Merge branch 'main' into texinfo

Author: Sparks29032

.pre-commit-config.yaml

@@ -22,7 +22,7 @@ repos:
     hooks:
       - id: black
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 6.1.0
     hooks:
       - id: flake8
   - repo: https://github.com/pycqa/isort

LICENSE.txt

@@ -1,7 +1,7 @@
 This program is part of the DiffPy open-source project at Columbia
 University and is available subject to the conditions and terms laid out below.
 
-Copyright © 2009-2019, Trustees of Columbia University in the City of New York,
+Copyright © 2009-2024, Trustees of Columbia University in the City of New York,
 all rights reserved.
 
 For more information please visit the diffpy web-page at http://diffpy.org or

README.rst

@@ -79,24 +79,18 @@ To create and activate a conda environment to use this software, run
 the following command from the command line ::
 	
 	conda create -n pdfmorph_env python=3 --yes
-	source activate pdfmorph_env
-
-If you're using Windows, replace ``source activate pdfmorph`` with 
-``activate pdfmorph_env``.
+	conda activate pdfmorph_env
 
 When you are finished with the session, exit the environment by running :: 
 
-	source deactivate pdfmorph_env
-
-or, on Windows, ``deactivate pdfmorph_env``.
+	conda deactivate pdfmorph_env
 
 For your future sessions with the application: Make sure to run the 
-``source activate pdfmorph_env`` or ``activate pdfmorph_env`` commands 
-from your command line beforehand to ensure access to the software.
+``conda activate pdfmorph_env`` command from your command line beforehand
+to ensure access to the software.
 
 Once in your desired conda environment, you can install from either the
-"diffpy" or "conda-forge" channels of Anaconda packages by running 
-either ::
+"conda-forge" channel of Anaconda packages by running ::
 
 	conda config --add channels conda-forge
 	conda install diffpy.pdfmorph
@@ -157,9 +151,9 @@ We welcome contributors from the community.  Please consider posting issues, and
 To ensure code quality and to prevent accidental commits into the default branch, please set up the use of our pre-commit
 hooks.
 
-1. Install pre-commit in your working environment by running ``conda install pre-commit``
+1. Install pre-commit in your working environment by running ``conda install pre-commit``.
 
-2. Initialize pre-commit (one time only) ``pre-commit install``
+2. Initialize pre-commit (one time only) ``pre-commit install``.
 
 Thereafter your code will be linted by black and isort and checked against flake8 before you can commit.
 If it fails by black or isort, just rerun and it should pass (black and isort will modify the files so should

doc/manual/source/conf.py

@@ -21,7 +21,7 @@
 
 project = "PDFmorph"
 project_full = "diffpy.pdfmorph"
-copyright = "2009-2019, Trustees of Columbia University in the City of New York, all rights reserved."
+copyright = "2009-2024, Trustees of Columbia University in the City of New York, all rights reserved"
 author = "Chris Farrow, Christopher J. Wright, Pavol Juhás, Chia-Hao (Timothy) Liu, S. Matthew Román, Simon J.L. Billinge"
 
 # The full version, including alpha/beta/rc tags

doc/manual/source/license.rst

@@ -5,7 +5,7 @@ This program is part of the DiffPy open-source project at Columbia
 University and is available subject to the conditions and terms laid out 
 below.
 
-Copyright © 2009-2019, Trustees of Columbia University in the City of 
+Copyright © 2009-2024, Trustees of Columbia University in the City of 
 New York, all rights reserved.
 
 For more information please visit the diffpy web-page at 

doc/manual/source/quickstart.rst

@@ -0,0 +1,8 @@
+Download Tutorial Files Here
+############################
+
+Quick start tutorial data:
+:download:`tutorialData.zip <../../../tutorial/tutorialData.zip>`
+
+Extra tutorial data:
+:download:`additionalData.zip <../../../tutorial/additionalData.zip>`

doc/manual/source/tutorialfiles.rst

@@ -249,7 +249,7 @@ def multiple_morph_output(
         header = "# Data generated by pdfmorph\n"
         header += f"# from morphing {morph_path_name}\n"
         header += f"# with target directory {target_path_name}"
-        reference_table = Path(save_directory).joinpath("Morph_Reference_Table.csv")
+        reference_table = Path(save_directory).joinpath("Morph_Reference_Table.txt")
         with open(reference_table, "w") as reference:
             print(f"{header}\n{inputs}\n{verbose_outputs}{table}", file=reference)
 

src/diffpy/pdfmorph/pdfmorph_io.py

@@ -53,7 +53,12 @@ def custom_error(self, msg):
                 "Use --help for help.",
             ]
         ),
-        epilog="Please report bugs to diffpy-dev@googlegroups.com.",
+        epilog="\n".join(
+            [
+                "Please report bugs to diffpy-users@googlegroups.com.",
+                "For more information, see the PDFmorph website at https://www.diffpy.org/diffpy.pdfmorph.",
+            ]
+        ),
     )
 
     parser.add_option("-V", "--version", action="version", help="Show program version and exit.")
@@ -90,65 +95,6 @@ def custom_error(self, msg):
  minimizing the residual.""",
     )
 
