Fix bugs to run tutorial CLI, update python, matplotlib API

doc/source/tutorial/abbreviations.txt

@@ -10,7 +10,7 @@
 .. |tar.gz| replace:: :source-release:`tar.gz`
 
 .. Image substitutions
-.. |images/extract_single_peak1.png| ge:: ../../examples/images/extract_single_peak1.png
+.. |images/extract_single_peak1.png| image:: ../../examples/images/extract_single_peak1.png
 .. |images/extract_single_peak2.png| image:: ../../examples/images/extract_single_peak2.png
 .. |images/extract_single_peak3.png| image:: ../../examples/images/extract_single_peak3.png
 .. |images/parameter_summary1.png| image:: ../../examples/images/parameter_summary1.png

news/entry-point-.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Configure entry point in pyproject.toml to run CLI commands
+
+**Security:**
+
+* <news item>

news/fix-api-bug.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* Update Python, matploblib API to run documentation CLI tutorials
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -45,6 +45,9 @@ template = "{tag}"
 dev_template = "{tag}"
 dirty_template = "{tag}"
 
+[project.scripts]
+srmise = "diffpy.srmise.applications.extract:main"
+
 [tool.setuptools.packages.find]
 where = ["src"] # list of folders that contain the packages (["."] by default)
 include = ["*"] # package names should match these glob patterns (["*"] by default)

src/diffpy/srmise/applications/extract.py

@@ -419,82 +419,85 @@ def main():
  from diffpy.srmise.pdfpeakextraction import PDFPeakExtraction
  from diffpy.srmise.srmiseerrors import SrMiseDataFormatError, SrMiseFileError
 
- try:
- options.peakfunction = eval("peaks." + options.peakfunction)
- except Exception as err:
- print(err)
- print("Could not create peak function '%s'. Exiting." % options.peakfunction)
- return
-
- try:
- options.modelevaluator = eval("modelevaluators." + options.modelevaluator)
- except Exception as err:
- print(err)
- print("Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator)
- return
-
- if options.bcrystal is not None:
+ if options.peakfunction:
+ try:
+ options.peakfunction = eval("peaks." + options.peakfunction)
+ except Exception as err:
+ print(err)
+ print("Could not create peak function '%s'. Exiting." % options.peakfunction)
+ return
+
+ if options.modelevaluator:
+ try:
+ options.modelevaluator = eval("modelevaluators." + options.modelevaluator)
+ except Exception as err:
+ print(err)
+ print("Could not find ModelEvaluator '%s'. Exiting." % options.modelevaluator)
+ return
+
+ if options.bcrystal:
  from diffpy.srmise.baselines.polynomial import Polynomial
 
  bl = Polynomial(degree=1)
  options.baseline = parsepars(bl, [options.bcrystal, "0c"])
  options.baseline.pars[0] = -4 * np.pi * options.baseline.pars[0]
- elif options.bsrmise is not None:
+ elif options.bsrmise:
  # use baseline from existing file
  blext = PDFPeakExtraction()
  blext.read(options.bsrmise)
  options.baseline = blext.extracted.baseline
- elif options.bpoly0 is not None:
+ elif options.bpoly0:
  from diffpy.srmise.baselines.polynomial import Polynomial
 
  bl = Polynomial(degree=0)
  options.baseline = parsepars(bl, [options.bpoly0])
- elif options.bpoly1 is not None:
+ elif options.bpoly1:
  from diffpy.srmise.baselines.polynomial import Polynomial
 
  bl = Polynomial(degree=1)
  options.baseline = parsepars(bl, options.bpoly1)
- elif options.bpoly2 is not None:
+ elif options.bpoly2:
  from diffpy.srmise.baselines.polynomial import Polynomial
 
  bl = Polynomial(degree=2)
  options.baseline = parsepars(bl, options.bpoly2)
- elif options.bseq is not None:
+ elif options.bseq:
  from diffpy.srmise.baselines.fromsequence import FromSequence
 
  bl = FromSequence(options.bseq)
  options.baseline = bl.actualize([], "internal")
- elif options.bspherical is not None:
+ elif options.bspherical:
  from diffpy.srmise.baselines.nanospherical import NanoSpherical
 
  bl = NanoSpherical()
  options.baseline = parsepars(bl, options.bspherical)
 
  try:
  options.baseline = eval("baselines." + options.baseline)
+
  except Exception as err:
  print(err)
  print("Could not create baseline '%s'. Exiting." % options.baseline)
  return
 
  filename = args[0]
 
