Fix bugs to run tutorial CLI, update python, matplotlib API (#137)

* Add entry point to srmise app

* Create entry-point-.rst

* Fix abbreviation for image 1

* Evaluate method only after option is true

* Fix matplotlib depreciate for inv_transform

* Remove unnecessary check for lenght

* Read .gr file, convert to utf-8:

* Add fix api bug news

* Apply pre-commit

* Remove print func

* Properly compare parameters, using a list

Author: bobleesj

Diff for: 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

Diff for: 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>

Diff for: 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>

Diff for: 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)

Diff for: 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:

Diff for: 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])
 

Diff for: 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."

Diff for: 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]") % (