From f8fec80c8ba4553e53867ab5921cdc6dfbb922b1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 15:22:48 +0100
Subject: [PATCH 01/19] install specifications

---
 README.md | 17 +++++++++++++++++
 1 file changed, 17 insertions(+)

diff --git a/README.md b/README.md
index fd50faf..e908c7d 100644
--- a/README.md
+++ b/README.md
@@ -5,3 +5,20 @@ also includes the line tension, a measure for the force transfer exclusively acr
 pyTFM includes an addon for the image annotation tool [clickpoints](https://clickpoints.readthedocs.io/en/latest/) allowing you to quickly analyze and vizualize large datasets.
 
 Please refer to the [Documentation](https://pytfm.readthedocs.io/en/latest/) of pyTFM for detailed instructions on installation and usage.
+
+## Conda enviroment creation
+You need to create python 3.7 enviroment.
+```
+conda create --name pyTFM python=3.7
+conda activate pyTFM
+```
+
+pyTFM package install
+```
+pip install git+https://github.com/fabrylab/pyTFM.git
+```
+
+If you want to use jupyterlab with black packge
+```
+conda install jupyterlab jupyterlab_code_formatter black isort -c conda-forge
+```

From 1f86b7ae4db69fc3b6dccf2a5592e2be73ed190d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:45:46 +0100
Subject: [PATCH 02/19] Create test_pyTFM.py

---
 testing/test_pyTFM.py | 104 ++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 testing/test_pyTFM.py

diff --git a/testing/test_pyTFM.py b/testing/test_pyTFM.py
new file mode 100644
index 0000000..0c47fdf
--- /dev/null
+++ b/testing/test_pyTFM.py
@@ -0,0 +1,104 @@
+import numpy as np
+import pytest
+import matplotlib.pyplot as plt
+import numpy as np
+import openpiv.filters
+import scipy.fft
+
+from openpiv.pyprocess import extended_search_area_piv
+import openpiv.scaling
+import openpiv.tools
+import openpiv.validation
+from matplotlib.colors import LinearSegmentedColormap
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+from pyTFM.utilities_TFM import suppress_warnings
+from scipy.ndimage.filters import median_filter, gaussian_filter
+from scipy.ndimage.filters import uniform_filter
+from pyTFM.TFM_functions import ffttc_traction
+from pyTFM.TFM_functions import get_xy_for_quiver
+
+def test_ffttc_traction_output_shape():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output shape is as expected
+    assert tx_filter.shape == (10, 10)
+    assert ty_filter.shape == (10, 10)
+
+def test_ffttc_traction_output_type():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is of the correct type
+    assert isinstance(tx_filter, np.ndarray)
+    assert isinstance(ty_filter, np.ndarray)
+
+def test_ffttc_traction_output_values():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is as expected
+    assert np.allclose(tx_filter, 0)
+    assert np.allclose(ty_filter, 0)
+
+def test_ffttc_traction_input_shape():
+    # create test inputs with incorrect shape
+    u = np.zeros((10, 10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a ValueError is raised for incorrect input shape
+    with pytest.raises(ValueError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+def test_ffttc_traction_input_type():
+    # create test inputs with incorrect type
+    u = np.zeros((10, 10))
+    v = "not an array"
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a TypeError is raised for incorrect input type
+    with pytest.raises(TypeError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+        
+########get_xy_for_quiver
+def test_get_xy_for_quiver():
+    u = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    xs, ys = get_xy_for_quiver(u)
+    
+    # Test the shape of xs and ys
+    assert np.shape(xs) == np.shape(u)
+    assert np.shape(ys) == np.shape(u)
+    
+    # Test the values of xs
+    for i in range(np.shape(u)[0]):
+        assert np.array_equal(xs[i, :], np.arange(0, np.shape(u)[1], 1))
+        
+    # Test the values of ys
+    for j in range(np.shape(u)[1]):
+        assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))

From 46cf963a07b2246ad87879378c7fc5497a17e297 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:51:10 +0100
Subject: [PATCH 03/19] Create python-package.yml

