Extend the notebook example by refining the Biso parameters

.github/workflows/test-ipynb.yml

@@ -0,0 +1,40 @@
+name: Testing Jupyter Notebooks
+
+on:
+  workflow_dispatch:
+  pull_request:
+    branches:
+      - "**"
+
+jobs:
+  test:
+    timeout-minutes: 30
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [macos-latest, ubuntu-latest, windows-latest]
+        python-version: ['3.10', '3.11', '3.12']
+
+    runs-on: ${{ matrix.os }}
+
+    steps:
+      - name: Check-out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python environment
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Upgrade package installer for Python
+        shell: bash
+        run: python -m pip install --upgrade pip
+
+      - name: Install Python dependences
+        shell: bash
+        run: pip install '.[dev]'
+
+      - name: Run tests on Jupyter Notebooks
+        shell: bash
+        run: pytest --nbmake examples/*ipynb --nbmake-timeout=300 -n=auto

README.md

@@ -14,6 +14,8 @@
 
 ## Getting Started
 
+Currently, easydiffraction is in beta and has not been released on PyPI. Please use the alternative method given below to install easydiffraction from our GitHub repository.
+
 ### Install EasyDiffraction python library
 
 * Create and go to, e.g., **easydiffraction** directory (*optional*)
@@ -31,7 +33,7 @@
   ```
 * Install **easydiffraction**
   ```
-  pip install easydiffraction
+  pip install easydiffraction --extra-index-url https://easyscience.github.io/pypi
   ```
 
 ## Examples
@@ -42,7 +44,7 @@
 
 * Install **easydiffraction**, including `charts` extras for visualization
   ```
-  pip install 'easydiffraction[charts]'
+  pip install 'easydiffraction[charts]' --extra-index-url https://easyscience.github.io/pypi
   ```
 * Install Jupyter Notebook
   ```

easydiffraction/Job.py

@@ -2,6 +2,7 @@
 # SPDX-License-Identifier: BSD-3-Clause
 # © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffraction
 
+import builtins
 import importlib.util
 import time
 from copy import deepcopy
@@ -59,6 +60,10 @@
 except ImportError:
     print("pandas not installed")
 
+try:
+    from IPython.display import display
+except ImportError:
+    pass
 
 T_ = TypeVar('T_')
 
@@ -744,7 +749,7 @@ def show_analysis_chart(self):
 
         y_calc = self.calculate_profile()
 
-        peak_idx, _ = find_peaks(y_calc)  #, prominence=1)
+        peak_idx, _ = find_peaks(y_calc)
         x_bragg = self.experiment.x.data[peak_idx]
         y_bragg = np.zeros_like(x_bragg)
 
@@ -759,8 +764,8 @@ def show_analysis_chart(self):
         )
 
         trace_bragg = go.Scatter(
-            x=x_bragg,  # np.random.uniform(low=self.experiment.x.data.min(), high=self.experiment.x.data.max(), size=(50,)),
-            y=y_bragg,  #np.zeros(50),
+            x=x_bragg,
+            y=y_bragg,
             xaxis='x2',
             yaxis='y2',
             line=dict(color='rgb(230, 171, 2)'),  #color=px.colors.qualitative.Plotly[9]),
@@ -778,7 +783,7 @@ def show_analysis_chart(self):
             y=self.background,
             xaxis='x3',
             yaxis='y3',
-            line=dict(color='gray'),  # default: width=2?
+            line=dict(color='gray'),
             mode='lines',
             name='Background (Ibkg)'
         )
@@ -841,27 +846,25 @@ def show_analysis_chart(self):
                 title_text=x_axis_title,
                 anchor='y',
                 range=[x_min, x_max],
-                # linecolor='blue',
                 showline=True, mirror=True, zeroline=False
             ),
             xaxis2=dict(
+                matches='x',
                 anchor='y2',
                 range=[x_min, x_max],
-                # linecolor='green',
                 showline=True, mirror=True, zeroline=False, showticklabels=False
             ),
             xaxis3=dict(
+                matches='x',
                 anchor='y3',
                 range=[x_min, x_max],
-                # linecolor='red',
                 showline=True, mirror=True, zeroline=False, showticklabels=False
             ),
             yaxis=dict(
                 title_text='Imeas - Icalc',
                 domain=[0, resid_height / full_height - 0.01],
                 range=[resid_y_min, resid_y_max],
                 tickvals=[int(resid_y_min), 0, int(resid_y_max)],
-                # nticks = 3,
                 showline=True, mirror=True, showgrid=False
             ),
             yaxis2=dict(
@@ -877,12 +880,14 @@ def show_analysis_chart(self):
         )
 
         fig = go.Figure(data=data, layout=layout)
-
-        # fig.update_xaxes(showline=True, mirror=True)
-        # fig.update_yaxes(showline=True, mirror=True)
-
         fig.show()
 
