fix broken import, remove deprecated pkg_resource (#50)

Author: stevenhua0320

Diff for: src/diffpy/srmise/basefunction.py

@@ -369,7 +369,7 @@ def factory(functionstr, baselist):
         # "key=value"->{"key":"value"}
         data = re.split(r"(?:[\r\n]+|\A)(\S+)=", data)
         ddict = {}
-        for i in range(len(data) / 2):
+        for i in range(len(data) // 2):
             ddict[data[2 * i + 1]] = data[2 * i + 2]
 
         # dictionary of parameters
@@ -442,7 +442,8 @@ def safefunction(f, fsafe):
 
 if __name__ == "__main__":
 
-    from diffpy.srmise.peaks import GaussianOverR, TerminationRipples
+    from diffpy.srmise.peaks.gaussianoverr import GaussianOverR
+    from diffpy.srmise.peaks.terminationripples import TerminationRipples
 
     p = GaussianOverR(0.8)
     outstr = p.writestr([])

Diff for: src/diffpy/srmise/modelcluster.py

@@ -26,9 +26,9 @@
 import numpy as np
 
 from diffpy.srmise import srmiselog
-from diffpy.srmise.baselines import Baseline
+from diffpy.srmise.baselines.base import Baseline
 from diffpy.srmise.modelparts import ModelParts
-from diffpy.srmise.peaks import Peak, Peaks
+from diffpy.srmise.peaks.base import Peak, Peaks
 from diffpy.srmise.srmiseerrors import (
     SrMiseDataFormatError,
     SrMiseEstimationError,

Diff for: src/diffpy/srmise/modelparts.py

@@ -20,21 +20,22 @@
 """
 
 import logging
+from importlib.metadata import version
 
 import matplotlib.pyplot as plt
 import numpy as np
 
 # Output of scipy.optimize.leastsq for a single parameter changed in scipy 0.8.0
 # Before it returned a scalar, later it returned an array of length 1.
-import pkg_resources as pr
+from packaging.version import parse
 from scipy.optimize import leastsq
 
 from diffpy.srmise import srmiselog
 from diffpy.srmise.srmiseerrors import SrMiseFitError, SrMiseStaticOwnerError, SrMiseUndefinedCovarianceError
 
 logger = logging.getLogger("diffpy.srmise")
-__spv__ = pr.get_distribution("scipy").version
-__oldleastsqbehavior__ = pr.parse_version(__spv__) < pr.parse_version("0.8.0")
+__spv__ = version("scipy")
+__oldleastsqbehavior__ = parse(__spv__) < parse("0.8.0")
 
 
 class ModelParts(list):
@@ -123,8 +124,8 @@ def fit(
                 freepars,  # initial parameters
                 args=args,  # arguments to residual, residual_jacobian
                 Dfun=self.residual_jacobian,  # explicit Jacobian
-                col_deriv=1,  # order of derivatives in Jacobian
-                full_output=1,
+                col_deriv=True,  # order of derivatives in Jacobian
+                full_output=True,
                 maxfev=ntrials,
             )
         except NotImplementedError:
@@ -136,8 +137,8 @@ def fit(
                 self.residual,  # minimize this function
                 freepars,  # initial parameters
                 args=args,  # arguments to residual
-                col_deriv=1,  # order of derivatives in Jacobian
-                full_output=1,
+                col_deriv=True,  # order of derivatives in Jacobian
+                full_output=True,
                 maxfev=ntrials,
             )
         except Exception:
@@ -202,7 +203,7 @@ def fit(
             try:
                 cov.transform(in_format="internal", out_format=cov_format)
             except SrMiseUndefinedCovarianceError:
-                logger.warn("Covariance not defined.  Fit may not have converged.")
+                logger.warning("Covariance not defined.  Fit may not have converged.")
 
         return
 
@@ -352,7 +353,7 @@ def __str__(self):
 
     def __getslice__(self, i, j):
         """Extends list.__getslice__"""
-        return self.__class__(list.__getslice__(self, i, j))
+        return self.__class__(list.__getitem__(self, i, j))
 
     def transform(self, in_format="internal", out_format="internal"):
         """Transforms format of parameters in this modelpart.

Diff for: src/diffpy/srmise/pdfdataset.py

@@ -201,7 +201,7 @@ def readStr(self, datastring):
 
         # find where the metadata starts
         metadata = ""
-        res = re.search(r"^#+\ +metadata\b\n", header, re.M)
+        res = re.search(r"^#+ +metadata\b\n", header, re.M)
         if res:
             metadata = header[res.end() :]
             header = header[: res.start()]
@@ -343,7 +343,7 @@ def writeStr(self):
         # metadata
         if len(self.metadata) > 0:
             lines.append("# metadata")
-            for k, v in self.metadata.iteritems():
+            for k, v in self.metadata.items():
                 lines.append("%s=%s" % (k, v))
         # write data:
         lines.append("##### start data")
@@ -408,10 +408,10 @@ class PDFDataFormatError(Exception):
     dataset = PDFDataSet("test")
     dataset.read(filename)
     print("== metadata ==")
-    for k, v in dataset.metadata.iteritems():
+    for k, v in dataset.metadata.items():
         print(k, "=", v)
     print("== data members ==")
-    for k, v in dataset.__dict__.iteritems():
+    for k, v in dataset.__dict__.items():
         if k in ("metadata", "robs", "Gobs", "drobs", "dGobs") or k[0] == "_":
             continue
         print(k, "=", v)