easydiffraction 0.1.6__tar.gz → 0.2.0__tar.gz

easydiffraction-0.2.0/.github/release-drafter.yml

@@ -0,0 +1,35 @@
+# This file is used to configure the Release Drafter GitHub Action
+# https://github.com/marketplace/actions/release-drafter
+
+name-template: 'EasyDiffraction $RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+categories:
+- title: 'Added'
+  labels:  # Labels to use to categorize a pull request as a feature
+    - 'enhancement'
+- title: 'Fixed'
+  labels:  # Labels to use to categorize a pull request as a bug fix
+    - 'bug'
+- title: 'Changed'
+  labels:  # Labels to use to categorize a pull request as a maintenance task
+    - 'chore'
+    - 'documentation'
+    - 'refactor'
+change-template: '- $TITLE (#$NUMBER)'
+change-title-escapes: '\<*_&' # You can add # and @ to disable mentions, and add ` to disable code blocks.
+version-resolver:
+  major:
+    labels:
+      - 'major'
+  minor:
+    labels:
+      - 'enhancement'
+  patch:
+    labels:
+      - 'bug'
+      - 'chore'
+      - 'documentation'
+      - 'refactor'
+  default: patch
+template: |
+  $CHANGES

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/delete-old-runs.yml

@@ -1,4 +1,5 @@
-# This workflow will delete old workflow runs based on the input parameters.
+# This workflow will delete old workflow runs based on the input
+# parameters.
 # https://github.com/Mattraks/delete-workflow-runs
 
 name: Delete old workflow runs

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/ossar-analysis.yml

@@ -1,4 +1,5 @@
-# Integrates a collection of open source static analysis tools with GitHub code scanning.
+# Integrates a collection of open source static analysis tools with
+# GitHub code scanning.
 # https://github.com/github/ossar-action
 
 name: Run security static analysis

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/pypi-publish.yml

@@ -1,4 +1,5 @@
-# Builds a Python package and publish it to PyPI when a new tag is created.
+# Builds a Python package and publish it to PyPI when a new tag is
+# created.
 
 name: Upload release to PyPI
 
@@ -19,6 +20,8 @@ jobs:
     steps:
     - name: Check-out repository
       uses: actions/checkout@v4
+      with:
+        fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
     - name: Set up Python
       uses: actions/setup-python@v5

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/release-drafter.yml

@@ -1,4 +1,5 @@
-# Drafts your next Release notes as pull requests are merged into default branch
+# Drafts your next Release notes as pull requests are merged into
+# default branch
 
 name: Update release draft
 
@@ -14,7 +15,7 @@ jobs:
 
     steps:
       - uses: release-drafter/release-drafter@v6
-        id: create_release
+        id: create-release
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
 
@@ -31,7 +32,7 @@ jobs:
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }} # This pulls from the create_release step above
+          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-0.1.6 → easydiffraction-0.2.0}/.github/workflows/test-code.yaml

@@ -44,6 +44,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -83,6 +85,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
+      with:
+        fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/test-ipynb.yml

@@ -34,6 +34,8 @@ jobs:
     steps:
       - name: Checkout repository
         uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
       - name: Set up Python
         uses: actions/setup-python@v5
@@ -69,6 +71,8 @@ jobs:
     steps:
       - name: Check-out repository
         uses: actions/checkout@v4
+        with:
+          fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
       - name: Set up Python environment
         uses: actions/setup-python@v5

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/test-package.yaml

@@ -51,6 +51,8 @@ jobs:
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
+      with:
+        fetch-depth: '0'  # full history with tags to get the version number by versioningit
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
@@ -104,6 +106,10 @@ jobs:
         name: EasyDiffractionLib_py${{ matrix.python-version }}_${{ matrix.os }}_${{ runner.arch }}
         path: .  # directory to extract downloaded zipped artifacts
 
+    # The local version must be higher than the PyPI version for pip to
+    # prefer the local version. So, after a new release and a new tag,
+    # remember to merge the master branch with the develop branch,
+    # and then create a new feature branch from the develop branch.
     - name: Install Python package from previous job with 'dev' extras
       run: pip install 'easydiffraction[dev]' --find-links=dist
 
@@ -117,7 +123,7 @@ jobs:
       shell: bash
       run: >
         pytest 
-        --nbmake examples 
+        --nbmake examples/
         --ignore-glob='examples/*emcee*'
         --nbmake-timeout=300 
         --color=yes

