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Adding testing to the CI. (#105)
Fix #104 Fix #109 --------- Co-authored-by: Taylor Hanayik <[email protected]>
1 parent a84e773 commit 7812824

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‎.github/workflows/ci.yml‎

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@@ -16,16 +16,28 @@ jobs:
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- uses: actions/setup-python@v5
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with:
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python-version: "3.12"
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- run: |
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# Run Ruff
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- name: Run Ruff
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run: |
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pip install uv
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uv pip install --system ruff
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ruff check
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# Run Codespell
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- name: Run Codespell
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run: |
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pip install codespell
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codespell codespell src/**/*.py
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Test:
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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.8", "3.9", "3.10", "3.11", "3.12"]
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python-version: ["3.9", "3.10", "3.11", "3.12"]
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os:
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- ubuntu-latest
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- macos-latest # arm64 (Apple Silicon)
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- macos-13 # latest Intel release
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- windows-latest
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steps:
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- uses: actions/checkout@v4
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with:
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python-version: ${{ matrix.python-version }}
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- run: |
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pipx install hatch
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hatch run test
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pip install pytest-notebook
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pip install pre-commit
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pre-commit run --all
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pre-commit install
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# pipx install hatch
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# hatch run test --cover --nb-test-files
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- name: Install IPyNiiVue & Deps
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run: pip install -e .
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- name: Test import
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run: |
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python -c "import ipyniivue"
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- name: Test IPyNiiVue
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run: |
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pip install pytest-cov
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pip install --upgrade pip ipython ipykernel
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ipython kernel install --name "python3" --user
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mkdir -p ./reports
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pytest --cov --cov-report=json:./reports/coverage.json --cov-report=xml:./reports/coverage.xml
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- name: Upload ipyniivue test coverage report
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uses: actions/upload-artifact@v4
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with:
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name: coverage_ipyniivue-${{ matrix.os }}-py${{ matrix.python-version }}
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path: ./reports/coverage.json
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- name: Generate Markdown summary of code coverage
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uses: irongut/[email protected]
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with:
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filename: ./reports/coverage.xml
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format: markdown
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output: both
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thresholds: "10 10"
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- name: Add test results to job summary
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run: |
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cat ./code-coverage-results.md >> $GITHUB_STEP_SUMMARY
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- name: Test example notebooks
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run: |
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pip install nbmake
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rm -rf ./reports
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mkdir -p ./reports
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pytest --nbmake examples/*ipynb --cov --cov-report=json:./reports/coverage.json --cov-report=xml:./reports/coverage.xml
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- name: Upload ipyniivue example notbooks coverage report
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uses: actions/upload-artifact@v4
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with:
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name: coverage_ipyniivue_notebooks-${{ matrix.os }}-py${{ matrix.python-version }}
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path: ./reports/coverage.json
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- name: Generate Markdown summary of code coverage
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uses: irongut/[email protected]
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with:
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filename: ./reports/coverage.xml
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format: markdown
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output: both
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thresholds: "10 10"
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- name: Add test results to job summary
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run: |
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cat ./code-coverage-results.md >> $GITHUB_STEP_SUMMARY
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# coverage run -m pytest --nb-test-files
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# nbt-test-files check for changes in the output of the notebook.
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# This does not work for our purpose since we wipe the output
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# before committing changes to facilitate integration with git.
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# - name: Upload coverage to codecov (Only do this for the ubuntu-latest job)
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# if: matrix.os == 'ubuntu-latest'
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# uses: codecov/codecov-action@v5
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# with:
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# token: ${{secrets.CODECOV_TOKEN}}
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#
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LintJavaScript:
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name: JavaScript / Lint
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runs-on: macos-14

‎examples/additive_voxels.ipynb‎

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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎examples/basic_multiplanar.ipynb‎

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"nv.is_colorbar = True\n",
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"nv.view_mode_hot_key = \"KeyN\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎examples/drawing.ipynb‎

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"for widget in widgetArray:\n",
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" display(widget[\"widget\"])"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "32e9b296-bae2-47c4-9912-e99e5cb6a85e",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.3"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎examples/example_sideview.ipynb‎

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{
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"cells": [
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "52de1125",
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"metadata": {},
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"outputs": [],
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"source": [
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"# This is not part of IPyNiiVue dependencies so it has to be installed independently\n",
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"!pip install ipylab"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"nv.volumes[0].opacity = 0.5\n",
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"nv.volumes[1].colormap = \"green\""
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "c7b34b44-2940-4f0e-99b5-2e16ad3d23f3",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎examples/mesh_and_volume.ipynb‎

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"\n",
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"nv"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "851a559d-59e8-40bc-b1f0-9380f9844855",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎examples/mesh_layers.ipynb‎

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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.12.3"
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"pygments_lexer": "ipython3"
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},
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"widgets": {
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"application/vnd.jupyter.widget-state+json": {

‎examples/prototypes/meshes_(GIfTI, FreeSurfer, MZ3, OBJ, STL, legacy VTK).ipynb‎

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"\n",
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"# nv1.setMeshShader(nv1.meshes[0].id, \"Outline\"); does not seem to exist yet."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎examples/prototypes/torso_regions.ipynb‎

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"}\n",
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"nv.setDrawColormap(cmap);"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "94a1c95a-308b-4259-ac29-7512c48239b2",
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"metadata": {},
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"outputs": [],
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

‎examples/prototypes/trajectory.ipynb‎

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"\n",
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"nv"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"metadata": {},
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"source": []
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}
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],
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"metadata": {
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"mimetype": "text/x-python",
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"name": "python",
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"nbconvert_exporter": "python",
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"pygments_lexer": "ipython3",
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"version": "3.11.6"
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"pygments_lexer": "ipython3"
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}
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},
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"nbformat": 4,

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