easydiffraction 0.1.3__tar.gz → 0.1.5__tar.gz

easydiffraction-0.1.5/.github/workflows/release-drafter.yml

@@ -0,0 +1,37 @@
+# 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
+  push:
+    branches: [master]
+
+jobs:
+  update-release-draft:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: release-drafter/release-drafter@v6
+        id: create_release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Check-out repository
+        uses: actions/checkout@v4
+
+      # Zips the examples directory
+      - name: Zip examples directory
+        run: zip -r examples.zip examples/
+
+      # Uploads the zipped examples directory to the release draft
+      - name: Upload zipped examples directory
+        uses: actions/upload-release-asset@v1
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the create_release step above
+          asset_path: ./examples.zip
+          asset_name: examples.zip
+          asset_content_type: application/zip

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/.github/workflows/test-ipynb.yml

@@ -86,7 +86,8 @@ jobs:
         shell: bash
         run: >
           pytest 
-          --nbmake examples/*ipynb 
+          --nbmake examples 
+          --ignore-glob='examples/*emcee*'
           --nbmake-timeout=300 
           --color=yes
           -n=auto

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/.github/workflows/test-package.yaml

@@ -117,7 +117,8 @@ jobs:
       shell: bash
       run: >
         pytest 
-        --nbmake examples/*ipynb 
+        --nbmake examples 
+        --ignore-glob='examples/*emcee*'
         --nbmake-timeout=300 
         --color=yes
         -n=auto  

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/PKG-INFO

@@ -1,12 +1,12 @@
 Metadata-Version: 2.3
 Name: easydiffraction
-Version: 0.1.3
+Version: 0.1.5
 Summary: Making diffraction data analysis and modelling easy
 Project-URL: homepage, https://easydiffraction.org
 Project-URL: documentation, https://docs.easydiffraction.org/lib
 Project-URL: source, https://github.com/EasyScience/EasyDiffractionLib
 Project-URL: tracker, https://github.com/EasyScience/EasyDiffractionLib/issues
-Author: EasyDiffractionLib contributors
+Author-email: EasyDiffraction contributors <support@easydiffraction.org>
 License: BSD 3-Clause License
         
         Copyright (c) 2024, EasyDiffractionLib contributors (https://github.com/EasyScience/EasyDiffractionLib)
@@ -36,7 +36,6 @@ License: BSD 3-Clause License
         CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
         OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
         OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
-License-File: LICENSE
 Classifier: Development Status :: 4 - Beta
 Classifier: License :: OSI Approved :: BSD License
 Classifier: Operating System :: OS Independent
@@ -51,18 +50,17 @@ Requires-Python: <3.13,>=3.9
 Requires-Dist: cryspy
 Requires-Dist: easycrystallography
 Requires-Dist: easyscience
+Requires-Dist: pooch
 Provides-Extra: charts
 Requires-Dist: darkdetect; extra == 'charts'
 Requires-Dist: pandas; extra == 'charts'
 Requires-Dist: plotly; extra == 'charts'
-Requires-Dist: pooch; extra == 'charts'
 Requires-Dist: py3dmol; extra == 'charts'
 Provides-Extra: dev
 Requires-Dist: build; extra == 'dev'
 Requires-Dist: jinja2; extra == 'dev'
 Requires-Dist: nbmake; extra == 'dev'
 Requires-Dist: nbqa; extra == 'dev'
-Requires-Dist: pooch; extra == 'dev'
 Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
 Requires-Dist: pytest-xdist; extra == 'dev'

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/easydiffraction/Job.py

@@ -63,6 +63,7 @@ except ImportError:
     print("pandas not installed")
 
 try:
+    from IPython.display import HTML
     from IPython.display import display
 except ImportError:
     pass
@@ -139,6 +140,7 @@ class DiffractionJob(JobBase):
         self.sample = sample # container for phases
         self.interface = self.sample._interface
         self.analysis = analysis
+        self.update_job_type()
         # necessary for the fitter
         # TODO: remove the dependency on kwargs
         self._kwargs = {}
@@ -328,7 +330,14 @@ class DiffractionJob(JobBase):
         self.type.is_tof = self.experiment.is_tof
         self.type.is_sc = self.experiment.is_single_crystal
         self.type.is_2d = self.experiment.is_2d
-
+        # radiation
+        if hasattr(self.sample, 'pattern') and self.sample.pattern is not None:
+            if self.type.is_xray:
+                self.sample.pattern.radiation = "x-ray"
+            elif self.type.is_neut:
+                self.sample.pattern.radiation = "neutron"
+
+        # axis
         if self.type.is_tof:
             self._x_axis_name = "time"
             if self.pattern is not None:
@@ -586,16 +595,27 @@ class DiffractionJob(JobBase):
         if result is None:
             raise ValueError("Fitting failed")
 
