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

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

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: diffpy.apps
-Version: 0.2.0rc0
+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/

{diffpy_apps-0.2.0rc0 → 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"

diffpy_apps-0.2.0rc1/src/diffpy/__init__.py

@@ -0,0 +1,14 @@
+#!/usr/bin/env python
+##############################################################################
+#
+# (c) 2026 diffpy.apps contributors.
+# All rights reserved.
+#
+# File coded by: Billinge Group members and community contributors.
+#
+# See GitHub contributions for a more detailed list of contributors.
+# https://github.com/diffpy/diffpy.apps/graphs/contributors
+#
+# See LICENSE.rst for license information.
+#
+##############################################################################

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

@@ -202,7 +202,6 @@ class PDFAdapter:
         delta1 and delta2 variables, and structure parameters
         constrained by the space group.
         """
-
         recipe = FitRecipe()
         recipe.add_contribution(self.contribution)
         qdamp = recipe.create_new_variable("qdamp", fixed=False, value=0.04)

{diffpy_apps-0.2.0rc0 → diffpy_apps-0.2.0rc1}/src/diffpy/apps/refinebase/parametric_model.py

@@ -199,8 +199,7 @@ class ParametricModelEquation(ParametricModel):
 
 class ParametricModelFunction(ParametricModel):
     def __init__(self, name, function, argnames=None):
-        """
-        Initialize a ParametricModelFunction instance.
+        """Initialize a ParametricModelFunction instance.
 
         function can be either a callable or a string representing
         the pre-defined function.
@@ -254,8 +253,7 @@ class ParametricModelPDF(ParametricModel):
         finite=False,
         run_parallel=True,
     ):
-        """
-        Create a ParametricModelPDF instance from a structure object.
+        """Create a ParametricModelPDF instance from a structure object.
 
         structure can be a raw diffpy.structure/pyobjcryst structure, or
         an existing DiffpyStructureParSet/ObjCrystCrystalParSet phase
@@ -615,10 +613,11 @@ def create_pdf_model_from_code(
     finite=False,
     run_parallel=True,
 ):
-    """Create a ParametricModelPDF by executing code that builds a structure.
+    """Create a ParametricModelPDF by executing code that builds a
+    structure.
 
-    The code must assign the structure/crystal object to a variable named
-    structure_name (default "structure") in its local namespace.
+    The code must assign the structure/crystal object to a variable
+    named structure_name (default "structure") in its local namespace.
     """
     local_namespace = {}
     exec(code, global_namespace, local_namespace)

{diffpy_apps-0.2.0rc0 → diffpy_apps-0.2.0rc1}/src/diffpy/apps/refinebase/refinement_server.py

@@ -102,7 +102,8 @@ async def set_profile_calculation_range(
     xmax: Annotated[float, "End of the calculation range"] = None,
     dx: Annotated[float, "Step size for the calculation range"] = None,
 ) -> str:
-    """Set the calculation range for a profile in the refinement session."""
+    """Set the calculation range for a profile in the refinement
+    session."""
     session.set_profile_calculation_range(
         profile_name, xmin=xmin, xmax=xmax, dx=dx
     )
@@ -191,8 +192,8 @@ async def add_pdf_model(
         bool, "Whether to run the PDF model in parallel"
     ] = True,
 ) -> str:
-    """
-    Add a structure-file-based parametric model to the refinement session.
+    """Add a structure-file-based parametric model to the refinement
+    session.
 
     Parameters
     ----------
@@ -247,8 +248,7 @@ async def add_function_model(
         list[str] | None, "Argument names for the function"
     ] = None,
 ) -> str:
-    """
-    Add a function model to the refinement session.
+    """Add a function model to the refinement session.
 
     function can be either a callable or a string representing
     the pre-defined function.
@@ -282,7 +282,8 @@ async def set_model_equation(
     model_name: Annotated[str, "Name of the parametric model"],
     equation: Annotated[str, "New equation for the parametric model"],
 ) -> str:
-    """Set the equation for an existing parametric model in the session."""
+    """Set the equation for an existing parametric model in the
+    session."""
     session.set_model_equation(model_name=model_name, equation=equation)
     return f"Equation for model {model_name} set successfully."
 
@@ -339,7 +340,8 @@ async def set_model_profile(
     model_name: Annotated[str, "Name of the parametric model"],
     profile_name: Annotated[str, "Name of the profile to set on the model"],
 ) -> str:
-    """Set the profile for a parametric model in the refinement session."""
+    """Set the profile for a parametric model in the refinement
+    session."""
     session.set_model_profile(model_name, profile_name)
     return f"Profile {profile_name} set for model {model_name} successfully."
 
@@ -365,7 +367,8 @@ async def get_profile_data(
     profile_name: Annotated[str, "Name of the profile to retrieve"],
     data_path: Annotated[str, "Path to the data to retrieve"],
 ) -> str:
-    """Get the details of a specific profile in the refinement session."""
+    """Get the details of a specific profile in the refinement
+    session."""
     profile = session.profiles_dict[profile_name]
     data = {"xobs": profile.xobs.tolist(), "yobs": profile.yobs.tolist()}
     with open(data_path, "w") as f:
@@ -395,8 +398,8 @@ async def constrain_pdf_model_space_group_symmetry(
 ) -> str:
     """Constrain a parametric model to a specific space group symmetry.
 
