easydiffraction 0.5.8__tar.gz → 0.6.0__tar.gz

easydiffraction-0.6.0/.github/workflows/draft-release-notes.yml

@@ -0,0 +1,47 @@
+# Drafts your next Release notes as pull requests are merged into
+# default branch
+
+name: Update release draft
+
+on:
+  # Runs on pushes targeting the default branch (updates the real draft release)
+  push:
+    branches:
+      - main
+      - master
+
+jobs:
+  draft-release-notes:
+    permissions:
+      # write permission is required to create a github release
+      contents: write
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Drafts the next release notes
+        uses: enhantica/drafterino@v1
+
+        with:
+          config: |
+            title: 'easydiffraction $COMPUTED_VERSION'
+            tag: 'v$COMPUTED_VERSION'
+            note-template: '- $PR_TITLE (#$PR_NUMBER)'
+
+            default-bump: post
+
+            major-bump-labels: ['[scope] significant']
+            minor-bump-labels: ['[scope] enhancement']
+            patch-bump-labels: ['[scope] bug', '[scope] maintenance']
+            post-bump-labels: ['[scope] documentation']
+
+            release-notes:
+              - title: 'Added'
+                labels: ['[scope] significant', '[scope] enhancement']
+              - title: 'Fixed'
+                labels: ['[scope] bug']
+              - title: 'Changed'
+                labels: ['[scope] maintenance', '[scope] documentation']
+
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/.github/workflows/test-code.yaml

@@ -197,6 +197,19 @@ jobs:
           export PYTHONPATH="$(pwd)/src${PYTHONPATH:+:$PYTHONPATH}"
           python -m pytest tests/functional_tests/ --color=yes -n auto
 
+      # Ensures a consistent high version like 999.0.0 when not on a tagged commit
+      # This is needed for testing the package in the next job, as its version
+      # must be higher than the PyPI version for pip to prefer the local version.
+      - name: Inject fallback version tag if not on a real tag
+        shell: bash
+        run: |
+          if ! git describe --tags --match "v*" --exact-match > /dev/null 2>&1; then
+            echo "Not on release tag — applying fallback 'v999.0.0'"
+            git tag v999.0.0
+          else
+            echo "On a valid tag"
+          fi
+
       - name: Create Python package for the next job
         shell: bash
         run: python -m build --wheel --outdir dist

easydiffraction-0.6.0/.prettierignore

@@ -0,0 +1 @@
+.pixi

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: easydiffraction
-Version: 0.5.8
+Version: 0.6.0
 Summary: Diffraction data analysis
 Project-URL: homepage, https://easydiffraction.org
 Project-URL: documentation, https://docs.easydiffraction.org/lib

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/docs/mkdocs.yml

@@ -27,9 +27,14 @@ extra:
       name: EasyDiffraction Library Source Code on GitHub
 
 # Jupyter notebooks
-#plugins:
-#  - mkdocs-jupyter:
-#      execute_ignore:
+plugins:
+  - mkdocs-jupyter:
+      execute_ignore:
+        - 'quick*.ipynb'
+        - 'basic*.ipynb'
+        - 'advanced*.ipynb'
+        - 'cryst*.ipynb'
+        - 'pdf*.ipynb'
 #        - '*emcee*.ipynb' # Ignore notebooks with 'emcee' in the name from execution
 
 ##################

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/docs/user-guide/analysis-workflow/experiment.md

@@ -132,7 +132,7 @@ which makes it easier to manage the experiment:
    depends on the experiment type, but generally includes columns for 2θ angle
    or TOF and intensity.
 
-### 1. Instrument Category
+### 1. Instrument Category { #instrument-category }
 
 ```python
 # Modify the default instrument parameters
@@ -140,7 +140,15 @@ project.experiments['hrpt'].instrument.setup_wavelength = 1.494
 project.experiments['hrpt'].instrument.calib_twotheta_offset = 0.6
 ```
 
-### 2. Peak Category
+### 2. Excluded Regions Category { #excluded-regions-category }
+
+```python
+# Add excluded regions to the experiment
+project.experiments['hrpt'].excluded_regions.add(start=0, end=10)
+project.experiments['hrpt'].excluded_regions.add(start=160, end=180)
+```
+
+### 3. Peak Category { #peak-category }
 
 ```python
 # Select the desired peak profile type
@@ -154,7 +162,7 @@ project.experiments['hrpt'].peak.broad_lorentz_x = 0
 project.experiments['hrpt'].peak.broad_lorentz_y = 0.1
 ```
 
-### 3. Background Category
+### 4. Background Category { #background-category }
 
 ```python
 # Select the desired background type
@@ -168,14 +176,14 @@ project.experiments['hrpt'].background.add(x=110, y=170)
 project.experiments['hrpt'].background.add(x=165, y=170)
 ```
 
