ratapi 0.0.0.dev9__tar.gz → 0.0.0.dev11__tar.gz

{ratapi-0.0.0.dev9/ratapi.egg-info → ratapi-0.0.0.dev11}/PKG-INFO

@@ -1,10 +1,9 @@
 Metadata-Version: 2.1
 Name: ratapi
-Version: 0.0.0.dev9
+Version: 0.0.0.dev11
 Summary: Python extension for the Reflectivity Analysis Toolbox (RAT)
-Home-page: https://github.com/RascalSoftware/python-RAT
-Author: 
-Author-email: 
+Project-URL: Documentation, https://rascalsoftware.github.io/RAT/
+Project-URL: Repository, https://github.com/RascalSoftware/python-RAT
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Provides-Extra: dev

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/cpp/RAT/applyHydration.cpp

@@ -43,7 +43,7 @@ namespace RAT
         //  Index 6 determines what we hydrate with
         //  Hydrate the real component of the SLD.
         //  Note that we never hydrate the imaginary component of the SLD.
-        if (layers[b_i + layers.size(0) * 5] == 1.0) {
+        if (layers[b_i + layers.size(0) * 5] == 0.0) {
           d = bulkIn;
         } else {
           d = bulkOut;

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/pyproject.toml

@@ -8,7 +8,7 @@ build-backend = 'setuptools.build_meta'
 
 [project]
 name = "ratapi"
-version = "0.0.0.dev9"
+version = "0.0.0.dev11"
 description = "Python extension for the Reflectivity Analysis Toolbox (RAT)"
 readme = "README.md"
 requires-python = ">=3.10"
@@ -22,6 +22,10 @@ dependencies = [
     "tqdm>=4.66.5",
 ]
 
+[project.urls]
+Documentation = "https://rascalsoftware.github.io/RAT/"
+Repository = "https://github.com/RascalSoftware/python-RAT"
+
 [project.optional-dependencies]
 dev = [
     "pytest>=7.4.0",

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/ratapi/controls.py

@@ -206,7 +206,7 @@ class Controls(BaseModel, validate_assignment=True, extra="forbid", use_attribut
     def initialise_IPC(self):
         """Set up the inter-process communication file."""
         IPC_obj, self._IPCFilePath = tempfile.mkstemp()
-        os.write(IPC_obj, b"0")
+        os.write(IPC_obj, b"\x00")
         os.close(IPC_obj)
         return None
 
@@ -221,7 +221,7 @@ class Controls(BaseModel, validate_assignment=True, extra="forbid", use_attribut
         """
         if os.path.isfile(self._IPCFilePath):
             with open(self._IPCFilePath, "wb") as f:
-                f.write(b"1")
+                f.write(b"\x01")
         else:
             warnings.warn("An IPC file was not initialised.", UserWarning, stacklevel=2)
         return None
@@ -230,6 +230,7 @@ class Controls(BaseModel, validate_assignment=True, extra="forbid", use_attribut
         """Delete the inter-process communication file."""
         with contextlib.suppress(FileNotFoundError):
             os.remove(self._IPCFilePath)
+        self._IPCFilePath = ""
         return None
 
     def save(self, filepath: str | Path = "./controls.json"):

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/ratapi/inputs.py

@@ -385,7 +385,7 @@ def make_problem(project: ratapi.Project) -> ProblemDefinition:
 
 def get_layer_details(project: ratapi.Project) -> list[int]:
     """Get parameter indices for all layers defined in the project."""
-    hydrate_id = {"bulk in": 1, "bulk out": 2}
+    hydrate_id = {"bulk in": 0, "bulk out": 1}
     layer_details = []
 
     # Get the thickness, SLD, roughness fields from the appropriate model

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/ratapi/outputs.py

@@ -538,6 +538,19 @@ class BayesResults(Results):
     nestedSamplerOutput: NestedSamplerOutput
     chain: np.ndarray
 
+    def from_procedure(self) -> Procedures:
+        """Return the procedure that created the result.
+
+        Returns
+        -------
+        procedure: Procedures
+            The procedure that created the result.
+        """
+        samples = self.nestedSamplerOutput.nestSamples
+        if samples.shape == (1, 2) and not np.any(samples):
+            return Procedures.DREAM
+        return Procedures.NS
+
     def save(self, filepath: str | Path = "./results.json"):
         """Save the BayesResults object to a JSON file.
 

