documentation moved to docs/src

EasyScience · May 6, 2024 · b517c24 · b517c24
1 parent fd5c13e
commit b517c24
Show file tree

Hide file tree

Showing 58 changed files with 21 additions and 21 deletions.
diff --git a/EasyReflectometry/calculators/refl1d/wrapper.py b/EasyReflectometry/calculators/refl1d/wrapper.py
@@ -6,7 +6,7 @@
 from refl1d import model
 from refl1d import names
 
-from EasyReflectometry.experiment.resolution_functions import is_constant_resolution_function
+from EasyReflectometry.experiment.resolution_functions import is_percentage_fhwm_resolution_function
 
 from ..wrapper_base import WrapperBase
 
@@ -148,7 +148,7 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
         sample = _build_sample(self.storage, model_name)
         dq_array = self._resolution_function(q_array)
 
-        if is_constant_resolution_function(self._resolution_function):
+        if is_percentage_fhwm_resolution_function(self._resolution_function):
             # Get percentage of Q and change from sigma to FWHM
             dq_array = dq_array * q_array / 100 / (2 * np.sqrt(2 * np.log(2)))
 

diff --git a/EasyReflectometry/calculators/refnx/wrapper.py b/EasyReflectometry/calculators/refnx/wrapper.py
@@ -5,7 +5,7 @@
 import numpy as np
 from refnx import reflect
 
-from EasyReflectometry.experiment.resolution_functions import is_constant_resolution_function
+from EasyReflectometry.experiment.resolution_functions import is_percentage_fhwm_resolution_function
 
 from ..wrapper_base import WrapperBase
 
@@ -131,7 +131,7 @@ def calculate(self, q_array: np.ndarray, model_name: str) -> np.ndarray:
         )
 
         dq_vector = self._resolution_function(q_array)
-        if is_constant_resolution_function(self._resolution_function):
+        if is_percentage_fhwm_resolution_function(self._resolution_function):
             # FWHM Percentage resolution is constant given as
             # For a constant resolution percentage refnx supports to pass a scalar value rather than a vector
             dq_vector = dq_vector[0]

diff --git a/EasyReflectometry/experiment/model.py b/EasyReflectometry/experiment/model.py
@@ -11,7 +11,7 @@
 from easyscience.Objects.ObjectClasses import BaseObj
 from easyscience.Objects.ObjectClasses import Parameter
 
-from EasyReflectometry.experiment.resolution_functions import is_constant_resolution_function
+from EasyReflectometry.experiment.resolution_functions import is_percentage_fhwm_resolution_function
 from EasyReflectometry.parameter_utils import get_as_parameter
 from EasyReflectometry.sample import BaseAssembly
 from EasyReflectometry.sample import Layer
@@ -175,7 +175,7 @@ def uid(self) -> int:
     @property
     def _dict_repr(self) -> dict[str, dict[str, str]]:
         """A simplified dict representation."""
-        if is_constant_resolution_function(self._resolution_function):
+        if is_percentage_fhwm_resolution_function(self._resolution_function):
             resolution_value = self._resolution_function([0])[0]
             resolution = f'{resolution_value} %'
         else:

diff --git a/EasyReflectometry/experiment/resolution_functions.py b/EasyReflectometry/experiment/resolution_functions.py
@@ -44,6 +44,6 @@ def _linear(q: np.array) -> np.array:
     return _linear
 
 
-def is_constant_resolution_function(resolution_function: Callable[[np.array], np.array]) -> bool:
+def is_percentage_fhwm_resolution_function(resolution_function: Callable[[np.array], np.array]) -> bool:
     """Check if the resolution function is a constant."""
     return 'constant' in resolution_function.__name__
diff --git a/docs/Makefile b/docs/Makefile
@@ -5,7 +5,7 @@
 SPHINXOPTS    =
 SPHINXBUILD   = python -msphinx
 SPHINXPROJ    = EasyReflectometry
-SOURCEDIR     = .
+SOURCEDIR     = ./src
 BUILDDIR      = _build
 
 # Put it first so that "make" without argument is like "make help".

diff --git a/docs/make.bat b/docs/make.bat
@@ -7,7 +7,7 @@ REM Command file for Sphinx documentation
 if "%SPHINXBUILD%" == "" (
 	set SPHINXBUILD=python -msphinx
 )
-set SOURCEDIR=.
+set SOURCEDIR=./src
 set BUILDDIR=_build
 set SPHINXPROJ=orsopy
 