---
 .github/workflows/python-package.yml | 40 ++++++++++++++++++++++++++++
 1 file changed, 40 insertions(+)
 create mode 100644 .github/workflows/python-package.yml

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
new file mode 100644
index 0000000..38c9a0c
--- /dev/null
+++ b/.github/workflows/python-package.yml
@@ -0,0 +1,40 @@
+# 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: Python package
+
+on:
+  push:
+    branches: [ "master" ]
+  pull_request:
+    branches: [ "master" ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.6", "3.7", "3.8", "3.9"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install flake8 pytest
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Lint with flake8
+      run: |
+        # stop the build if there are Python syntax errors or undefined names
+        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+    - name: Test with pytest
+      run: |
+        pytest testing/test_pyTFM.py

From 9120ecedb8a291167899f41ef78aa02e2a2ed317 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:53:01 +0100
Subject: [PATCH 04/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 10 ++--------
 1 file changed, 2 insertions(+), 8 deletions(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 38c9a0c..51a29c8 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9"]
+        python-version: ["3.7", "3.8", "3.9"]
 
     steps:
     - uses: actions/checkout@v3
@@ -27,14 +27,8 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install flake8 pytest
+        python -m pip install pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
-    - name: Lint with flake8
-      run: |
-        # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
-        # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest
       run: |
         pytest testing/test_pyTFM.py

From 58fe9d13bfcda30c2df5e6dba67316386b2dd4c2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:55:32 +0100
Subject: [PATCH 05/19] Create test_pyTFM.py

---
 pyTFM/test_pyTFM.py | 104 ++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 pyTFM/test_pyTFM.py

diff --git a/pyTFM/test_pyTFM.py b/pyTFM/test_pyTFM.py
new file mode 100644
index 0000000..0c47fdf
--- /dev/null
+++ b/pyTFM/test_pyTFM.py
@@ -0,0 +1,104 @@
+import numpy as np
+import pytest
+import matplotlib.pyplot as plt
+import numpy as np
+import openpiv.filters
+import scipy.fft
+
+from openpiv.pyprocess import extended_search_area_piv
+import openpiv.scaling
+import openpiv.tools
+import openpiv.validation
+from matplotlib.colors import LinearSegmentedColormap
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+from pyTFM.utilities_TFM import suppress_warnings
+from scipy.ndimage.filters import median_filter, gaussian_filter
+from scipy.ndimage.filters import uniform_filter
+from pyTFM.TFM_functions import ffttc_traction
+from pyTFM.TFM_functions import get_xy_for_quiver
+
+def test_ffttc_traction_output_shape():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output shape is as expected
+    assert tx_filter.shape == (10, 10)
+    assert ty_filter.shape == (10, 10)
+
+def test_ffttc_traction_output_type():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is of the correct type
+    assert isinstance(tx_filter, np.ndarray)
+    assert isinstance(ty_filter, np.ndarray)
+
+def test_ffttc_traction_output_values():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is as expected
+    assert np.allclose(tx_filter, 0)
+    assert np.allclose(ty_filter, 0)
+
+def test_ffttc_traction_input_shape():
+    # create test inputs with incorrect shape
+    u = np.zeros((10, 10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a ValueError is raised for incorrect input shape
+    with pytest.raises(ValueError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+def test_ffttc_traction_input_type():
+    # create test inputs with incorrect type
+    u = np.zeros((10, 10))
+    v = "not an array"
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a TypeError is raised for incorrect input type
+    with pytest.raises(TypeError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+        
+########get_xy_for_quiver
+def test_get_xy_for_quiver():
+    u = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    xs, ys = get_xy_for_quiver(u)
+    
+    # Test the shape of xs and ys
+    assert np.shape(xs) == np.shape(u)
+    assert np.shape(ys) == np.shape(u)
+    
+    # Test the values of xs
+    for i in range(np.shape(u)[0]):
+        assert np.array_equal(xs[i, :], np.arange(0, np.shape(u)[1], 1))
+        
+    # Test the values of ys
+    for j in range(np.shape(u)[1]):
+        assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))

