From 60274b473bfb2daae924ae083081aa934e660fac Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 3 Oct 2023 20:48:39 +0000
Subject: [PATCH 01/12] Bump pillow from 10.0.0 to 10.0.1

Bumps [pillow](https://github.com/python-pillow/Pillow) from 10.0.0 to 10.0.1.
- [Release notes](https://github.com/python-pillow/Pillow/releases)
- [Changelog](https://github.com/python-pillow/Pillow/blob/main/CHANGES.rst)
- [Commits](https://github.com/python-pillow/Pillow/compare/10.0.0...10.0.1)

---
updated-dependencies:
- dependency-name: pillow
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 129 +++++++++++++++++++++++++++++-----------------------
 1 file changed, 71 insertions(+), 58 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 795a51f..d220b0b 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.5.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.6.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
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@@ -461,6 +462,7 @@ files = [
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@@ -469,6 +471,7 @@ files = [
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@@ -477,6 +480,7 @@ files = [
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@@ -1001,6 +1005,7 @@ optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, !=3.6.*"
 files = [
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+    {file = "jsonpointer-2.4.tar.gz", hash = "sha256:585cee82b70211fa9e6043b7bb89db6e1aa49524340dde8ad6b63206ea689d88"},
 ]
 
 [[package]]
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@@ -2007,67 +2022,65 @@ files = [
 
 [[package]]
 name = "pillow"
-version = "10.0.0"
+version = "10.0.1"
 description = "Python Imaging Library (Fork)"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.extras]

From e946c3892e0c8b4451504ea9c3a09d59a1b7cc42 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Tue, 17 Oct 2023 20:55:12 +0000
Subject: [PATCH 02/12] Bump urllib3 from 2.0.4 to 2.0.7

Bumps [urllib3](https://github.com/urllib3/urllib3) from 2.0.4 to 2.0.7.
- [Release notes](https://github.com/urllib3/urllib3/releases)
- [Changelog](https://github.com/urllib3/urllib3/blob/main/CHANGES.rst)
- [Commits](https://github.com/urllib3/urllib3/compare/2.0.4...2.0.7)

---
updated-dependencies:
- dependency-name: urllib3
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 poetry.lock | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index d220b0b..28cb833 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -3282,13 +3282,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.0.4"
+version = "2.0.7"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "urllib3-2.0.4-py3-none-any.whl", hash = "sha256:de7df1803967d2c2a98e4b11bb7d6bd9210474c46e8a0401514e3a42a75ebde4"},
-    {file = "urllib3-2.0.4.tar.gz", hash = "sha256:8d22f86aae8ef5e410d4f539fde9ce6b2113a001bb4d189e0aed70642d602b11"},
+    {file = "urllib3-2.0.7-py3-none-any.whl", hash = "sha256:fdb6d215c776278489906c2f8916e6e7d4f5a9b602ccbcfdf7f016fc8da0596e"},
+    {file = "urllib3-2.0.7.tar.gz", hash = "sha256:c97dfde1f7bd43a71c8d2a58e369e9b2bf692d1334ea9f9cae55add7d0dd0f84"},
 ]
 
 [package.extras]

From 7065b9598b649a631b311f166239cc425e858d4b Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 10:56:46 +0200
Subject: [PATCH 03/12] fix fit normalization to linear and not quadratic - is
 more in line with the integral, and still evaluations higher Q with more
 preference

---
 glassure/core/calc.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/glassure/core/calc.py b/glassure/core/calc.py
index c659134..c6113e7 100644
--- a/glassure/core/calc.py
+++ b/glassure/core/calc.py
@@ -69,7 +69,7 @@ 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 +103,7 @@ 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

From a7b4bea0f6fa6a37ba3a8cb50bcf80fc8468670c Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 10:59:27 +0200
Subject: [PATCH 04/12] fix error with S0 auto evaluation for brown and hubbell
 form factors.

