Add more pycrysfml integration

.copier-answers.yml

@@ -1,6 +1,6 @@
 # WARNING: Do not edit this file manually.
 # Any changes will be overwritten by Copier.
-_commit: v0.10.1-33-g0f85abf
+_commit: v0.10.1-40-g29e2ccf
 _src_path: gh:easyscience/templates
 app_docs_url: https://easyscience.github.io/diffraction-app
 app_doi: 10.5281/zenodo.18163581

.github/workflows/backmerge.yml

@@ -20,6 +20,11 @@ concurrency:
   group: backmerge-master-into-develop
   cancel-in-progress: false
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   backmerge:
     runs-on: ubuntu-latest

.github/workflows/cleanup.yml

@@ -61,6 +61,11 @@ on:
           - 'false'
           - 'true'
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   del-runs:
     runs-on: ubuntu-latest

.github/workflows/coverage.yml

@@ -26,6 +26,9 @@ concurrency:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Run docstring coverage

.github/workflows/dashboard.yml

@@ -14,6 +14,9 @@ env:
   DEVELOP_BRANCH: develop
   REPO_OWNER: ${{ github.repository_owner }}
   REPO_NAME: ${{ github.event.repository.name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   dashboard:

.github/workflows/docs.yml

@@ -48,6 +48,9 @@ env:
   IS_RELEASE_TAG: ${{ startsWith(github.ref, 'refs/tags/v') }}
   GITHUB_REPOSITORY: ${{ github.repository }}
   NOTEBOOKS_DIR: tutorials
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Single job that builds and deploys documentation.

.github/workflows/issues-labels.yml

@@ -11,6 +11,11 @@ on:
 permissions:
   issues: write
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   check-labels:
     if: github.actor != 'easyscience[bot]'

.github/workflows/lint-format.yml

@@ -34,6 +34,9 @@ permissions:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   lint-format:

.github/workflows/pypi-publish.yml

@@ -10,6 +10,11 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   pypi-publish:
     runs-on: ubuntu-latest

.github/workflows/pypi-test.yml

@@ -20,6 +20,9 @@ permissions:
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
   DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Test installation from PyPI on multiple OS

.github/workflows/release-notes.yml

@@ -10,6 +10,11 @@ on:
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   draft-release-notes:
     permissions:

.github/workflows/release-pr.yml

@@ -24,6 +24,9 @@ permissions:
 env:
   DEFAULT_BRANCH: ${{ github.event.repository.default_branch }}
   SOURCE_BRANCH: ${{ inputs.source_branch || 'develop' }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   create-pull-request:

.github/workflows/security.yml

@@ -44,6 +44,11 @@ permissions:
   contents: read
   security-events: write
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   codeql:
     name: Code scanning

.github/workflows/test-trigger.yml

@@ -10,6 +10,11 @@ on:
 permissions:
   contents: read
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   code-tests-trigger:
     runs-on: ubuntu-latest

.github/workflows/test.yml

@@ -46,6 +46,9 @@ env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
   PY_VERSIONS: '3.12 3.14'
   PIXI_ENVS: 'py-312-env py-314-env'
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Set up environment variables
@@ -214,7 +217,14 @@ jobs:
             # platform-specific deps so this is a no-op on Linux/Windows.
             echo "Adding libc++ for macOS (required by diffpy.pdffit2)"
             pixi add --platform osx-arm64 libcxx
-            pixi add --platform osx-64 libcxx
+
+            # Doing this in a hacky way, as pixi does not support adding 
+            # dependencies from a custom PyPI index with a CLI command without
+            # specifying full wheel name.
+            echo "Adding pycrysfml from custom PyPI index"
+            echo '' >> pixi.toml
+            echo '[pypi-dependencies]' >> pixi.toml
+            echo 'pycrysfml = { version = ">=0.2.1", index = "https://easyscience.github.io/pypi/" }' >> pixi.toml
 
             echo "Looking for wheel in ../dist/py$py_ver/"
             ls -l "../dist/py$py_ver/"

.github/workflows/tutorial-tests-trigger.yml

@@ -10,6 +10,11 @@ on:
 permissions:
   contents: read
 
+# Opt into Node.js 24 for all JavaScript actions.
+# Remove once all referenced actions natively target Node 24.
+env:
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
+
 jobs:
   tutorial-tests-trigger:
     runs-on: ubuntu-latest