-    If no space group is provided, the model will be constrained to
-    its current space group parsed from its structure.
+    If no space group is provided, the model will be constrained to its
+    current space group parsed from its structure.
     """
     session.constrain_pdf_model_space_group_symmetry(model_name, space_group)
     return (
@@ -428,9 +431,8 @@ async def combine_models(
         list[str], "Names of the child parametric models"
     ],
 ) -> str:
-    """
-    Combine two parametric models by registering the child to the parent model.
-    """
+    """Combine two parametric models by registering the child to the
+    parent model."""
     session.combine_models(parent_model_name, child_model_names)
     return (
         f"Models {parent_model_name} and "
@@ -445,9 +447,7 @@ async def set_variables_value(
         dict, "Mapping of variable names to the values to set them to"
     ],
 ) -> str:
-    """
-    Set the value of a specific variable in a parametric model.
-    """
+    """Set the value of a specific variable in a parametric model."""
     session.set_variables_value(name_value_dict)
 
     return f"Variables '{name_value_dict}' are set."
@@ -458,9 +458,7 @@ async def set_variables_value(
 async def get_variable(
     variable_name: Annotated[str, "Name of the variable"],
 ) -> str:
-    """
-    Get the value of a specific variable in a parametric model.
-    """
+    """Get the value of a specific variable in a parametric model."""
     variable = session.get_variable(variable_name)
     return f"Variable '{variable_name}': {variable['value']}"
 
@@ -473,9 +471,7 @@ async def list_model_parameters(
         bool, "Whether to list only independent parameters"
     ] = True,
 ) -> str:
-    """
-    List all parameters of a specific parametric model.
-    """
+    """List all parameters of a specific parametric model."""
     if model_name not in session.models_dict:
         raise ValueError(f"Model with ID {model_name} does not exist.")
 
@@ -495,9 +491,7 @@ async def list_model_parameters(
 @mcp.tool()
 @tool_errors
 async def clear() -> str:
-    """
-    Clear the current refinement session.
-    """
+    """Clear the current refinement session."""
     session.clear()
     return "Refinement session cleared successfully."
 
@@ -507,9 +501,7 @@ async def clear() -> str:
 async def list_recipe_parameters(
     recipe_name: Annotated[str, "Name of the recipe"],
 ) -> str:
-    """
-    List all parameters of a specific recipe.
-    """
+    """List all parameters of a specific recipe."""
     if recipe_name not in session.recipes_dict:
         raise ValueError(f"Recipe with ID {recipe_name} does not exist.")
 
@@ -552,8 +544,8 @@ async def solve(
         bool, "Whether to also include sgpars from the models automatically"
     ] = False,
 ) -> str:
-    """
-    Initiate a refinement using the specified profiles, models, and variables.
+    """Initiate a refinement using the specified profiles, models, and
+    variables.
 
     Parameters
     ----------

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

@@ -1,9 +1,9 @@
 Metadata-Version: 2.4
 Name: diffpy.apps
-Version: 0.2.0rc0
+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/

{diffpy_apps-0.2.0rc0 → diffpy_apps-0.2.0rc1}/tests/test_agentify.py

@@ -28,7 +28,7 @@ pytestmark = pytest.mark.skipif(
                 update=False,
             ),
             "cwd",
-            ".claude/skills/cmi-skill",
+            ".claude/skills/diffpy-playbook",
         ),
         # C2: diffpy.apps agentify --system
         #   Deploys system claude skill.
@@ -40,7 +40,7 @@ pytestmark = pytest.mark.skipif(
                 update=False,
             ),
             "home",
-            ".claude/skills/cmi-skill",
+            ".claude/skills/diffpy-playbook",
         ),
         # C3: diffpy.apps agentify --agent codex
         #   Deploys workspace codex skill.
@@ -52,7 +52,7 @@ pytestmark = pytest.mark.skipif(
                 update=False,
             ),
             "cwd",
-            ".codex/skills/cmi-skill",
+            ".codex/skills/diffpy-playbook",
         ),
         # C4: diffpy.apps agentify --agent codex --system
         #   Deploys system codex skill.
@@ -64,7 +64,7 @@ pytestmark = pytest.mark.skipif(
                 update=False,
             ),
             "home",
-            ".codex/skills/cmi-skill",
+            ".codex/skills/diffpy-playbook",
         ),
     ],
 )
@@ -94,14 +94,17 @@ def test_agentify_update():
                 update=False,
             )
             agentify(args)
-            skill_path = Path(tmp) / "cwd" / ".claude" / "skills" / "cmi-skill"
+            skill_path = (
+                Path(tmp) / "cwd" / ".claude" / "skills" / "diffpy-playbook"
+            )
             assert skill_path.exists()
             args.update = True
             agentify(args)
             pytest.raises(
                 FileExistsError,
                 match=re.escape(
-                    f"Agentic skill cmi-skill already exists at {skill_path}. "
+                    "Agentic skill diffpy-playbook already exists at "
+                    f"{skill_path}. "
                     "To overwrite, pass '--update' flag to update the skill"
                 ),
             )