+        # Print fitting result. If in a notebook, use emojis.
+        success_msg = "Success"
+        failure_msg = "Failure"
+        duration_msg = f"{end - start:.2f} s"
+        if self.is_notebook():
+            success_msg = f'🥳 {success_msg}'
+            failure_msg = f'😩 {failure_msg}'
+            duration_msg = f'⌛ {duration_msg}'
+        print("Fitting result")
         if result.success:
-            print("Fitting successful")
-            print(f"Duration: {end - start:.2f} s")
-            print(f"Reduced chi: {result.reduced_chi:.2f}")
+            reduced_chi_msg = f"{result.reduced_chi:.2f}"
+            if self.is_notebook():
+                reduced_chi_msg = f'👍 {reduced_chi_msg}'
+            print(f'Status: {success_msg}')
+            print(f'Duration: {duration_msg}')
+            print(f'Reduced χ²: {reduced_chi_msg}')
         else:
-            print("Fitting failed.")
+            print(f'Status: {failure_msg}')
 
         self.fitting_results = result
 
-
     ###### UTILITY METHODS ######
     def add_datastore(self, datastore: xr.Dataset):
         '''
@@ -631,7 +651,7 @@ class DiffractionJob(JobBase):
         phase = self.phases[id]
         cif = phase.cif
 
-        structure_view = py3Dmol.view(linked=False)
+        structure_view = py3Dmol.view(width=540, height=480, linked=False)
         structure_view.addModel(cif, 'cif')
         structure_view.setStyle({'sphere': {'colorscheme': 'Jmol', 'scale': .2},
                                  'stick': {'colorscheme': 'Jmol', 'radius': 0.1}})
@@ -639,8 +659,8 @@ class DiffractionJob(JobBase):
             structure_view.setBackgroundColor('#111')
         structure_view.addUnitCell()
         structure_view.replicateUnitCell(2, 2, 2)
-        structure_view.zoomTo()
-        structure_view.show()
+        structure_view.zoomTo()  # To zoom in to the center of the structure
+        structure_view.show()  # To display the contents of the view object on Jupyter notebook.
 
     def print_data(self):
         '''
@@ -727,6 +747,62 @@ class DiffractionJob(JobBase):
 
         fig.show()
 
+    def show_simulation_chart(self, show_legend=True):
+        '''
+        Show the simulation chart.
+        '''
+        if importlib.util.find_spec("plotly") is None:
+            print("Warning: Plotly not installed. Try `pip install plotly`.")
+            return
+
+        if self.type.is_pd and self.type.is_cwl:
+            x_axis_title = '2θ (degree)'
+            x = np.arange(self.instrument.twotheta_range_min.raw_value,
+                          self.instrument.twotheta_range_max.raw_value + self.instrument.twotheta_range_inc.raw_value,
+                          self.instrument.twotheta_range_inc.raw_value)
+        elif self.type.is_pd and self.type.is_tof:
+            x_axis_title = 'TOF (µs)'
+            x = np.arange(self.instrument.tof_range_min.raw_value,
+                          self.instrument.tof_range_max.raw_value + self.instrument.tof_range_inc.raw_value,
+                          self.instrument.tof_range_inc.raw_value)
+        else:
+            print(f"Warning: Simulation chart not available for this type of job '{self.type}'")
+            print("Supported types: 'pd-cwl' and 'pd-tof'")
+
+        y_calc = self.calculate_profile(x)
+
+        main_y_range = y_calc.max() - y_calc.min()
+        main_y_min = y_calc.min() - main_y_range / 10
+        main_y_max = y_calc.max() + main_y_range / 10
+
+        trace_calc = go.Scatter(
+            x=x,
+            y=y_calc,
+            line=dict(color='rgb(214, 39, 40)'),
+            mode='lines',
+            name='Total calculated (Icalc)'
+        )
+
+        data = [trace_calc]
+
+        layout = go.Layout(
+            autosize=True,
+            margin=dict(autoexpand=True,
+                        r=30, t=30, b=45),
+            legend=dict(yanchor="top", y=1.0,
+                        xanchor="right", x=1.0),
+            xaxis=dict(title_text=x_axis_title),
+            yaxis=dict(title_text='Icalc', range=[main_y_min, main_y_max]),
+        )
+
+        fig = go.Figure(data=data, layout=layout)
+
+        fig.update_xaxes(showline=True, mirror=True, zeroline=False)
+        fig.update_yaxes(showline=True, mirror=True, zeroline=False)
+        fig.update_layout(showlegend=show_legend)
+
+        fig.show()
+
     def show_analysis_chart(self, show_legend=True):
         '''
         Show the analysis chart.
@@ -939,27 +1015,27 @@ class DiffractionJob(JobBase):
         return f'{parent_name}.{display_name}'
 