-### 4. Linked Phases Category
+### 5. Linked Phases Category { #linked-phases-category }
 
 ```python
 # Link the sample model defined in the previous step to the experiment
 project.experiments['hrpt'].linked_phases.add(id='lbco', scale=10.0)
 ```
 
-### 5. Measured Data Category
+### 6. Measured Data Category { #measured-data-category }
 
 If you do not have a CIF file for your experiment, you can load measured data
 from a file in a supported format. The measured data will be automatically

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/docs/user-guide/analysis-workflow/model.md

@@ -79,21 +79,21 @@ to manage the model:
 3. **Atom Sites Category**: Describes the positions and properties of atoms
    within the unit cell.
 
-### 1. Space Group Category
+### 1. Space Group Category { #space-group-category }
 
 ```python
 # Set space group
 project.sample_models['nacl'].space_group.name_h_m = 'F m -3 m'
 ```
 
-### 2. Cell Category
+### 2. Cell Category { #cell-category }
 
 ```python
 # Define unit cell parameters
 project.sample_models['nacl'].cell.length_a = 5.691694
 ```
 
-### 3. Atom Sites Category
+### 3. Atom Sites Category { #atom-sites-category }
 
 ```python
 # Add atomic sites

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/docs/user-guide/first-steps.md

@@ -87,8 +87,11 @@ example datasets without having to manually download them.
 
 EasyDiffraction provides several helper methods to display supported engines for
 calculation, minimization, and plotting. These methods can be called on the
-`Project` instance to display the available options for each category. For
-example, you can use the `show_supported_calculators()` method to see which
+`Project` instance to display the available options for different categories.
+
+### Supported calculators
+
+For example, you can use the `show_supported_calculators()` method to see which
 calculation engines are available for use in your project:
 
 ```python
@@ -105,8 +108,19 @@ An example of the output for the `show_supported_calculators()` method is:
 | cryspy     | CrysPy library for crystallographic calculations            |
 | pdffit     | PDFfit2 library for pair distribution function calculations |
 
-Other helper methods include those for showing the available parameters grouped
-in different categories. For example, you can use:
+### Supported minimizers
+
+You can also check the available minimizers using the
+`show_available_minimizers()` method:
+
+```python
+project.show_available_minimizers()
+```
+
+### Available parameters
+
+EasyDiffraction provides several methods for showing the available parameters
+grouped in different categories. For example, you can use:
 
 - `project.analysis.show_all_params()` – to display all available parameters for
   the analysis step.
@@ -135,6 +149,22 @@ method is:
 | 60  | project.experiments['hrpt'].peak.broad_gauss_v         | hrpt.peak.broad_gauss_v          |
 | 61  | project.experiments['hrpt'].peak.broad_gauss_w         | hrpt.peak.broad_gauss_w          |
 
+### Supported plotters
+
+To see the available plotters, you can use the `show_available_plotters()`
+method on the `plotter` attribute of the `Project` instance:
+
+```python
+project.plotter.show_supported_engines()
+```
+
+An example of the output is:
+
+| Engine       | Description                                |
+| ------------ | ------------------------------------------ |
+| asciichartpy | Console ASCII line charts                  |
+| plotly       | Interactive browser-based graphing library |
+
 ## Data analysis workflow
 
 Once the EasyDiffraction package is imported, you can proceed with the **data

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/pyproject.toml

@@ -16,9 +16,9 @@ classifiers = [
   'Operating System :: OS Independent',
   'Programming Language :: Python :: 3 :: Only',
   'Programming Language :: Python :: 3',
-  "Programming Language :: Python :: 3.11",
-  "Programming Language :: Python :: 3.12",
-  "Programming Language :: Python :: 3.13",
+  'Programming Language :: Python :: 3.11',
+  'Programming Language :: Python :: 3.12',
+  'Programming Language :: Python :: 3.13',
 ]
 requires-python = '>=3.11,<3.14'
 dependencies = [
@@ -113,10 +113,13 @@ source = 'versioningit' # Use versioningit to manage the version
 # source code.
 