---
 changelog.rst                        | 6 ++++++
 glassure/gui/model/glassure_model.py | 2 +-
 tests/gui_tests/test_functional.py   | 8 ++++++++
 3 files changed, 15 insertions(+), 1 deletion(-)

diff --git a/changelog.rst b/changelog.rst
index a7a6c75..f2ac1b3 100644
--- a/changelog.rst
+++ b/changelog.rst
@@ -1,3 +1,9 @@
+1.4.1 (under development)
+-------------------------
+
+Bug fixes:
+    - fix error with s0 auto calculation when using brown hubbell form factors.
+
 1.4.0 (2023/09/03)
 ------------------
 
diff --git a/glassure/gui/model/glassure_model.py b/glassure/gui/model/glassure_model.py
index 433b8c1..6ae1a36 100644
--- a/glassure/gui/model/glassure_model.py
+++ b/glassure/gui/model/glassure_model.py
@@ -570,7 +570,7 @@ def perform_extrapolation(self):
 
         extrapolation_method = self.extrapolation_config.method
         if self.extrapolation_config.s0_auto:
-            self.extrapolation_config.s0 = calculate_s0(self.composition)
+            self.extrapolation_config.s0 = calculate_s0(self.composition, self.sf_source)
 
         s0 = self.extrapolation_config.s0
 
diff --git a/tests/gui_tests/test_functional.py b/tests/gui_tests/test_functional.py
index 4abb6e7..90fc830 100644
--- a/tests/gui_tests/test_functional.py
+++ b/tests/gui_tests/test_functional.py
@@ -196,3 +196,11 @@ def test_using_different_fourier_transform_methods(main_controller: GlassureCont
     assert not np.array_equal(prev_gr_data, pattern_widget.gr_items[0].getData())
 
     # he is satisfied with the small changes and will continue to use the fft method
+
+
+def test_adding_elements_with_brown_hubbell(main_controller: GlassureController, main_widget: GlassureWidget,
+                                            composition_widget: CompositionWidget, model: GlassureModel):
+    composition_widget.source_cb.setCurrentIndex(1)
+    assert composition_widget.source_cb.currentText() == "brown_hubbell"
+    click_button(composition_widget.add_element_btn)
+    click_checkbox(main_widget.left_control_widget.extrapolation_widget.activate_cb)

From 52e01d2e0bb876edb51c5666c34ce2a5b0f0d79e Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 16:25:06 +0200
Subject: [PATCH 05/12] added continuous delivery script (adapted from
 xypattern)

---
 .github/workflows/CD.yml | 62 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 .github/workflows/CD.yml

diff --git a/.github/workflows/CD.yml b/.github/workflows/CD.yml
new file mode 100644
index 0000000..5552489
--- /dev/null
+++ b/.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
\ No newline at end of file

From b218d46dc3bdb1049542b28fb00b865d7bf3e328 Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 16:29:12 +0200
Subject: [PATCH 06/12] converted changelog into markdown format

---
 changelog.md  | 39 +++++++++++++++++++++++++++++++++++++++
 changelog.rst | 44 --------------------------------------------
 2 files changed, 39 insertions(+), 44 deletions(-)
 create mode 100644 changelog.md
 delete mode 100644 changelog.rst

diff --git a/changelog.md b/changelog.md
new file mode 100644
index 0000000..4f11d3d
--- /dev/null
+++ b/changelog.md
@@ -0,0 +1,39 @@
+## 1.4.1 (2023/10/27)
+
+### Bug fixes:
+- fix error with s0 auto calculation when using brown hubbell form factors.
+
+## 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
diff --git a/changelog.rst b/changelog.rst
deleted file mode 100644
index f2ac1b3..0000000
--- a/changelog.rst
+++ /dev/null
@@ -1,44 +0,0 @@
-1.4.1 (under development)
--------------------------
-
-Bug fixes:
-    - fix error with s0 auto calculation when using brown hubbell form factors.
-
-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
-