     def _parameters(self):
-        parameters = {'name': [], 'value': [], 'error': [], 'unit': [], 'min': [], 'max': [], 'vary': []}
+        parameters = {'name': [], 'value': [], 'unit': [], 'error': [], 'min': [], 'max': [], 'vary': []}
         for parameter in self.get_parameters():
             if parameter.enabled:
                 name = self.get_full_parameter_name(parameter.unique_name, parameter.display_name, parameter.url)
-                parameters['name'].append(name)
+                parameters['name'].append(f'<name>{name}</name>')
                 parameters['value'].append(parameter.raw_value)
+                parameters['unit'].append(f'<unit>{parameter.unit:~P}</unit>')
                 parameters['error'].append(parameter.error) if parameter.error else parameters['error'].append('')
-                parameters['unit'].append(f'{parameter.unit:~P}')
                 parameters['min'].append(parameter.min)
                 parameters['max'].append(parameter.max)
                 parameters['vary'].append(parameter.free) if parameter.free else parameters['vary'].append('')
         return parameters
 
     def _free_parameters(self):
-        parameters = {'name': [], 'value': [], 'error': [], 'unit': []}
+        parameters = {'name': [], 'value': [], 'unit': [], 'error': []}
         for parameter in self.get_fit_parameters():
             name = self.get_full_parameter_name(parameter.unique_name, parameter.display_name, parameter.url)
-            parameters['name'].append(name)
+            parameters['name'].append(f'<name>{name}</name>')
             parameters['value'].append(parameter.raw_value)
+            parameters['unit'].append(f'<unit>{parameter.unit:~P}</unit>')
             parameters['error'].append(parameter.error)
-            parameters['unit'].append(f'{parameter.unit:~P}')
         return parameters
 
     def _show_parameters(self, parameters):
@@ -970,11 +1046,19 @@ class DiffractionJob(JobBase):
             df = pd.DataFrame(parameters)
             df.index += 1
             if self.is_notebook():
-                display(df.
-                        style.  # apply styles from below
-                        set_table_styles([dict(selector='th', props=[('text-align', 'left')])]).  # align header to left
-                        set_properties(subset=['name'], **{'text-align': 'left'}).  # align column 'name' to left
-                        format(precision=5))  # set precision
+                # convert the DataFrame to HTML
+                html = df.to_html(escape=False)
+                # align the header of the column 'name' to the left
+                html = html.replace('<th>name', '<th style="text-align: left;">name')
+                # remove the header of the column 'unit'
+                html = html.replace('<th>unit', '<th>')
+                # align the cells in the column 'name' to the left
+                html = html.replace('<td><name>', '<td style="text-align: left;">')
+                html = html.replace('</name></td>', '</td>')
+                # align the cells in the column 'unit' to the left and remove the left padding
+                html = html.replace('<td><unit>', '<td style="text-align: left; padding-left: 0px">')
+                html = html.replace('</unit></td>', '</td>')
+                display(HTML(html))
             else:
                 print(df)
         else:

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/easydiffraction/Profiles/P1D.py

@@ -14,6 +14,7 @@ from typing import Union
 
 from easyscience.Datasets.xarray import xr
 from easyscience.Objects.ObjectClasses import BaseObj
+from easyscience.Objects.ObjectClasses import Descriptor
 from easyscience.Objects.ObjectClasses import Parameter
 
 from easydiffraction.components.polarization import PolarizedBeam
@@ -244,6 +245,48 @@ class Instrument1DCWParameters(BaseObj):
             "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_instr/",
             "value": 0.0,
             "fixed": True,
+        },
+        "twotheta_range_min": {
+            "name": "twotheta_range_min",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 10.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "twotheta_range_max": {
+            "name": "twotheta_range_max",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 170.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "twotheta_range_inc": {
+            "name": "twotheta_range_inc",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 0.1,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_min": {
+            "name": "tof_range_min",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 10000.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_max": {
+            "name": "tof_range_max",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 100000.0,
+            "fixed": True,
+            "enabled": False,
+        },
+        "tof_range_inc": {
+            "name": "tof_range_inc",
+            "url": "https://docs.easydiffraction.org/lib/project/dictionaries/_pd_meas/",
+            "value": 5.0,
+            "fixed": True,
+            "enabled": False,
         }
     }
 
