easyscience · henrikjacobsenfys · Mar 20, 2025 · Nov 27, 2024 · Nov 27, 2024 · Nov 27, 2024
diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml
@@ -34,7 +34,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc

diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
@@ -30,7 +30,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ['3.9', '3.10', '3.11', '3.12']
+        python-version: ['3.10', '3.11', '3.12']
         os: [ubuntu-latest, macos-latest, windows-latest]
 
     runs-on: ${{ matrix.os }}
@@ -74,7 +74,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.11
 
     - name: Install dependencies and build
       run: |

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11','3.12']
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
 
     steps:

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -27,7 +27,7 @@ jobs:
 
     - uses: actions/setup-python@v5
       with:
-        python-version: 3.9
+        python-version: 3.10
 
     - name: Install dependencies and build
       run: |

diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst
@@ -102,7 +102,7 @@ Before you submit a pull request, check that it meets these guidelines:
 2. If the pull request adds functionality, the docs should be updated. Put
    your new functionality into a function with a docstring, and add the
    feature to the list in README.md.
-3. The pull request should work for Python 3.9, 3.10, and 3.11, and for PyPy. Check
+3. The pull request should work for Python, 3.10, 3.11 and 3.12, and for PyPy. Check
    https://travis-ci.com/easyScience/EasyReflectometryLib/pull_requests
    and make sure that the tests pass for all supported Python versions.
 

diff --git a/docs/src/calculators.rst b/docs/src/calculators.rst
diff --git a/docs/src/dictionay.rst b/docs/src/dictionay.rst
diff --git a/docs/src/index.rst b/docs/src/index.rst
@@ -7,11 +7,7 @@
 
    installation
    usage
-   sample/sample
-   calculators
-   model/model
    tutorials/tutorials
-   dictionary
    contributing
    authors
    api/api

diff --git a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb
diff --git a/docs/src/tutorials/sample/multiple.ort → ...rc/tutorials/advancedfitting/multiple.ort b/docs/src/tutorials/sample/multiple.ort → ...rc/tutorials/advancedfitting/multiple.ort
diff --git a/docs/src/sample/assemblies_library.rst → ...rc/tutorials/basic/assemblies_library.rst b/docs/src/sample/assemblies_library.rst → ...rc/tutorials/basic/assemblies_library.rst
@@ -1,15 +1,16 @@
-Assemblies
+Creating multilayers and surfactant layers
 ==========
 
-:py:mod:`easyreflectometry` is designed to be used with a broad range of different assemblies.
-These assemblies offer flexibility for the user and enable more powerful analysis by making chemical and pysical constraints available with limited code. 
+:py:mod:`easyreflectometry` is designed to be used with a broad range of different assemblies.  
+Assemblies are collective layers behaving as a single object, for example, a multilayer or a surfactant layer.
+These assemblies offer flexibility for the user and enable more powerful analysis by making chemical and physical constraints available with limited code. 
 In this page, we will document the assemblies that are available with simple examples of the constructors that exist.
 Full API documentation is also available for the :py:mod:`easyreflectometry.sample.assemblies` module.
 
 :py:class:`Multilayer`
 ----------------------
 
-This assembly should be used for a series of layers that, for whatever reason, should be thought of as a single object. 
+This assembly should be used for a series of layers that should be thought of as a single object. 
 For example, in the `simple fitting tutorial`_ this assembly type is used to combine the silicon and silicon dioxide layer that as formed into a single object. 
 All of the separate layers in these objects will be fitted individually, i.e. there is no constraints present, however, there is some cognative benefit to grouping layers together. 
 

diff --git a/docs/src/sample/layer_library.rst → docs/src/tutorials/basic/layer_library.rst b/docs/src/sample/layer_library.rst → docs/src/tutorials/basic/layer_library.rst
@@ -1,4 +1,4 @@
-Layers
+Defining Layers
 ======
 
 Similar to a range of different `materials`_, there are a few different ways that a layer can be defined in :py:mod:`easyreflectometry`.

diff --git a/docs/src/sample/material_library.rst → .../src/tutorials/basic/material_library.rst b/docs/src/sample/material_library.rst → .../src/tutorials/basic/material_library.rst
@@ -1,9 +1,9 @@
-Materials
+Defining materials
 =========
 
 In order to support a wide range of applications (and to build complex `assemblies`_) there are a few different types of material that can be utilised in :py:mod:`easyreflectometry`. 
-These can include constraints or enabel the user to define the material based on chemical or physical properties. 
-Full API documentation for the :py:mod:`easyreflectometry.sample.elements.material` mdoule is also available, but here we will give some simple uses for them. 
+These can include constraints or enable the user to define the material based on chemical or physical properties. 
+Full API documentation for the :py:mod:`easyreflectometry.sample.elements.material` module is also available, but here we will give some simple uses for them. 
 
