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Pin sphinx version #145

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merged 3 commits into from
Mar 14, 2024
Merged

Pin sphinx version #145

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48d1c67
Update docs and set docutils pin in requirements.txt
hkjeldsberg Mar 14, 2024
8849f3d
Pin sphinx installation
hkjeldsberg Mar 14, 2024
992bbd5
Add blank space
hkjeldsberg Mar 14, 2024
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14 changes: 5 additions & 9 deletions .github/workflows/deploy_pages.yml
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Expand Up @@ -31,7 +31,7 @@ jobs:
- name: Upgrade pip and setuptools
run: |
python3 -m pip install pip setuptools --upgrade

# See: https://github.com/marketplace/actions/setup-miniconda
- name: Setup Mambaforge
uses: conda-incubator/setup-miniconda@v2
Expand All @@ -56,21 +56,17 @@ jobs:
run: mamba env update -n vampy -f environment.yml
if: steps.cache.outputs.cache-hit != 'true'

# Install requirements, with downgraded docutils to fix layout-bug
# https://github.com/executablebooks/jupyter-book/issues/1997
- name: Install dependencies
run: |
pip install -r requirements.txt
run: pip install -r requirements.txt

- name: Install VaMPy
run: python3 -m pip install .[test]

# https://github.com/executablebooks/jupyter-book/issues/1997
- name: Downgrade docutils to fix layout-bug
run: python3 -m pip install docutils==0.17.1

# Build the book
- name: Build the book
run: |
jupyter-book build docs
run: jupyter-book build docs

# Deploy the book's HTML to gh-pages branch
- name: GitHub Pages action
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2 changes: 1 addition & 1 deletion docs/api.rst
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Expand Up @@ -35,7 +35,7 @@ Pre-processing scripts
:undoc-members:
:show-inheritance:

.. automodule:: vampy.automatedPreprocessing.ToolRepairSTL
.. automodule:: vampy.automatedPreprocessing.repair_tools
:members:
:undoc-members:
:show-inheritance:
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2 changes: 1 addition & 1 deletion docs/movingatrium.md
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Expand Up @@ -106,7 +106,7 @@ $ oasismove NSfracStepMove problem=MovingAtrium mesh_path=../../../models/moving

Upon completion of the simulation, the results, along with the associated mesh, are stored in a concise HDF5 format.
Additionally, the residence time $T_R$ and the velocity field are saved in the XDMF files `blood.xdmf`
and `velocity.xdmf`, respectively, which includes the mesh deformation. {numref}`moving_results` presents the volumetric
and `velocity.xdmf`, respectively, which includes the mesh deformation. The animation below presents the volumetric
representation of the blood residence time and velocity field throughout the four cardiac cycles. It's noteworthy to
observe the accumulating $T_R$ within the left atrial appendage over time.

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4 changes: 3 additions & 1 deletion requirements.txt
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Expand Up @@ -3,4 +3,6 @@ matplotlib
numpy
ghp-import
cppimport
scipy
scipy
sphinx==5.3.0
docutils==0.17.1
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