@@ -257,6 +300,12 @@ class Instrument1DCWParameters(BaseObj):
     reflex_asymmetry_p2: ClassVar[Parameter]
     reflex_asymmetry_p3: ClassVar[Parameter]
     reflex_asymmetry_p4: ClassVar[Parameter]
+    twotheta_range_min: ClassVar[Descriptor]
+    twotheta_range_max: ClassVar[Descriptor]
+    twotheta_range_inc: ClassVar[Descriptor]
+    tof_range_min: ClassVar[Descriptor]
+    tof_range_max: ClassVar[Descriptor]
+    tof_range_inc: ClassVar[Descriptor]
 
     def __init__(
         self,
@@ -270,6 +319,12 @@ class Instrument1DCWParameters(BaseObj):
         reflex_asymmetry_p2: Optional[Union[Parameter, float]] = None,
         reflex_asymmetry_p3: Optional[Union[Parameter, float]] = None,
         reflex_asymmetry_p4: Optional[Union[Parameter, float]] = None,
+        twotheta_range_min: Optional[Union[Descriptor, float]] = None,
+        twotheta_range_max: Optional[Union[Descriptor, float]] = None,
+        twotheta_range_inc: Optional[Union[Descriptor, float]] = None,
+        tof_range_min: Optional[Union[Descriptor, float]] = None,
+        tof_range_max: Optional[Union[Descriptor, float]] = None,
+        tof_range_inc: Optional[Union[Descriptor, float]] = None,
         interface: Optional[iF] = None,
     ):
         super(Instrument1DCWParameters, self).__init__(
@@ -299,6 +354,18 @@ class Instrument1DCWParameters(BaseObj):
             self.reflex_asymmetry_p3 = reflex_asymmetry_p3
         if reflex_asymmetry_p4 is not None:
             self.reflex_asymmetry_p4 = reflex_asymmetry_p4
+        if twotheta_range_min is not None:
+            self.twotheta_range_min = twotheta_range_min
+        if twotheta_range_max is not None:
+            self.twotheta_range_max = twotheta_range_max
+        if twotheta_range_inc is not None:
+            self.twotheta_range_inc = twotheta_range_inc
+        if tof_range_min is not None:
+            self.tof_range_min = tof_range_min
+        if tof_range_max is not None:
+            self.tof_range_max = tof_range_max
+        if tof_range_inc is not None:
+            self.tof_range_inc = tof_range_inc
         self.name = self._name
         self.interface = interface
 

{easydiffraction-0.1.3 → easydiffraction-0.1.5}/easydiffraction/__init__.py

@@ -9,6 +9,7 @@ from .components.phase import Phase as Phase
 from .components.phase import Phases as Phases
 from .components.site import Atoms as Atoms
 from .components.site import Site as Site
+from .io.download import download_from_repository
 from .Job import DiffractionJob as Job
 
-__all__ = ['Job']
+__all__ = ['Job', 'download_from_repository']

easydiffraction-0.1.5/easydiffraction/io/download.py

@@ -0,0 +1,24 @@
+# SPDX-FileCopyrightText: 2024 EasyDiffraction contributors
+# SPDX-License-Identifier: BSD-3-Clause
+# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffraction
+
+import pooch
+
+
+def download_from_repository(fname : str, branch : str = 'master', destination : str = 'data'):
+    '''
+    This function downloads a file from the EasyDiffraction repository on GitHub.
+    :param fname: The name of the file to download
+    :param destination: The destination folder to save the file
+    :return: None
+    '''
+    organisation = 'EasyScience'
+    repository = 'EasyDiffractionLib'
+    source = 'examples/data'
+    url = f'https://raw.githubusercontent.com/{organisation}/{repository}/refs/heads/{branch}/{source}/{fname}'
+    pooch.retrieve(
+        url=url,
+        known_hash=None,
+        fname=fname,
+        path=destination,
+    )