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/.github/workflows/verify-pr-labels.yml

@@ -1,4 +1,5 @@
-# Verifies if a pull request has at least one label from a set of valid labels before it can be merged.
+# Verifies if a pull request has at least one label from a set of valid
+# labels before it can be merged.
 
 name: Verify pull request labels
 
@@ -18,6 +19,6 @@ jobs:
       uses: jesusvasquez333/verify-pr-label-action@v1.4.0
       with:
         github-token: ${{ secrets.GITHUB_TOKEN }}
-        valid-labels: chore, fix, bugfix, bug, enhancement, feature, dependencies, documentation
+        valid-labels: 'enhancement, bug, chore, documentation, refactor'
         pull-request-number: ${{ github.event.pull_request.number }}
         disable-reviews: false

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/DEVELOPMENT.md

@@ -1,6 +1,6 @@
 # Development
 
-This is an example of a workflow that describes the development process. 
+This is an example of a workflow that describes the development process.
 
 * Clone EasyDiffractionLib repository
   ```console
@@ -27,18 +27,19 @@ This is an example of a workflow that describes the development process.
   ```console
   python -m pip install --upgrade pip
   ```
-* Install easydiffraction from root with `dev` extras for development 
+* Install easydiffraction from root with `dev` extras for development
   ```console
   pip install '.[dev]'
   ```
 * Make changes in the code
 * Run Ruff - Python linter and code formatter (configuration is in pyproject.toml)
   ```console
-  ruff check . --fix 
+  ruff check --fix  # Linting (overwriting files)
+  ruff format       # Formatting (overwriting files)
   ```
 * Run python tests
   ```console
-  pytest tests/ --color=yes -n auto 
+  pytest tests/ --color=yes -n auto
   ```
 * Clear all Jupyter notebooks output
   ```console

{easydiffraction-0.1.6 → easydiffraction-0.2.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: easydiffraction
-Version: 0.1.6
+Version: 0.2.0
 Summary: Making diffraction data analysis and modelling easy
 Project-URL: homepage, https://easydiffraction.org
 Project-URL: documentation, https://docs.easydiffraction.org/lib
@@ -65,6 +65,7 @@ Requires-Dist: pytest; extra == 'dev'
 Requires-Dist: pytest-cov; extra == 'dev'
 Requires-Dist: pytest-xdist; extra == 'dev'
 Requires-Dist: ruff; extra == 'dev'
+Requires-Dist: versioningit; extra == 'dev'
 Description-Content-Type: text/markdown
 
 <img src="https://raw.githubusercontent.com/EasyScience/EasyDiffractionApp/master/resources/images/ed_logo.svg" height="65">

