Merge pull request #270 from thomas-rocke/DislFixes

MAINT: Upper bound numpy version <2.0.0

docs/Makefile

@@ -52,7 +52,7 @@ clean:
 	rm -rf $(BUILDDIR)/*
 
 html:
-	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	$(SPHINXBUILD) --show-traceback -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
 

docs/conf.py

@@ -284,7 +284,8 @@
 # Raise Error (not default Warning) when a notebook execution fails
 # (due to code error, timeout, etc.)
 nb_execution_raise_on_error = True
-nb_execution_timeout = 60
+nb_execution_show_tb = True
+nb_execution_timeout = 90
 
 # -- Extension configuration -------------------------------------------------
 

matscipy/calculators/eam/io.py

@@ -148,11 +148,11 @@ def read_eam(eam_file, kind="eam/alloy"):
     supported_kinds = ["eam", "eam/alloy", "eam/fs"]
     if kind not in supported_kinds: 
         raise ValueError(f"EAM kind {kind} not supported")
-    with open(eam_file, 'r') as file:
-        eam = file.readlines()
+    # with open(eam_file, 'r', encoding='utf-8') as file:
+    #     eam = file.readlines()
 
     if kind == "eam":
-        with open(eam_file, 'r') as file:
+        with open(eam_file, 'r', encoding='utf-8') as file:
             # ignore comment characters on first line but strip them from subsequent lines
             lines = [file.readline()]
             lines.extend(_strip_comments_from_line(line) for line in file.readlines())
@@ -216,7 +216,7 @@ def read_eam(eam_file, kind="eam/alloy"):
 
     if kind in ["eam/alloy", "eam/fs"]:
         """eam/alloy and eam/fs have almost the same structure, except for the electron density section"""
-        with open(eam_file, 'r') as file:
+        with open(eam_file, 'r', encoding='utf-8') as file:
             # ignore comment characters on first line but strip them from subsequent lines
             lines = [file.readline() for _ in range(3)]
             lines.extend(_strip_comments_from_line(line) for line in file.readlines())

matscipy/dislocation.py

@@ -3493,6 +3493,7 @@ def inf_line_transform(p, z_max):
             # Start by translating by z_max (periodicity) such that there are points below the cell
             n = np.ceil(np.min(p[:, 2]) / z_max)
             p_off = n * z_max
+            p = np.copy(p) # Needed as sphinx-build/myst_nb was making `p` read-only for some reason.
             p[:, 2] -= p_off
 
             # Now start from the point with negative z closest to z=0
@@ -4064,7 +4065,7 @@ def build_cylinder(self,
         bulk, disloc, core_positions, cyl_mask, fix_mask = self._build_bulk_cyl(radius, core_positions, fix_width, extension,
                                                             fixed_points, self_consistent, method, verbose, cyl_mask=cyl_mask, **kwargs)
 
-        if partial_distance > 0:
+        if not np.allclose(core_positions[0, :], core_positions[1, :]):
             # Specify left & right dislocation separately
             disloc.info["core_positions"] = [list(core_positions[0, :]), list(core_positions[1, :])]
             disloc.info["burgers_vectors"] = [list(self.left_dislocation.burgers), list(self.right_dislocation.burgers)]

pyproject.toml

@@ -24,7 +24,7 @@ classifiers = [
 requires-python = ">=3.8.0"
 dynamic = ["version"]
 dependencies = [
-    "numpy>=1.16.0",
+    "numpy>=1.16.0, <2.0.0",
     "scipy>=1.2.3",
     "ase>=3.23.0",
     "packaging"
@@ -35,22 +35,24 @@ test = [
     "pytest",
     "pytest-subtests",
     "pytest-timeout",
-    "sympy",
-    "atomman",
-    "ovito"
+    "matscipy[dislocation]",
+    "sympy"
+]
+dislocation = [
+    "nglview==3.0.8",  # resolves https://github.com/libAtoms/matscipy/issues/222
+    "ovito",
+    "atomman"
 ]
 docs = [
+    "matscipy[dislocation]",
     "sphinx",
     "myst_nb",
     "numpydoc",
-    "atomman",
-    "ovito",
     "sphinx_copybutton",
     "sphinx_rtd_theme",
     "sphinxcontrib-spelling",
     "pydata-sphinx-theme",
-    "jupytext",
-    "nglview==3.0.8"  # resolves https://github.com/libAtoms/matscipy/issues/222
+    "jupytext"
 ]
 cli = [
     "argcomplete"