easyscience · damskii9992 · Apr 15, 2025 · Apr 3, 2025 · Apr 7, 2025
diff --git a/.github/workflows/documentation-build.yml b/.github/workflows/documentation-build.yml
@@ -34,15 +34,17 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: 3.10.12
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc
+        pip install sphinx==8.1.3
         pip install . '.[dev,docs]'
     - name: Build and Commit
       uses: sphinx-notes/pages@master
       with:
-        install_requirements: true
+        install_requirements: false
+        sphinx_version: 8.1.3
         documentation_path: docs/src
     - name: Push changes
       uses: ad-m/github-push-action@master

diff --git a/docs/src/api/data.rst b/docs/src/api/data.rst
@@ -1,4 +1,4 @@
-.. automodule:: easyreflectometry.data
+.. automodule:: easyreflectometry.data.measurement
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/src/api/model.rst b/docs/src/api/model.rst
@@ -1,4 +1,4 @@
-.. automodule:: easyreflectometry.model
+.. automodule:: easyreflectometry.model.model
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/src/api/sample.rst b/docs/src/api/sample.rst
@@ -1,5 +1,4 @@
-
-.. automodule:: easyreflectometry.sample
+.. automodule:: easyreflectometry.sample.collections.sample
     :members:
     :undoc-members:
     :show-inheritance:
diff --git a/docs/src/conf.py b/docs/src/conf.py
@@ -25,8 +25,7 @@
 
 import easyreflectometry
 
-# sys.path.insert(0, os.path.abspath('../src'))
-sys.path.insert(0, str(Path(__file__).resolve().parents[2] / "src"))
+sys.path.insert(0, os.path.abspath('../src'))
 
 main_root = Path(__file__).parents[2]
 sys.path.append(str(main_root))

diff --git a/docs/src/index.rst b/docs/src/index.rst
@@ -5,12 +5,12 @@
    :hidden:
    :caption: Contents:
 
-   installation
-   usage
-   tutorials/tutorials
-   contributing
-   authors
-   api/api
+   installation.rst
+   usage.rst
+   tutorials/tutorials.rst
+   contributing.rst
+   authors.rst
+   api/api.rst
 
 
 Indices and tables

diff --git a/docs/src/tutorials/advancedfitting/advancedfitting.rst b/docs/src/tutorials/advancedfitting/advancedfitting.rst
@@ -0,0 +1,9 @@
+Advanced Fitting
+================
+
+These are advanced fitting examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities.
+
+.. toctree:: 
+   :maxdepth: 1
+
+   multi_contrast.ipynb
diff --git a/docs/src/tutorials/advancedfitting/multi_contrast.ipynb b/docs/src/tutorials/advancedfitting/multi_contrast.ipynb
diff --git a/docs/src/tutorials/basic/assemblies_library.rst b/docs/src/tutorials/basic/assemblies_library.rst
@@ -1,5 +1,5 @@
 Creating multilayers and surfactant layers
-==========
+===========================================
 
 :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.

diff --git a/docs/src/tutorials/basic/sample.rst → docs/src/tutorials/basic/basic.rst b/docs/src/tutorials/basic/sample.rst → docs/src/tutorials/basic/basic.rst
@@ -1,12 +1,13 @@
 Basic
-======
+=====
 
 The :py:mod:`easyreflectometry` package is focused on making easy to use functionality for specific modelling approaches. 
 In order to achieve this, we have a sample library with different functionality. 
 
