {}

prody/dynamics/signature.py

@@ -1648,7 +1648,7 @@ def showSignatureDistribution(signature, **kwargs):
     bins = kwargs.pop('bins', 'auto')
     if bins == 'auto':
         _, bins = np.histogram(W.flatten(), bins='auto')
-    elif np.isscalar(bins) and isinstance(bins, (int, np.integer)):
+    elif np.isscalar(bins) and isinstance(bins, int):
         step = (W.max() - W.min())/bins
         bins = np.arange(W.min(), W.max(), step)
 

prody/sequence/msa.py

@@ -154,7 +154,7 @@ def __getitem__(self, index):
         if isinstance(rows, list):
             rows = self.getIndex(rows) or rows
         elif isinstance(rows, int):
-            return Sequence(self._msa[rows, cols].tostring(),
+            return Sequence(self._msa[rows, cols].tobytes(),
                             self._labels[rows])
         elif isinstance(rows, str):
             try:
@@ -164,7 +164,7 @@ def __getitem__(self, index):
                                .format(index))
             else:
                 if isinstance(rows, int):
-                    return Sequence(self._msa[rows, cols].tostring(),
+                    return Sequence(self._msa[rows, cols].tobytes(),
                                     self._labels[rows])
 
         if cols is None:
@@ -546,7 +546,7 @@ def refineMSA(msa, index=None, label=None, rowocc=None, seqid=None, colocc=None,
                 from prody.utilities import GAP_PENALTY, GAP_EXT_PENALTY, ALIGNMENT_METHOD
 
                 chseq = chain.getSequence()
-                algn = alignBioPairwise(pystr(arr[index].tostring().upper()), pystr(chseq),
+                algn = alignBioPairwise(pystr(arr[index].tobytes().upper()), pystr(chseq),
                                         "local",
                                         MATCH_SCORE, MISMATCH_SCORE,
                                         GAP_PENALTY, GAP_EXT_PENALTY,

prody/sequence/msafile.py

@@ -433,7 +433,7 @@ def setSlice(self, slice):
                 else:
                     self._slice = slice
                     self._slicer = lambda seq, slc=slice: fromstring(seq,
-                                                        '|S1')[slc].tostring()
+                                                        '|S1')[slc].tobytes()
             else:
                 self._slice = slice
                 self._slicer = lambda seq, slc=slice: seq[slc]

prody/sequence/sequence.py

@@ -49,9 +49,9 @@ def _array(self):
     def __str__(self):
 
         if PY3K:
-            return self._array.tostring().decode()
+            return self._array.tobytes().decode()
         else:
-            return self._array.tostring()
+            return self._array.tobytes()
 
     def __len__(self):
 

prody/tests/apps/test_prody_anm.py

@@ -5,10 +5,8 @@
 
 from numpy.testing import *
 
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 

prody/tests/apps/test_prody_catdcd.py

@@ -4,10 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import parsePDB, DCDFile, parseDCD
 

prody/tests/apps/test_prody_examples.py

@@ -6,10 +6,9 @@
 from subprocess import Popen, PIPE
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import LOGGER
 LOGGER.verbosity = None

prody/tests/apps/test_prody_gnm.py

@@ -4,10 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 

prody/tests/apps/test_prody_pca.py

@@ -4,10 +4,9 @@
 from prody.tests import TestCase, skipIf, skipUnless
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody.tests.datafiles import TEMPDIR, pathDatafile
 

prody/tests/atomic/test_select.py

@@ -5,17 +5,16 @@
 import inspect
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
 
 from prody import *
 from prody import LOGGER
 from prody.tests import unittest
 from prody.tests.datafiles import *
 from prody.atomic.atommap import DUMMY
 
+from prody.utilities import importDec
+dec = importDec()
+
 prody.atomic.select.DEBUG = False
 LOGGER.verbosity = 'none'
 

prody/tests/database/test_pfam.py

@@ -37,7 +37,7 @@ def testUniprotAccMulti(self):
             'searchPfam failed to return a dict instance')
 
         self.assertEqual(sorted(list(a.keys()))[:2], ['PF00060', 'PF00497'],
-                         'searchPfam failed to return the right domain family IDs')
+                           'searchPfam failed to return the right domain family IDs')
 
     def testPdbIdChMulti(self):
         """Test the outcome of a simple search scenario using a PDB ID

prody/tests/dynamics/test_enms.py

@@ -3,10 +3,9 @@
 import numpy as np
 from numpy import arange
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/dynamics/test_pca.py

@@ -3,10 +3,9 @@
 import numpy as np
 from numpy import arange
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/proteins/test_ciffile.py

@@ -5,10 +5,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/proteins/test_dssp.py

@@ -1,10 +1,9 @@
 """This module contains unit tests for :mod:`~prody.proteins`."""
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/proteins/test_insty.py

