chore: update the dependency to pass matrix tests

cookiecutter.json

@@ -13,7 +13,7 @@
   "package_dir_name": "diffpy.apps",
   "project_short_description": "User applications to help with tasks using diffpy packages",
   "project_keywords": "diffraction, PDF, X-ray, neutron",
-  "minimum_supported_python_version": "3.11",
+  "minimum_supported_python_version": "3.12",
   "maximum_supported_python_version": "3.13",
   "project_needs_c_code_compiled": "No",
   "project_has_gui_tests": "No"

news/fix-matrix.rst

@@ -0,0 +1,23 @@
+**Added:**
+
+* No news added: Fix the dependency to pass matrix-and-codecov tests
+
+**Changed:**
+
+* <news item>
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>

pyproject.toml

@@ -15,7 +15,7 @@ maintainers = [
 description = "User applications to help with tasks using diffpy packages"
 keywords = ['diffraction', 'PDF', 'X-ray', 'neutron']
 readme = "README.rst"
-requires-python = ">=3.11, <3.14"
+requires-python = ">=3.12, <3.14"
 classifiers = [
         'Development Status :: 5 - Production/Stable',
         'Environment :: Console',
@@ -25,7 +25,6 @@ classifiers = [
         'Operating System :: Microsoft :: Windows',
         'Operating System :: POSIX',
         'Operating System :: Unix',
-        'Programming Language :: Python :: 3.11',
         'Programming Language :: Python :: 3.12',
         'Programming Language :: Python :: 3.13',
         'Topic :: Scientific/Engineering :: Physics',

requirements/conda.txt

@@ -1,10 +1,10 @@
+diffpy.cmi
+diffpy.srfit >=3.4.0
+diffpy.srreal
 numpy
 scipy
-psutil
 textx
+psutil
 pyyaml
-diffpy.srfit
-diffpy.srreal
-diffpy.structure
 networkx
 mcp

tests/test_agentify.py

@@ -82,16 +82,14 @@ def test_agentify_update(mock_clone_skills):
         Path(tmp) / "cwd_dir" / ".claude" / "skills" / "diffpy-playbook"
     )
     assert skill_path.exists()
-    args.update = True
-    agentify(args)
-    pytest.raises(
-        FileExistsError,
+    with pytest.warns(
+        UserWarning,
         match=re.escape(
-            "Agentic skill diffpy-playbook already exists at "
-            f"{skill_path}. "
-            "To overwrite, pass '--update' flag to update the skill"
+            f"Skill at {skill_path} already exists. "
+            "Use '--update' flag to overwrite."
         ),
-    )
+    ):
+        agentify(args)
     # C2: Deploy again with --update flag when skill already exists
     #  with a dummy file in the skill directory.
     #  Expect no error to be raised, and the skill is updated.