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

NiklasVin · BenjaminRodenberg · web-flow · commit a67bad1d161f · 2024-10-19T13:59:26.000+02:00
* Add requirements.txt files.
* Update run.sh files.

---------

Co-authored-by: Benjamin Rodenberg &lt;benjamin.rodenberg@cit.tum.de&gt;
diff --git a/channel-transport-reaction/chemical-fenics/requirements.txt b/channel-transport-reaction/chemical-fenics/requirements.txt
@@ -0,0 +1,11 @@
+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
+
diff --git a/channel-transport-reaction/chemical-fenics/run.sh b/channel-transport-reaction/chemical-fenics/run.sh
@@ -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
diff --git a/channel-transport-reaction/fluid-fenics/requirements.txt b/channel-transport-reaction/fluid-fenics/requirements.txt
@@ -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
diff --git a/channel-transport-reaction/fluid-fenics/run.sh b/channel-transport-reaction/fluid-fenics/run.sh
@@ -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
diff --git a/elastic-tube-1d/fluid-python/requirements.txt b/elastic-tube-1d/fluid-python/requirements.txt
@@ -1,3 +1,3 @@
 matplotlib
 numpy >1, <2
-pyprecice~=3.0
+pyprecice~=3.0
diff --git a/elastic-tube-3d/solid-fenics/requirements.txt b/elastic-tube-3d/solid-fenics/requirements.txt
@@ -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
diff --git a/elastic-tube-3d/solid-fenics/run.sh b/elastic-tube-3d/solid-fenics/run.sh
@@ -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
diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt b/flow-around-controlled-moving-cylinder/controller-fmi/requirements.txt
@@ -0,0 +1 @@
+fmiprecice
diff --git a/flow-around-controlled-moving-cylinder/controller-fmi/run.sh b/flow-around-controlled-moving-cylinder/controller-fmi/run.sh
@@ -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
diff --git a/flow-around-controlled-moving-cylinder/solid-python/requirements.txt b/flow-around-controlled-moving-cylinder/solid-python/requirements.txt
@@ -0,0 +1,2 @@
+pyprecice~=3.0
+numpy >1, <2
diff --git a/flow-around-controlled-moving-cylinder/solid-python/run.sh b/flow-around-controlled-moving-cylinder/solid-python/run.sh
@@ -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
diff --git a/flow-over-heated-plate/solid-fenics/requirements.txt b/flow-over-heated-plate/solid-fenics/requirements.txt
@@ -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
diff --git a/flow-over-heated-plate/solid-fenics/run.sh b/flow-over-heated-plate/solid-fenics/run.sh
@@ -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
diff --git a/oscillator-overlap/mass-left-python/run.sh b/oscillator-overlap/mass-left-python/run.sh
@@ -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
diff --git a/oscillator-overlap/mass-right-python/run.sh b/oscillator-overlap/mass-right-python/run.sh
@@ -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
diff --git a/oscillator-overlap/solver-python/requirements.txt b/oscillator-overlap/solver-python/requirements.txt
diff --git a/oscillator/mass-left-fmi/requirements.txt b/oscillator/mass-left-fmi/requirements.txt
@@ -0,0 +1 @@
+fmiprecice
diff --git a/oscillator/mass-left-fmi/run.sh b/oscillator/mass-left-fmi/run.sh
@@ -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
 
diff --git a/oscillator/mass-left-python/requirements.txt b/oscillator/mass-left-python/requirements.txt
diff --git a/oscillator/mass-left-python/run.sh b/oscillator/mass-left-python/run.sh
@@ -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
diff --git a/oscillator/mass-right-fmi/requirements.txt b/oscillator/mass-right-fmi/requirements.txt
@@ -0,0 +1 @@
+fmiprecice
diff --git a/oscillator/mass-right-fmi/run.sh b/oscillator/mass-right-fmi/run.sh
@@ -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
 
diff --git a/oscillator/mass-right-python/requirements.txt b/oscillator/mass-right-python/requirements.txt
diff --git a/oscillator/mass-right-python/run.sh b/oscillator/mass-right-python/run.sh
@@ -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
diff --git a/oscillator/solver-fmi/requirements.txt b/oscillator/solver-fmi/requirements.txt
@@ -0,0 +1 @@
+fmiprecice
diff --git a/oscillator/solver-python/requirements.txt b/oscillator/solver-python/requirements.txt
diff --git a/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh b/partitioned-heat-conduction-complex/dirichlet-fenics/run.sh
@@ -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
diff --git a/partitioned-heat-conduction-complex/neumann-fenics/run.sh b/partitioned-heat-conduction-complex/neumann-fenics/run.sh
@@ -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
diff --git a/partitioned-heat-conduction-complex/solver-fenics/requirements.txt b/partitioned-heat-conduction-complex/solver-fenics/requirements.txt
@@ -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
diff --git a/partitioned-heat-conduction-overlap/left-fenics/run.sh b/partitioned-heat-conduction-overlap/left-fenics/run.sh
@@ -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
diff --git a/partitioned-heat-conduction-overlap/right-fenics/run.sh b/partitioned-heat-conduction-overlap/right-fenics/run.sh
@@ -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
diff --git a/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt b/partitioned-heat-conduction-overlap/solver-fenics/requirements.txt
@@ -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
diff --git a/partitioned-heat-conduction/neumann-fenics/run.sh b/partitioned-heat-conduction/neumann-fenics/run.sh
@@ -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
diff --git a/perpendicular-flap/solid-fenics/requirements.txt b/perpendicular-flap/solid-fenics/requirements.txt
@@ -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
diff --git a/perpendicular-flap/solid-fenics/run.sh b/perpendicular-flap/solid-fenics/run.sh
@@ -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
diff --git a/volume-coupled-diffusion/drain-fenics/run.sh b/volume-coupled-diffusion/drain-fenics/run.sh
@@ -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
diff --git a/volume-coupled-diffusion/solver-fenics/requirements.txt b/volume-coupled-diffusion/solver-fenics/requirements.txt
@@ -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
diff --git a/volume-coupled-diffusion/source-fenics/run.sh b/volume-coupled-diffusion/source-fenics/run.sh
@@ -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