From 2e719e5f7314e4abfc5aaa3d12553e3e4b6fc99c Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 16:33:07 +0200
Subject: [PATCH 07/12] cleaning up unnecssary old files

---
 .travis.yml | 56 -----------------------------------------------------
 MANIFEST.in |  2 --
 2 files changed, 58 deletions(-)
 delete mode 100644 .travis.yml
 delete mode 100644 MANIFEST.in

diff --git a/.travis.yml b/.travis.yml
deleted file mode 100644
index 29c0c54..0000000
--- a/.travis.yml
+++ /dev/null
@@ -1,56 +0,0 @@
-# Config file for automatic testing at travis-ci.org
-language: python
-
-python:
-  - 2.7
-  - 3.6
-  
-cache:
-  pip: true
-  directories:
-    - /home/travis/miniconda2
-    - /home/travis/miniconda3
-  
-before_install:
-  # install anaconda
-  - echo $TRAVIS_PYTHON_VERSION
-  - if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ]; then
-      if [ ! -d "/home/travis/miniconda2/bin" ]; then
-        rm -rf /home/travis/miniconda2;
-        wget http://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh;
-        chmod +x miniconda.sh;
-        ./miniconda.sh -b;
-      fi
-    fi
-  - if [ "$TRAVIS_PYTHON_VERSION" == "3.6" ]; then
-      if [ ! -d "/home/travis/miniconda3/bin" ]; then
-        rm -rf /home/travis/miniconda3;
-        wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-        chmod +x miniconda.sh;
-        ./miniconda.sh -b;
-      fi
-    fi
-    
-  - if [ "$TRAVIS_PYTHON_VERSION" == "2.7" ]; then
-      export PATH=/home/travis/miniconda2/bin:$PATH;
-    else
-      export PATH=/home/travis/miniconda3/bin:$PATH;
-    fi
-    
-  - conda update --yes conda
-  - export PYTHONPATH=$PWD/glassure:$PYTHONPATH
-
-  #start x-server
-  - export DISPLAY=:99.0
-  - sh -e /etc/init.d/xvfb start
-
-install:
-  - conda install --yes python=$TRAVIS_PYTHON_VERSION numpy scipy pyqt pytest pytest-cov pandas mock
-  - pip install pyqtgraph lmfit coveralls coverage
-
-script:
-  - coverage run --source glassure -m py.test
-  - coverage report -m
-
-after_success:
-  coveralls
diff --git a/MANIFEST.in b/MANIFEST.in
deleted file mode 100644
index 65a30b5..0000000
--- a/MANIFEST.in
+++ /dev/null
@@ -1,2 +0,0 @@
-include versioneer.py
-include glassure/core/_version.py

From 53ba2f76d8cf51ca8f07b325724587cc7c862fef Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 16:40:47 +0200
Subject: [PATCH 08/12] added matrix and coverage to CI workflow

---
 .github/workflows/CI.yml | 46 +++++++++++++++++-----------------------
 1 file changed, 20 insertions(+), 26 deletions(-)

diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml
index 7ef175d..5867dea 100644
--- a/.github/workflows/CI.yml
+++ b/.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 }}

From 450b88aa2460d96fba3bf59a1ebfbc38785d06fd Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 17:23:44 +0200
Subject: [PATCH 09/12] refactor usage of StrEnum (python >3.11) to Enum, since
 we want to keep backward compatibility

