Documentation fixes

.github/workflows/documentation-build.yml

@@ -23,6 +23,16 @@ jobs:
   # This workflow contains a single job called "build"
   build_documentation:
     runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+
+    # Grant GITHUB_TOKEN the permissions required to make a Pages deployment
+    permissions:
+      contents: read    # to clone the repository
+      pages: write      # to deploy to Pages
+      id-token: write   # to verify the deployment originates from an appropriate source
+
     steps:
     - name: Checkout
       uses: actions/checkout@master
@@ -34,16 +44,21 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v5
       with:
-        python-version: 3.11
+        python-version: 3.12
     - name: Install Pandoc, repo and dependencies
       run: |
         sudo apt install pandoc
+        sudo apt install libcairo2-dev
         pip install sphinx==8.1.3
         pip install . '.[dev,docs]'
+
+    - name: Install Jupyter kernel
+      run: |
+        python -m ipykernel install --user --name=python3
+
     - name: Build and Commit
-      uses: sphinx-notes/pages@master
+      uses: sphinx-notes/pages@v3
       with:
-        install_requirements: false
         sphinx_version: 8.1.3
         documentation_path: docs/src
     - name: Push changes

.github/workflows/ossar-analysis.yml

@@ -13,7 +13,7 @@ jobs:
   OSSAR-Scan:
     # OSSAR runs on windows-latest.
     # ubuntu-latest and macos-latest support coming soon
-    runs-on: windows-latest
+    runs-on: windows-2022
 
     steps:
       # Checkout your code repository to scan

.github/workflows/python-ci.yml

@@ -31,7 +31,7 @@ jobs:
       max-parallel: 4
       matrix:
         python-version: ['3.11', '3.12']
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        os: [ubuntu-latest, macos-latest, windows-2022]
 
     runs-on: ${{ matrix.os }}
     if: "!contains(github.event.head_commit.message, '[ci skip]')"

docs/src/tutorials/advancedfitting/multi_contrast.ipynb

@@ -251,7 +251,7 @@
     ")\n",
     "d13d2o.constrain_area_per_molecule = True\n",
     "d13d2o.conformal_roughness = True\n",
-    "d13d2o.constrain_solvent_roughness(d2o_layer)"
+    "d13d2o.constrain_solvent_roughness(d2o_layer.roughness)"
    ]
   },
   {
@@ -291,7 +291,7 @@
     ")\n",
     "d70d2o.constrain_area_per_molecule = True\n",
     "d70d2o.conformal_roughness = True\n",
-    "d70d2o.constrain_solvent_roughness(d2o_layer)"
+    "d70d2o.constrain_solvent_roughness(d2o_layer.roughness)"
    ]
   },
   {
@@ -331,7 +331,7 @@
     ")\n",
     "d83acmw.constrain_area_per_molecule = True\n",
     "d83acmw.conformal_roughness = True\n",
-    "d83acmw.constrain_solvent_roughness(acmw_layer)"
+    "d83acmw.constrain_solvent_roughness(acmw_layer.roughness)"
    ]
   },
   {
@@ -341,8 +341,8 @@
    "source": [
     "## Introducing constraints\n",
     "\n",
-    "Then to ensure that the structure (thicknesss, area per molecule, etc.) is kept the same between the different contrasts we constain these (`layer2` is the head layer and `layer1`, which the neutron are incident on first are the tail layer). \n",
-    "The `constrain_multiple_contrast` method allows this, not that is it important that a chain of constraints is produced, one constraining the next. "
+    "To ensure that the structure (thicknesss, area per molecule, etc.) is kept the same between the different contrasts we constrain these (`layer2` is the head layer and `layer1`, which the neutron are incident on first are the tail layer). \n",
+    "The `constrain_multiple_contrast` method allows this, note that it is important that a chain of constraints is produced, one constraining the next. "
    ]
   },
   {
@@ -352,12 +352,6 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "# These four lines should be removed in future\n",
-    "d70d2o.head_layer.area_per_molecule_parameter.enabled = True\n",
-    "d70d2o.tail_layer.area_per_molecule_parameter.enabled = True\n",
-    "d83acmw.head_layer.area_per_molecule_parameter.enabled = True\n",
-    "d83acmw.tail_layer.area_per_molecule_parameter.enabled = True\n",
-    "\n",
     "d70d2o.constrain_multiple_contrast(d13d2o)\n",
     "d83acmw.constrain_multiple_contrast(d70d2o)"
    ]
@@ -571,7 +565,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,

docs/src/tutorials/fitting/monolayer.ipynb

@@ -382,7 +382,7 @@
     "calculator = CalculatorFactory()\n",
     "model.interface = calculator\n",
     "fitter = MultiFitter(model)\n",
-    "fitter.switch_minimizer(AvailableMinimizers.LMFit_differential_evolution)\n",
+    "# fitter.switch_minimizer(AvailableMinimizers.LMFit_differential_evolution)\n",
     "analysed = fitter.fit(data)"
    ]
   },
@@ -487,7 +487,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,

docs/src/tutorials/fitting/repeating.ipynb

@@ -274,7 +274,7 @@
    "outputs": [],
    "source": [
     "fitter = MultiFitter(model)\n",
-    "fitter.switch_minimizer(AvailableMinimizers.LMFit_differential_evolution)\n",
+    "# fitter.switch_minimizer(AvailableMinimizers.LMFit_differential_evolution)\n",
     "analysed = fitter.fit(data)\n",
     "analysed"
    ]
@@ -341,7 +341,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.9"
+   "version": "3.12.11"
   }
  },
  "nbformat": 4,

