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Add missing requirements.txt and venvs for Python tutorials (#563)
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* Add requirements.txt files.
* Update run.sh files.

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Co-authored-by: Benjamin Rodenberg <[email protected]>
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@NiklasVin @BenjaminRodenberg
NiklasVin and BenjaminRodenberg authored Oct 19, 2024
1 parent 62e2e18 commit a67bad1
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Showing 38 changed files with 175 additions and 24 deletions.
11 changes: 11 additions & 0 deletions channel-transport-reaction/chemical-fenics/requirements.txt
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numpy >1, <2
fenicsprecice~=2.0

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0

6 changes: 5 additions & 1 deletion channel-transport-reaction/chemical-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-package .venv
. .venv/bin/activate
pip install -r requirements.txt

python3 chemical-reaction-advection-diffusion.py

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10 changes: 10 additions & 0 deletions channel-transport-reaction/fluid-fenics/requirements.txt
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numpy >1, <2
fenicsprecice~=2.0

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
5 changes: 5 additions & 0 deletions channel-transport-reaction/fluid-fenics/run.sh
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Expand Up @@ -4,6 +4,11 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-package .venv
. .venv/bin/activate
pip install -r requirements.txt


python3 fluid.py

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2 changes: 1 addition & 1 deletion elastic-tube-1d/fluid-python/requirements.txt
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@@ -1,3 +1,3 @@
matplotlib
numpy >1, <2
pyprecice~=3.0
pyprecice~=3.0
10 changes: 10 additions & 0 deletions elastic-tube-3d/solid-fenics/requirements.txt
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fenicsprecice~=2.0
numpy >1, <2

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
7 changes: 7 additions & 0 deletions elastic-tube-3d/solid-fenics/run.sh
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@@ -1,4 +1,11 @@
#!/usr/bin/env bash
set -e -u

. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-package .venv
. .venv/bin/activate
pip install -r requirements.txt

python3 solid.py
1 change: 1 addition & 0 deletions flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt
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fmiprecice
4 changes: 4 additions & 0 deletions flow-around-controlled-moving-cylinder/controller-fmi/run.sh
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Expand Up @@ -15,6 +15,10 @@ if [ ! -f PIDcontroller.fmu ]; then
cd ../../
fi

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

fmiprecice ./fmi-settings.json ./precice-settings.json

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2 changes: 2 additions & 0 deletions flow-around-controlled-moving-cylinder/solid-python/requirements.txt
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pyprecice~=3.0
numpy >1, <2
4 changes: 4 additions & 0 deletions flow-around-controlled-moving-cylinder/solid-python/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

python3 solid.py ../precice-config.xml

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10 changes: 10 additions & 0 deletions flow-over-heated-plate/solid-fenics/requirements.txt
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fenicsprecice~=2.0
numpy >1, <2

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
4 changes: 4 additions & 0 deletions flow-over-heated-plate/solid-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r requirements.txt

python3 solid.py

close_log
8 changes: 4 additions & 4 deletions oscillator-overlap/mass-left-python/run.sh
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@@ -1,13 +1,13 @@
#!/usr/bin/env bash
set -e -u

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv .venv
. .venv/bin/activate
pip install -r ../solver-python/requirements.txt

python3 ../solver-python/oscillator.py Mass-Left

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8 changes: 4 additions & 4 deletions oscillator-overlap/mass-right-python/run.sh
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@@ -1,13 +1,13 @@
#!/usr/bin/env bash
set -e -u

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv .venv
. .venv/bin/activate
pip install -r ../solver-python/requirements.txt

python3 ../solver-python/oscillator.py Mass-Right

close_log
0 ...overlap/mass-left-python/requirements.txt → ...or-overlap/solver-python/requirements.txt
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1 change: 1 addition & 0 deletions oscillator/mass-left-fmi/requirements.txt
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fmiprecice
4 changes: 4 additions & 0 deletions oscillator/mass-left-fmi/run.sh
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Expand Up @@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then
cd ../../../mass-left-fmi
fi

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

fmiprecice fmi-settings.json precice-settings.json
python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Left

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3 changes: 0 additions & 3 deletions oscillator/mass-left-python/requirements.txt
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8 changes: 4 additions & 4 deletions oscillator/mass-left-python/run.sh
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@@ -1,13 +1,13 @@
#!/usr/bin/env bash
set -e -u