 :py:class:`Material`
 --------------------

diff --git a/docs/src/model/model.rst → docs/src/tutorials/basic/model.rst b/docs/src/model/model.rst → docs/src/tutorials/basic/model.rst
@@ -1,4 +1,4 @@
-Model
+Creating a model
 =====
 
 The main component of an experiment in :py:mod:`easyreflectometry` is the :py:class:`Model`. 

diff --git a/docs/src/sample/sample.rst → docs/src/tutorials/basic/sample.rst b/docs/src/sample/sample.rst → docs/src/tutorials/basic/sample.rst
@@ -1,4 +1,4 @@
-Sample
+Basic
 ======
 
 The :py:mod:`easyreflectometry` package is focused on making easy to use functionality for specific modelling approaches. 

diff --git a/docs/src/tutorials/sample/dspc.png → docs/src/tutorials/fitting/dspc.png b/docs/src/tutorials/sample/dspc.png → docs/src/tutorials/fitting/dspc.png
diff --git a/.../tutorials/sample/material_solvated.ipynb → ...tutorials/fitting/material_solvated.ipynb b/.../tutorials/sample/material_solvated.ipynb → ...tutorials/fitting/material_solvated.ipynb
@@ -20,7 +20,7 @@
    "id": "f404875e",
    "metadata": {},
    "source": [
-    "First configure matplotlib to place figures in notebook and import needed modules"
+    "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`"
    ]
   },
   {
@@ -354,7 +354,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "erl_d",
+   "display_name": ".venv2",
    "language": "python",
    "name": "python3"
   },
@@ -368,7 +368,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.5"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

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/src/tutorials/sample/monolayer.ipynb → docs/src/tutorials/fitting/monolayer.ipynb b/docs/src/tutorials/sample/monolayer.ipynb → docs/src/tutorials/fitting/monolayer.ipynb
@@ -17,7 +17,7 @@
    "id": "e46c0e41",
    "metadata": {},
    "source": [
-    "First configure matplotlib to place figures in notebook and import needed modules"
+    "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`"
    ]
   },
   {
@@ -151,7 +151,7 @@
     "Now we can create the `SurfactantLayer` object, this takes a large number of parameters, that we will introduce gradually. \n",
     "\n",
     "<center>\n",
-    "    <img src='dspc.png' alt='The chemical structure for the DSPC molecule.' width='400px'></img>\n",
+    "    <img src='dspc.png' alt='The chemical structure for the DSPC molecule.'></img>\n",
     "</center>\n",
     "<center>\n",
     "    The chemical structure for the DSPC molecule. By <a href='https://commons.wikimedia.org/w/index.php?curid=97726650'>Graeme Bartlett - Self Drawn, CC0</a>\n",
@@ -474,7 +474,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": ".venv2",
    "language": "python",
    "name": "python3"
   },
@@ -488,7 +488,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/src/tutorials/sample/monolayer.png → docs/src/tutorials/fitting/monolayer.png b/docs/src/tutorials/sample/monolayer.png → docs/src/tutorials/fitting/monolayer.png
diff --git a/docs/src/tutorials/sample/monolayer.svg → docs/src/tutorials/fitting/monolayer.svg b/docs/src/tutorials/sample/monolayer.svg → docs/src/tutorials/fitting/monolayer.svg
diff --git a/docs/src/tutorials/fitting/repeating.ipynb b/docs/src/tutorials/fitting/repeating.ipynb
@@ -21,7 +21,7 @@
    "id": "f5d0bd58",
    "metadata": {},
    "source": [
-    "First configure matplotlib to place figures in notebook and import needed modules"
+    "First configure matplotlib to place figures in notebook and import needed modules. Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`"
    ]
   },
   {
@@ -327,7 +327,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": ".venv2",
    "language": "python",
    "name": "python3"
   },
@@ -341,7 +341,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,

diff --git a/docs/src/tutorials/fitting/simple_fitting.ipynb b/docs/src/tutorials/fitting/simple_fitting.ipynb
@@ -17,7 +17,8 @@
    "id": "d0fea80b",
    "metadata": {},
    "source": [
-    "First configure matplotlib to place figures in notebook and import needed modules"
+    "First configure matplotlib to place figures in notebook and import needed modules.\n",
+    "Note that the plot function needs installation of `plopp` seperately or installation of `easyreflectometry[dev]`"
    ]
   },
   {
@@ -523,7 +524,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": ".test",
    "language": "python",
    "name": "python3"
   },
@@ -537,7 +538,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.10"
+   "version": "3.11.9"
   }
  },
  "nbformat": 4,
-Original file line number
+Diff line change
@@ -1,4 +1,4 @@
-    Sample
+    Basic
     ======
     The :py:mod:`easyreflectometry` package is focused on making easy to use functionality for specific modelling approaches.
@@ Expand Down @@