From 44762d2ccf42538a486c7b32dbb77eee76198c9d Mon Sep 17 00:00:00 2001 From: ViktorvdV Date: Tue, 5 Jan 2021 16:25:18 +0100 Subject: [PATCH 1/2] 'CI:Use_Netlify_for_notebooks_tests' --- .github/workflows/notebook-test.yml | 17 ----------------- .github/workflows/notebooks-test.yml | 25 +++++++++++++++++++++++++ examples/requirements.txt | 11 ++++++----- 3 files changed, 31 insertions(+), 22 deletions(-) delete mode 100644 .github/workflows/notebook-test.yml create mode 100644 .github/workflows/notebooks-test.yml diff --git a/.github/workflows/notebook-test.yml b/.github/workflows/notebook-test.yml deleted file mode 100644 index 8697b354..00000000 --- a/.github/workflows/notebook-test.yml +++ /dev/null @@ -1,17 +0,0 @@ -name: Notebook tests - -on: [push, pull_request] - -jobs: - run: - runs-on: ubuntu-latest - name: Run notebooks on treebeard - steps: - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 - - uses: treebeardtech/treebeard@v0.1.1 - with: - docker-username: thewtex - docker-password: "${{ secrets.DOCKER_PASSWORD }}" - docker-image-name: insighttoolkit/itk-elastix - notebooks: examples/*.ipynb diff --git a/.github/workflows/notebooks-test.yml b/.github/workflows/notebooks-test.yml new file mode 100644 index 00000000..75b2d1e1 --- /dev/null +++ b/.github/workflows/notebooks-test.yml @@ -0,0 +1,25 @@ +name: Notebooks tests + +on: [push, pull_request] + +jobs: + test-elastix: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v2 + - name: Set Up Python + uses: actions/setup-python@v2 + with: + python-version: 3.7 + - run: | + cd examples + pip install -r requirements.txt + pip install pytest-tornasync + python -m ipykernel install --user --name elastixenv + pip install pytest 'nbmake[html]' + - run: | + pytest --nbmake --path-output=. +# - if: failure() + - run: | + netlify deploy --dir=_build/html --auth=${{ secrets.NETLIFY_TOKEN }} --site=${{ secrets.NETLIFY_SITE_API_ID }} + diff --git a/examples/requirements.txt b/examples/requirements.txt index 0e5861a4..cc0d8224 100644 --- a/examples/requirements.txt +++ b/examples/requirements.txt @@ -1,4 +1,4 @@ -itk-elastix>=0.7.0 +itk-elastix>=0.8.0 itk==5.1.1.post1 itk-core==5.1.1.post1 itk-numerics==5.1.1.post1 @@ -7,8 +7,9 @@ itk-registration==5.1.1.post1 itk-segmentation==5.1.1.post1 itkwidgets>=0.32.0 jupyterlab==1.2.5 -imageio +imageio>=2.5.0 ipywidgets>=7.5.1 -ipympl>=0.4.1 -voila>=0.1.21 -pyinstaller \ No newline at end of file +ipympl==0.5.7 +voila>=0.2.3 +pyinstaller>=4.0 +sphinxcontrib-bibtex==1.0.0 From 5b3c4d510102c7f18d8c1b2525701fe37a8a21c5 Mon Sep 17 00:00:00 2001 From: ViktorvdV Date: Thu, 14 Jan 2021 11:03:03 +0100 Subject: [PATCH 2/2] BUG:Same_virtual_env_in_all_notebooks --- examples/ITK_Example10_Transformix_Jacobian.ipynb | 6 +++--- examples/ITK_Example11_Transformix_DeformationField.ipynb | 6 +++--- examples/ITK_UnitTestExample1_RigidRegistration.ipynb | 6 +++--- examples/ITK_UnitTestExample2_AffineRegistration.ipynb | 6 +++--- examples/ITK_UnitTestExample6_PointSetTransformation.ipynb | 6 +++--- 5 files changed, 15 insertions(+), 15 deletions(-) diff --git a/examples/ITK_Example10_Transformix_Jacobian.ipynb b/examples/ITK_Example10_Transformix_Jacobian.ipynb index 0a3be859..67d5600b 100644 --- a/examples/ITK_Example10_Transformix_Jacobian.ipynb +++ b/examples/ITK_Example10_Transformix_Jacobian.ipynb @@ -186,9 +186,9 @@ ], "metadata": { "kernelspec": { - "display_name": "ElastixEnv2", + "display_name": "ElastixEnv", "language": "python", - "name": "elastixenv2" + "name": "elastixenv" }, "language_info": { "codemirror_mode": { @@ -200,7 +200,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.5" } }, "nbformat": 4, diff --git a/examples/ITK_Example11_Transformix_DeformationField.ipynb b/examples/ITK_Example11_Transformix_DeformationField.ipynb index a42adac7..dcc56b63 100644 --- a/examples/ITK_Example11_Transformix_DeformationField.ipynb +++ b/examples/ITK_Example11_Transformix_DeformationField.ipynb @@ -265,9 +265,9 @@ ], "metadata": { "kernelspec": { - "display_name": "ElastixEnv2", + "display_name": "ElastixEnv", "language": "python", - "name": "elastixenv2" + "name": "elastixenv" }, "language_info": { "codemirror_mode": { @@ -279,7 +279,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.5" } }, "nbformat": 4, diff --git a/examples/ITK_UnitTestExample1_RigidRegistration.ipynb b/examples/ITK_UnitTestExample1_RigidRegistration.ipynb index 15c14f3b..54779f47 100644 --- a/examples/ITK_UnitTestExample1_RigidRegistration.ipynb +++ b/examples/ITK_UnitTestExample1_RigidRegistration.ipynb @@ -121,9 +121,9 @@ ], "metadata": { "kernelspec": { - "display_name": "ITKTestEnvDebug", + "display_name": "ElastixEnv", "language": "python", - "name": "itktestenvdebug" + "name": "elastixenv" }, "language_info": { "codemirror_mode": { @@ -135,7 +135,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.5" } }, "nbformat": 4, diff --git a/examples/ITK_UnitTestExample2_AffineRegistration.ipynb b/examples/ITK_UnitTestExample2_AffineRegistration.ipynb index f72962ec..91568f6b 100644 --- a/examples/ITK_UnitTestExample2_AffineRegistration.ipynb +++ b/examples/ITK_UnitTestExample2_AffineRegistration.ipynb @@ -122,9 +122,9 @@ ], "metadata": { "kernelspec": { - "display_name": "ITKTestEnvDebug", + "display_name": "ElastixEnv", "language": "python", - "name": "itktestenvdebug" + "name": "elastixenv" }, "language_info": { "codemirror_mode": { @@ -136,7 +136,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.5" } }, "nbformat": 4, diff --git a/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb b/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb index ea4a06b6..827b7975 100644 --- a/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb +++ b/examples/ITK_UnitTestExample6_PointSetTransformation.ipynb @@ -162,9 +162,9 @@ ], "metadata": { "kernelspec": { - "display_name": "ITKTestEnvDebug", + "display_name": "ElastixEnv", "language": "python", - "name": "itktestenvdebug" + "name": "elastixenv" }, "language_info": { "codemirror_mode": { @@ -176,7 +176,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.7.9" + "version": "3.8.5" } }, "nbformat": 4,