easydiffraction-0.2.0/docs/dev/diagrams/classes.md

@@ -0,0 +1,95 @@
+* src
+  * easydiffraction (as before)
+    * calculators (as before)
+      * cryspy
+        * calculator.py (instead of calculators/cryspy.py)
+          * class Cryspy (as before)
+        * wrapper.py (instead of Interfaces/cryspyV2.py)
+          * class CryspyWrapper (instead of CryspyV2)
+      * pdffit2
+        * calculator.py (instead of calculators/pdffit2.py)
+          * class Pdffit2 (as before)
+        * wrapper.py (instead of Interfaces/pdffit2.py)
+          * class Pdffit2Wrapper (instead of Pdffit2)
+      * pycrysfml
+        * calculator.py (instead of calculators/CFML.py)
+          * class Pycrysfml (instead of CFML)
+        * wrapper.py (instead of Interfaces/CFML.py)
+          * class PycrysfmlWrapper (instead of CFML)
+      * \_\_init\_\_.py
+      * calculator_base.py (no equivalent in old API? Do we need it?)
+        * class CalculatorBase (no equivalent in old API? Do we need it?)
+      * wrapper_factory.py ??? (instead of interface.py)
+        * class WrapperFactory ??? (instead of InterfaceFactory)
+      * wrapper_base.py (instead of Interfaces/interfaceTemplate.py)
+        * class WrapperBase (instead of InterfaceTemplate)
+
+
+
+
+## Old structure
+
+* easydiffraction - As before
+  * calculators - As before
+    * \_\_init\_\_.py - As before
+    * CFML.py - Move to src/easydiffraction/calculators/pycrysfml/calculator.py
+      * class CFML - Rename to Pycrysfml
+    * cryspy.py - Move to src/easydiffraction/calculators/cryspy/calculator.py
+      * class Cryspy - As before
+    * GSASII.py - Remove
+    * pdffit2.py - Move to src/easydiffraction/calculators/pdffit2/calculator.py
+      * class Pdffit2 - As before
+  * components - Temporarily as before
+    * \_\_init\_\_.py
+    * phase.py
+    * polarization.py
+    * site.py
+  * elements - Temporarily as before
+    * Backgrounds
+      * \_\_init\_\_.py
+      * Background.py
+      * Factorial.py
+      * Point.py
+    * Experiments
+      * \_\_init\_\_.py
+      * Experiment.py
+      * Pattern.py
+    * \_\_init\_\_.py
+  * Interfaces
+    * \_\_init\_\_.py
+    * CFML.py - Move to src/easydiffraction/calculators/pycrysfml/wrapper.py
+      * class CFML - Rename to PycrysfmlWrapper
+    * cryspy.py - Remove
+    * cryspyV2.py - Move to src/easydiffraction/calculators/cryspy/wrapper.py
+      * class CryspyV2 - Rename to CryspyWrapper
+    * GSASII.py - Remove
+    * interfaceTemplate.py - Move to src/easydiffraction/calculators/wrapper_base.py
+      * class InterfaceTemplate - Rename to WrapperBase
+    * pdffit2.py - Move to src/easydiffraction/calculators/pdffit2/wrapper.py
+      * class Pdffit2 - Rename to Pdffit2Wrapper
+    * types.py
+  * io - Remove
+    * \_\_init\_\_.py - Remove
+    * cif.py - Remove
+    * cif_reader.py - From EDB. Move to EasyCrystallography
+    * cryspy_parser.py - Move to calculators/cryspy/...
+    * download.py - Remove
+      * def download_from_repository -> Move to easydiffraction/utils.py
+    * helpers.py - Remove
+  * Profiles - Temporarily as before
+    * \_\_init\_\_.py
+    * Analysis.py
+    * common.py
+    * Container.py
+    * Experiment.py
+    * JobType.py
+    * P1D.py
+    * Sample.py
+  * \_\_init\_\_.py - As before
+  * interfaces.py - Move to src/easydiffraction/calculators/wrapper_factory.py
+    * class InterfaceFactory - Rename to WrapperFactory
+  * Job.py - Rename to job.py
+  * Jobs.py - Remove
+  * main.py - As before
+  * Runner.py - Remove
+  * sample.py - Temporarily as before