From 879fbcbcccf1c69e7d52c091ce8374f3218ce014 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:55:47 +0100
Subject: [PATCH 06/19] Delete testing directory

---
 testing/test_pyTFM.py | 104 ------------------------------------------
 1 file changed, 104 deletions(-)
 delete mode 100644 testing/test_pyTFM.py

diff --git a/testing/test_pyTFM.py b/testing/test_pyTFM.py
deleted file mode 100644
index 0c47fdf..0000000
--- a/testing/test_pyTFM.py
+++ /dev/null
@@ -1,104 +0,0 @@
-import numpy as np
-import pytest
-import matplotlib.pyplot as plt
-import numpy as np
-import openpiv.filters
-import scipy.fft
-
-from openpiv.pyprocess import extended_search_area_piv
-import openpiv.scaling
-import openpiv.tools
-import openpiv.validation
-from matplotlib.colors import LinearSegmentedColormap
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-from pyTFM.utilities_TFM import suppress_warnings
-from scipy.ndimage.filters import median_filter, gaussian_filter
-from scipy.ndimage.filters import uniform_filter
-from pyTFM.TFM_functions import ffttc_traction
-from pyTFM.TFM_functions import get_xy_for_quiver
-
-def test_ffttc_traction_output_shape():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output shape is as expected
-    assert tx_filter.shape == (10, 10)
-    assert ty_filter.shape == (10, 10)
-
-def test_ffttc_traction_output_type():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output is of the correct type
-    assert isinstance(tx_filter, np.ndarray)
-    assert isinstance(ty_filter, np.ndarray)
-
-def test_ffttc_traction_output_values():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output is as expected
-    assert np.allclose(tx_filter, 0)
-    assert np.allclose(ty_filter, 0)
-
-def test_ffttc_traction_input_shape():
-    # create test inputs with incorrect shape
-    u = np.zeros((10, 10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # assert that a ValueError is raised for incorrect input shape
-    with pytest.raises(ValueError):
-        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-def test_ffttc_traction_input_type():
-    # create test inputs with incorrect type
-    u = np.zeros((10, 10))
-    v = "not an array"
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # assert that a TypeError is raised for incorrect input type
-    with pytest.raises(TypeError):
-        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-        
-########get_xy_for_quiver
-def test_get_xy_for_quiver():
-    u = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
-    xs, ys = get_xy_for_quiver(u)
-    
-    # Test the shape of xs and ys
-    assert np.shape(xs) == np.shape(u)
-    assert np.shape(ys) == np.shape(u)
-    
-    # Test the values of xs
-    for i in range(np.shape(u)[0]):
-        assert np.array_equal(xs[i, :], np.arange(0, np.shape(u)[1], 1))
-        
-    # Test the values of ys
-    for j in range(np.shape(u)[1]):
-        assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))

From c518aa9e4b44e0f1b55acd58b9679f4c0e4ab445 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 16:56:05 +0100
Subject: [PATCH 07/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 51a29c8..520d1e8 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -31,4 +31,4 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - name: Test with pytest
       run: |
-        pytest testing/test_pyTFM.py
+        pytest test_pyTFM.py

From 7473e10f981048aa1451b1c3100f87d585bfaec6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:31:33 +0100
Subject: [PATCH 08/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 9 ++++++++-
 1 file changed, 8 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 520d1e8..b60c84e 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -29,6 +29,13 @@ jobs:
         python -m pip install --upgrade pip
         python -m pip install pytest
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    # Display the Python version being used
+    - name: Display Python version
+      run: python -c "import sys; print(sys.version)"
+    # Install the package using the setup.py
+    - name: Install package
+      run: python setup.py install
+    # Install pytest (you can use some other testing utility)
     - name: Test with pytest
       run: |
-        pytest test_pyTFM.py
+        pytest pyTFM/pyTFM/test_pyTFM.py

