Release: merge develop into master

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-23-g55e8e0e
+_commit: v0.10.1-25-ga5301e9
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/test.yml

@@ -74,7 +74,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-15, windows-2022]
 
     runs-on: ${{ matrix.os }}
 
@@ -163,7 +163,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-24.04, macos-14, windows-2022]
+        os: [ubuntu-24.04, macos-15, windows-2022]
 
     runs-on: ${{ matrix.os }}
 
@@ -202,11 +202,8 @@ jobs:
             echo "Adding Python $py_ver"
             pixi add "python=$py_ver"
 
-            echo "Adding Conda dependencies"
-            pixi add gsl
-
-            #echo "Adding PyPI dependencies"
-            #pixi add --pypi pytest pytest-xdist
+            echo "Setting macOS 14.0 as minimum required"
+            pixi project system-requirements add macos 14.0
 
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"

README.md

@@ -9,8 +9,9 @@
   </picture>
 </p>
 
-**EasyDynamics** is a software for plotting and fitting QENS and INS
-powder data.
+**EasyDynamics** is a software package for plotting and fitting neutron
+spectroscopy data (QENS and INS), mainly dedicated to amorphous
+materials and crystalline powders.
 
 <!-- HOME REPOSITORY SECTION -->
 

docs/docs/index.md

@@ -1,6 +1,6 @@
 ![](assets/images/logo_dark.svg#gh-dark-mode-only)![](assets/images/logo_light.svg#gh-light-mode-only)
 
-# QENS data analysis
+# Neutron spectroscopy data analysis
 
 Here is a brief overview of the main documentation sections:
 

docs/docs/introduction/index.md

@@ -6,8 +6,9 @@ icon: material/information-slab-circle
 
 ## Description
 
-**EasyDynamics** is a software for plotting and fitting QENS and INS
-powder data.
+**EasyDynamics** is a software package for plotting and fitting neutron
+spectroscopy data (QENS and INS), mainly dedicated to amorphous
+materials and crystalline powders
 
 **EasyDynamics** is developed both as a Python library and as a
 cross-platform desktop application.

docs/docs/tutorials/analysis1d.ipynb

@@ -81,8 +81,7 @@
     ")\n",
     "\n",
     "fit_result = my_analysis.fit()\n",
-    "fig = my_analysis.plot_data_and_model()\n",
-    "fig"
+    "my_analysis.plot_data_and_model()"
    ]
   }
  ],
@@ -102,7 +101,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.13"
+   "version": "3.12.12"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/components.ipynb

@@ -26,6 +26,7 @@
     "from easydynamics.sample_model import DampedHarmonicOscillator\n",
     "from easydynamics.sample_model import DeltaFunction\n",
     "from easydynamics.sample_model import Exponential\n",
+    "from easydynamics.sample_model import ExpressionComponent\n",
     "from easydynamics.sample_model import Gaussian\n",
     "from easydynamics.sample_model import Lorentzian\n",
     "from easydynamics.sample_model import Polynomial\n",
@@ -123,11 +124,37 @@
     "plt.legend()\n",
     "plt.show()"
    ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9a113170",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "expr = ExpressionComponent(\n",
+    "    'A * exp(-(x - x0)**2 / (2*sigma**2)) +B*sin(2*pi*x/period)',\n",
+    "    parameters={'A': 10, 'x0': 0, 'sigma': 1},\n",
+    ")\n",
+    "\n",
+    "expr.A = 5\n",
+    "expr.sigma = 0.5\n",
+    "\n",
+    "expr.period = 2.0\n",
+    "\n",
+    "x = np.linspace(-5, 5, 100)\n",
+    "y = expr.evaluate(x)\n",
+    "\n",
+    "plt.figure()\n",
+    "plt.plot(x, y, label='Expression Component')\n",
+    "plt.legend()\n",
+    "plt.show()"
+   ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "easydynamics_newbase",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -141,7 +168,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/convolution.ipynb

@@ -30,7 +30,7 @@
     "from easydynamics.sample_model import Gaussian\n",
     "from easydynamics.sample_model import Lorentzian\n",
     "from easydynamics.sample_model.component_collection import ComponentCollection\n",
-    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor\n",
+    "from easydynamics.utils import detailed_balance_factor\n",
     "\n",
     "%matplotlib widget"
    ]

docs/docs/tutorials/detailed_balance.ipynb

@@ -25,7 +25,7 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "\n",
-    "from easydynamics.utils import _detailed_balance_factor as detailed_balance_factor\n",
+    "from easydynamics.utils import detailed_balance_factor\n",
     "\n",
     "%matplotlib widget"
    ]