- if filename is not None:
+ if filename:
  ext = PDFPeakExtraction()
  try:
  ext.read(filename)
  except (SrMiseDataFormatError, SrMiseFileError, Exception):
  ext.loadpdf(filename)
 
  pdict = {}
- if options.peakfunction is not None:
+ if options.peakfunction:
  pdict["pf"] = [options.peakfunction]
- if options.baseline is not None:
+ if options.baseline:
  pdict["baseline"] = options.baseline
- if options.cres is not None:
+ if options.cres:
  pdict["cres"] = options.cres
  if options.dg_mode is None:
- if options.dg is not None:
+ if options.dg:
  options.dg_mode = "absolute"
  elif ext.dy is None:
  options.dg_mode = "max-fraction"
@@ -510,17 +513,17 @@ def main():
  pdict["effective_dy"] = options.dg * ext.y.ptp() * np.ones(len(ext.y))
  elif options.dg_mode == "dG-fraction":
  pdict["effective_dy"] = options.dg * ext.dy
- if options.rng is not None:
+ if options.rng:
  pdict["rng"] = list(options.rng)
- if options.qmax is not None:
+ if options.qmax:
  pdict["qmax"] = options.qmax if options.qmax == "automatic" else float(options.qmax)
- if options.nyquist is not None:
+ if options.nyquist:
  pdict["nyquist"] = options.nyquist
- if options.supersample is not None:
+ if options.supersample:
  pdict["supersample"] = options.supersample
- if options.scale is not None:
+ if options.scale:
  pdict["scale"] = options.scale
- if options.modelevaluator is not None:
+ if options.modelevaluator:
  pdict["error_method"] = options.modelevaluator
 
  if options.liveplot:
@@ -532,23 +535,24 @@ def main():
  cov = None
  if options.performextraction:
  cov = ext.extract()
+ print(cov)
 
- if options.savefile is not None:
+ if options.savefile:
  try:
  ext.write(options.savefile)
  except SrMiseFileError as err:
  print(err)
  print("Could not save result to '%s'." % options.savefile)
 
- if options.pwafile is not None:
+ if options.pwafile:
  try:
  ext.writepwa(options.pwafile)
  except SrMiseFileError as err:
  print(err)
  print("Could not save pwa summary to '%s'." % options.pwafile)
 
  print(ext)
- if cov is not None:
+ if cov:
  print(cov)
 
  if options.plot:

src/diffpy/srmise/applications/plot.py

@@ -504,7 +504,7 @@ def on_draw(event):
  invisiblelabel.set_visible(True)
  visiblelabel = labeldict[fig]
  bbox = invisiblelabel.get_window_extent(invisiblelabel._renderer)
- bbox = bbox.inverse_transformed(ax_main.transAxes)
+ bbox = bbox.transformed(ax_main.transAxes.inverted())
  bbox = bbox.get_points()
  xpos = np.mean(np.transpose(bbox)[0])
 

src/diffpy/srmise/basefunction.py

@@ -100,6 +100,7 @@ def __init__(
  The class (not instance) which implements caching of BaseFunction
  evaluations.
  """
+
  self.parameterdict = parameterdict
  self.npars = len(self.parameterdict)
 
@@ -114,9 +115,13 @@ def __init__(
  if not isinstance(p, str):
  emsg = "Argument parameterdict's keys must be strings."
  raise ValueError(emsg)
- vals = self.parameterdict.values()
+
+ # Convert values to list and sort
+ vals = list(self.parameterdict.values())
  vals.sort()
- if vals != range(self.npars):
+
+ # Check if the sorted values match the sequence from 0 to npars-1
+ if vals != list(range(self.npars)):
  emsg = (
  "Argument parameterdict's values must uniquely specify "
  + "the index of each parameter defined by its keys."

src/diffpy/srmise/pdfdataset.py

@@ -202,7 +202,10 @@ def read(self, filename):
  self
  """
  try:
- self.readStr(open(filename, "rb").read())
+ # Open the file in binary mode, read it, and decode to convert bytes to string
+ with open(filename, "rb") as file:
+ file_content = file.read().decode("utf-8")
+ self.readStr(file_content)
  except PDFDataFormatError as err:
  basename = os.path.basename(filename)
  emsg = ("Could not open '%s' due to unsupported file format " + "or corrupted data. [%s]") % (