---
 glassure/core/calc.py                   | 12 ++++++-----
 glassure/core/methods.py                | 25 +++++++++++++++++++++++
 glassure/gui/model/configuration.py     | 27 ++-----------------------
 glassure/gui/widgets/control/options.py |  5 +++--
 4 files changed, 37 insertions(+), 32 deletions(-)
 create mode 100644 glassure/core/methods.py

diff --git a/glassure/core/calc.py b/glassure/core/calc.py
index c6113e7..843f582 100644
--- a/glassure/core/calc.py
+++ b/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']
@@ -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]
 
diff --git a/glassure/core/methods.py b/glassure/core/methods.py
new file mode 100644
index 0000000..f2345d2
--- /dev/null
+++ b/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'
diff --git a/glassure/gui/model/configuration.py b/glassure/gui/model/configuration.py
index 54ae062..686906d 100644
--- a/glassure/gui/model/configuration.py
+++ b/glassure/gui/model/configuration.py
@@ -1,12 +1,13 @@
 # -*- coding: utf-8 -*/:
 from __future__ import annotations
-from enum import StrEnum
+from enum import Enum
 from colorsys import hsv_to_rgb
 from copy import deepcopy
 
 import numpy as np
 
 from ...core.pattern import Pattern
+from ...core.methods import SqMethod, NormalizationMethod, FourierTransformMethod
 
 
 class TransformConfiguration(object):
@@ -273,30 +274,6 @@ def get_pattern_or_none(pattern_dict):
         return config
 
 
-class SqMethod(StrEnum):
-    """
-    Enum class for the different methods to calculate the structure factor.
-    """
-    FZ = 'FZ'
-    AL = 'AL'
-
-
-class NormalizationMethod(StrEnum):
-    """
-    Enum class for the different methods to perform an intensity normalization.
-    """
-    INTEGRAL = 'integral'
-    FIT = 'fit'
-
-
-class FourierTransformMethod(StrEnum):
-    """
-    Enum class for the different methods to perform a Fourier transform.
-    """
-    FFT = 'fft'
-    INTEGRAL = 'integral'
-
-
 def calculate_color(ind):
     s = 0.8
     v = 0.8
diff --git a/glassure/gui/widgets/control/options.py b/glassure/gui/widgets/control/options.py
index e716002..7ba4d7e 100644
--- a/glassure/gui/widgets/control/options.py
+++ b/glassure/gui/widgets/control/options.py
@@ -3,7 +3,8 @@
 from qtpy import QtCore, QtWidgets
 from ..custom import HorizontalLine, FloatLineEdit, DragSlider
 import numpy as np
-from ...model.configuration import NormalizationMethod, SqMethod, TransformConfiguration, FourierTransformMethod
+from ...model.configuration import TransformConfiguration
+from ....core.methods import SqMethod, NormalizationMethod, FourierTransformMethod
 
 
 class OptionsWidget(QtWidgets.QWidget):
@@ -165,7 +166,7 @@ def get_fourier_transform_method(self):
             return FourierTransformMethod.INTEGRAL
 
     def set_fourier_transform_method(self, method):
-        if method == 'fft':
+        if method == 'fft' or method == FourierTransformMethod.FFT:
             self.fft_cb.setChecked(True)
         else:
             self.fft_cb.setChecked(False)

From eeac7421d471c240ed2492bcc5884cd35a298408 Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 17:30:45 +0200
Subject: [PATCH 10/12] import future annotation to make | for types work

---
 glassure/gui/widgets/custom/pattern.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/glassure/gui/widgets/custom/pattern.py b/glassure/gui/widgets/custom/pattern.py
index 7e02f80..4dae220 100644
--- a/glassure/gui/widgets/custom/pattern.py
+++ b/glassure/gui/widgets/custom/pattern.py
@@ -1,5 +1,5 @@
 # -*- coding: utf-8 -*-
-
+from __future__ import annotations
 import pyqtgraph as pg
 import numpy as np
 from qtpy import QtCore, QtWidgets

From 56075d91179006a8fecff2cb0cfda887ff5eceaa Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 17:35:35 +0200
Subject: [PATCH 11/12] remove unused density optimizer class