-    group = optparse.OptionGroup(
-        parser,
-        "Multiple Morphs",
-        """This program can morph a PDF against multiple targets in one command.
- See -s and Plot Options for how saving and plotting functionality changes when performing multiple morphs.""",
-    )
-    parser.add_option_group(group)
-    group.add_option(
-        "--multiple",
-        dest="multiple",
-        action="store_true",
-        help=f"""Changes usage to \'{prog_short} [options] FILE DIRECTORY\'. FILE
- will be morphed with each file in DIRECTORY as target.
- Files in DIRECTORY are sorted by alphabetical order unless a field is
- specified by --sort-by.""",
-    )
-    group.add_option(
-        "--sort-by",
-        metavar="FIELD",
-        dest="field",
-        help="""Used with --multiple to sort files in DIRECTORY by FIELD from lowest to highest.
- FIELD must be included in the header of all the PDF files.""",
-    )
-    group.add_option(
-        "--reverse",
-        dest="reverse",
-        action="store_true",
-        help="""Sort from highest to lowest instead.""",
-    )
-    group.add_option(
-        "--serial-file",
-        metavar="SERIALFILE",
-        dest="serfile",
-        help="""Look for FIELD in a serial file instead.
- Must specify name of serial file SERIALFILE.""",
-    )
-    group.add_option(
-        "--save-names-file",
-        metavar="NAMESFILE",
-        dest="snamesfile",
-        help=f"""Used when both -s and --multiple are enabled.
- Specify names for each manipulated PDF when saving (see -s) using a serial file
- NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
- is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
- whose value specifies the name to save the manipulated PDF as.
-(See sample names files in the PDFmorph tutorial).""",
-    )
-    group.add_option(
-        "--plot-parameter",
-        metavar="PLOTPARAM",
-        dest="plotparam",
-        help="""Used when both plotting and --multiple are enabled.
- Choose a PLOTPARAM to plot for each morph (i.e. adding --pp=Pearson means the program
- will display a plot of the Pearson correlation coefficient for each morph-target pair).
- PLOTPARAM is not case sensitive, so both Pearson and pearson indicate the same parameter.
- When PLOTPARAM is not specified, Rw values for each morph-target pair will be plotted.
- PLOTPARAM will be displayed as the vertical axis label for the plot.""",
-    )
-
     # Manipulations
     group = optparse.OptionGroup(
         parser,
@@ -199,7 +145,7 @@ def custom_error(self, msg):
         "--qdamp",
         type="float",
         metavar="QDAMP",
-        help="Dampen PDF by a factor QDAMP. (See PDFGui manual.)",
+        help="Dampen PDF by a factor QDAMP.",
     )
     group.add_option(
         "--radius",
@@ -255,20 +201,82 @@ def custom_error(self, msg):
         "--mlabel",
         metavar="MLABEL",
         dest="mlabel",
-        help="Set label for morphed data to MLABEL on plot. Ignored if using file names as labels.",
+        help="Set label for morphed data to MLABEL on plot. Default label is FILE1.",
     )
     group.add_option(
         "--tlabel",
         metavar="TLABEL",
         dest="tlabel",
-        help="Set label for target data to TLABEL on plot. Ignored if using file names as labels.",
+        help="Set label for target data to TLABEL on plot. Default label is FILE2.",
     )
     group.add_option("--pmin", type="float", help="Minimum r-value to plot. Defaults to RMIN.")
     group.add_option("--pmax", type="float", help="Maximum r-value to plot. Defaults to RMAX.")
-    group.add_option("--maglim", type="float", help="Magnify plot curves beyond MAGLIM by MAG.")
-    group.add_option("--mag", type="float", help="Magnify plot curves beyond MAGLIM by MAG.")
+    group.add_option("--maglim", type="float", help="Magnify plot curves beyond r=MAGLIM by MAG.")
+    group.add_option("--mag", type="float", help="Magnify plot curves beyond r=MAGLIM by MAG.")
     group.add_option("--lwidth", type="float", help="Line thickness of plotted curves.")
 