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv .venv
. .venv/bin/activate
pip install -r ../solver-python/requirements.txt

python3 ../solver-python/oscillator.py Mass-Left

close_log
1 change: 1 addition & 0 deletions oscillator/mass-right-fmi/requirements.txt
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fmiprecice
4 changes: 4 additions & 0 deletions oscillator/mass-right-fmi/run.sh
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Expand Up @@ -16,6 +16,10 @@ if [ ! -f ../solver-fmi/Oscillator.fmu ]; then
cd ../../../mass-right-fmi
fi

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

fmiprecice fmi-settings.json precice-settings.json
python3 ../solver-fmi/calculate-error.py ../mass-left-fmi/fmi-settings.json ../mass-left-fmi/precice-settings.json ../mass-right-fmi/fmi-settings.json ../mass-right-fmi/precice-settings.json Mass-Right

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3 changes: 0 additions & 3 deletions oscillator/mass-right-python/requirements.txt
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8 changes: 4 additions & 4 deletions oscillator/mass-right-python/run.sh
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@@ -1,13 +1,13 @@
#!/usr/bin/env bash
set -e -u

python3 -m venv .venv
. .venv/bin/activate
pip install -r requirements.txt

. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv .venv
. .venv/bin/activate
pip install -r ../solver-python/requirements.txt

python3 ../solver-python/oscillator.py Mass-Right

close_log
1 change: 1 addition & 0 deletions oscillator/solver-fmi/requirements.txt
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fmiprecice
0 ...verlap/mass-right-python/requirements.txt → oscillator/solver-python/requirements.txt
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4 changes: 4 additions & 0 deletions partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/heat.py -d -i complex

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4 changes: 4 additions & 0 deletions partitioned-heat-conduction-complex/neumann-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/heat.py -n -i complex

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11 changes: 11 additions & 0 deletions partitioned-heat-conduction-complex/solver-fenics/requirements.txt
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fenicsprecice~=2.0
numpy >1, <2
sympy

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
4 changes: 4 additions & 0 deletions partitioned-heat-conduction-overlap/left-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/heat.py Left

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4 changes: 4 additions & 0 deletions partitioned-heat-conduction-overlap/right-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/heat.py Right

close_log
10 changes: 10 additions & 0 deletions partitioned-heat-conduction-overlap/solver-fenics/requirements.txt
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@@ -0,0 +1,10 @@
fenicsprecice~=2.0
numpy >1, <2

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
4 changes: 4 additions & 0 deletions partitioned-heat-conduction/neumann-fenics/run.sh
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Expand Up @@ -8,6 +8,10 @@ pip install -r ../solver-fenics/requirements.txt
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/heat.py Neumann

close_log
11 changes: 11 additions & 0 deletions perpendicular-flap/solid-fenics/requirements.txt
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fenicsprecice~=2.0
numpy >1, <2
matplotlib

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
4 changes: 4 additions & 0 deletions perpendicular-flap/solid-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r requirements.txt

python3 solid.py

close_log
4 changes: 4 additions & 0 deletions volume-coupled-diffusion/drain-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/volume-coupled-diffusion.py --drain

close_log
10 changes: 10 additions & 0 deletions volume-coupled-diffusion/solver-fenics/requirements.txt
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@@ -0,0 +1,10 @@
fenicsprecice~=2.0
numpy >1, <2

# Assuming FEniCS from ppa:fenics-packages/fenics was installed https://fenicsproject.org/download/archive/
# Use --system-site-packages in venv
fenics-dijitso==2019.2.0.dev0
fenics-dolfin==2019.2.0.13.dev0
fenics-ffc==2019.2.0.dev0
fenics-fiat==2019.2.0.dev0
fenics-ufl-legacy==2022.3.0
4 changes: 4 additions & 0 deletions volume-coupled-diffusion/source-fenics/run.sh
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Expand Up @@ -4,6 +4,10 @@ set -e -u
. ../../tools/log.sh
exec > >(tee --append "$LOGFILE") 2>&1

python3 -m venv --system-site-packages .venv
. .venv/bin/activate
pip install -r ../solver-fenics/requirements.txt

python3 ../solver-fenics/volume-coupled-diffusion.py --source

close_log

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