---
 glassure/gui/model/density_optimization.py | 101 ---------------------
 glassure/gui/model/glassure_model.py       |  26 ------
 2 files changed, 127 deletions(-)
 delete mode 100644 glassure/gui/model/density_optimization.py

diff --git a/glassure/gui/model/density_optimization.py b/glassure/gui/model/density_optimization.py
deleted file mode 100644
index 85ff1ce..0000000
--- a/glassure/gui/model/density_optimization.py
+++ /dev/null
@@ -1,101 +0,0 @@
-# -*- coding: utf-8 -*-
-
-import numpy as np
-from qtpy import QtGui
-from lmfit import Parameters, minimize, report_fit
-
-from ...core.calculator import StandardCalculator
-from ...core.utility import convert_density_to_atoms_per_cubic_angstrom
-
-
-class DensityOptimizer(object):
-    def __init__(self,
-                 original_pattern, background_pattern, initial_background_scaling,
-                 elemental_abundances, initial_density,
-                 density_min, density_max, bkg_min, bkg_max, r_cutoff,
-                 use_modification_fcn=False, extrapolation_method=None,extrapolation_parameters=None, r=np.linspace(0, 10, 1000),
-                 output_txt=None):
-        self.original_pattern = original_pattern
-        self.background_pattern = background_pattern
-        self.background_scaling = initial_background_scaling
-        self.elemental_abundances = elemental_abundances
-        self.density = initial_density
-        self.r = r
-        self.minimization_r = np.linspace(0, r_cutoff, r_cutoff * 100)
-        self.r_cutoff = r_cutoff
-
-        self.bkg_min = bkg_min
-        self.bkg_max = bkg_max
-        self.density_min = density_min
-        self.density_max = density_max
-        self.use_modification_fcn = use_modification_fcn
-        self.extrapolation_method = extrapolation_method
-        self.extrapolation_parameters = extrapolation_parameters
-        self.output_txt = output_txt
-        self.iteration = 1
-
-    def optimize(self, optimization_iterations=10,  fcn_callback=None):
-        params = Parameters()
-        params.add("density", value=self.density, min=self.density_min, max=self.density_max)
-        params.add("background_scaling", value=self.background_scaling, min=self.bkg_min, max=self.bkg_max)
-
-        def fcn_optimization(params):
-            density = params['density'].value
-            background_scaling = params['background_scaling'].value
-
-            self.background_pattern.scaling = background_scaling
-            calculator = StandardCalculator(
-                original_pattern=self.original_pattern,
-                background_pattern=self.background_pattern,
-                composition=self.elemental_abundances,
-                density=density,
-                r=self.r,
-                extrapolation_method=self.extrapolation_method,
-                extrapolation_parameters=self.extrapolation_parameters,
-                use_modification_fcn=self.use_modification_fcn
-            )
-            calculator.optimize_sq(
-                r_cutoff=self.minimization_r,
-                iterations=optimization_iterations
-            )
-
-            if fcn_callback is not None:
-                fr_pattern = calculator.calc_fr()
-                gr_pattern = calculator.calc_gr()
-                fcn_callback(background_scaling, density, fr_pattern, gr_pattern)
-
-            r, fr = calculator.calc_fr(self.minimization_r).data
-
-            output = (-fr - 4 * np.pi * convert_density_to_atoms_per_cubic_angstrom(self.elemental_abundances, density) *
-                    self.minimization_r) ** 2
-
-
-            self.write_output(u'{} X: {:.3f} Den: {:.3f}'.format(self.iteration, np.sum(output)/(r[1]-r[0]), density))
-            self.iteration+=1
-            return output
-
-        self.output_txt.setPlainText('')
-        minimize(fcn_optimization, params)
-        self.write_fit_result(params)
-        report_fit(params)
-
-    def write_output(self, msg):
-        if self.output_txt is None:
-            print(msg)
-        else:
-            previous_txt = str(self.output_txt.toPlainText())
-            new_txt = previous_txt + "\n" + str(msg)
-            self.output_txt.setPlainText(new_txt)
-            # QtGui.QApplication.processEvents()
-            self.output_txt.verticalScrollBar().setValue(self.output_txt.verticalScrollBar().maximum())
-            QtGui.QApplication.processEvents()
-            self.output_txt.verticalScrollBar().setValue(self.output_txt.verticalScrollBar().maximum())
-            QtGui.QApplication.processEvents()
-
-    def write_fit_result(self, params):
-        output =  '\nFit Results:\n'
-        output += '-Background Scaling:\n  % .3g +/- %.3g\n' % (params['background_scaling'].value,
-                                                              params['background_scaling'].stderr)
-        output += '-Density:\n  % .3g +/- %.3g\n' % (params['density'].value,
-                                                   params['density'].stderr)
-        self.write_output(output)
diff --git a/glassure/gui/model/glassure_model.py b/glassure/gui/model/glassure_model.py
index 6ae1a36..fb4bf3c 100644
--- a/glassure/gui/model/glassure_model.py
+++ b/glassure/gui/model/glassure_model.py
@@ -8,7 +8,6 @@
 from qtpy import QtGui, QtCore
 
