Merge pull request prody#1959 from jamesmkrieger/rtbtools_upgrade_fix

Fix rtbtools to permit numpy upgrade

.github/workflows/main.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11"]
+        python-version: ["2.7", "3.8", "3.9", "3.10", "3.11", "3.12"]
 
     steps:
     - uses: actions/checkout@v2

docs/apps/docapps.py

@@ -1,15 +1,18 @@
 #!/usr/bin/python
 
 import os
-import imp
+import sys
 import importlib
 from subprocess import Popen, PIPE
 
-path = [importlib.util.find_spec("prody").submodule_search_locations[0]]
-apps = imp.load_module('prody.apps',
-                           *imp.find_module('apps', path))
+from prody.utilities.misctools import impLoadModule
 
-for cmd, subcmds in [('prody', apps.PRODY_APPS), ('evol', apps.EVOL_APPS)]:
+path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+
+prody_apps = impLoadModule('prody.apps.prody_apps', path_apps + '/prody_apps/', '__init__')
+evol_apps = impLoadModule('prody.apps.evol_apps', path_apps + '/evol_apps/', '__init__')
+
+for cmd, subcmds in [('prody', prody_apps.PRODY_APPS), ('evol', evol_apps.EVOL_APPS)]:
 
     pipe = Popen([cmd, '-h'], stdout=PIPE, stderr=PIPE)
     with open(os.path.join(cmd, cmd + '.txt'), 'w') as rst:

prody/apps/evol_apps/__init__.py

@@ -1,6 +1,5 @@
 """This module defines some sequence evolution applications."""
 
-import imp
 import importlib
 import sys
 
@@ -9,14 +8,22 @@
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('evol_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('evol_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/evol_apps/'
 
 EVOL_APPS = ['search', 'fetch', 'filter', 'refine', 'merge', 'occupancy',
              'conserv', 'coevol', 'rankorder']
@@ -81,8 +88,7 @@
 
 for cmd in EVOL_APPS:
     cmd = 'evol_' + cmd
-    mod = imp.load_module('prody.apps.evol_apps.' + cmd,
-                          *imp.find_module(cmd, [path_apps]))
+    mod = impLoadModule('prody.apps.evol_apps.', cmd, path_apps)
     mod.APP.addApplication(evol_commands)
 
 

prody/apps/prody_apps/__init__.py

@@ -1,6 +1,5 @@
 """This module defines structure and dynamics analysis applications."""
 
-import imp
 import importlib
 import sys
 
@@ -9,14 +8,22 @@
 except ImportError:
     from .. import argparse
 
-from ..apptools import *
+from prody.apps.apptools import *
+from prody.utilities.misctools import impLoadModule
 
 if sys.version_info[0] == 2:
+    import imp
     path_prody = imp.find_module('prody')[1]
 else:
     path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-path_apps = imp.find_module('apps', [path_prody])[1]
-path_apps = imp.find_module('prody_apps', [path_apps])[1]
+
+try:
+    import imp
+    path_apps = imp.find_module('apps', [path_prody])[1]
+    path_apps = imp.find_module('prody_apps', [path_apps])[1]
+except ModuleNotFoundError:
+    path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+    path_apps += '/prody_apps/'
 
 PRODY_APPS = ['anm', 'gnm', 'pca', 'eda', 'align', 'blast', 'biomol',
                   'catdcd', 'contacts', 'fetch', 'select', 'energy', 
@@ -44,11 +51,9 @@
 
 for cmd in PRODY_APPS:
     cmd = 'prody_' + cmd
-    mod = imp.load_module('prody.apps.prody_apps.' + cmd,
-                          *imp.find_module(cmd, [path_apps]))
+    mod = impLoadModule('prody.apps.prody_apps.', cmd, path_apps)
     mod.addCommand(prody_commands)
 
-
 def prody_main():
 
     if len(sys.argv) == 1:

prody/dynamics/rtbtools.c

@@ -419,7 +419,7 @@ void cross(double x[], double y[], double z[])
 int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB, 
 			int nres, int nblx, int bmx)
 {
-  double **X, **I, **IC, *CM, *W, **A, **ISQT;
+  double **X, **Ii, **IC, *CM, *W, **A, **ISQT;
   double x, tr, dd, df;
   int *IDX, nbp, b, i, j, k, ii, jj, aa, bb, elm;
 
@@ -429,7 +429,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
   X = dmatrix(1, bmx, 1, 3);
   IDX = ivector(1, bmx);
   CM = dvector(1, 3);
-  I = dmatrix(1, 3, 1, 3);
+  Ii = dmatrix(1, 3, 1, 3);
   IC = dmatrix(1, 3, 1, 3);
   W = dvector(1, 3);
   A = dmatrix(1, 3, 1, 3);
@@ -442,7 +442,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
     for(j=1; j<=3; j++)
     {
       CM[j] = 0.0;
-      for(i=1; i<=3; i++) I[i][j] = 0.0;
+      for(i=1; i<=3; i++) Ii[i][j] = 0.0;
       for(i=1; i<=bmx; i++) X[i][j] = 0.0;
     }
 
@@ -478,19 +478,19 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
       }
       for(i=1; i<=3; i++)
       {
-        I[i][i] += (dd - X[k][i] * X[k][i]);
+        Ii[i][i] += (dd - X[k][i] * X[k][i]);
         for(j=i+1; j<=3; j++)
         {
-          I[i][j] -= X[k][i]*X[k][j];
-          I[j][i] = I[i][j];
+          Ii[i][j] -= X[k][i]*X[k][j];
+          Ii[j][i] = Ii[i][j];
 	      }
       }
     }
 