 [tool.versioningit.format]
-distance = '{base_version}.post{distance}'       # example: 1.2.3.post42
-dirty = '{base_version}'                         # example: 1.2.3
-distance-dirty = '{base_version}.post{distance}' # example: 1.2.3.post42
+distance = '{base_version}+d{distance}'       # example: 0.5.8+d3, 1.2.3.post4+d2
+dirty = '{base_version}'                      # example: 0.5.8, 1.2.3.post4
+distance-dirty = '{base_version}+d{distance}' # 
 
+# Configure how versioningit detects versions from Git
+# - 'match' ensures it only considers tags starting with 'v'
+# - 'default-tag' is used as a fallback when no matching tag is found
 [tool.versioningit.vcs]
 method = 'git'
 match = ['v*']

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/analysis/calculators/calculator_crysfml.py

@@ -20,7 +20,8 @@ try:
 
     print("✅ 'pycrysfml' calculation engine is successfully imported.")
 except ImportError:
-    print("⚠️ 'pycrysfml' module not found. This calculation engine will not be available.")
+    # TODO: Add the following print to debug mode
+    # print("⚠️ 'pycrysfml' module not found. This calculation engine will not be available.")
     cfml_py_utilities = None
 
 

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/analysis/calculators/calculator_cryspy.py

@@ -23,7 +23,8 @@ try:
 
     print("✅ 'cryspy' calculation engine is successfully imported.")
 except ImportError:
-    print("⚠️ 'cryspy' module not found. This calculation engine will not be available.")
+    # TODO: Add the following print to debug mode
+    # print("⚠️ 'cryspy' module not found. This calculation engine will not be available.")
     cryspy = None
 
 

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/analysis/calculators/calculator_pdffit.py

@@ -19,7 +19,8 @@ try:
     redirect_stdout(open(os.path.devnull, 'w'))  # silence the C++ engine output
     print("✅ 'pdffit' calculation engine is successfully imported.")
 except ImportError:
-    print("⚠️ 'pdffit' module not found. This calculation engine will not be available.")
+    # TODO: Add the following print to debug mode
+    # print("⚠️ 'pdffit' module not found. This calculation engine will not be available.")
     pdffit = None
 
 

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/analysis/minimizers/minimizer_factory.py

@@ -55,6 +55,9 @@ class MinimizerFactory:
 
     @classmethod
     def show_available_minimizers(cls) -> None:
+        # TODO: Rename this method to `show_supported_minimizers` for
+        #  consistency with other methods in the library. E.g.
+        #  `show_supported_calculators`, etc.
         """
         Display a table of available minimizers and their descriptions.
         """

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/experiments/collections/excluded_regions.py

@@ -21,23 +21,23 @@ class ExcludedRegion(Component):
     def cif_category_key(self) -> str:
         return 'excluded_region'
 
-    def __init__(self, minimum: float, maximum: float):
+    def __init__(self, start: float, end: float):
         super().__init__()
 
-        self.minimum = Descriptor(
-            value=minimum,
-            name='minimum',
-            cif_name='minimum',
+        self.start = Descriptor(
+            value=start,
+            name='start',
+            cif_name='start',
         )
-        self.maximum = Parameter(
-            value=maximum,
-            name='maximum',
-            cif_name='maximum',
+        self.end = Parameter(
+            value=end,
+            name='end',
+            cif_name='end',
         )
 
         # Select which of the input parameters is used for the
         # as ID for the whole object
-        self._entry_id = f'{minimum}-{maximum}'
+        self._entry_id = f'{start}-{end}'
 
         # Lock further attribute additions to prevent
         # accidental modifications by users
@@ -65,7 +65,7 @@ class ExcludedRegions(Collection):
         pattern = experiment.datastore.pattern
 
         # Boolean mask for points within the new excluded region
-        in_region = (pattern.full_x >= item.minimum.value) & (pattern.full_x <= item.maximum.value)
+        in_region = (pattern.full_x >= item.start.value) & (pattern.full_x <= item.end.value)
 
         # Update the exclusion mask
         pattern.excluded[in_region] = True
@@ -79,13 +79,13 @@ class ExcludedRegions(Collection):
         # TODO: Consider moving this to the base class
         #  to avoid code duplication with implementations in Background, etc.
         #  Consider using parameter names as column headers
-        columns_headers: List[str] = ['minimum', 'maximum']
+        columns_headers: List[str] = ['start', 'end']
         columns_alignment = ['left', 'left']
         columns_data: List[List[float]] = []
         for region in self._items.values():
-            minimum = region.minimum.value
-            maximum = region.maximum.value
-            columns_data.append([minimum, maximum])
+            start = region.start.value
+            end = region.end.value
+            columns_data.append([start, end])
 
         print(paragraph('Excluded regions'))
         render_table(

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/plotting/plotters/plotter_base.py

@@ -7,9 +7,8 @@ from abc import abstractmethod
 import numpy as np
 
 from easydiffraction.utils.utils import is_notebook
-from easydiffraction.utils.utils import is_pycharm
 
-DEFAULT_ENGINE = 'plotly' if is_notebook() or is_pycharm() else 'asciichartpy'
+DEFAULT_ENGINE = 'plotly' if is_notebook() else 'asciichartpy'
 DEFAULT_HEIGHT = 9
 DEFAULT_MIN = -np.inf
 DEFAULT_MAX = np.inf