 .. toctree:: 
    :maxdepth: 1
-
+
+   model
    material_library
    layer_library
    assemblies_library
diff --git a/docs/src/tutorials/basic/layer_library.rst b/docs/src/tutorials/basic/layer_library.rst
@@ -1,5 +1,5 @@
 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/tutorials/basic/material_library.rst b/docs/src/tutorials/basic/material_library.rst
@@ -1,5 +1,5 @@
 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 enable the user to define the material based on chemical or physical properties. 

diff --git a/docs/src/tutorials/basic/model.rst b/docs/src/tutorials/basic/model.rst
@@ -1,5 +1,5 @@
 Creating a model
-=====
+================
 
 The main component of an experiment in :py:mod:`easyreflectometry` is the :py:class:`Model`. 
 This is a description of the :py:class:`Sample` and the environment in which the experiment is performed. 

diff --git a/docs/src/tutorials/extra/extra.rst b/docs/src/tutorials/extra/extra.rst
@@ -0,0 +1,7 @@
+Extra
+=====
+
+These are extra examples using the :py:mod:`easyreflectometry` library, to get an understanding of the possibilities.
+
+.. toctree:: 
+   :maxdepth: 1
diff --git a/docs/src/tutorials/fitting/d70d2o.ort b/docs/src/tutorials/fitting/d70d2o.ort
@@ -0,0 +1,91 @@
+# # ORSO reflectivity data file | 0.1 standard | YAML encoding | https://www.reflectometry.org/
+# data_source:
+#     owner:
+#         name: Andrew McCluskey
+#         affiliation: European Spallation Source
+#         contact: andrew.mccluskey@ess.eu
+#     experiment:
+#         facility: ISIS
+#         start_date: 2015-05-20
+#         title: A single contrast of DSPC
+#         instrument: surf
+#         probe: neutron
+#     sample:
+#         name: DSPC monolayer
+#         category: air / liquid
+#         composition: air / d70DSPC / D2O
+#     measurement:
+#         instrument_settings:
+#             wavelength:
+#                magnitude: 12
+#                unit: angstrom
+#             incident_angle: 
+#                magnitude: 0.2
+#                unit: deg
+#         data_files:
+#             - Unknown.nxs
+#         scheme: angle-dispersive
+# reduction:
+#     software: mantid
+#     timestamp: 2015-08-27T15:33:59+01:00
+#     corrections:
+#          - footprint
+#          - incident intensity
+#          - detector efficiency
+# columns:
+#     - {name: Qz, unit: 1/angstrom, dimension: WW transfer}
+#     - {name: R, dimension: reflectivity}
+#     - {name: sR, dimension: error-reflectivity}
+#     - {name: sQz, unit: 1/angstrom, dimension: resolution-WW transfer}
+##                  Qz                    RQz                     sR                    sQz        
+5.1792999999999999e-02 1.4254000000000000e-04 2.9187999999999999e-06 2.5896500000000002e-03
+5.4383000000000001e-02 1.1424000000000000e-04 2.3277000000000002e-06 2.7191500000000000e-03
+5.7102000000000000e-02 9.5197000000000004e-05 1.9168000000000000e-06 2.8551000000000002e-03
+5.9957000000000003e-02 7.4925000000000005e-05 1.5375000000000001e-06 2.9978500000000003e-03
+6.2954999999999997e-02 6.1081999999999996e-05 1.2839999999999999e-06 3.1477499999999999e-03
+6.6102999999999995e-02 5.2451000000000003e-05 1.0896999999999999e-06 3.3051499999999998e-03
+6.9407999999999997e-02 4.3195000000000002e-05 9.3939000000000000e-07 3.4704000000000002e-03
+7.2877999999999998e-02 3.5877999999999998e-05 8.0683999999999999e-07 3.6439000000000003e-03
+7.6522000000000007e-02 2.8937000000000001e-05 6.8090000000000002e-07 3.8261000000000007e-03
+8.0348000000000003e-02 2.7223999999999999e-05 6.3740000000000003e-07 4.0174000000000000e-03