easydiffraction-0.2.0/pyproject.toml

@@ -0,0 +1,147 @@
+###############################
+# Configuration for the project
+###############################
+
+[project]
+name = 'easydiffraction'
+dynamic = ['version']  # Use versioningit to manage the version
+description = 'Making diffraction data analysis and modelling easy'
+authors = [
+    { name = 'EasyDiffraction contributors', email = 'support@easydiffraction.org' }
+]
+readme = 'README.md'
+license = { file = 'LICENSE' }
+classifiers = [
+    'Topic :: Scientific/Engineering',
+    'Development Status :: 4 - Beta',
+    'License :: OSI Approved :: BSD License',
+    'Operating System :: OS Independent',
+    'Programming Language :: Python :: 3 :: Only',
+    'Programming Language :: Python :: 3',
+    'Programming Language :: Python :: 3.9',
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12'
+]
+requires-python = '>=3.9,<3.13'
+dependencies = [
+    'cryspy',  # For calculations of diffraction patterns
+    'pooch',  # For data fetching
+    'easyscience',  # The base library of the EasyScience framework
+    'easycrystallography',  # Crystallography tools of the EasyScience framework
+]
+
+[project.optional-dependencies]
+dev = [
+    'build',  # For building the package
+    'pytest',  # For testing
+    'pytest-xdist',  # For parallel testing
+    'pytest-cov',  # For coverage
+    'ruff',  # For linting
+    'nbmake',  # For building notebooks
+    'nbqa',  # For linting notebooks
+    'jinja2',  # For templating
+    'versioningit',  # For versioning
+]
+charts = [
+    'darkdetect',  # For dark mode detection
+    'plotly',  # For interactive plots
+    'py3Dmol',  # For visualisation of crystal structures
+    'pandas',  # For displaying tables in juptyer notebooks
+]
+
+[project.urls]
+homepage = 'https://easydiffraction.org'
+documentation = 'https://docs.easydiffraction.org/lib'
+source = 'https://github.com/EasyScience/EasyDiffractionLib'
+tracker = 'https://github.com/EasyScience/EasyDiffractionLib/issues'
+
+############################
+# Build system configuration
+############################
+
+# Build system 'hatch' -- Python project manager
+# https://hatch.pypa.io/
+
+# Versioning system 'versioningit' -- Versioning from git tags
+# https://versioningit.readthedocs.io/
+
+[build-system]
+build-backend = 'hatchling.build'
+requires = [
+  'hatchling',
+  'versioningit'
+]
+
+#############################
+# Configuration for hatchling
+#############################
+
+[tool.hatch.build.targets.wheel]
+packages = ['src/easydiffraction']
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.version]
+source = 'versioningit'  # Use versioningit to manage the version
+
+################################
+# Configuration for versioningit
+################################
+
+# Versioningit generates versions from git tags, so we don't need to
+# either specify them statically in pyproject.toml or save them in the
+# 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
+
+[tool.versioningit.vcs]
+method = 'git'
+match = ['v*']
+default-tag = 'v999.0.0'
+
+########################
+# Configuration for ruff
+########################
+
+# 'ruff' -- Python linter and code formatter
+# https://docs.astral.sh/ruff/rules/
+
+[tool.ruff]
+exclude = [
+  'examples',
+  'examples_old',
+  'tests'
+]
+indent-width = 4
+line-length = 127
+
+[tool.ruff.format]
+docstring-code-format = true  # Whether to format code snippets in docstrings
+indent-style = 'space'  # PEP 8 recommends using spaces over tabs
+line-ending = 'lf'  # Line endings will be converted to \n
+quote-style = 'single'  # But double quotes in docstrings (PEP 8, PEP 257)
+
+[tool.ruff.lint]
+select = [
+    'E9', 'F63', 'F7', 'F82',  # flake8 settings from existing CI setup
+    'E', 'W',  # pycodestyle
+    'F',  # Pyflakes
+    'I',  # isort
+    'S',  # flake8-bandit
+]
+
+[tool.ruff.lint.isort]
+force-single-line = true
+
+[tool.ruff.lint.per-file-ignores]
+# allow asserts in test files
+'*test_*.py' = ['S101']
+
+#[tool.ruff.lint.pycodestyle]
+#max-line-length = 79  # https://peps.python.org/pep-0008/#maximum-line-length
+#max-doc-length = 72  # https://peps.python.org/pep-0008/#maximum-line-length

{easydiffraction-0.1.6 → easydiffraction-0.2.0/src}/easydiffraction/Profiles/Analysis.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2024 EasyDiffraction contributors
 # SPDX-License-Identifier: BSD-3-Clause
-# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffraction
+# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/EasyScience/EasyDiffraction>
 
 from typing import Union
 
@@ -10,32 +10,33 @@ from easyscience.fitting.fitter import Fitter as CoreFitter
 from easyscience.fitting.minimizers.factory import AvailableMinimizers
 from easyscience.Objects.job.analysis import AnalysisBase as coreAnalysis
 
-from easydiffraction.interface import InterfaceFactory
+from easydiffraction.calculators.wrapper_factory import WrapperFactory
 
 
 class Analysis(coreAnalysis):
     """
     Diffraction-specific Experiment object.
     """
+
     def __init__(self, name: str, interface=None, *args, **kwargs):
         super(Analysis, self).__init__(name, *args, **kwargs)
         self.name = name
         if interface is None:
-            interface = InterfaceFactory()
+            interface = WrapperFactory()
         self.interface = interface
         self._fitter = CoreFitter(self, self.interface.fit_func)
 
     def calculate_theory(self, x: Union[xr.DataArray, np.ndarray], **kwargs) -> np.ndarray:
-        '''
+        """
         Implementation of the abstract method from JobBase.
         Just a wrapper around the profile calculation.
-        '''
+        """
         return self.calculate_profile(x, **kwargs)
 
     def calculate_profile(self, x: Union[xr.DataArray, np.ndarray] = None, coord=None, **kwargs) -> np.ndarray:
-        '''
+        """
         Calculate the profile based on current phase.
-        '''
+        """
         x_store, f = coord.EasyScience.fit_prep(
             self.interface.fit_func,
             bdims=xr.broadcast(coord.transpose()),
@@ -43,13 +44,16 @@ class Analysis(coreAnalysis):
         y = xr.apply_ufunc(f, *x_store, kwargs=kwargs)
         return y
 
