🎉 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: v0.12.0
+_commit: v0.13.1-3-g44c0369
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/dynamics-app
 app_doi: 10.5281/zenodo.18877180

.github/workflows/docs.yml

@@ -83,6 +83,9 @@ jobs:
           fi
           echo "RELEASE_VERSION=${RELEASE_VERSION}" >> "$GITHUB_ENV"
           echo "DOCS_VERSION=${DOCS_VERSION}" >> "$GITHUB_ENV"
+          # Artifact names cannot contain '/', so sanitize the (possibly slash-containing)
+          # branch name for use in the uploaded artifact name.
+          echo "ARTIFACT_SUFFIX=${RELEASE_VERSION//\//-}" >> "$GITHUB_ENV"
 
       # Check out the repository source code.
       # Note: The gh-pages branch is fetched separately later for mike deployment.
@@ -123,16 +126,19 @@ jobs:
 
       # Build the static files for the documentation site for local inspection
       # Input: docs/ directory containing the Markdown files
-      # Output: site/ directory containing the generated HTML files
+      # Output: docs/site/ directory containing the generated HTML files
+      # Also verifies that mkdocstrings generated docs/site/objects.inv.
       - name: Build site for local check
-        run: pixi run docs-build-local
+        run: |
+          pixi run docs-build-local
+          pixi run docs-inventory-check
 
-      # Upload the static files from the site/ directory to be used for
+      # Upload the static files from the docs/site/ directory to be used for
       # local check
       - name: Upload built site as artifact
         uses: ./.github/actions/upload-artifact
         with:
-          name: site-local_easydynamics-lib-${{ env.RELEASE_VERSION }}
+          name: site-local_easydynamics-lib-${{ env.ARTIFACT_SUFFIX }}
           path: docs/site/
 
       # Create GitHub App token for pushing to gh-pages as easyscience[bot].

.github/workflows/pypi-test.yml

@@ -43,11 +43,15 @@ jobs:
           frozen: false
 
       - name: Init pixi project
-        run: pixi init easydynamics
+        run:
+          pixi init --platform linux-64 --platform osx-arm64 --platform win-64
+          easydynamics
 
-      - name: Set the minimum system requirements
+      - name: Configure pixi platforms
         working-directory: easydynamics
-        run: pixi project system-requirements add macos 14.0
+        run: |
+          pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+          pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
 
       - name: Add Python 3.14 from Conda
         working-directory: easydynamics

.github/workflows/test.yml

@@ -211,15 +211,16 @@ jobs:
             echo "🔹🔸🔹🔸🔹 Python: $py_ver 🔹🔸🔹🔸🔹"
 
             echo "Initializing pixi project"
-            pixi init easydynamics_py$py_ver
+            pixi init --platform linux-64 --platform osx-arm64 --platform win-64 easydynamics_py$py_ver
             cd easydynamics_py$py_ver
 
+            echo "Configure pixi platforms"
+            pixi workspace platform edit linux-64 --glibc 2.35 --no-install
+            pixi workspace platform edit osx-arm64 --macos 14.0 --no-install
+
             echo "Adding Python $py_ver"
             pixi add "python=$py_ver"
 
-            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/"
 

.gitignore

@@ -44,3 +44,4 @@ CMakeLists.txt.user*
 .cache/
 *.log
 *.zip
+.claude/

CONTRIBUTING.md

@@ -42,8 +42,7 @@ Please make sure you follow the EasyScience organization-wide
 If you are not planning to contribute code, you may want to:
 
 - 🐞 Report a bug — see [Reporting Issues](#11-reporting-issues)
-- 🛡 Report a security issue — see
-  [Security Issues](#12-security-issues)
+- 🛡 Report a security issue — see [Security Issues](#12-security-issues)
 - 💬 Ask a question or start a discussion at
   [Project Discussions](https://github.com/easyscience/dynamics-lib/discussions)
 