From 4e29aec2adff6add788a7f5a04d96c42f2287fef Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:35:00 +0100
Subject: [PATCH 09/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index b60c84e..ec401c4 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -34,7 +34,7 @@ jobs:
       run: python -c "import sys; print(sys.version)"
     # Install the package using the setup.py
     - name: Install package
-      run: python setup.py install
+      run: pip install git+https://github.com/fabrylab/pyTFM.git
     # Install pytest (you can use some other testing utility)
     - name: Test with pytest
       run: |

From c04447d90e9790af4a9b6620a812d82684dd2b79 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:41:13 +0100
Subject: [PATCH 10/19] Create test_pyTFM.py

---
 test_pyTFM.py | 104 ++++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 104 insertions(+)
 create mode 100644 test_pyTFM.py

diff --git a/test_pyTFM.py b/test_pyTFM.py
new file mode 100644
index 0000000..0c47fdf
--- /dev/null
+++ b/test_pyTFM.py
@@ -0,0 +1,104 @@
+import numpy as np
+import pytest
+import matplotlib.pyplot as plt
+import numpy as np
+import openpiv.filters
+import scipy.fft
+
+from openpiv.pyprocess import extended_search_area_piv
+import openpiv.scaling
+import openpiv.tools
+import openpiv.validation
+from matplotlib.colors import LinearSegmentedColormap
+from mpl_toolkits.axes_grid1 import make_axes_locatable
+from pyTFM.utilities_TFM import suppress_warnings
+from scipy.ndimage.filters import median_filter, gaussian_filter
+from scipy.ndimage.filters import uniform_filter
+from pyTFM.TFM_functions import ffttc_traction
+from pyTFM.TFM_functions import get_xy_for_quiver
+
+def test_ffttc_traction_output_shape():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output shape is as expected
+    assert tx_filter.shape == (10, 10)
+    assert ty_filter.shape == (10, 10)
+
+def test_ffttc_traction_output_type():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is of the correct type
+    assert isinstance(tx_filter, np.ndarray)
+    assert isinstance(ty_filter, np.ndarray)
+
+def test_ffttc_traction_output_values():
+    # create test inputs
+    u = np.zeros((10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # call the function
+    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+    # assert that the output is as expected
+    assert np.allclose(tx_filter, 0)
+    assert np.allclose(ty_filter, 0)
+
+def test_ffttc_traction_input_shape():
+    # create test inputs with incorrect shape
+    u = np.zeros((10, 10, 10))
+    v = np.zeros((10, 10))
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a ValueError is raised for incorrect input shape
+    with pytest.raises(ValueError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+
+def test_ffttc_traction_input_type():
+    # create test inputs with incorrect type
+    u = np.zeros((10, 10))
+    v = "not an array"
+    pixelsize1 = 0.1
+    pixelsize2 = 0.1
+    young = 1e6
+
+    # assert that a TypeError is raised for incorrect input type
+    with pytest.raises(TypeError):
+        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
+        
+########get_xy_for_quiver
+def test_get_xy_for_quiver():
+    u = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
+    xs, ys = get_xy_for_quiver(u)
+    
+    # Test the shape of xs and ys
+    assert np.shape(xs) == np.shape(u)
+    assert np.shape(ys) == np.shape(u)
+    
+    # Test the values of xs
+    for i in range(np.shape(u)[0]):
+        assert np.array_equal(xs[i, :], np.arange(0, np.shape(u)[1], 1))
+        
+    # Test the values of ys
+    for j in range(np.shape(u)[1]):
+        assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))

From 8fb4c6f4de7815658a830d8ebe0917db0cf8504e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:41:27 +0100
Subject: [PATCH 11/19] Delete test_pyTFM.py