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/plotting/plotters/plotter_plotly.py

@@ -104,6 +104,11 @@ class PlotlyPlotter(PlotterBase):
             layout=layout,
         )
 
+        # Format the axes ticks
+        # Keeps decimals for small numbers; groups thousands for large ones
+        fig.update_xaxes(tickformat=',.6~g', separatethousands=True)
+        fig.update_yaxes(tickformat=',.6~g', separatethousands=True)
+
         # Show the figure
 
         # In GitHub CI builds (e.g., during Jupyter Book generation), avoid

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/src/easydiffraction/utils/utils.py

@@ -5,6 +5,7 @@
 General utilities and helpers for easydiffraction.
 """
 
+import importlib
 import os
 import re
 from typing import List
@@ -79,14 +80,19 @@ def is_notebook() -> bool:
     if IPython is None:
         return False
 
+    if is_pycharm():  # Running inside PyCharm
+        return True
+    elif is_colab():  # Running inside Google Colab
+        return True
+
     try:
         shell = get_ipython().__class__.__name__  # noqa: F821
-        if shell == 'ZMQInteractiveShell':
-            return True  # Jupyter notebook or qtconsole
-        elif shell == 'TerminalInteractiveShell':
-            return False  # Terminal running IPython
-        else:
-            return False  # Other type (unlikely)
+        if shell == 'ZMQInteractiveShell':  # Jupyter notebook or qtconsole
+            return True
+        elif shell == 'TerminalInteractiveShell':  # Terminal running IPython
+            return False
+        else:  # Other type (unlikely)
+            return False
     except NameError:
         return False  # Probably standard Python interpreter
 
@@ -101,6 +107,19 @@ def is_pycharm() -> bool:
     return os.environ.get('PYCHARM_HOSTED') == '1'
 
 
+def is_colab() -> bool:
+    """
+    Determines if the current environment is Google Colab.
+
+    Returns:
+        bool: True if running in Google Colab PyCharm, False otherwise.
+    """
+    try:
+        return importlib.util.find_spec('google.colab') is not None
+    except ModuleNotFoundError:
+        return False
+
+
 def is_github_ci() -> bool:
     """
     Determines if the current process is running in GitHub Actions CI.

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/tests/functional_tests/fitting/test_powder-diffraction_multiphase.py

@@ -56,7 +56,7 @@ def test_single_fit_neutron_pd_tof_mcstas_lbco_si() -> None:
     project.experiments.add(expt)
 
     # Exclude regions from fitting
-    project.experiments['mcstas'].excluded_regions.add(minimum=108000, maximum=200000)
+    project.experiments['mcstas'].excluded_regions.add(start=108000, end=200000)
 
     # Prepare for fitting
     project.analysis.current_calculator = 'cryspy'

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/tools/prepare_notebooks.py

@@ -79,6 +79,13 @@ def ensure_bootstrap(nb) -> bool:
 
 def process_notebook(path: Path) -> int:
     nb = nbformat.read(path, as_version=4)
+
+    # Remove all 'tags' metadata from cells
+    for cell in nb.cells:
+        if 'tags' in cell.metadata:
+            cell.metadata.pop('tags')
+
+    # Add the bootstrap cell if needed
     changed = 0
     if ensure_bootstrap(nb):
         changed += 1

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/tutorials/cryst-struct_pd-neut-tof_multidata_NCAF-WISH.py

@@ -206,12 +206,12 @@ expt47.linked_phases.add('ncaf', scale=2.0)
 # #### Set Excluded Regions
 
 # %%
-expt56.excluded_regions.add(minimum=0, maximum=10010)
-expt56.excluded_regions.add(minimum=100010, maximum=200000)
+expt56.excluded_regions.add(start=0, end=10010)
+expt56.excluded_regions.add(start=100010, end=200000)
 
 # %%
-expt47.excluded_regions.add(minimum=0, maximum=10006)
-expt47.excluded_regions.add(minimum=100004, maximum=200000)
+expt47.excluded_regions.add(start=0, end=10006)
+expt47.excluded_regions.add(start=100004, end=200000)
 
 # %% [markdown]
 # ## Define Project

{easydiffraction-0.5.8 → easydiffraction-0.6.0}/tutorials/cryst-struct_pd-neut-tof_multiphase-LBCO-Si_McStas.py

@@ -240,8 +240,8 @@ project.plot_meas(expt_name='mcstas')
 # Add excluded regions.
 
 # %%
-experiment.excluded_regions.add(minimum=0, maximum=40000)
-experiment.excluded_regions.add(minimum=108000, maximum=200000)
+experiment.excluded_regions.add(start=0, end=40000)
+experiment.excluded_regions.add(start=108000, end=200000)
 
 # %% [markdown]
 # Show excluded regions.