Merge branch 'develop' into main

.github/workflows/CD.yml

@@ -0,0 +1,62 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CD
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build_package:
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.12" ]
+
+    runs-on: "ubuntu-latest"
+
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Install Poetry
+        uses: snok/install-poetry@v1
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Build Package
+        run: poetry build
+
+      - name: Upload wheels to artifact
+        uses: actions/upload-artifact@v3
+        with:
+          name: wheels
+          path: dist/*
+
+  pypi-publish:
+    name: Upload release to PyPI
+    needs: build_package
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/glassure/
+    permissions:
+      id-token: write
+    steps:
+      - uses: actions/download-artifact@v3
+        with:
+          name: wheels
+          path: dist
+
+      - name: check the dist folder
+        run: ls dist
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/CI.yml

@@ -12,16 +12,26 @@ jobs:
     env:
       QT_QPA_PLATFORM: offscreen
 
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: [ "3.9", "3.10", "3.11" ]
+
     steps:
       #----------------------------------------------
       #       check-out repo and set-up python
       #----------------------------------------------
       - name: Check out repository
         uses: actions/checkout@v3
-      - name: Set up Python 3.11
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.11'
+          python-version: ${{ matrix.python-version }}
+          cache: 'poetry'
 
       #----------------------------------------------
       #  -----  install apt dependencies  -----
@@ -35,36 +45,20 @@ jobs:
           libxcb-shm0-dev libxcb-icccm4-dev libxcb-sync0-dev libxcb-xfixes0-dev libxcb-shape0-dev \
           libxcb-randr0-dev libxcb-render-util0-dev libegl1
 
-      #----------------------------------------------
-      #  -----  install & configure poetry  -----
-      #----------------------------------------------
-      - name: Install Poetry
-        uses: snok/install-poetry@v1
-        with:
-          virtualenvs-create: true
-          virtualenvs-in-project: true
-          installer-parallel: true
 
       #----------------------------------------------
-      #       load cached venv if cache exists
-      #----------------------------------------------
-      - name: Load cached venv
-        id: cached-poetry-dependencies
-        uses: actions/cache@v3
-        with:
-          path: .venv
-          key: venv-${{ runner.os }}-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
-
-      #----------------------------------------------
-      # install dependencies if cache does not exist
+      #            install dependencies
       #----------------------------------------------
       - name: Install dependencies
-        if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
-        run: poetry install --no-interaction --no-root
+        run: poetry install
       #----------------------------------------------
       #              run test suite
       #----------------------------------------------
       - name: Run tests
         run: |
-          poetry run pytest tests/core_tests
-          poetry run pytest tests/gui_tests
+          poetry run pytest tests --cov=glassure --cov-report=xml
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v3
+        env:
+          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

changelog.md

@@ -0,0 +1,40 @@
+## 1.4.1 (2023/10/27)
+
+### Bug fixes:
+- fix error with s0 auto calculation when using brown hubbell form factors.
+- fix python compatibility for 3.9 and 3.10 
+
+## 1.4.0 (2023/09/03)
+
+### New features:
+- the chosen scattering factor source can now be applied per configuration and are not global anymore
+- added support for ionic scattering factors when using the brown et al. 2006 scattering factors
+- calculations now also work correctly without specifying a background pattern
+- added typehints to the core calculation functions
+- the normalization method can now be chosen in the GUI - previously only integral was available and now also
+  fitting can be chosen
+- the Structure Factor calculation method can be chosen in the GUI - now Faber-Ziman and Ashcroft-Langreth are
+  available
+- fft has been set to be default for the Fourier transform in the GUI and a checkbox has been added to also allow
+  the usage of integration method when necessary
+- the extrapolation of the S(Q) to zero in the GUI will now calculate the theoretical value for S(Q) at Q=0, using
+  the form factors - the value can also be set manually (e.g. for data with very low compressibility)
+- the current configurations can be saved as a json file and loaded later for continuing work on these data, or as
+  documentation for the data processing
+- created basic documentation for the core functions, available under (glassure.readthedocs.io)
+
+
+### Bug fixes:
+- consistent naming for patterns - file endings will now always be omitted
+- removing a configuration now correctly switches to the correct configuration and updates the parameters in the gui
+- renaming configurations is now persistent after removing a configuration
+- visibility of configurations is now persistent after removing or freezing a configuration
+- float numbers can now be entered with a comma as decimal separator, it will be converted to a dot automatically
+- data and background patterns are correctly updated in the plot when switching between configurations
+
+## 1.3.0 (2023/04/26)
+
+### New features:
+- changed to pyqt 6 which should reduce issues with high dpi screens
+- added support for brown et al. 2006 scattering factors (from international tables of crystallography) and hubbell et 
+  al.1975 compton scattering intensities

glassure/__init__.py

@@ -1,3 +1,3 @@
 # -*- coding: utf8 -*-
-__version__ = '1.4.0'
+__version__ = '1.4.1'
 

glassure/core/calc.py

@@ -7,6 +7,8 @@
 from .utility import calculate_incoherent_scattering, calculate_f_squared_mean, calculate_f_mean_squared, \
     convert_density_to_atoms_per_cubic_angstrom
 