diff --git a/docs/_static/favicon.ico → docs/src/_static/favicon.ico b/docs/_static/favicon.ico → docs/src/_static/favicon.ico
diff --git a/docs/_static/logo.png → docs/src/_static/logo.png b/docs/_static/logo.png → docs/src/_static/logo.png
diff --git a/docs/_static/logo.svg → docs/src/_static/logo.svg b/docs/_static/logo.svg → docs/src/_static/logo.svg
diff --git a/docs/api/api.rst → docs/src/api/api.rst b/docs/api/api.rst → docs/src/api/api.rst
diff --git a/docs/api/assemblies/gradient_layer.rst → docs/src/api/assemblies/gradient_layer.rst b/docs/api/assemblies/gradient_layer.rst → docs/src/api/assemblies/gradient_layer.rst
diff --git a/docs/api/assemblies/multilayer.rst → docs/src/api/assemblies/multilayer.rst b/docs/api/assemblies/multilayer.rst → docs/src/api/assemblies/multilayer.rst
diff --git a/docs/api/assemblies/repeating_multilayer.rst → ...c/api/assemblies/repeating_multilayer.rst b/docs/api/assemblies/repeating_multilayer.rst → ...c/api/assemblies/repeating_multilayer.rst
diff --git a/docs/api/assemblies/surfactant_layer.rst → docs/src/api/assemblies/surfactant_layer.rst b/docs/api/assemblies/surfactant_layer.rst → docs/src/api/assemblies/surfactant_layer.rst
diff --git a/docs/api/data.rst → docs/src/api/data.rst b/docs/api/data.rst → docs/src/api/data.rst
diff --git a/docs/api/elements/layer.rst → docs/src/api/elements/layer.rst b/docs/api/elements/layer.rst → docs/src/api/elements/layer.rst
diff --git a/.../api/elements/layer_area_per_molecule.rst → .../api/elements/layer_area_per_molecule.rst b/.../api/elements/layer_area_per_molecule.rst → .../api/elements/layer_area_per_molecule.rst
diff --git a/docs/api/elements/material.rst → docs/src/api/elements/material.rst b/docs/api/elements/material.rst → docs/src/api/elements/material.rst
diff --git a/docs/api/elements/material_density.rst → docs/src/api/elements/material_density.rst b/docs/api/elements/material_density.rst → docs/src/api/elements/material_density.rst
diff --git a/docs/api/elements/material_mixture.rst → docs/src/api/elements/material_mixture.rst b/docs/api/elements/material_mixture.rst → docs/src/api/elements/material_mixture.rst
diff --git a/docs/api/elements/material_solvated.rst → docs/src/api/elements/material_solvated.rst b/docs/api/elements/material_solvated.rst → docs/src/api/elements/material_solvated.rst
diff --git a/docs/api/model.rst → docs/src/api/model.rst b/docs/api/model.rst → docs/src/api/model.rst
diff --git a/docs/api/sample.rst → docs/src/api/sample.rst b/docs/api/sample.rst → docs/src/api/sample.rst
diff --git a/docs/authors.rst → docs/src/authors.rst b/docs/authors.rst → docs/src/authors.rst
diff --git a/docs/calculators.rst → docs/src/calculators.rst b/docs/calculators.rst → docs/src/calculators.rst
diff --git a/docs/conf.py → docs/src/conf.py b/docs/conf.py → docs/src/conf.py
@@ -23,9 +23,9 @@
 import toml
 from pathlib import Path
 
-sys.path.insert(0, os.path.abspath('..'))
+sys.path.insert(0, os.path.abspath('../..'))
 
-main_root = Path(__file__).parents[1]
+main_root = Path(__file__).parents[2]
 sys.path.append(str(main_root))
 project_info = toml.load(os.path.join(main_root, 'pyproject.toml'))
 

