diffpy.apps 0.1.1rc0__tar.gz → 0.2.0rc1__tar.gz

{diffpy_apps-0.1.1rc0/src/diffpy.apps.egg-info → diffpy_apps-0.2.0rc1}/PKG-INFO

@@ -1,9 +1,10 @@
 Metadata-Version: 2.4
 Name: diffpy.apps
-Version: 0.1.1rc0
+Version: 0.2.0rc1
 Summary: User applications to help with tasks using diffpy packages
-Author-email: Yuchen Xiao <yx2924@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
-Maintainer-email: Yuchen Xiao <yx2924@columbia.edu>, Simon Billinge <sbillinge@ucsb.edu>
+Author-email: Yuchen Xiao <xiaoyuch@msu.edu>, Simon Billinge <sbillinge@ucsb.edu>
+Maintainer-email: Simon Billinge <sbillinge@ucsb.edu>
+License-Expression: BSD-3-Clause
 Project-URL: Homepage, https://github.com/diffpy/diffpy.apps/
 Project-URL: Issues, https://github.com/diffpy/diffpy.apps/issues/
 Keywords: diffraction,PDF,X-ray,neutron
@@ -11,7 +12,6 @@ Classifier: Development Status :: 5 - Production/Stable
 Classifier: Environment :: Console
 Classifier: Intended Audience :: Developers
 Classifier: Intended Audience :: Science/Research
-Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: MacOS :: MacOS X
 Classifier: Operating System :: Microsoft :: Windows
 Classifier: Operating System :: POSIX
@@ -71,6 +71,7 @@ contains
 
 - `runmacro`: A runner for DiffPy macro files.
 - `agentify`: A deployer for diffpy.cmi agentic skills.
+- `Diffpy MCP server`: A local server for the DiffPy MCP instance.
 
 For more information about the diffpy.apps library, please consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_.
 

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/README.rst

@@ -41,6 +41,7 @@ contains
 
 - `runmacro`: A runner for DiffPy macro files.
 - `agentify`: A deployer for diffpy.cmi agentic skills.
+- `Diffpy MCP server`: A local server for the DiffPy MCP instance.
 
 For more information about the diffpy.apps library, please consult our `online documentation <https://diffpy.github.io/diffpy.apps>`_.
 

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/pyproject.toml

@@ -6,11 +6,10 @@ build-backend = "setuptools.build_meta"
 name = "diffpy.apps"
 dynamic=['version', 'dependencies']
 authors = [
-  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
+  {name='Yuchen Xiao', email='xiaoyuch@msu.edu'},
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 maintainers = [
-  {name='Yuchen Xiao', email='yx2924@columbia.edu'},
   {name='Simon Billinge', email='sbillinge@ucsb.edu'},
 ]
 description = "User applications to help with tasks using diffpy packages"
@@ -22,7 +21,6 @@ classifiers = [
         'Environment :: Console',
         'Intended Audience :: Developers',
         'Intended Audience :: Science/Research',
-        'License :: OSI Approved :: BSD License',
         'Operating System :: MacOS :: MacOS X',
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
@@ -33,6 +31,7 @@ classifiers = [
         'Topic :: Scientific/Engineering :: Physics',
         'Topic :: Scientific/Engineering :: Chemistry',
 ]
+license = "BSD-3-Clause"
 
 [project.urls]
 Homepage = "https://github.com/diffpy/diffpy.apps/"

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/requirements/conda.txt

@@ -6,3 +6,7 @@ pyyaml
 diffpy.srfit
 diffpy.srreal
 diffpy.structure
+networkx
+mcp[cli]
+mp-api
+pymatgen

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/src/diffpy/__init__.py

@@ -1,7 +1,7 @@
 #!/usr/bin/env python
 ##############################################################################
 #
-# (c) 2026 The Trustees of Columbia University in the City of New York.
+# (c) 2026 diffpy.apps contributors.
 # All rights reserved.
 #
 # File coded by: Billinge Group members and community contributors.

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/src/diffpy/apps/app_agentify.py

@@ -2,10 +2,10 @@ import shutil
 import socket
 import subprocess
 import tempfile
+import warnings
 from pathlib import Path
 
 REPO_URL = "https://github.com/diffpy/cmi-agent-skills"
-DIR_NAME = "cmi-skill"
 
