test

devutils/makesdist

@@ -17,11 +17,11 @@ sys.path.insert(0, BASEDIR)
 from setup import versiondata
 timestamp = versiondata.getint('DEFAULT', 'timestamp')
 
-print 'Run "setup.py sdist --formats=tar"',
+print('Run "setup.py sdist --formats=tar"',)
 cmd_sdist = [sys.executable] + 'setup.py sdist --formats=tar'.split()
 ec = subprocess.call(cmd_sdist, cwd=BASEDIR, stdout=open(os.devnull, 'w'))
 if ec:  sys.exit(ec)
-print "[done]"
+print("[done]")
 
 tarname = max(glob.glob(BASEDIR + '/dist/*.tar'), key=os.path.getmtime)
 
@@ -36,8 +36,8 @@ def fixtarinfo(tinfo):
     return tinfo
 
 
-print 'Filter %s --> %s.gz' % (2 * (os.path.basename(tarname),)),
+print('Filter %s --> %s.gz' % (2 * (os.path.basename(tarname),)),)
 for ti in tfin:
     tfout.addfile(fixtarinfo(ti), tfin.extractfile(ti))
 os.remove(tarname)
-print "[done]"
+print("[done]")

devutils/prep.py

@@ -8,6 +8,8 @@
 
 __basedir__ = os.getcwdu()
 
+from numpy.compat import unicode
+
 # Example imports
 
 
@@ -18,20 +20,21 @@ def __init__(self):
 
     def test(self, call, *args, **kwds):
         m = sys.modules[call.__module__]
-        testname = m.__name__+'.'+call.__name__
+        testname = m.__name__ + "." + call.__name__
         path = os.path.dirname(m.__file__)
         os.chdir(path)
         try:
             call(*args, **kwds)
-            self.messages.append("%s: success" %testname)
-        except Exception, e:
-            self.messages.append("%s: error, details below.\n%s" %(testname, e))
+            self.messages.append("%s: success" % testname)
+        except Exception as e:
+            self.messages.append("%s: error, details below.\n%s" % (testname, e))
         finally:
             os.chdir(__basedir__)
 
     def report(self):
-        print '==== Results of Tests ===='
-        print '\n'.join(self.messages)
+        print("==== Results of Tests ====")
+        print("\n".join(self.messages))
+
 
 def scrubeol(directory, filerestr):
     """Use unix-style endlines for files in directory matched by regex string.
@@ -50,11 +53,11 @@ def scrubeol(directory, filerestr):
         text = unicode(original.read())
         original.close()
 
-        updated = io.open(f, 'w', newline='\n')
+        updated = io.open(f, "w", newline="\n")
         updated.write(text)
         updated.close()
 
-        print "Updated %s to unix-style endlines." %f
+        print("Updated %s to unix-style endlines." % f)
 
 
 def rm(directory, filerestr):
@@ -72,30 +75,31 @@ def rm(directory, filerestr):
     for f in files:
         os.remove(f)
 
-        print "Deleted %s." %f
-
+        print("Deleted %s." % f)
 
 
 if __name__ == "__main__":
 
     # Temporarily add examples to path
-    lib_path = os.path.abspath(os.path.join('..','doc','examples'))
+    lib_path = os.path.abspath(os.path.join("..", "doc", "examples"))
     sys.path.append(lib_path)
 
     # Delete existing files that don't necessarily have a fixed name.
     rm("../doc/examples/output", r"known_dG.*\.pwa")
     rm("../doc/examples/output", r"unknown_dG.*\.pwa")
 
-    ### Testing examples
+    # Testing examples
     examples = Test()
-    test_names = ["extract_single_peak",
-                  "parameter_summary",
-                  "fit_initial",
-                  "query_results",
-                  "multimodel_known_dG1",
-                  "multimodel_known_dG2",
-                  "multimodel_unknown_dG1",
-                  "multimodel_unknown_dG2"]
+    test_names = [
+        "extract_single_peak",
+        "parameter_summary",
+        "fit_initial",
+        "query_results",
+        "multimodel_known_dG1",
+        "multimodel_known_dG2",
+        "multimodel_unknown_dG1",
+        "multimodel_unknown_dG2",
+    ]
 
     test_modules = []
     for test in test_names:
@@ -106,10 +110,8 @@ def rm(directory, filerestr):
 
     examples.report()
 
-    ### Convert output of example files to Unix-style endlines for sdist.
-    if os.linesep != '\n':
-        print "==== Scrubbing Endlines ===="
+    # Convert output of example files to Unix-style endlines for sdist.
+    if os.linesep != "\n":
+        print("==== Scrubbing Endlines ====")
         # All *.srmise and *.pwa files in examples directory.
         scrubeol("../doc/examples/output", r".*(\.srmise|\.pwa)")
-
-

diffpy/srmise/__init__.py

@@ -2,7 +2,8 @@
 ##############################################################################
 #
 # SrMise            by Luke Granlund
-#                   (c) 2014 trustees of the Michigan State University.
+#                   (c) 2014 trustees of the Michigan State University
+#                   (c) 2024 trustees of Columia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund
@@ -13,28 +14,5 @@
 
 """Tools for peak extraction from PDF."""
 
-__all__ = [
-    "basefunction",
-    "srmiseerrors",
-    "srmiselog",
-    "dataclusters",
-    "modelcluster",
-    "modelparts",
-    "pdfdataset",
-    "pdfpeakextraction",
-    "peakextraction",
-    "peakstability",
-    "multimodelselection",
-]
-
-from basefunction import BaseFunction
-from dataclusters import DataClusters
-from modelcluster import ModelCluster, ModelCovariance
-from modelparts import ModelPart, ModelParts
-from multimodelselection import MultimodelSelection
-from pdfdataset import PDFDataSet
-from pdfpeakextraction import PDFPeakExtraction
-from peakextraction import PeakExtraction
-from peakstability import PeakStability
 
 from diffpy.srmise.version import __version__

diffpy/srmise/applications/__init__.py

@@ -2,7 +2,8 @@
 ##############################################################################
 #
 # SrMise            by Luke Granlund
-#                   (c) 2014 trustees of the Michigan State University.
+#                   (c) 2014 trustees of the Michigan State University
+#                   (c) 2024 trustees of Columia University in the City of New York
 #                   All rights reserved.
 #
 # File coded by:    Luke Granlund