Merge pull request #178 from EasyScience/develop

Version 1.10.0

Author: andped10

docs/src/dictionay.rst

@@ -0,0 +1,20 @@
+Dictionary
+==========
+The following serves to clarify what we mean by the terms we use in this project.
+
+Sample
+------
+A sample is an ideal representation of a the full physical setup.
+This includes the layer(s) under investigation, the surrounding superphase, and the subphase.
+
+Calculator
+----------
+A calculator is the physics engine which calculates the reflectivity curve from our inputted sample parameters.
+We rely on third party software to provide the necessary calculators.
+Different calculators might have different capabilities and limitations. 
+
+Model
+-----
+A model combines a sample and calculator.
+The model is also responsible for including instrumental effects such as background, scale, and resolution.
+

docs/src/index.rst

@@ -11,6 +11,7 @@
    calculators
    experiment/experiment
    tutorials/tutorials
+   dictionary
    contributing
    authors
    api/api

docs/src/sample/material_library.rst

@@ -22,7 +22,7 @@ The construction of a :py:class:`Material` is achieved as shown below.
         name='Boron'
     )
 
-The above object will have the properties of :py:attr:`sld` and :py:attr:`isld`, which will have values of :code:`6.908 1 / angstrom ** 2` and :code:`-0.278 1 / angstrom ** 2` respectively. 
+The above object will have the properties of :py:attr:`sld` and :py:attr:`isld`, which will have values of :code:`6.908 1/angstrom^2` and :code:`-0.278 1/angstrom^2` respectively. 
 As is shown in the `tutorials`_, a material can be used to construct a :py:class:`Layer` from which `slab models`_ are created.
 
 :py:class:`MaterialDensity`
@@ -78,7 +78,7 @@ So to produce a :py:class:`MaterialSolvated` that is 20 % D2O in a polymer, the
         name='Solvated Polymer'
     )
 
-For the :py:attr:`solvated_polymer` object, the :py:attr:`sld` will be :code:`2.872 1 / angstrom ** 2` (the weighted average of the two scattering length densities). 
+For the :py:attr:`solvated_polymer` object, the :py:attr:`sld` will be :code:`2.872 1/angstrom^2` (the weighted average of the two scattering length densities). 
 The :py:class:`MaterialSolvated` includes a constraint such that if the value of either constituent scattering length densities (both real and imaginary components) or the fraction changes, then the resulting material :py:attr:`sld` and :py:attr:`isld` will change appropriately. 
 
 .. _`assemblies`: ./assemblies_library.html

docs/src/tutorials/fitting/repeating.ipynb

@@ -35,8 +35,11 @@
     "\n",
     "import numpy as np\n",
     "import scipp as sc\n",
-    "import easyreflectometry\n",
+    "import pooch\n",
     "import refl1d\n",
+    "\n",
+    "import easyreflectometry\n",
+    "\n",
     "from easyreflectometry.data import load\n",
     "from easyreflectometry.sample import Layer\n",
     "from easyreflectometry.sample import Sample\n",
@@ -46,7 +49,8 @@
     "from easyreflectometry.experiment import PercentageFhwm\n",
     "from easyreflectometry.calculators import CalculatorFactory\n",
     "from easyreflectometry.fitting import Fitter\n",
-    "from easyreflectometry.plot import plot"
+    "from easyreflectometry.plot import plot\n",
+    "from easyscience.fitting import AvailableMinimizers"
    ]
   },
   {
@@ -78,18 +82,22 @@
     "## Reading in experimental data\n",
     "\n",
     "The data that we will investigate in this tutorial was generated with [GenX](https://aglavic.github.io/genx/) and is stored in an `.ort` [format file](https://github.com/reflectivity/file_format/blob/master/specification.md).\n",
-    "Use link to [download](repeating_layers.ort) the ort data."
+    "We use `pooch` to fetch the file from the repository."
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "609174e5-1371-412d-a29f-cb05bfe36df0",
+   "id": "7121c7e9",
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = load('repeating_layers.ort')\n",
-    "data"
+    "file_path = pooch.retrieve(\n",
+    "    # URL to one of Pooch's test files\n",
+    "    url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/repeating_layers.ort\",\n",
+    "    known_hash=\"a5ffca9fd24f1d362266251723aec7ce9f34f123e39a38dfc4d829c758e6bf90\",\n",
+    ")\n",
+    "data = load(file_path)"
    ]
   },
   {
@@ -265,7 +273,8 @@
    "outputs": [],
    "source": [
     "fitter = Fitter(model)\n",
-    "analysed = fitter.fit(data, method='differential_evolution')\n",
+    "fitter.switch_minimizer(AvailableMinimizers.LMFit_differential_evolution)\n",
+    "analysed = fitter.fit(data)\n",
     "analysed"
    ]
   },
@@ -316,8 +325,22 @@
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "erl_1_311",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

docs/src/tutorials/fitting/simple_fitting.ipynb

@@ -29,8 +29,11 @@
    "source": [
     "%matplotlib inline\n",
     "\n",
-    "import easyreflectometry\n",
+    "import pooch\n",
     "import refnx\n",
+    "\n",
+    "import easyreflectometry\n",
+    "\n",
     "from easyreflectometry.data import load\n",
     "from easyreflectometry.sample import Layer\n",
     "from easyreflectometry.sample import Sample\n",
@@ -71,7 +74,7 @@
     "\n",
     "`easyreflectometry` has support for the `.ort` file format, a [standard file format for reduced reflectivity data developed by the Open Reflectometry Standards Organisation](https://www.reflectometry.org/working_groups/file_formats/).\n",
     "To load in a dataset, we use the `load` function.\n",
-    "Use link to [download](example.ort) the ort data."
+    "We use `pooch` to fetch the file from the repository."
    ]
   },
   {
@@ -81,7 +84,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "data = load('example.ort')"
+    "file_path = pooch.retrieve(\n",
+    "    # URL to one of Pooch's test files\n",
+    "    url=\"https://raw.githubusercontent.com/EasyScience/EasyReflectometryLib/master/docs/src/tutorials/fitting/example.ort\",\n",
+    "    known_hash=\"82d0c95c069092279a799a8131ad3710335f601d9f1080754b387f42e407dfab\",\n",
+    ")\n",
+    "data = load(file_path)"
    ]
   },
   {
@@ -514,8 +522,22 @@
   }
  ],
  "metadata": {
+  "kernelspec": {
+   "display_name": "erl_1_311",
+   "language": "python",
+   "name": "python3"
+  },
   "language_info": {
-   "name": "python"
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,