 
 def ensure_setup():
@@ -35,21 +35,31 @@ def agentify(args):
     elif agent == "codex":
         skills_dir = ".codex/skills"
     if system_flag:
-        destination = Path().home() / skills_dir / DIR_NAME
+        dest_dir = Path().home() / skills_dir
     else:
-        destination = Path().cwd() / skills_dir / DIR_NAME
-    if destination.exists() and not args.update:
-        raise FileExistsError(
-            f"Agentic skill {DIR_NAME} already exists at {destination}. "
-            "To overwrite, pass '--update' flag to update the skill"
-        )
+        dest_dir = Path().cwd() / skills_dir
     with tempfile.TemporaryDirectory() as tmp:
         tmp_path = Path(tmp)
         subprocess.run(
             ["git", "clone", REPO_URL, str(tmp_path)],
             check=True,
         )
-        if destination.exists():
-            shutil.rmtree(destination)
-        shutil.copytree(tmp_path / DIR_NAME, destination, dirs_exist_ok=True)
-    print(f"Agentic skill {DIR_NAME} has been deployed to {destination}")
+        for item in tmp_path.iterdir():
+            if item.is_dir():
+                destination = dest_dir / item.name
+                if destination.exists():
+                    if args.update:
+                        shutil.rmtree(destination)
+                        shutil.copytree(item, destination, dirs_exist_ok=True)
+                        print(f"Updated existing skill at {destination}")
+                    else:
+                        warnings.warn(
+                            f"Skill at {destination} already exists. "
+                            "Use '--update' flag to overwrite."
+                        )
+                        continue
+                else:
+                    shutil.copytree(item, destination, dirs_exist_ok=True)
+                    print(
+                        f"Skill {item.name} has been deployed to {destination}"
+                    )

{diffpy_apps-0.1.1rc0 → diffpy_apps-0.2.0rc1}/src/diffpy/apps/pdfadapter.py

@@ -65,8 +65,8 @@ class PDFAdapter:
         """
         profile = Profile()
         parser = PDFParser()
-        parser.parseString(Path(profile_path).read_text())
-        profile.loadParsedData(parser)
+        parser.parse_file(profile_path)
+        profile.load_parsed_data(parser)
         if q_range is not None:
             profile.meta["qmin"] = q_range[0]
             profile.meta["qmax"] = q_range[1]
@@ -77,7 +77,7 @@ class PDFAdapter:
                     "xmax": calculation_range[1],
                     "dx": calculation_range[2],
                 }
-            profile.setCalculationRange(**calculation_range)
+            profile.set_calculation_range(**calculation_range)
         self.profile = profile
 
     def initialize_structures(
@@ -185,10 +185,10 @@ class PDFAdapter:
         """
         equation = equation[0] if equation is not None else None
         contribution = FitContribution("pdfcontribution")
-        contribution.setProfile(self.profile)
+        contribution.set_profile(self.profile)
         for pdfgenerator in self.pdfgenerators:
-            contribution.addProfileGenerator(pdfgenerator)
-        contribution.setEquation(equation)
+            contribution.add_profile_generator(pdfgenerator)
+        contribution.set_equation(equation)
         self.contribution = contribution
         return self.contribution
 
@@ -202,11 +202,10 @@ class PDFAdapter:
         delta1 and delta2 variables, and structure parameters
         constrained by the space group.
         """
-
         recipe = FitRecipe()
-        recipe.addContribution(self.contribution)
-        qdamp = recipe.newVar("qdamp", fixed=False, value=0.04)
-        qbroad = recipe.newVar("qbroad", fixed=False, value=0.02)
+        recipe.add_contribution(self.contribution)
+        qdamp = recipe.create_new_variable("qdamp", fixed=False, value=0.04)
+        qbroad = recipe.create_new_variable("qbroad", fixed=False, value=0.02)
         for i, (pdfgenerator, spacegroup) in enumerate(
             zip(self.pdfgenerators, self.spacegroups)
         ):
@@ -215,23 +214,23 @@ class PDFAdapter:
                 "delta2",
             ]:
                 par = getattr(pdfgenerator, pname)
-                recipe.addVar(
+                recipe.add_variable(
                     par, name=f"{pdfgenerator.name}_{pname}", fixed=False
                 )
-            recipe.constrain(pdfgenerator.qdamp, qdamp)
-            recipe.constrain(pdfgenerator.qbroad, qbroad)
+            recipe.add_constraint(pdfgenerator.qdamp, qdamp)
+            recipe.add_constraint(pdfgenerator.qbroad, qbroad)
             stru_parset = pdfgenerator.phase
             spacegroupparams = constrainAsSpaceGroup(stru_parset, spacegroup)
             for par in spacegroupparams.xyzpars:
-                recipe.addVar(
+                recipe.add_variable(
                     par, name=f"{pdfgenerator.name}_{par.name}", fixed=False
                 )
             for par in spacegroupparams.latpars:
-                recipe.addVar(
+                recipe.add_variable(
                     par, name=f"{pdfgenerator.name}_{par.name}", fixed=False
                 )
             for par in spacegroupparams.adppars:
-                recipe.addVar(
+                recipe.add_variable(
                     par, name=f"{pdfgenerator.name}_{par.name}", fixed=False
                 )
         recipe.fithooks[0].verbose = 0
@@ -247,7 +246,7 @@ class PDFAdapter:
             e.g. 's0' for scale factor.
         """
         for var_name in variable_names:
-            self.recipe.addVar(
+            self.recipe.add_variable(
                 getattr(self.contribution, var_name),
                 name=var_name,
                 fixed=False,
@@ -275,7 +274,7 @@ class PDFAdapter:
             Mapping from recipe variable names to new values.
         """
         for vname, vvalue in variable_name_to_value.items():
-            self.recipe._parameters[vname].setValue(vvalue)
+            self.recipe._parameters[vname].set_value(vvalue)
 
     def get_results(self):
         """Return the current fit results as a JSON-compatible