     /* DIAGONALIZE INERTIA TENSOR */
     for (i=1; i<=3; i++)
       for (j=1; j<=3; j++)
-	      IC[i][j]=I[i][j];
+	      IC[i][j]=Ii[i][j];
     dsvdcmp(IC, 3, 3, W, A);
     deigsrt(W, A, 3);
     righthand2(W, A, 3);
@@ -545,7 +545,7 @@ int dblock_projections2(dSparse_Matrix *PP, PDB_File *PDB,
   free_dmatrix(X, 1, bmx, 1, 3);
   free_ivector(IDX, 1, bmx);
   free_dvector(CM, 1, 3);
-  free_dmatrix(I, 1, 3, 1, 3);
+  free_dmatrix(Ii, 1, 3, 1, 3);
   free_dmatrix(IC, 1, 3, 1, 3);
   free_dvector(W, 1, 3);
   free_dmatrix(A, 1, 3, 1, 3);

prody/tests/dynamics/test_lda.py

@@ -3,10 +3,8 @@
 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_fixer.py

@@ -1,10 +1,8 @@
 """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_waterbridges.py

@@ -2,10 +2,8 @@
 
 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/utilities/doctools.py

@@ -45,7 +45,7 @@ def joinTerms(terms, sep=', ', last=None, sort=False):
 
 
 def wrapText(text, width=70, join='\n', **kwargs):
-    """Returns wrapped lines from :func:`textwrap.wrap` after *join*\ing them.
+    """Returns wrapped lines from :func:`textwrap.wrap` after *join*ing them.
     """
 
     try:

prody/utilities/misctools.py

@@ -22,7 +22,7 @@
            'getValue', 'indentElement', 'isPDB', 'isURL', 'isListLike', 'isSymmetric', 'makeSymmetric',
            'getDistance', 'fastin', 'createStringIO', 'div0', 'wmean', 'bin2dec', 'wrapModes', 
            'fixArraySize', 'decToHybrid36', 'hybrid36ToDec', 'DTYPE', 'checkIdentifiers', 'split', 'mad',
-           'importDec']
+           'importDec', 'impLoadModule']
 
 DTYPE = array(['a']).dtype.char  # 'S' for PY2K and 'U' for PY3K
 CURSORS = []
@@ -788,17 +788,37 @@ def _mad(x):
 
 
 def importDec():
-    """Returns one of :mod:`scipy.linalg` or :mod:`numpy.linalg`."""
+    """Returns an imported module equivalent to numpy testing decorators."""
 
     try:
         import numpy.testing.decorators as dec
-    except ImportError:
+    except ModuleNotFoundError:
         try:
             from numpy.testing import dec
         except ImportError:
             try:
                 import numpy.testing._private.decorators as dec
-            except ImportError:
+            except ModuleNotFoundError:
                 from pytest import mark as dec    
 
     return dec
+
+
+def impLoadModule(name, cmd, path):
+    """Returns an  an imported module equivalent to imp."""
+
+    if not name.endswith('.'):
+        name += '.'
+
+    try:
+        import imp
+        mod = imp.load_module(name + cmd,
+                              *imp.find_module(cmd, [path]))
+    except ImportError:
+        import importlib
+        loader = importlib.machinery.SourceFileLoader(name + cmd,
+                                                      path + cmd + '.py')
+        mod = importlib.util.types.ModuleType(loader.name)
+        loader.exec_module(mod)
+
+    return mod

pyproject.toml

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

scripts/evol

@@ -1,13 +1,10 @@
 #!/usr/bin/env python
 
-import imp
+from prody.utilities.misctools import impLoadModule
 import importlib
-if sys.version_info[0] == 2:
-    path_prody = imp.find_module('prody')[1]
-else:
-    path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-apps = imp.find_module('apps', [path])
-apps = imp.load_module('prody.apps', *apps)
+
+path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+apps = impLoadModule('prody.apps.evol_apps', path_apps + '/evol_apps/', '__init__')
 
 if __name__ == '__main__':
     apps.evol_main()

scripts/prody

@@ -1,13 +1,10 @@
 #!/usr/bin/env python
 
-import imp
+from prody.utilities.misctools import impLoadModule
 import importlib
-if sys.version_info[0] == 2:
-    path_prody = imp.find_module('prody')[1]
-else:
-    path_prody = importlib.util.find_spec("prody").submodule_search_locations[0]
-apps = imp.find_module('apps', [path])
-apps = imp.load_module('prody.apps', *apps)
+
+path_apps = importlib.util.find_spec("prody.apps").submodule_search_locations[0]
+apps = impLoadModule('prody.apps.prody_apps', path_apps + '/prody_apps/', '__init__')
 
 if __name__ == '__main__':
     apps.prody_main()

setup.py

@@ -16,7 +16,7 @@
 if sys.version_info[:2] == (2, 7) or sys.version_info[:2] <= (3, 5):
     INSTALL_REQUIRES=['numpy>=1.10', 'biopython<=1.76', 'pyparsing', 'scipy']
 else:
-    INSTALL_REQUIRES=['numpy>=1.10,<1.24', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
+    INSTALL_REQUIRES=['numpy>=1.10,<2', 'biopython', 'pyparsing<=3.1.1', 'scipy', 'setuptools']
 
 if sys.version_info[0] == 3 and sys.version_info[1] < 6:
     sys.stderr.write('Python 3.5 and older is not supported\n')