diff --git a/docs/contributing.rst → docs/src/contributing.rst b/docs/contributing.rst → docs/src/contributing.rst
diff --git a/docs/experiment/experiment.rst → docs/src/experiment/experiment.rst b/docs/experiment/experiment.rst → docs/src/experiment/experiment.rst
diff --git a/docs/index.rst → docs/src/index.rst b/docs/index.rst → docs/src/index.rst
diff --git a/docs/installation.rst → docs/src/installation.rst b/docs/installation.rst → docs/src/installation.rst
diff --git a/docs/sample/assemblies_library.rst → docs/src/sample/assemblies_library.rst b/docs/sample/assemblies_library.rst → docs/src/sample/assemblies_library.rst
diff --git a/docs/sample/layer_library.rst → docs/src/sample/layer_library.rst b/docs/sample/layer_library.rst → docs/src/sample/layer_library.rst
diff --git a/docs/sample/material_library.rst → docs/src/sample/material_library.rst b/docs/sample/material_library.rst → docs/src/sample/material_library.rst
diff --git a/docs/sample/sample.rst → docs/src/sample/sample.rst b/docs/sample/sample.rst → docs/src/sample/sample.rst
diff --git a/docs/tutorials/_static/d70d2o.ort → docs/src/tutorials/_static/d70d2o.ort b/docs/tutorials/_static/d70d2o.ort → docs/src/tutorials/_static/d70d2o.ort
diff --git a/docs/tutorials/_static/dspc.png → docs/src/tutorials/_static/dspc.png b/docs/tutorials/_static/dspc.png → docs/src/tutorials/_static/dspc.png
diff --git a/docs/tutorials/_static/example.ort → docs/src/tutorials/_static/example.ort b/docs/tutorials/_static/example.ort → docs/src/tutorials/_static/example.ort
diff --git a/docs/tutorials/_static/monolayer.png → docs/src/tutorials/_static/monolayer.png b/docs/tutorials/_static/monolayer.png → docs/src/tutorials/_static/monolayer.png
diff --git a/docs/tutorials/_static/monolayer.svg → docs/src/tutorials/_static/monolayer.svg b/docs/tutorials/_static/monolayer.svg → docs/src/tutorials/_static/monolayer.svg
diff --git a/docs/tutorials/_static/multiple.ort → docs/src/tutorials/_static/multiple.ort b/docs/tutorials/_static/multiple.ort → docs/src/tutorials/_static/multiple.ort
diff --git a/docs/tutorials/_static/polymer_film.png → docs/src/tutorials/_static/polymer_film.png b/docs/tutorials/_static/polymer_film.png → docs/src/tutorials/_static/polymer_film.png
diff --git a/docs/tutorials/_static/polymer_film.svg → docs/src/tutorials/_static/polymer_film.svg b/docs/tutorials/_static/polymer_film.svg → docs/src/tutorials/_static/polymer_film.svg
diff --git a/docs/tutorials/_static/repeating.png → docs/src/tutorials/_static/repeating.png b/docs/tutorials/_static/repeating.png → docs/src/tutorials/_static/repeating.png
diff --git a/docs/tutorials/_static/repeating.svg → docs/src/tutorials/_static/repeating.svg b/docs/tutorials/_static/repeating.svg → docs/src/tutorials/_static/repeating.svg
diff --git a/docs/tutorials/_static/repeating_layers.ort → ...rc/tutorials/_static/repeating_layers.ort b/docs/tutorials/_static/repeating_layers.ort → ...rc/tutorials/_static/repeating_layers.ort
diff --git a/...mod_pointwise_two_layer_sample_dq-0.0.ort → ...mod_pointwise_two_layer_sample_dq-0.0.ort b/...mod_pointwise_two_layer_sample_dq-0.0.ort → ...mod_pointwise_two_layer_sample_dq-0.0.ort
diff --git a/...mod_pointwise_two_layer_sample_dq-1.0.ort → ...mod_pointwise_two_layer_sample_dq-1.0.ort b/...mod_pointwise_two_layer_sample_dq-1.0.ort → ...mod_pointwise_two_layer_sample_dq-1.0.ort
diff --git a/...od_pointwise_two_layer_sample_dq-10.0.ort → ...od_pointwise_two_layer_sample_dq-10.0.ort b/...od_pointwise_two_layer_sample_dq-10.0.ort → ...od_pointwise_two_layer_sample_dq-10.0.ort
diff --git a/docs/tutorials/_static/two_layers.png → docs/src/tutorials/_static/two_layers.png b/docs/tutorials/_static/two_layers.png → docs/src/tutorials/_static/two_layers.png
diff --git a/docs/tutorials/_static/two_layers.svg → docs/src/tutorials/_static/two_layers.svg b/docs/tutorials/_static/two_layers.svg → docs/src/tutorials/_static/two_layers.svg
diff --git a/docs/tutorials/material_solvated.ipynb → docs/src/tutorials/material_solvated.ipynb b/docs/tutorials/material_solvated.ipynb → docs/src/tutorials/material_solvated.ipynb
@@ -43,7 +43,7 @@
     "from EasyReflectometry.sample import MaterialSolvated\n",
     "from EasyReflectometry.sample import Multilayer\n",
     "from EasyReflectometry.experiment import Model\n",
-    "from EasyReflectometry.experiment import constant_resolution_function\n",
+    "from EasyReflectometry.experiment import percentage_fhwm_resolution_function\n",
     "from EasyReflectometry.calculators import CalculatorFactory\n",
     "from EasyReflectometry.fitting import Fitter\n",
     "from EasyReflectometry.plot import plot"
@@ -182,7 +182,7 @@
     "\n",
     "subphase = Layer(material=d2o, thickness=0, roughness=3, name='D2O Subphase')\n",
     "\n",
-    "resolution_function = constant_resolution_function(0.02)\n",
+    "resolution_function = percentage_fhwm_resolution_function(0.02)\n",
     "sample = Sample(superphase, solvated_film_layer, subphase, name='Film Structure')\n",
     "model = Model(\n",
     "    sample=sample,\n",