---
 pyTFM/test_pyTFM.py | 104 --------------------------------------------
 1 file changed, 104 deletions(-)
 delete mode 100644 pyTFM/test_pyTFM.py

diff --git a/pyTFM/test_pyTFM.py b/pyTFM/test_pyTFM.py
deleted file mode 100644
index 0c47fdf..0000000
--- a/pyTFM/test_pyTFM.py
+++ /dev/null
@@ -1,104 +0,0 @@
-import numpy as np
-import pytest
-import matplotlib.pyplot as plt
-import numpy as np
-import openpiv.filters
-import scipy.fft
-
-from openpiv.pyprocess import extended_search_area_piv
-import openpiv.scaling
-import openpiv.tools
-import openpiv.validation
-from matplotlib.colors import LinearSegmentedColormap
-from mpl_toolkits.axes_grid1 import make_axes_locatable
-from pyTFM.utilities_TFM import suppress_warnings
-from scipy.ndimage.filters import median_filter, gaussian_filter
-from scipy.ndimage.filters import uniform_filter
-from pyTFM.TFM_functions import ffttc_traction
-from pyTFM.TFM_functions import get_xy_for_quiver
-
-def test_ffttc_traction_output_shape():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output shape is as expected
-    assert tx_filter.shape == (10, 10)
-    assert ty_filter.shape == (10, 10)
-
-def test_ffttc_traction_output_type():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output is of the correct type
-    assert isinstance(tx_filter, np.ndarray)
-    assert isinstance(ty_filter, np.ndarray)
-
-def test_ffttc_traction_output_values():
-    # create test inputs
-    u = np.zeros((10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # call the function
-    tx_filter, ty_filter = ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-    # assert that the output is as expected
-    assert np.allclose(tx_filter, 0)
-    assert np.allclose(ty_filter, 0)
-
-def test_ffttc_traction_input_shape():
-    # create test inputs with incorrect shape
-    u = np.zeros((10, 10, 10))
-    v = np.zeros((10, 10))
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # assert that a ValueError is raised for incorrect input shape
-    with pytest.raises(ValueError):
-        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-
-def test_ffttc_traction_input_type():
-    # create test inputs with incorrect type
-    u = np.zeros((10, 10))
-    v = "not an array"
-    pixelsize1 = 0.1
-    pixelsize2 = 0.1
-    young = 1e6
-
-    # assert that a TypeError is raised for incorrect input type
-    with pytest.raises(TypeError):
-        ffttc_traction(u, v, pixelsize1, pixelsize2, young)
-        
-########get_xy_for_quiver
-def test_get_xy_for_quiver():
-    u = np.array([[1, 2, 3], [4, 5, 6], [7, 8, 9]])
-    xs, ys = get_xy_for_quiver(u)
-    
-    # Test the shape of xs and ys
-    assert np.shape(xs) == np.shape(u)
-    assert np.shape(ys) == np.shape(u)
-    
-    # Test the values of xs
-    for i in range(np.shape(u)[0]):
-        assert np.array_equal(xs[i, :], np.arange(0, np.shape(u)[1], 1))
-        
-    # Test the values of ys
-    for j in range(np.shape(u)[1]):
-        assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))

From 5663d0e886097c513475ccd22401d12e24421326 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:42:01 +0100
Subject: [PATCH 12/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index ec401c4..890dd54 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -38,4 +38,4 @@ jobs:
     # Install pytest (you can use some other testing utility)
     - name: Test with pytest
       run: |
-        pytest pyTFM/pyTFM/test_pyTFM.py
+        pytest test_pyTFM.py

From a835c83745a305003974683bca22940780c48380 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:50:32 +0100
Subject: [PATCH 13/19] Update python-package.yml

---
 .github/workflows/python-package.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/python-package.yml b/.github/workflows/python-package.yml
index 890dd54..40fa2fb 100644
--- a/.github/workflows/python-package.yml
+++ b/.github/workflows/python-package.yml
@@ -16,7 +16,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9"]
+        python-version: ["3.7"] #["3.7", "3.8", "3.9"]
 
     steps:
     - uses: actions/checkout@v3

From af6dcfd2b6c613685a62385f995b8917ea22a008 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 9 Feb 2023 17:52:58 +0100
Subject: [PATCH 14/19] Update README.md