docs/docs/tutorials/analysis.ipynb

@@ -23,18 +23,8 @@
     "# Imports\n",
     "import pooch\n",
     "\n",
-    "from easydynamics.analysis.analysis import Analysis\n",
-    "from easydynamics.experiment import Experiment\n",
-    "from easydynamics.sample_model import BrownianTranslationalDiffusion\n",
-    "from easydynamics.sample_model import ComponentCollection\n",
-    "from easydynamics.sample_model import DeltaFunction\n",
-    "from easydynamics.sample_model import Gaussian\n",
-    "from easydynamics.sample_model import Lorentzian\n",
-    "from easydynamics.sample_model import Polynomial\n",
-    "from easydynamics.sample_model.background_model import BackgroundModel\n",
-    "from easydynamics.sample_model.instrument_model import InstrumentModel\n",
-    "from easydynamics.sample_model.resolution_model import ResolutionModel\n",
-    "from easydynamics.sample_model.sample_model import SampleModel\n",
+    "import easydynamics as edyn\n",
+    "import easydynamics.sample_model as sm\n",
     "\n",
     "%matplotlib widget"
    ]
@@ -47,7 +37,7 @@
    "outputs": [],
    "source": [
     "# Load the vanadium data\n",
-    "vanadium_experiment = Experiment('Vanadium')\n",
+    "vanadium_experiment = edyn.Experiment('Vanadium')\n",
     "file_path = pooch.retrieve(\n",
     "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
     "    known_hash='16cc1b327c303feeb88fb9dda5390dc4880b62396b1793f98c6fef0b27c7b873',\n",
@@ -66,34 +56,34 @@
     "# Example of Analysis with a simple sample model and instrument model\n",
     "# The scattering from vanadium is purely elastic, so we model it with a\n",
     "# delta function\n",
-    "delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
-    "sample_model = SampleModel(\n",
+    "delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=1)\n",
+    "sample_model = sm.SampleModel(\n",
     "    components=delta_function,\n",
     ")\n",
     "\n",
     "# The resolution is in this case modeled as a Gaussian. However, we can\n",
     "# add as many components as we like to the resolution model\n",
-    "res_gauss = Gaussian(width=0.1)\n",
+    "res_gauss = sm.Gaussian(width=0.1)\n",
     "res_gauss.area.fixed = True\n",
-    "resolution_components = ComponentCollection()\n",
+    "resolution_components = sm.ComponentCollection()\n",
     "resolution_components.append_component(res_gauss)\n",
-    "resolution_model = ResolutionModel(components=resolution_components)\n",
+    "resolution_model = sm.ResolutionModel(components=resolution_components)\n",
     "\n",
     "# The background model is created in the same way. In this case, we use\n",
     "# a flat background\n",
-    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
     "\n",
     "# We combine the resolution abd background model into an instrument\n",
     "# model. This model also contains a small energy offset to account for\n",
     "# instrument misalignment.\n",
     "\n",
-    "instrument_model = InstrumentModel(\n",
+    "instrument_model = sm.InstrumentModel(\n",
     "    resolution_model=resolution_model,\n",
     "    background_model=background_model,\n",
     ")\n",
     "\n",
     "# Collect everything into an analysis object.\n",
-    "vanadium_analysis = Analysis(\n",
+    "vanadium_analysis = edyn.Analysis(\n",
     "    display_name='Vanadium Full Analysis',\n",
     "    experiment=vanadium_experiment,\n",
     "    sample_model=sample_model,\n",
@@ -180,7 +170,7 @@
    "source": [
     "# Now it's time to look at the data we want to fit. We first load the\n",
     "# data\n",
-    "diffusion_experiment = Experiment('Diffusion')\n",
+    "diffusion_experiment = edyn.Experiment('Diffusion')\n",
     "\n",
     "file_path = pooch.retrieve(\n",
     "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/diffusion_data_example.h5',\n",
@@ -200,23 +190,23 @@
     "# Now we set up the model, similarly to how we set up the model for the\n",
     "# vanadium data.\n",
     "\n",
-    "delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
-    "lorentzian = Lorentzian(display_name='Lorentzian', area=0.5, width=0.3)\n",
-    "component_collection = ComponentCollection(\n",
+    "delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
+    "lorentzian = sm.Lorentzian(display_name='Lorentzian', area=0.5, width=0.3)\n",
+    "component_collection = sm.ComponentCollection(\n",
     "    components=[delta_function, lorentzian],\n",
     ")\n",
     "\n",
-    "sample_model = SampleModel(\n",
+    "sample_model = sm.SampleModel(\n",
     "    components=component_collection,\n",
     ")\n",
     "\n",
-    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
     "\n",
-    "instrument_model = InstrumentModel(\n",
+    "instrument_model = sm.InstrumentModel(\n",
     "    background_model=background_model,\n",
     ")\n",
     "\n",
-    "diffusion_analysis = Analysis(\n",
+    "diffusion_analysis = edyn.Analysis(\n",
     "    display_name='Diffusion Full Analysis',\n",
     "    experiment=diffusion_experiment,\n",
     "    sample_model=sample_model,\n",
@@ -265,17 +255,6 @@
     "diffusion_analysis.plot_parameters(names=['Lorentzian width', 'Lorentzian area'])"
    ]
   },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "eb226c8f",
-   "metadata": {},
-   "outputs": [],
-   "source": [
-    "# It will be possible to fit this to a DiffusionModel, but that will\n",
-    "# come later."
-   ]
-  },
   {
    "cell_type": "code",
    "execution_count": null,
@@ -286,26 +265,26 @@
     "# Let us now fit directly to a diffusion model. We replace the\n",
     "# Lorentzian with a Brownian translational diffusion model and keep the\n",
     "# other parameters the same.\n",
-    "delta_function = DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
-    "component_collection = ComponentCollection(\n",
+    "delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=0.2)\n",
+    "component_collection = sm.ComponentCollection(\n",
     "    components=[delta_function],\n",
     ")\n",
-    "diffusion_model = BrownianTranslationalDiffusion(\n",
+    "diffusion_model = sm.BrownianTranslationalDiffusion(\n",
     "    display_name='Brownian Translational Diffusion', diffusion_coefficient=2.4e-9, scale=0.5\n",
     ")\n",
     "\n",
-    "sample_model = SampleModel(\n",
+    "sample_model = sm.SampleModel(\n",
     "    components=component_collection,\n",
     "    diffusion_models=diffusion_model,\n",
     ")\n",
     "\n",
-    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
     "\n",
-    "instrument_model = InstrumentModel(\n",
+    "instrument_model = sm.InstrumentModel(\n",
     "    background_model=background_model,\n",
     ")\n",
     "\n",
-    "diffusion_model_analysis = Analysis(\n",
+    "diffusion_model_analysis = edyn.Analysis(\n",
     "    display_name='Diffusion Full Analysis',\n",
     "    experiment=diffusion_experiment,\n",
     "    sample_model=sample_model,\n",
@@ -342,13 +321,13 @@
    "outputs": [],
    "source": [
     "# Let us look at the fitted diffusion coefficient\n",
-    "diffusion_model.get_all_parameters()"
+    "diffusion_model.get_fittable_parameters()"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "default",
    "language": "python",
    "name": "python3"
   },
@@ -362,7 +341,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.4"
+   "version": "3.14.5"
   }
  },
  "nbformat": 4,