+    def is_notebook(self):
+        '''
+        Check if the code is running in a Jupyter notebook.
+        '''
+        return hasattr(builtins, "__IPYTHON__")
+
     def print_free_parameters(self):
         '''
         Print the free parameters.
@@ -893,11 +898,14 @@ def print_free_parameters(self):
                 parameters['names'].append(parameter.display_name)
                 parameters['values'].append(parameter.raw_value)
                 parameters['errors'].append(parameter.error)
-                parameters['units'].append(f'{parameter.unit:~H}')
+                parameters['units'].append(f'{parameter.unit:~P}')
             df = pd.DataFrame(parameters)
             df.index += 1
             df.style.format(precision=5)
-            return df
+            if self.is_notebook():
+                display(df)
+            else:
+                print(df)
         else:
             for parameter in self.get_fit_parameters():
                 print(parameter)

examples/Change_minimizer.ipynb

@@ -52,7 +52,7 @@
     "    print(\"Running in Google Colab\")\n",
     "    # Install the easydiffraction library if it is not installed (including charts extras)\n",
     "    if importlib.util.find_spec(\"easydiffraction\") is None:\n",
-    "        !pip install 'easydiffraction[charts]'\n",
+    "        !pip install 'easydiffraction[charts]' --extra-index-url https://easyscience.github.io/pypi\n",
     "    # Download the data files to be read in notebook\n",
     "    for fname in ['lbco.cif', 'hrpt.xye']:\n",
     "        pooch.retrieve(\n",

examples/Fitting_PD-NEUT-TOF_NCAF-WISH.ipynb

@@ -52,7 +52,7 @@
     "    print(\"Running in Google Colab\")\n",
     "    # Install the easydiffraction library if it is not installed (including charts extras)\n",
     "    if importlib.util.find_spec(\"easydiffraction\") is None:\n",
-    "        !pip install 'easydiffraction[charts]'\n",
+    "        !pip install 'easydiffraction[charts]' --extra-index-url https://easyscience.github.io/pypi\n",
     "    # Download the data files to be read in notebook\n",
     "    for fname in ['ncaf.cif', 'wish.xye']:\n",
     "        pooch.retrieve(\n",

examples/Fitting_PD-NEUT-TOF_Si-SEPD.ipynb

@@ -38,8 +38,8 @@
      "colab"
     ],
     "ExecuteTime": {
-     "end_time": "2024-10-21T21:25:54.088976Z",
-     "start_time": "2024-10-21T21:25:54.072841Z"
+     "end_time": "2024-10-22T10:09:35.372871Z",
+     "start_time": "2024-10-22T10:09:35.339954Z"
     }
    },
    "source": [
@@ -52,7 +52,7 @@
     "    print(\"Running in Google Colab\")\n",
     "    # Install the easydiffraction library if it is not installed (including charts extras)\n",
     "    if importlib.util.find_spec(\"easydiffraction\") is None:\n",
-    "        !pip install 'easydiffraction[charts]'\n",
+    "        !pip install 'easydiffraction[charts]' --extra-index-url https://easyscience.github.io/pypi\n",
     "    # Download the data files to be read in notebook\n",
     "    for fname in ['sepd.xye']:\n",
     "        pooch.retrieve(\n",

examples/data/lbco.cif

@@ -19,7 +19,7 @@ _atom_site.fract_z
 _atom_site.occupancy
 _atom_site.ADP_type
 _atom_site.B_iso_or_equiv
-La La 0 0 0 0.5 Biso 0.49
-Ba Ba 0 0 0 0.5 Biso 0.49
-Co Co 0.5 0.5 0.5 1 Biso 0.26
-O O 0 0.5 0.5 1 Biso 1.40
+La La 0 0 0 0.5 Biso 0.1
+Ba Ba 0 0 0 0.5 Biso 0.1
+Co Co 0.5 0.5 0.5 1 Biso 0.1
+O O 0 0.5 0.5 1 Biso 0.1

pyproject.toml

@@ -4,7 +4,7 @@ build-backend = 'hatchling.build'
 
 [project]
 name = 'easydiffraction'
-version = '0.1.0'
+version = '0.1.1'
 description = 'Making diffraction data analysis and modelling easy'
 authors = [{name = 'EasyDiffractionLib contributors'}]
 readme = 'README.md'
@@ -23,9 +23,9 @@ classifiers = [
 ]
 requires-python = '>=3.9,<3.13'
 dependencies = [
-    'cryspy @ git+https://github.com/ikibalin/cryspy.git@beta',
+    'cryspy @ git+https://github.com/EasyScience/cryspy.git@beta',
     'EasyScience @ git+https://github.com/EasyScience/EasyScience.git@free-params',
-    'easycrystallography @ git+https://github.com/EasyScience/EasyCrystallography.git@develop',
+    'easycrystallography @ git+https://github.com/EasyScience/EasyCrystallography.git@adp_cif_naming',
     'pycifrw>=4.4.1',
     'pooch',
     'funcy'
@@ -41,12 +41,14 @@ dev = [
     'flake8>=6.0.0',
     'pytest>=5.2',
     'pytest-cov>=3.0.0',
+    'pytest-xdist',  # used with nbmake to run parallel tests
+    'nbmake',  # testing jupyter notebooks
+    'playwright',  # needed for nbmake
+    'jinja2',  # nedeed for nbmake
     'ruff',
     'toml>=0.10',
     'yapf>=0.31.0',
     'requests',
-    'py3Dmol',
-    'bokeh',
     'gemmi',
     'periodictable',
 ]