+    # Multiple morph options
+    group = optparse.OptionGroup(
+        parser,
+        "Multiple Morphs",
+        """This program can morph a PDF against multiple targets in one command.
+ See -s and Plot Options for how saving and plotting functionality changes when performing multiple morphs.""",
+    )
+    parser.add_option_group(group)
+    group.add_option(
+        "--multiple",
+        dest="multiple",
+        action="store_true",
+        help=f"""Changes usage to \'{prog_short} [options] FILE DIRECTORY\'. FILE
+ will be morphed with each file in DIRECTORY as target.
+ Files in DIRECTORY are sorted by alphabetical order unless a field is
+ specified by --sort-by.""",
+    )
+    group.add_option(
+        "--sort-by",
+        metavar="FIELD",
+        dest="field",
+        help="""Used with --multiple to sort files in DIRECTORY by FIELD.
+ If the FIELD being used has a numerical value, sort from lowest to highest.
+ Otherwise, sort in ASCII sort order.
+ FIELD must be included in the header of all the PDF files.""",
+    )
+    group.add_option(
+        "--reverse",
+        dest="reverse",
+        action="store_true",
+        help="""Sort from highest to lowest instead.""",
+    )
+    group.add_option(
+        "--serial-file",
+        metavar="SERIALFILE",
+        dest="serfile",
+        help="""Look for FIELD in a serial file instead.
+ Must specify name of serial file SERIALFILE.""",
+    )
+    group.add_option(
+        "--save-names-file",
+        metavar="NAMESFILE",
+        dest="snamesfile",
+        help=f"""Used when both -s and --multiple are enabled.
+ Specify names for each manipulated PDF when saving (see -s) using a serial file
+ NAMESFILE. The format of NAMESFILE should be as follows: each target PDF
+ is an entry in NAMESFILE. For each entry, there should be a key {__save_morph_as__}
+ whose value specifies the name to save the manipulated PDF as. An example .json
+ serial file is shown in the PDFmorph manual.""",
+    )
+    group.add_option(
+        "--plot-parameter",
+        metavar="PLOTPARAM",
+        dest="plotparam",
+        help="""Used when both plotting and --multiple are enabled.
+ Choose a PLOTPARAM to plot for each morph (i.e. adding --plot-parameter=Pearson means the
+ program will display a plot of the Pearson correlation coefficient for each morph-target
+ pair). PLOTPARAM is not case sensitive, so both Pearson and pearson indicate the same
+ parameter. When PLOTPARAM is not specified, Rw values for each morph-target pair will be
+ plotted. PLOTPARAM will be displayed as the vertical axis label for the plot.""",
+    )
+
     # Defaults
     parser.set_defaults(multiple=False)
     parser.set_defaults(reverse=False)
@@ -330,10 +338,11 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
         chain.append(helpers.TransformXtalRDFtoPDF())
         refpars.append("smear")
         config["smear"] = opts.smear
+        # Set baselineslope if not given
         config["baselineslope"] = opts.baselineslope
         if opts.baselineslope is None:
-            refpars.append("baselineslope")
             config["baselineslope"] = -0.5
+        refpars.append("baselineslope")
     # Size
     radii = [opts.radius, opts.pradius]
     nrad = 2 - radii.count(None)
@@ -370,8 +379,7 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
 
     # Now remove non-refinable parameters
     if opts.exclude is not None:
-        refpars = set(refpars) - set(opts.exclude)
-        refpars = list(refpars)
+        refpars = list(set(refpars) - set(opts.exclude))
 
     # Refine or execute the morph
     refiner = refine.Refiner(chain, x_morph, y_morph, x_target, y_target)
@@ -387,12 +395,15 @@ def single_morph(parser, opts, pargs, stdout_flag=True):
                 if "scale" in refpars:
                     rptemp.append("scale")
                 refiner.refine(*rptemp)
+            # Adjust all parameters
             refiner.refine(*refpars)
         except ValueError as e:
             parser.custom_error(str(e))
-    elif "smear" in refpars and opts.baselineslope is None:
+    # Smear is not being refined, but baselineslope needs to refined to apply smear
+    # Note that baselineslope is only added to the refine list if smear is applied
+    elif "baselineslope" in refpars:
         try:
-            refiner.refine("baselineslope", baselineslope=-0.5)
+            refiner.refine("baselineslope", baselineslope=config["baselineslope"])
         except ValueError as e:
             parser.custom_error(str(e))
     else:
@@ -475,8 +486,13 @@ def multiple_morphs(parser, opts, pargs, stdout_flag=True):
     if not target_directory.is_dir():
         parser.custom_error(f"{target_directory} is not a directory. Go to --help for usage.")
 
-    # Do not morph morph_file against itself if it is in the same directory
+    # Get list of files from target directory
     target_list = list(target_directory.iterdir())
+    for target in target_list:
+        if target.is_dir():
+            target_list.remove(target)
+
+    # Do not morph morph_file against itself if it is in the same directory
     if morph_file in target_list:
         target_list.remove(morph_file)
 

src/diffpy/pdfmorph/pdfmorphapp.py

@@ -114,14 +114,14 @@ def refine(self, *args, **kw):
             return 0.0
 
         initial = [config[p] for p in self.pars]
-        out = leastsq(self.residual, initial, full_output=1)
-        fvec = out[2]["fvec"]
-        if out[4] not in (1, 2, 3, 4):
-            mesg = out[3]
-            raise ValueError(mesg)
+        sol, cov_sol, infodict, emesg, ier = leastsq(self.residual, initial, full_output=1)
+        fvec = infodict["fvec"]
+        if ier not in (1, 2, 3, 4):
+            emesg
+            raise ValueError(emesg)
 
         # Place the fit parameters in config
-        vals = out[0]
+        vals = sol
         if not hasattr(vals, "__iter__"):
             vals = [vals]
         self.chain.config.update(zip(self.pars, vals))