---
 README.md | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/README.md b/README.md
index e908c7d..6a77932 100644
--- a/README.md
+++ b/README.md
@@ -1,3 +1,7 @@
+[![Python package](https://github.com/martinschatz-cz/pyTFM/actions/workflows/python-package.yml/badge.svg?event=push)](https://github.com/martinschatz-cz/pyTFM/actions/workflows/python-package.yml)
+
+[![Python 3.7](https://img.shields.io/badge/python-3.7-green.svg)]() [![Python 3.8](https://img.shields.io/badge/python-3.8-red.svg)]() [![Python 3.9](https://img.shields.io/badge/python-3.9-red.svg)]()
+
 ## Readme
 
 pyTFM is a python package that allows you to analyze force generation and stresses in cell colonies and confluent cell layers growing on a 2 dimensional surface. This package implements the procedures of [Traction Force Microscopy](https://www.ncbi.nlm.nih.gov/pubmed/11832345) and [Monolayer Stress Microscopy](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0055172). In addition to the standard measures for stress and force generation, it

From 235622a8dcd7aabcbc54ebe696a1f99410b2c48e Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Fri, 10 Feb 2023 08:53:30 +0100
Subject: [PATCH 15/19] contractillity and strain_energy_points test

---
 test_pyTFM.py | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/test_pyTFM.py b/test_pyTFM.py
index 0c47fdf..7a0a459 100644
--- a/test_pyTFM.py
+++ b/test_pyTFM.py
@@ -16,6 +16,8 @@
 from scipy.ndimage.filters import uniform_filter
 from pyTFM.TFM_functions import ffttc_traction
 from pyTFM.TFM_functions import get_xy_for_quiver
+from pyTFM.TFM_functions import strain_energy_points
+from pyTFM.TFM_functions import contractillity
 
 def test_ffttc_traction_output_shape():
     # create test inputs
@@ -102,3 +104,28 @@ def test_get_xy_for_quiver():
     # Test the values of ys
     for j in range(np.shape(u)[1]):
         assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))
+        
+        
+def test_contractility():
+    tx = np.array([1, 2, 3, 4, 5])
+    ty = np.array([1, 2, 3, 4, 5])
+    pixelsize = 10
+    mask = np.array([True, True, True, True, True])
+
+    expected_output = (30.0, np.array([5.5, 11.0, 16.5, 22.0, 27.5]), np.array([5.5, 11.0, 16.5, 22.0, 27.5]), np.array([2.5, 2.5]))
+    output = contractillity(tx, ty, pixelsize, mask)
+
+    assert output == expected_output, f"Expected {expected_output}, but got {output}"
+
+def test_strain_energy_points():
+    u = np.array([1, 2, 3, 4, 5])
+    v = np.array([1, 2, 3, 4, 5])
+    tx = np.array([1, 2, 3, 4, 5])
+    ty = np.array([1, 2, 3, 4, 5])
+    pixelsize1 = 10
+    pixelsize2 = 10
+
+    expected_output = np.array([12.5, 25.0, 37.5, 50.0, 62.5])
+    output = strain_energy_points(u, v, tx, ty, pixelsize1, pixelsize2)
+
+    assert np.array_equal(output, expected_output), f"Expected {expected_output}, but got {output}"

From b126fa8b9c1b84761d75b5bf598098a4402b4f48 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Fri, 10 Feb 2023 08:57:52 +0100
Subject: [PATCH 16/19] clean

---
 test_pyTFM.py | 25 -------------------------
 1 file changed, 25 deletions(-)