diff --git a/docs/tutorials/monolayer.ipynb → docs/src/tutorials/monolayer.ipynb b/docs/tutorials/monolayer.ipynb → docs/src/tutorials/monolayer.ipynb
@@ -41,7 +41,7 @@
     "from EasyReflectometry.sample import Layer\n",
     "from EasyReflectometry.sample import Sample\n",
     "from EasyReflectometry.experiment import Model\n",
-    "from EasyReflectometry.experiment import constant_resolution_function\n",
+    "from EasyReflectometry.experiment import percentage_fhwm_resolution_function\n",
     "from EasyReflectometry.fitting import Fitter\n",
     "from EasyReflectometry.plot import plot\n",
     "\n"
@@ -317,7 +317,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = constant_resolution_function(5)\n",
+    "resolution_function = percentage_fhwm_resolution_function(5)\n",
     "sample = Sample(air_layer, dspc, d2o_layer)\n",
     "model = Model(\n",
     "    sample=sample,\n",

diff --git a/docs/tutorials/multi_contrast.ipynb → docs/src/tutorials/multi_contrast.ipynb b/docs/tutorials/multi_contrast.ipynb → docs/src/tutorials/multi_contrast.ipynb
@@ -39,7 +39,7 @@
     "from EasyReflectometry.sample import LayerAreaPerMolecule\n",
     "from EasyReflectometry.sample import Sample\n",
     "from EasyReflectometry.experiment import Model\n",
-    "from EasyReflectometry.experiment import constant_resolution_function\n",
+    "from EasyReflectometry.experiment import percentage_fhwm_resolution_function\n",
     "from EasyReflectometry.calculators import CalculatorFactory\n",
     "from EasyReflectometry.fitting import Fitter\n",
     "print(f'EasyReflectometry: {EasyReflectometry.__version__}')\n",
@@ -405,7 +405,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = constant_resolution_function(5)\n",
+    "resolution_function = percentage_fhwm_resolution_function(5)\n",
     "\n",
     "d13d2o_sample = Sample(air_layer, d13d2o, d2o_layer)\n",
     "d70d2o_sample = Sample(air_layer, d70d2o, d2o_layer)\n",

diff --git a/docs/tutorials/repeating.ipynb → docs/src/tutorials/repeating.ipynb b/docs/tutorials/repeating.ipynb → docs/src/tutorials/repeating.ipynb
@@ -43,7 +43,7 @@
     "from EasyReflectometry.sample import Material\n",
     "from EasyReflectometry.sample import RepeatingMultilayer\n",
     "from EasyReflectometry.experiment import Model\n",
-    "from EasyReflectometry.experiment import constant_resolution_function\n",
+    "from EasyReflectometry.experiment import percentage_fhwm_resolution_function\n",
     "from EasyReflectometry.calculators import CalculatorFactory\n",
     "from EasyReflectometry.fitting import Fitter\n",
     "from EasyReflectometry.plot import plot"
@@ -191,7 +191,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = constant_resolution_function(0)\n",
+    "resolution_function = percentage_fhwm_resolution_function(0)\n",
     "sample = Sample(superphase, rep_multilayer, subphase, name='Multilayer Structure')\n",
     "model = Model(\n",
     "    sample=sample,\n",

diff --git a/docs/tutorials/resolution_functions.ipynb → .../src/tutorials/resolution_functions.ipynb b/docs/tutorials/resolution_functions.ipynb → .../src/tutorials/resolution_functions.ipynb
diff --git a/docs/tutorials/simple_fitting.ipynb → docs/src/tutorials/simple_fitting.ipynb b/docs/tutorials/simple_fitting.ipynb → docs/src/tutorials/simple_fitting.ipynb
@@ -37,7 +37,7 @@
     "from EasyReflectometry.sample import Material\n",
     "from EasyReflectometry.sample import Multilayer\n",
     "from EasyReflectometry.experiment import Model\n",
-    "from EasyReflectometry.experiment import constant_resolution_function\n",
+    "from EasyReflectometry.experiment import percentage_fhwm_resolution_function\n",
     "from EasyReflectometry.calculators import CalculatorFactory\n",
     "from EasyReflectometry.fitting import Fitter\n",
     "from EasyReflectometry.plot import plot"
@@ -297,7 +297,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "resolution_function = constant_resolution_function(0.02)\n",
+    "resolution_function = percentage_fhwm_resolution_function(0.02)\n",
     "model = Model(\n",
     "    sample=sample,\n",
     "    scale=1,\n",

diff --git a/docs/tutorials/tutorials.rst → docs/src/tutorials/tutorials.rst b/docs/tutorials/tutorials.rst → docs/src/tutorials/tutorials.rst
diff --git a/docs/usage.rst → docs/src/usage.rst b/docs/usage.rst → docs/src/usage.rst