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/ratapi/utils/convert.py

@@ -291,7 +291,14 @@ def r1_to_project(filename: str | PathLike) -> Project:
         if Path(custom_filepath).suffix != ".m":
             custom_filepath += ".m"
         model_name = Path(custom_filepath).stem
-        custom_file = ClassList([CustomFile(name=model_name, filename=custom_filepath, language=Languages.Matlab)])
+        # Assume the custom file is in the same directory as the mat file
+        custom_file = ClassList(
+            [
+                CustomFile(
+                    name=model_name, filename=custom_filepath, language=Languages.Matlab, path=Path(filename).parent
+                )
+            ]
+        )
         layers = ClassList()
         for contrast in contrasts:
             contrast.model = [model_name]

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/ratapi/utils/plotting.py

@@ -76,9 +76,9 @@ def _extract_plot_data(event_data: PlotEventData, q4: bool, show_error_bar: bool
         for j in range(len(sld)):
             results["sld"][-1].append([sld[j][:, 0], sld[j][:, 1]])
 
+        results["sld_resample"].append([])
         if event_data.resample[i] == 1 or event_data.modelType == "custom xy":
             layers = event_data.resampledLayers[i][0]
-            results["sld_resample"].append([])
             for j in range(len(event_data.resampledLayers[i])):
                 layer = event_data.resampledLayers[i][j]
                 if layers.shape[1] == 4:
@@ -198,15 +198,14 @@ def plot_ref_sld_helper(
                 sld_min, sld_max = confidence_intervals["sld"][i][j]
                 sld_plot.fill_between(plot_data["sld"][i][j][0], sld_min, sld_max, alpha=0.6, color="grey")
 
-        if plot_data["sld_resample"]:
-            for j in range(len(plot_data["sld_resample"][i])):
-                sld_plot.plot(
-                    plot_data["sld_resample"][i][j][0],
-                    plot_data["sld_resample"][i][j][1],
-                    color=color,
-                    linewidth=1,
-                    animated=animated,
-                )
+        for j in range(len(plot_data["sld_resample"][i])):
+            sld_plot.plot(
+                plot_data["sld_resample"][i][j][0],
+                plot_data["sld_resample"][i][j][1],
+                color=color,
+                linewidth=1,
+                animated=animated,
+            )
 
     # Format the axis
     ref_plot.set_yscale("log")
@@ -493,6 +492,8 @@ class BlittingSupport:
         """
         if self.figure is not None:
             self.figure.clf()
+
+        self.figure.tight_layout()
         plot_ref_sld_helper(
             data,
             self.figure,
@@ -503,7 +504,6 @@ class BlittingSupport:
             show_legend=self.show_legend,
             animated=True,
         )
-        self.figure.tight_layout(pad=1)
         self.figure.canvas.draw()
         self.bg = self.figure.canvas.copy_from_bbox(self.figure.bbox)
         for line in self.figure.axes[0].lines:
@@ -544,11 +544,10 @@ class BlittingSupport:
                 self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
                 i += 1
 
-            if plot_data["sld_resample"]:
-                for resampled in plot_data["sld_resample"][j]:
-                    self.figure.axes[1].lines[i].set_data(resampled[0], resampled[1])
-                    self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
-                    i += 1
+            for resampled in plot_data["sld_resample"][j]:
+                self.figure.axes[1].lines[i].set_data(resampled[0], resampled[1])
+                self.figure.axes[1].draw_artist(self.figure.axes[1].lines[i])
+                i += 1
 
         for i, container in enumerate(self.figure.axes[0].containers):
             self.adjust_error_bar(

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11/ratapi.egg-info}/PKG-INFO

@@ -1,10 +1,9 @@
 Metadata-Version: 2.1
 Name: ratapi
-Version: 0.0.0.dev9
+Version: 0.0.0.dev11
 Summary: Python extension for the Reflectivity Analysis Toolbox (RAT)
-Home-page: https://github.com/RascalSoftware/python-RAT
-Author: 
-Author-email: 
+Project-URL: Documentation, https://rascalsoftware.github.io/RAT/
+Project-URL: Repository, https://github.com/RascalSoftware/python-RAT
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
 Provides-Extra: dev

{ratapi-0.0.0.dev9 → ratapi-0.0.0.dev11}/setup.py

@@ -69,7 +69,7 @@ class BuildExt(build_ext):
     }
 
     if sys.platform == "darwin":
-        darwin_opts = ["-stdlib=libc++", "-mmacosx-version-min=10.9"]
+        darwin_opts = ["-stdlib=libc++"]
         c_opts["unix"] = [*darwin_opts, "-fopenmp", "-O2"]
         l_opts["unix"] = [*darwin_opts, "-lomp"]
 
@@ -151,12 +151,6 @@ class BuildClib(build_clib):
 
 setup(
     name=PACKAGE_NAME,
-    author="",
-    author_email="",
-    url="https://github.com/RascalSoftware/python-RAT",
-    description="Python extension for the Reflectivity Analysis Toolbox (RAT)",
-    long_description=LONG_DESCRIPTION,
-    long_description_content_type="text/markdown",
     packages=find_packages(exclude=("tests",)),
     include_package_data=True,
     package_data={"": [get_shared_object_name(libevent[0])], "ratapi.examples": ["data/*.dat"]},