docs/docs/tutorials/analysis1d.ipynb

@@ -18,15 +18,9 @@
    "source": [
     "import pooch\n",
     "\n",
+    "import easydynamics as edyn\n",
+    "import easydynamics.sample_model as sm\n",
     "from easydynamics.analysis.analysis1d import Analysis1d\n",
-    "from easydynamics.experiment import Experiment\n",
-    "from easydynamics.sample_model import DeltaFunction\n",
-    "from easydynamics.sample_model import Gaussian\n",
-    "from easydynamics.sample_model import Polynomial\n",
-    "from easydynamics.sample_model.background_model import BackgroundModel\n",
-    "from easydynamics.sample_model.instrument_model import InstrumentModel\n",
-    "from easydynamics.sample_model.resolution_model import ResolutionModel\n",
-    "from easydynamics.sample_model.sample_model import SampleModel\n",
     "\n",
     "%matplotlib widget"
    ]
@@ -38,7 +32,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "vanadium_experiment = Experiment('Vanadium')\n",
+    "vanadium_experiment = edyn.Experiment('Vanadium')\n",
     "\n",
     "file_path = pooch.retrieve(\n",
     "    url='https://github.com/easyscience/dynamics-lib/raw/refs/heads/master/docs/docs/tutorials/data/vanadium_data_example.h5',\n",
@@ -56,18 +50,18 @@
    "outputs": [],
    "source": [
     "# Example of Analysis1d with a simple sample model and instrument model\n",
-    "delta_function = DeltaFunction(display_name='DeltaFunction', area=1)\n",
-    "sample_model = SampleModel(\n",
+    "delta_function = sm.DeltaFunction(display_name='DeltaFunction', area=1)\n",
+    "sample_model = sm.SampleModel(\n",
     "    components=delta_function,\n",
     ")\n",
     "\n",
-    "res_gauss = Gaussian(width=0.1)\n",
-    "resolution_model = ResolutionModel(components=res_gauss)\n",
+    "res_gauss = sm.Gaussian(width=0.1)\n",
+    "resolution_model = sm.ResolutionModel(components=res_gauss)\n",
     "\n",
     "\n",
-    "background_model = BackgroundModel(components=Polynomial(coefficients=[0.001]))\n",
+    "background_model = sm.BackgroundModel(components=sm.Polynomial(coefficients=[0.001]))\n",
     "\n",
-    "instrument_model = InstrumentModel(\n",
+    "instrument_model = sm.InstrumentModel(\n",
     "    resolution_model=resolution_model,\n",
     "    background_model=background_model,\n",
     ")\n",
@@ -87,7 +81,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3",
+   "display_name": "default",
    "language": "python",
    "name": "python3"
   },
@@ -101,7 +95,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.14.5"
+   "version": "3.14.6"
   }
  },
  "nbformat": 4,