diff --git a/test_pyTFM.py b/test_pyTFM.py
index 7a0a459..9658d7d 100644
--- a/test_pyTFM.py
+++ b/test_pyTFM.py
@@ -104,28 +104,3 @@ def test_get_xy_for_quiver():
     # Test the values of ys
     for j in range(np.shape(u)[1]):
         assert np.array_equal(ys[:, j], np.arange(0, np.shape(u)[0], 1))
-        
-        
-def test_contractility():
-    tx = np.array([1, 2, 3, 4, 5])
-    ty = np.array([1, 2, 3, 4, 5])
-    pixelsize = 10
-    mask = np.array([True, True, True, True, True])
-
-    expected_output = (30.0, np.array([5.5, 11.0, 16.5, 22.0, 27.5]), np.array([5.5, 11.0, 16.5, 22.0, 27.5]), np.array([2.5, 2.5]))
-    output = contractillity(tx, ty, pixelsize, mask)
-
-    assert output == expected_output, f"Expected {expected_output}, but got {output}"
-
-def test_strain_energy_points():
-    u = np.array([1, 2, 3, 4, 5])
-    v = np.array([1, 2, 3, 4, 5])
-    tx = np.array([1, 2, 3, 4, 5])
-    ty = np.array([1, 2, 3, 4, 5])
-    pixelsize1 = 10
-    pixelsize2 = 10
-
-    expected_output = np.array([12.5, 25.0, 37.5, 50.0, 62.5])
-    output = strain_energy_points(u, v, tx, ty, pixelsize1, pixelsize2)
-
-    assert np.array_equal(output, expected_output), f"Expected {expected_output}, but got {output}"

From efdcc02c597c73dc0f3bc273e06bac9934c63dde Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Thu, 23 Mar 2023 15:19:58 +0100
Subject: [PATCH 17/19] compatibility update

---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index 6a77932..eda896e 100644
--- a/README.md
+++ b/README.md
@@ -22,7 +22,9 @@ pyTFM package install
 pip install git+https://github.com/fabrylab/pyTFM.git
 ```
 
-If you want to use jupyterlab with black packge
+If you want to use jupyterlab
 ```
-conda install jupyterlab jupyterlab_code_formatter black isort -c conda-forge
+pip install jupyterlab
+jupyter-lab
 ```
+Sometimes it is necessary to reinstall pyTFM again through the JupyterLab because of scikit-image package.

From e1c17b3e30f658c4d860ad6be3ff66e5b30e3bc6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Wed, 30 Aug 2023 15:32:11 +0200
Subject: [PATCH 18/19] Update README.md

---
 README.md | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/README.md b/README.md
index eda896e..ca247b1 100644
--- a/README.md
+++ b/README.md
@@ -11,12 +11,14 @@ pyTFM includes an addon for the image annotation tool [clickpoints](https://clic
 Please refer to the [Documentation](https://pytfm.readthedocs.io/en/latest/) of pyTFM for detailed instructions on installation and usage.
 
 ## Conda enviroment creation
-You need to create python 3.7 enviroment.
+You need to create python 3.6 enviroment. 
 ```
-conda create --name pyTFM python=3.7
+conda create --name pyTFM python=3.6
 conda activate pyTFM
 ```
 
+Note: python 3.7 works too, but clickpoints need python 3.6.
+
 pyTFM package install
 ```
 pip install git+https://github.com/fabrylab/pyTFM.git

From 60e919eca1dbc98c86ae2ab7ff86c22f0e4876e3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Martin=20Sch=C3=A4tz?=
 <61615369+martinschatz-cz@users.noreply.github.com>
Date: Wed, 30 Aug 2023 15:34:09 +0200
Subject: [PATCH 19/19] Update of python info

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/README.md b/README.md
index ca247b1..4b8abce 100644
--- a/README.md
+++ b/README.md
@@ -1,6 +1,6 @@
 [![Python package](https://github.com/martinschatz-cz/pyTFM/actions/workflows/python-package.yml/badge.svg?event=push)](https://github.com/martinschatz-cz/pyTFM/actions/workflows/python-package.yml)
 
-[![Python 3.7](https://img.shields.io/badge/python-3.7-green.svg)]() [![Python 3.8](https://img.shields.io/badge/python-3.8-red.svg)]() [![Python 3.9](https://img.shields.io/badge/python-3.9-red.svg)]()
+[![Python 3.6](https://img.shields.io/badge/python-3.6-green.svg)]() [![Python 3.7](https://img.shields.io/badge/python-3.7-green.svg)]() [![Python 3.8](https://img.shields.io/badge/python-3.8-red.svg)]() [![Python 3.9](https://img.shields.io/badge/python-3.9-red.svg)]()
 
 ## Readme