@@ -35,25 +35,25 @@ def setUp(self):
             np.save('test_2k39_all.npy', self.data_all, allow_pickle=True)
 
             self.data_hbs = calcHydrogenBondsTrajectory(self.ATOMS)
-            np.save('test_2k39_hbs.npy', self.data_hbs, allow_pickle=True)
+            np.save('test_2k39_hbs.npy', np.array(self.data_hbs, dtype=object), allow_pickle=True)
 
             self.data_sbs = calcSaltBridgesTrajectory(self.ATOMS)
-            np.save('test_2k39_sbs.npy', self.data_sbs, allow_pickle=True)
+            np.save('test_2k39_sbs.npy', np.array(self.data_sbs, dtype=object), allow_pickle=True)
 
             self.data_rib = calcRepulsiveIonicBondingTrajectory(self.ATOMS)
-            np.save('test_2k39_rib.npy', self.data_rib, allow_pickle=True)
+            np.save('test_2k39_rib.npy', np.array(self.data_rib, dtype=object), allow_pickle=True)
 
             self.data_PiStack = calcPiStackingTrajectory(self.ATOMS)
-            np.save('test_2k39_PiStack.npy', self.data_PiStack, allow_pickle=True)
+            np.save('test_2k39_PiStack.npy', np.array(self.data_PiStack, dtype=object), allow_pickle=True)
 
             self.data_PiCat = calcPiCationTrajectory(self.ATOMS)
-            np.save('test_2k39_PiCat.npy', self.data_PiCat, allow_pickle=True)
+            np.save('test_2k39_PiCat.npy', np.array(self.data_PiCat, dtype=object), allow_pickle=True)
 
             self.data_hph = calcHydrophobicTrajectory(self.ATOMS)
-            np.save('test_2k39_hph.npy', self.data_hph, allow_pickle=True)
+            np.save('test_2k39_hph.npy', np.array(self.data_hph, dtype=object), allow_pickle=True)
 
             self.data_disu = calcDisulfideBondsTrajectory(self.ATOMS)
-            np.save('test_2k39_disu.npy', self.data_disu, allow_pickle=True)
+            np.save('test_2k39_disu.npy', np.array(self.data_disu, dtype=object), allow_pickle=True)
 
     def testAllInsteractions(self):
         """Test for all types of interactions."""

prody/tests/proteins/test_localpdb.py

@@ -4,10 +4,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/proteins/test_pdbfile.py

@@ -4,10 +4,9 @@
 
 import numpy as np
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/proteins/test_wwpdb.py

@@ -3,10 +3,9 @@
 import os
 
 from numpy.testing import *
-try:
-    import numpy.testing.decorators as dec
-except ImportError:
-    from numpy.testing import dec
+
+from prody.utilities import importDec
+dec = importDec()
 
 from prody import *
 from prody import LOGGER

prody/tests/sequence/test_msafile.py

@@ -5,12 +5,13 @@
 from os.path import join
 
 from numpy import array, log, zeros, char
-from numpy.testing import assert_array_equal, dec
+from numpy.testing import assert_array_equal
 
 from prody.tests.datafiles import *
 from prody.tests import TEMPDIR
 from prody import MSA, MSAFile, parseMSA, LOGGER, writeMSA
-from prody.utilities import createStringIO
+from prody.utilities import createStringIO, importDec
+dec = importDec()
 
 LOGGER.verbosity = None
 

prody/utilities/misctools.py

@@ -21,7 +21,8 @@
            'getDataPath', 'openData', 'chr2', 'toChararray', 'interpY', 'cmp', 'pystr',
            'getValue', 'indentElement', 'isPDB', 'isURL', 'isListLike', 'isSymmetric', 'makeSymmetric',
            'getDistance', 'fastin', 'createStringIO', 'div0', 'wmean', 'bin2dec', 'wrapModes', 
-           'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad']
+           'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad',
+           'importDec']
 
 DTYPE = array(['a']).dtype.char  # 'S' for PY2K and 'U' for PY3K
 CURSORS = []
@@ -784,3 +785,20 @@ def _mad(x):
                 return median(abs(x - med))
 
     return _mad(x)
+
+
+def importDec():
+    """Returns one of :mod:`scipy.linalg` or :mod:`numpy.linalg`."""
+
+    try:
+        import numpy.testing.decorators as dec
+    except ImportError:
+        try:
+            from numpy.testing import dec
+        except ImportError:
+            try:
+                import numpy.testing._private.decorators as dec
+            except ImportError:
+                from pytest import mark as dec    
+
+    return dec

pyproject.toml

@@ -1,2 +1,2 @@
 [build-system]
-requires = ["setuptools", "wheel", "numpy>=1.10,<1.24", "pyparsing", "scipy"]
+requires = ["setuptools", "wheel", "numpy>=1.10,<1.25", "pyparsing<=3.1.1", "scipy"]

setup.py

@@ -12,14 +12,13 @@
     sys.exit()
 
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython<=1.76', 'pyparsing', 'scipy']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.25', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython', 'pyparsing', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
 
-if sys.version_info[0] == 3:
-    if sys.version_info[1] < 6:
-        sys.stderr.write('Python 3.5 and older is not supported\n')
-        sys.exit()
+if sys.version_info[0] == 3 and sys.version_info[1] < 6:
+    sys.stderr.write('Python 3.5 and older is not supported\n')
+    sys.exit()
 
 if os.name == 'java':
     sys.stderr.write('JavaOS is not supported\n')