docs/docs/tutorials/tutorial1_brownian.ipynb

@@ -330,7 +330,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "diffusion_experiment.plot_data(slicer=True)"
+    "diffusion_experiment.plot_data(slicer=True, ymax=4)"
    ]
   },
   {
@@ -366,7 +366,7 @@
    "id": "927b8fb5",
    "metadata": {},
    "source": [
-    "We also create a new instrument_model and attach it to our analysis. We want to use the resolutin that we determined from the vanadium data. Ideally, we'd just attach it to the instrument model like before. However, this is currently not possible due to a small issue in EasyDynamics that will be fixed asap. For now, we need to hack it a bit."
+    "We also create a new instrument_model and attach it to our analysis, giving it the resolution model determined in the vanadium analysis. We further fix all parameters in the resolution model and normalize it."
    ]
   },
   {
@@ -378,20 +378,16 @@
    "source": [
     "instrument_model = InstrumentModel(\n",
     "    background_model=background_model,\n",
+    "    resolution_model=vanadium_analysis.instrument_model.resolution_model,\n",
     ")\n",
+    "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "diffusion_analysis = Analysis(\n",
     "    display_name='Diffusion Analysis',\n",
     "    experiment=diffusion_experiment,\n",
     "    sample_model=sample_model,\n",
     "    instrument_model=instrument_model,\n",
-    ")\n",
-    "\n",
-    "# We need to hack in the resolution model from the vanadium analysis,\n",
-    "# since the setters and getters overwrite the model. This will be fixed\n",
-    "# asap.\n",
-    "diffusion_analysis.instrument_model._resolution_model = (\n",
-    "    vanadium_analysis.instrument_model.resolution_model\n",
     ")"
    ]
   },
@@ -403,17 +399,6 @@
     "We don't want to fit our resolution anymore, so we fix all the parameters in it."
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "18e2f0bf",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# We fix all parameters of the resolution model.\n",
-    "diffusion_analysis.instrument_model.resolution_model.fix_all_parameters()"
-   ]
-  },
   {
    "cell_type": "markdown",
    "id": "e366a05d",
@@ -506,10 +491,19 @@
     "    diffusion_models=diffusion_model,\n",
     ")\n",
     "\n",
-    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
-    "\n",
+    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "48370156",
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "instrument_model = InstrumentModel(\n",
     "    background_model=background_model,\n",
+    "    resolution_model=vanadium_analysis.instrument_model.resolution_model,\n",
     ")"
    ]
   },
@@ -518,7 +512,7 @@
    "id": "8bb4abe9",
    "metadata": {},
    "source": [
-    "We attach all our models to a new `Analysis` object, again being mindful that we need to hack in the resolution. I promise this will be fixed soon!"
+    "We attach all our models to a new `Analysis` object."
    ]
   },
   {
@@ -535,12 +529,6 @@
     "    instrument_model=instrument_model,\n",
     ")\n",
     "\n",
-    "# We again need to hack in the resolution model from the vanadium\n",
-    "# analysis, since the setters and getters overwrite the model. This will\n",
-    "# be fixed asap.\n",
-    "diffusion_model_analysis.instrument_model._resolution_model = (\n",
-    "    vanadium_analysis.instrument_model.resolution_model\n",
-    ")\n",
     "diffusion_model_analysis.instrument_model.resolution_model.fix_all_parameters()"
    ]
   },
@@ -578,7 +566,7 @@
    "outputs": [],
    "source": [
     "diffusion_model_analysis.fit(fit_method='simultaneous')\n",
-    "diffusion_model_analysis.plot_data_and_model()"
+    "diffusion_model_analysis.plot_data_and_model(ymax=2)"
    ]
   },
   {

docs/docs/tutorials/tutorial2_nanoparticles.ipynb

@@ -275,14 +275,17 @@
     "background_model.components = polynomial\n",
     "\n",
     "\n",
-    "instrument_model = InstrumentModel(background_model=background_model)\n",
+    "instrument_model = InstrumentModel(\n",
+    "    background_model=background_model,\n",
+    "    resolution_model=res_analysis.instrument_model.resolution_model,\n",
+    ")\n",
+    "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "\n",
     "analysis = Analysis(\n",
     "    experiment=experiment, sample_model=sample_model, instrument_model=instrument_model\n",
     ")\n",
-    "analysis.instrument_model._resolution_model = res_analysis.instrument_model.resolution_model\n",
-    "analysis.instrument_model.resolution_model.fix_all_parameters()\n",
     "\n",
     "analysis.plot_data_and_model(logy=True)"
    ]
@@ -410,15 +413,17 @@
     "polynomial = Polynomial(coefficients=[0.15])\n",
     "background_model.components = polynomial\n",
     "\n",
-    "instrument_model = InstrumentModel(background_model=background_model)\n",
-    "\n",
+    "instrument_model = InstrumentModel(\n",
+    "    background_model=background_model,\n",
+    "    resolution_model=res_analysis.instrument_model.resolution_model,\n",
+    ")\n",
+    "instrument_model.resolution_model.fix_all_parameters()\n",
+    "instrument_model.normalize_resolution()\n",
     "\n",
     "# Create the analysis object\n",
     "mag_analysis = Analysis(\n",
     "    experiment=experiment, sample_model=mag_sample_model, instrument_model=instrument_model\n",
-    ")\n",
-    "mag_analysis.instrument_model._resolution_model = res_analysis.instrument_model.resolution_model\n",
-    "mag_analysis.instrument_model.resolution_model.fix_all_parameters()"
+    ")"
    ]
   },
   {
@@ -614,7 +619,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.12"
+   "version": "3.12.13"
   }
  },
  "nbformat": 4,

docs/docs/user-guide/concept.md

@@ -1,5 +1,5 @@
-The goal of EasyDynamics is to make it easy to fit QENS and powder INS
-data.
+EasyDynamics is a a fitting tool for neutron spectroscopy, mainly
+dedicated to amorphous materials and crystalline powders.
 
 The fit is carried out by an `Analysis` object, which contains an
 `Experiment` that contains the data, a `SampleModel` that describes the
@@ -44,10 +44,10 @@ like this:
 
 ```python
 gaussian = Gaussian()
-gaussian.area=2.0
-gaussian.area.fixed=True
-gaussian.width.fixed=False
-gaussian.width.min=0.5
+gaussian.area = 2.0
+gaussian.area.fixed = True
+gaussian.width.fixed = False
+gaussian.width.min = 0.5
 ```
 
 And so on.