 from ...core.pattern import Pattern
-from .density_optimization import DensityOptimizer
 from ...core.utility import calculate_incoherent_scattering, convert_density_to_atoms_per_cubic_angstrom
 from ...core import calculate_sq, calculate_gr, calculate_fr
 from ...core.optimization import optimize_sq
@@ -602,31 +601,6 @@ def calculate_gr(self):
         self.gr_pattern = calculate_gr(
             self.fr_pattern, self.density, self.composition)
 
-    def optimize_density_and_scaling2(self, density_min, density_max, bkg_min,
-                                      bkg_max, iterations, output_txt=None):
-        optimizer = DensityOptimizer(
-            original_pattern=self.original_pattern.limit(
-                self.q_min, self.q_max),
-            background_pattern=self.background_pattern.limit(
-                self.q_min, self.q_max),
-            initial_background_scaling=self.background_scaling,
-            elemental_abundances=self.composition,
-            initial_density=self.density,
-            r_cutoff=self.r_cutoff,
-            r=np.linspace(self.r_min, self.r_max, 1000),
-            density_min=density_min,
-            density_max=density_max,
-            bkg_min=bkg_min,
-            bkg_max=bkg_max,
-            use_modification_fcn=self.use_modification_fcn,
-            extrapolation_method=self.extrapolation_config.method,
-            extrapolation_parameters={
-                'q_max': self.extrapolation_config.fit_q_max,
-                'replace': self.extrapolation_config.fit_replace},
-            output_txt=output_txt
-        )
-
-        optimizer.optimize(iterations)
 
     def optimize_density_and_scaling(self, density_min, density_max, bkg_min, bkg_max, iterations, callback_fcn=None,
                                      output_txt=None):

From 6048db76f657abf6304bb45215452124c7db76ae Mon Sep 17 00:00:00 2001
From: Clemens Prescher <clemens.prescher@gmail.com>
Date: Fri, 27 Oct 2023 17:37:03 +0200
Subject: [PATCH 12/12] prepare for 1.4.1 release

---
 changelog.md         | 1 +
 glassure/__init__.py | 2 +-
 pyproject.toml       | 2 +-
 3 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/changelog.md b/changelog.md
index 4f11d3d..0efa518 100644
--- a/changelog.md
+++ b/changelog.md
@@ -2,6 +2,7 @@
 
 ### 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)
 
diff --git a/glassure/__init__.py b/glassure/__init__.py
index f9da9e9..41de290 100644
--- a/glassure/__init__.py
+++ b/glassure/__init__.py
@@ -1,3 +1,3 @@
 # -*- coding: utf8 -*-
-__version__ = '1.4.0'
+__version__ = '1.4.1'
 
diff --git a/pyproject.toml b/pyproject.toml
index 6a4ef7a..121e263 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "glassure"
-version = "1.4.0"
+version = "1.4.1"
 description = "API and GUI for analysis of X-ray total scattering data"
 authors = ["Clemens Prescher <clemens.prescher@gmail.com>"]
 license = "MIT"