+from .methods import SqMethod, NormalizationMethod, FourierTransformMethod
+
 __all__ = ['calculate_normalization_factor_raw', 'calculate_normalization_factor', 'fit_normalization_factor',
            'calculate_sq', 'calculate_sq_raw', 'calculate_sq_from_fr', 'calculate_sq_from_gr',
            'calculate_fr', 'calculate_gr_raw', 'calculate_gr']
@@ -69,7 +71,7 @@ def calculate_normalization_factor(sample_pattern: Pattern, density: float, comp
 
 
 def fit_normalization_factor(sample_pattern: Pattern, composition: dict[str, float], q_cutoff: float = 3,
-                             method: str = "squared", use_incoherent_scattering: bool = True,
+                             method: str = "linear", use_incoherent_scattering: bool = True,
                              sf_source: str = 'hajdu') -> float:
     """
     Estimates the normalization factor n for calculating S(Q) by fitting
@@ -103,7 +105,7 @@ def fit_normalization_factor(sample_pattern: Pattern, composition: dict[str, flo
 
     params = lmfit.Parameters()
     params.add("n", value=1, min=0)
-    params.add("multiple", value=1, min=0)
+    params.add("multiple", value=0, min=0)
 
     def optimization_fcn(params, x, sample_intensity, theory_intensity):
         n = params['n'].value
@@ -139,10 +141,10 @@ def calculate_sq_raw(sample_pattern: Pattern, f_squared_mean: np.ndarray, f_mean
     if incoherent_scattering is None:
         incoherent_scattering = np.zeros_like(q)
 
-    if method == 'FZ':
+    if method == 'FZ' or method == SqMethod.FZ:
         sq = (normalization_factor * intensity - incoherent_scattering - f_squared_mean + f_mean_squared) / \
              f_mean_squared
-    elif method == 'AL':
+    elif method == 'AL' or method == SqMethod.AL:
         sq = (normalization_factor * intensity - incoherent_scattering) / f_squared_mean
     else:
         raise NotImplementedError('{} method is not implemented'.format(method))
@@ -188,7 +190,7 @@ def calculate_sq(sample_pattern: Pattern, density: float, composition: dict[str,
         incoherent_scattering = None
 
     atomic_density = convert_density_to_atoms_per_cubic_angstrom(composition, density)
-    if normalization_method == 'fit':
+    if normalization_method == 'fit' or normalization_method == NormalizationMethod.FIT:
         normalization_factor = fit_normalization_factor(sample_pattern,
                                                         composition,
                                                         use_incoherent_scattering,
@@ -238,9 +240,9 @@ def calculate_fr(sq_pattern: Pattern, r: Optional[np.ndarray] = None, use_modifi
     else:
         modification = 1
 
-    if method == 'integral':
+    if method == 'integral' or method == FourierTransformMethod.INTEGRAL:
         fr = 2.0 / np.pi * np.trapz(modification * q * (sq - 1) * np.array(np.sin(np.outer(q.T, r))).T, q)
-    elif method == 'fft':
+    elif method == 'fft' or method == FourierTransformMethod.FFT:
         q_step = q[1] - q[0]
         r_step = r[1] - r[0]
 

glassure/core/methods.py

@@ -0,0 +1,25 @@
+from enum import Enum
+
+
+class SqMethod(Enum):
+    """
+    Enum class for the different methods to calculate the structure factor.
+    """
+    FZ = 'FZ'
+    AL = 'AL'
+
+
+class NormalizationMethod(Enum):
+    """
+    Enum class for the different methods to perform an intensity normalization.
+    """
+    INTEGRAL = 'integral'
+    FIT = 'fit'
+
+
+class FourierTransformMethod(Enum):
+    """
+    Enum class for the different methods to perform a Fourier transform.
+    """
+    FFT = 'fft'
+    INTEGRAL = 'integral'