calphy 1.4.2__tar.gz → 1.4.3__tar.gz

{calphy-1.4.2/calphy.egg-info → calphy-1.4.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.2
+Version: 1.4.3
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.2 → calphy-1.4.3}/calphy/__init__.py

@@ -4,7 +4,7 @@ from calphy.solid import Solid
 from calphy.alchemy import Alchemy
 from calphy.routines import MeltingTemp
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 
 def addtest(a,b):
     return a+b

{calphy-1.4.2 → calphy-1.4.3}/calphy/input.py

@@ -48,7 +48,7 @@ from pyscal3.core import structure_dict, element_dict, _make_crystal
 from ase.io import read, write
 import shutil
 
-__version__ = "1.4.2"
+__version__ = "1.4.3"
 
 
 def _check_equal(val):

{calphy-1.4.2 → calphy-1.4.3}/calphy/phase_diagram.py

@@ -314,7 +314,10 @@ def prepare_inputs_for_phase_diagram(inputyamlfile, calculation_base_name=None):
 
         comps = phase['composition']
         reference_element = comps["reference_element"]
-        use_composition_scaling = bool(comps["use_composition_scaling"])
+        if "use_composition_scaling" in comps.keys():
+            use_composition_scaling = bool(comps["use_composition_scaling"])
+        else:
+            use_composition_scaling = True
         if str(phase_reference_state) == 'liquid':
             use_composition_scaling = False
 

{calphy-1.4.2 → calphy-1.4.3}/calphy/solid.py

@@ -299,7 +299,7 @@ class Solid(cph.Phase):
             lmp.command(f'pair_style {self.calc._pair_style_with_options[0]}')
 
         #set up structure
-        lmp = ph.create_structure(lmp, self.calc, species=self.calc.n_elements+self.calc._ghost_element_count)
+        lmp = ph.create_structure(lmp, self.calc)
 
         if self.calc.potential_file is None:
             lmp.command(f'pair_coeff {self.calc.pair_coeff[0]}')

{calphy-1.4.2 → calphy-1.4.3/calphy.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: calphy
-Version: 1.4.2
+Version: 1.4.3
 Summary: free energy calculation for python
 Home-page: https://github.com/ICAMS/calphy
 Author: Sarath Menon, Yury Lysogorskiy, Ralf Drautz

{calphy-1.4.2 → calphy-1.4.3}/calphy.egg-info/SOURCES.txt

@@ -28,6 +28,7 @@ calphy.egg-info/entry_points.txt
 calphy.egg-info/not-zip-safe
 calphy.egg-info/requires.txt
 calphy.egg-info/top_level.txt
+tests/test_ex07.py
 tests/test_helpers.py
 tests/test_integrators.py
 tests/test_options.py

{calphy-1.4.2 → calphy-1.4.3}/setup.py

@@ -53,7 +53,7 @@ setup(
     packages=find_packages(include=['calphy', 'calphy.*']),
     test_suite='tests',
     url='https://github.com/ICAMS/calphy',
-    version='1.4.2',
+    version='1.4.3',
     zip_safe=False,
     entry_points={
         'console_scripts': [

calphy-1.4.3/tests/test_ex07.py

@@ -0,0 +1,25 @@
+def test_ex07():
+    import calphy
+    from calphy.postprocessing import read_report
+
+# def test_example07_first_cell_runs():
+#     notebook_path = os.path.abspath(os.path.join(os.path.dirname(__file__), '../examples/example_07/analysis.ipynb'))
+
+#     with open(notebook_path, "r", encoding="utf-8") as f:
+#         nb = nbformat.read(f, as_version=4)
+
+#     # Filter just the first code cell
+#     first_code_cell = next((cell for cell in nb.cells if cell.cell_type == "code"), None)
+
+#     if not first_code_cell:
+#         pytest.fail("No code cell found in example07.ipynb")
+
+#     # Create a minimal notebook with only the first cell
+#     nb_single = nbformat.v4.new_notebook()
+#     nb_single.cells = [first_code_cell]
+
+#     try:
+#         client = NotebookClient(nb_single, timeout=60, kernel_name="pyiron")
+#         client.execute()
+#     except Exception as e:
+#         pytest.fail(f"First code cell in example07.analysis.ipynb failed: {e}")