+8.4364999999999996e-02 2.3142999999999998e-05 5.5753000000000004e-07 4.2182499999999998e-03
+8.8583999999999996e-02 1.9910000000000001e-05 4.8592000000000000e-07 4.4292000000000003e-03
+9.3012999999999998e-02 1.7467000000000001e-05 4.3365000000000002e-07 4.6506500000000001e-03
+9.7664000000000001e-02 1.5252000000000001e-05 3.8785999999999998e-07 4.8832000000000007e-03
+1.0255000000000000e-01 1.4654999999999999e-05 3.6547000000000000e-07 5.1275000000000001e-03
+1.0767000000000000e-01 1.3203000000000000e-05 3.3522000000000001e-07 5.3835000000000003e-03
+1.1305999999999999e-01 1.2407000000000000e-05 3.1808000000000000e-07 5.6530000000000000e-03
+1.1871000000000000e-01 1.1365999999999999e-05 3.0100000000000001e-07 5.9354999999999998e-03
+1.2465000000000000e-01 1.0529000000000000e-05 2.7911000000000002e-07 6.2325000000000002e-03
+1.3088000000000000e-01 9.5791999999999997e-06 2.6436000000000002e-07 6.5440000000000003e-03
+1.3741999999999999e-01 8.5473000000000003e-06 2.5890999999999998e-07 6.8709999999999995e-03
+1.4429000000000000e-01 8.2166000000000002e-06 2.5923000000000003e-07 7.2145000000000004e-03
+1.5151000000000001e-01 7.1802000000000003e-06 2.5376999999999998e-07 7.5755000000000006e-03
+1.5908000000000000e-01 6.9426000000000002e-06 2.6561000000000001e-07 7.9540000000000010e-03
+1.6703999999999999e-01 5.5822999999999999e-06 7.3669999999999997e-07 8.3520000000000000e-03
+1.7538999999999999e-01 5.1837000000000000e-06 4.6409999999999998e-07 8.7694999999999995e-03
+1.8415999999999999e-01 3.9739000000000002e-06 3.0730000000000001e-07 9.2079999999999992e-03
+1.9336999999999999e-01 4.1088999999999997e-06 9.5290000000000002e-07 9.6685000000000000e-03
+2.0304000000000000e-01 3.0409000000000000e-06 2.3160000000000001e-07 1.0152000000000001e-02
+2.1318999999999999e-01 2.7470999999999999e-06 4.2269999999999999e-07 1.0659500000000001e-02
+2.2384999999999999e-01 2.3638000000000001e-06 1.4970000000000000e-07 1.1192500000000001e-02
+2.3504000000000000e-01 2.3843000000000002e-06 8.1460000000000000e-07 1.1752000000000000e-02
+2.4679000000000001e-01 1.5583000000000000e-06 1.0840000000000000e-07 1.2339500000000002e-02
+2.5913000000000003e-01 1.2864000000000001e-06 4.7440000000000001e-07 1.2956500000000003e-02
+2.7209000000000000e-01 1.1920000000000000e-06 1.8839999999999999e-07 1.3604500000000000e-02
+2.8569000000000000e-01 1.2465000000000001e-06 3.9385000000000000e-07 1.4284500000000000e-02
+2.9998000000000002e-01 9.1670000000000005e-07 2.3955000000000000e-07 1.4999000000000002e-02
+3.1497000000000003e-01 8.8736999999999998e-07 3.5324000000000001e-07 1.5748500000000002e-02
+3.3072000000000001e-01 8.5180000000000004e-07 5.0846000000000004e-07 1.6536000000000002e-02
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+3.8285000000000002e-01 8.5601999999999996e-07 2.9493000000000001e-07 1.9142500000000003e-02
+4.0200000000000002e-01 7.8897999999999996e-07 2.3347000000000001e-07 2.0100000000000003e-02
+4.2209999999999998e-01 7.1536999999999998e-07 3.3494000000000001e-07 2.1104999999999999e-02
+4.4319999999999998e-01 1.0234000000000000e-06 2.3370999999999999e-07 2.2159999999999999e-02
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+4.8863000000000001e-01 8.2964000000000001e-07 6.0419000000000001e-07 2.4431500000000002e-02
+5.1305999999999996e-01 5.2732000000000004e-07 3.4821999999999998e-07 2.5652999999999999e-02
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+5.8877000000000002e-01 5.6128999999999997e-07 4.3959999999999999e-07 2.9438500000000003e-02