.github/workflows/tutorial-tests.yml

@@ -27,6 +27,9 @@ concurrency:
 # Set the environment variables to be used in all jobs defined in this workflow
 env:
   CI_BRANCH: ${{ github.head_ref || github.ref_name }}
+  # Opt into Node.js 24 for all JavaScript actions.
+  # Remove once all referenced actions natively target Node 24.
+  FORCE_JAVASCRIPT_ACTIONS_TO_NODE24: true
 
 jobs:
   # Job 1: Test tutorials as scripts and notebooks on multiple OS

.gitignore

@@ -44,3 +44,8 @@ CMakeLists.txt.user*
 .cache/
 *.log
 *.zip
+
+# ED
+# Used to fetch tutorials data during their runtime. Need to have '/' at
+# the beginning to avoid ignoring 'data' module in the src/.
+/data/

docs/docs/tutorials/ed-1.ipynb

@@ -3,7 +3,7 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "id": "e1c6f514",
+   "id": "9cc849f9",
    "metadata": {
     "tags": [
      "hide-in-docs"
@@ -108,6 +108,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# Add structure from downloaded CIF\n",
     "project.structures.add_from_cif_path(structure_path)"
    ]
   },
@@ -137,6 +138,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# Add experiment from downloaded CIF\n",
     "project.experiments.add_from_cif_path(expt_path)"
    ]
   },
@@ -145,7 +147,7 @@
    "id": "11",
    "metadata": {},
    "source": [
-    "## Step 4: Perform Analysis"
+    "## Step 4: Perform Analysis (cryspy)"
    ]
   },
   {
@@ -168,7 +170,7 @@
    "outputs": [],
    "source": [
     "# Show fit results summary\n",
-    "project.analysis.show_fit_results()"
+    "project.analysis.display.fit_results()"
    ]
   },
   {
@@ -178,6 +180,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "# Show defined experiment names\n",
     "project.experiments.show_names()"
    ]
   },
@@ -188,15 +191,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "project.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)"
+    "# Plot measured vs. calculated diffraction patterns\n",
+    "project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)"
    ]
   },
   {
    "cell_type": "markdown",
    "id": "16",
    "metadata": {},
    "source": [
-    "## Step 5: Show Project Summary"
+    "## Step 5: Perform Analysis (crysfml)"
    ]
   },
   {
@@ -206,7 +210,42 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "project.summary.show_report()"
+    "# Change calculation engine from 'cryspy' to 'crysfml'\n",
+    "project.experiments['hrpt'].show_supported_calculator_types()\n",
+    "project.experiments['hrpt'].calculator_type = 'crysfml'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "18",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Start refinement\n",
+    "project.analysis.fit()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "19",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Show fit results summary\n",
+    "project.analysis.display.fit_results()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "20",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Plot measured vs. calculated diffraction patterns\n",
+    "project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)"
    ]
   }
  ],

docs/docs/tutorials/ed-1.py

@@ -40,6 +40,7 @@
 structure_path = ed.download_data(id=1, destination='data')
 
 # %%
+# Add structure from downloaded CIF
 project.structures.add_from_cif_path(structure_path)
 
 # %% [markdown]
@@ -50,10 +51,11 @@
 expt_path = ed.download_data(id=2, destination='data')
 
 # %%
+# Add experiment from downloaded CIF
 project.experiments.add_from_cif_path(expt_path)
 
 # %% [markdown]
-# ## Step 4: Perform Analysis
+# ## Step 4: Perform Analysis (cryspy)
 
 # %%
 # Start refinement. All parameters, which have standard uncertainties
@@ -65,13 +67,29 @@
 project.analysis.display.fit_results()
 
 # %%
+# Show defined experiment names
 project.experiments.show_names()
 
 # %%
+# Plot measured vs. calculated diffraction patterns
 project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)
 
 # %% [markdown]
-# ## Step 5: Show Project Summary
+# ## Step 5: Perform Analysis (crysfml)
 
 # %%
-project.summary.show_report()
+# Change calculation engine from 'cryspy' to 'crysfml'
+project.experiments['hrpt'].show_supported_calculator_types()
+project.experiments['hrpt'].calculator_type = 'crysfml'
+
+# %%
+# Start refinement
+project.analysis.fit()
+
+# %%
+# Show fit results summary
+project.analysis.display.fit_results()
+
+# %%
+# Plot measured vs. calculated diffraction patterns
+project.plotter.plot_meas_vs_calc(expt_name='hrpt', show_residual=True)