docs/src/tutorials/simulation/magnetism.ipynb

@@ -43,7 +43,8 @@
     "from easyreflectometry.sample import Layer\n",
     "from easyreflectometry.sample import Material\n",
     "from easyreflectometry.sample import Multilayer\n",
-    "from easyreflectometry.sample import Sample"
+    "from easyreflectometry.sample import Sample\n",
+    "from easyreflectometry.calculators.refl1d.wrapper import _get_polarized_probe"
    ]
   },
   {
@@ -331,15 +332,17 @@
     "    refl1d_sld_4(100, 0, magnetism=refl1d.names.Magnetism(rhoM=10, thetaM=70)) | \n",
     "    refl1d_vacuum(0, 0)\n",
     ") \n",
-    "probe = refl1d.names.QProbe(\n",
-    "        Q=model_coords,\n",
-    "        dQ=np.zeros(len(model_coords)),\n",
-    "        intensity=1,\n",
-    "        background=0,\n",
-    "    )\n",
+    "model_name = model.unique_name\n",
+    "storage = {'model': {model_name: {}}}\n",
+    "storage['model'][model_name]['scale'] = 10.0\n",
+    "storage['model'][model_name]['bkg'] = 20.0\n",
+    "\n",
+    "polarized_probe = _get_polarized_probe(\n",
+    "    q_array=model_coords,\n",
+    "    dq_array=np.zeros(len(model_coords)),\n",
+    "    model_name=model_name,\n",
+    "    storage=storage)\n",
     "\n",
-    "four_probes = [probe, None, None, None]\n",
-    "polarized_probe = refl1d.names.PolarizedQProbe(xs=four_probes, name='polarized')\n",
     "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)\n",
     "model_data_magnetism_ref1d = experiment.reflectivity()[0][1]\n",
     "plt.plot(model_coords, model_data_magnetism_ref1d, '-k', label='Refl1d', linewidth=4)\n",
@@ -413,34 +416,28 @@
     "    refl1d_vacuum(0, 0)\n",
     ") \n",
     "\n",
-    "probe_pp = refl1d.names.QProbe(\n",
-    "        Q=model_coords,\n",
-    "        dQ=np.zeros(len(model_coords)),\n",
-    "        intensity=1,\n",
-    "        background=0,\n",
-    "    )\n",
-    "probe_pm = refl1d.names.QProbe(\n",
-    "        Q=model_coords,\n",
-    "        dQ=np.zeros(len(model_coords)),\n",
-    "        intensity=1,\n",
-    "        background=0,\n",
-    "    )\n",
-    "probe_mp = refl1d.names.QProbe(\n",
-    "        Q=model_coords,\n",
-    "        dQ=np.zeros(len(model_coords)),\n",
-    "        intensity=1,\n",
-    "        background=0,\n",
-    "    )\n",
-    "probe_mm = refl1d.names.QProbe(\n",
-    "        Q=model_coords,\n",
-    "        dQ=np.zeros(len(model_coords)),\n",
-    "        intensity=1,\n",
-    "        background=0,\n",
-    "    )\n",
+    "model_name = model.unique_name\n",
+    "storage = {'model': {model_name: {}}}\n",
+    "storage['model'][model_name]['scale'] = 1.0\n",
+    "storage['model'][model_name]['bkg'] = 0.0\n",
     "\n",
-    "four_probes = [probe_pp, probe_pm, probe_mp, probe_mm]\n",
-    "polarized_probe = refl1d.names.PolarizedQProbe(xs=four_probes, name='polarized')\n",
-    "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)\n",
+    "polarized_probe = _get_polarized_probe(\n",
+    "    q_array=model_coords,\n",
+    "    dq_array=np.zeros(len(model_coords)),\n",
+    "    model_name=model_name,\n",
+    "    storage=storage,\n",
+    "    all_polarizations=True)\n",
+    "\n",
+    "experiment = refl1d.names.Experiment(probe=polarized_probe, sample=refl1d_sample)\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "239e2a04",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "model_data_magnetism_ref1d_raw_pp = experiment.reflectivity()[0][1]\n",
     "model_data_magnetism_ref1d_raw_pm = experiment.reflectivity()[1][1]\n",
     "model_data_magnetism_ref1d_raw_mp = experiment.reflectivity()[2][1]\n",
@@ -555,7 +552,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": ".venv2",
+   "display_name": "era",
    "language": "python",
    "name": "python3"
   },
@@ -569,7 +566,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.11.9"
+   "version": "3.11.12"
   }
  },
  "nbformat": 4,

pyproject.toml

@@ -29,11 +29,13 @@ classifiers = [
 requires-python = ">=3.11,<3.13"
 
 dependencies = [
+    #"easyscience @ git+https://github.com/easyscience/corelib.git@dict_size_changed_bug",
     "easyscience",
     "scipp",
     "refnx",
     "refl1d>=1.0.0rc0",
     "orsopy",
+    "svglib<1.6 ; platform_system=='Linux'",
     "xhtml2pdf",
     "bumps",
 ]
@@ -60,7 +62,7 @@ dev = [
 docs = [
     "myst_parser",
     "nbsphinx",
-    "sphinx==8.1.3",
+    "sphinx<=8.1.3",
     "sphinx_autodoc_typehints",
     "sphinx_book_theme",
     "sphinx-copybutton",
@@ -142,7 +144,7 @@ python =
 PLATFORM =
     ubuntu-latest: linux
     macos-latest: macos
-    windows-latest: windows
+    windows-latest: 2022
 [testenv]
 passenv =
     CI