-    def fit(self, x: Union[xr.DataArray, np.ndarray],
-                  y: Union[xr.DataArray, np.ndarray],
-                  e: Union[xr.DataArray, np.ndarray],
-                  **kwargs):
-        '''
+    def fit(
+        self,
+        x: Union[xr.DataArray, np.ndarray],
+        y: Union[xr.DataArray, np.ndarray],
+        e: Union[xr.DataArray, np.ndarray],
+        **kwargs,
+    ):
+        """
         Fit the profile based on current phase and experiment.
-        '''
+        """
         # cursory checks
         if x is None or y is None or e is None:
             return None
@@ -73,7 +77,7 @@ class Analysis(coreAnalysis):
             res = self._fitter.fit(x, y, **kwargs)
 
         except Exception as ex:
-            print(f"Error in fitting: {ex}")
+            print(f'Error in fitting: {ex}')
             return None
         return res
 
@@ -101,7 +105,7 @@ class Analysis(coreAnalysis):
         """
         # Convert the string to an enum
         if minimizer not in AvailableMinimizers.__members__:
-            raise ValueError(f"Minimizer {minimizer} not available")
+            raise ValueError(f'Minimizer {minimizer} not available')
         minimizer = AvailableMinimizers[minimizer]
         self._fitter.switch_minimizer(minimizer)
 
@@ -111,8 +115,8 @@ class Analysis(coreAnalysis):
         Load the analysis from a CIF file
         """
         # TODO: Implement this
-        return Analysis("Analysis")
+        return Analysis('Analysis')
 
     # required dunder methods
     def __str__(self):
-        return f"Analysis: {self.name}"
+        return f'Analysis: {self.name}'

{easydiffraction-0.1.6 → easydiffraction-0.2.0/src}/easydiffraction/Profiles/Container.py

@@ -1,6 +1,6 @@
 # SPDX-FileCopyrightText: 2024 EasyDiffraction contributors
 # SPDX-License-Identifier: BSD-3-Clause
-# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/easyscience/EasyDiffraction
+# © 2021-2024 Contributors to the EasyDiffraction project <https://github.com/EasyScience/EasyDiffraction>
 
 from easyscience.Objects.core import ComponentSerializer
 
@@ -9,7 +9,6 @@ from easydiffraction.Profiles.Sample import Sample
 
 
 class DataContainer(ComponentSerializer):
-
     def __init__(self, sim_store: Sample, exp_store: Experiment):
         self._simulations = sim_store
         self._experiments = exp_store
@@ -29,21 +28,20 @@ class DataContainer(ComponentSerializer):
                 """
                 :return: Json-able dictionary representation.
                 """
-                d = {"@module": self.__class__.__module__,
-                    "@class": self.__class__.__name__}
-                d["simulations"] = self._dataset.as_dict()
+                d = {'@module': self.__class__.__module__, '@class': self.__class__.__name__}
+                d['simulations'] = self._dataset.as_dict()
                 return d
 
         class Experiment(experiment_class):
             def __init__(self, sim_prefix):
                 super(Experiment, self).__init__(sim_prefix, dataset)
+
             def as_dict(self, skip=None):
                 """
                 :return: Json-able dictionary representation.
                 """
-                d = {"@module": self.__class__.__module__,
-                    "@class": self.__class__.__name__}
-                d["simulations"] = self._dataset.as_dict()
+                d = {'@module': self.__class__.__module__, '@class': self.__class__.__name__}
+                d['simulations'] = self._dataset.as_dict()
                 return d
 
         s = Simulation(dataset=dataset)
@@ -63,10 +61,9 @@ class DataContainer(ComponentSerializer):
         """
         :return: Json-able dictionary representation.
         """
-        d = {"@module": self.__class__.__module__,
-             "@class": self.__class__.__name__}
-        d["simulations"] = self._simulations.as_dict()
-        d["experiments"] = self._experiments.as_dict()
+        d = {'@module': self.__class__.__module__, '@class': self.__class__.__name__}
+        d['simulations'] = self._simulations.as_dict()
+        d['experiments'] = self._experiments.as_dict()
         return d
 
     @classmethod
@@ -75,4 +72,4 @@ class DataContainer(ComponentSerializer):
         :param d: Dict representation.
         :return: Species.
         """
-        return cls(d["simulations"], d["experiments"])
+        return cls(d['simulations'], d['experiments'])