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Merged
merged 12 commits into from
Oct 19, 2024
Merged

Add missing requirements.txt and venvs for Python tutorials #563

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fa820d0
Add requirements to oscillator tutorial
NiklasVin Aug 19, 2024
48a0a04
Apply suggestions from code review
BenjaminRodenberg Aug 29, 2024
14c80f7
Update run.sh and add requirements.txt for overlapping oscillator.
BenjaminRodenberg Aug 29, 2024
58f9e7c
Add requirements.txt for python tutorials and modified run scripts ac…
NiklasVin Aug 31, 2024
9ee418a
Merge branch 'precice:develop' into i547
NiklasVin Aug 31, 2024
fca16cc
Add requirements.txt for fmi cases
NiklasVin Aug 31, 2024
e1efdce
Add remaining requirements files and remove redundant requirements files
NiklasVin Aug 31, 2024
e1c6a36
Suggested changes
NiklasVin Sep 5, 2024
1c0b737
Merge branch 'develop' into i547
NiklasVin Sep 5, 2024
1df7f76
Accidentally deleted requirement
NiklasVin Sep 6, 2024
12243a8
Merge branch 'i547' of github.com:NiklasVin/tutorials into i547
NiklasVin Sep 6, 2024
c27d9ec
Add suggested changes
NiklasVin Sep 15, 2024
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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

close_log
close_log
10 changes: 10 additions & 0 deletions channel-transport-reaction/fluid-fenics/requirements.txt
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@@ -0,0 +1,10 @@
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

close_log
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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@@ -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
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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@@ -0,0 +1 @@
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

close_log
2 changes: 2 additions & 0 deletions flow-around-controlled-moving-cylinder/solid-python/requirements.txt
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@@ -0,0 +1,2 @@
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

close_log
10 changes: 10 additions & 0 deletions flow-over-heated-plate/solid-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 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

close_log
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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This file was deleted.

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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@@ -0,0 +1 @@
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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This file was deleted.

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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@@ -0,0 +1 @@
fmiprecice
0 ...verlap/mass-right-python/requirements.txt → oscillator/solver-python/requirements.txt
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File renamed without changes.
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

close_log
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

close_log
11 changes: 11 additions & 0 deletions partitioned-heat-conduction-complex/solver-fenics/requirements.txt
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@@ -0,0 +1,11 @@
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

close_log
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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@@ -0,0 +1,11 @@
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