precice · BenjaminRodenberg · Jan 25, 2024 · Jan 15, 2024 · Jan 15, 2024 · Jan 17, 2024
diff --git a/channel-transport/fluid-nutils/requirements.txt b/channel-transport/fluid-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/channel-transport/fluid-nutils/run.sh b/channel-transport/fluid-nutils/run.sh
@@ -1,4 +1,7 @@
 #!/bin/sh
 set -e -u
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 python3 fluid.py
diff --git a/flow-over-heated-plate/solid-nutils/requirements.txt b/flow-over-heated-plate/solid-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/flow-over-heated-plate/solid-nutils/run.sh b/flow-over-heated-plate/solid-nutils/run.sh
@@ -1,5 +1,7 @@
 #!/bin/bash
 set -e -u
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 python3 solid.py
-
diff --git a/partitioned-heat-conduction-direct/nutils/requirements.txt b/partitioned-heat-conduction-direct/nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/partitioned-heat-conduction-direct/nutils/run.sh b/partitioned-heat-conduction-direct/nutils/run.sh
@@ -8,6 +8,10 @@ if [ -z "$*" ] ; then
         usage
 fi
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 while getopts ":dn" opt; do
   case ${opt} in
   d)

diff --git a/partitioned-heat-conduction/nutils/requirements.txt b/partitioned-heat-conduction/nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/partitioned-heat-conduction/nutils/run.sh b/partitioned-heat-conduction/nutils/run.sh
@@ -8,6 +8,10 @@ if [ -z "$*" ] ; then
         usage
 fi
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 while getopts ":dn" opt; do
   case ${opt} in
   d)

diff --git a/perpendicular-flap/fluid-nutils/requirements.txt b/perpendicular-flap/fluid-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==6
+pyprecice==3.0.0.0dev2
diff --git a/perpendicular-flap/fluid-nutils/run.sh b/perpendicular-flap/fluid-nutils/run.sh
@@ -1,4 +1,7 @@
 #!/bin/sh
 set -e -u
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 python3 fluid.py
diff --git a/perpendicular-flap/solid-nutils/requirements.txt b/perpendicular-flap/solid-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==8
+pyprecice==3.0.0.0dev2
diff --git a/perpendicular-flap/solid-nutils/run.sh b/perpendicular-flap/solid-nutils/run.sh
@@ -1,4 +1,7 @@
 #!/bin/sh
 set -e -u
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 python3 solid.py richoutput=no
diff --git a/two-scale-heat-conduction/macro-nutils/requirements.txt b/two-scale-heat-conduction/macro-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/two-scale-heat-conduction/macro-nutils/run.sh b/two-scale-heat-conduction/macro-nutils/run.sh
@@ -1,4 +1,7 @@
 #!/bin/sh
 set -e -u
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
 NUTILS_RICHOUTPUT=no python3 macro.py
diff --git a/two-scale-heat-conduction/micro-nutils/requirements.txt b/two-scale-heat-conduction/micro-nutils/requirements.txt
@@ -0,0 +1,2 @@
+nutils==7
+pyprecice==3.0.0.0dev2
diff --git a/two-scale-heat-conduction/micro-nutils/run.sh b/two-scale-heat-conduction/micro-nutils/run.sh
@@ -3,6 +3,10 @@ set -e -u
 
 usage() { echo "Usage: cmd [-s] [-p n]" 1>&2; exit 1; }
 
+python3 -m venv .venv
+. .venv/bin/activate
+pip install -r requirements.txt
+
 # Check if no input argument was provided
 if [ -z "$*" ] ; then
         echo "No input argument provided. Micro Manager is launched in serial"
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		nutils==7
		pyprecice==3.0.0.0dev2
Comment on lines +1 to +2 Copy link Member MakisH Jan 18, 2024 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. Since we are adding a `requirements.txt`, I think we should also specify here the non-preCICE dependencies. For this script: from nutils import function, mesh, cli, solver, export import treelog as log import numpy as np import precice from mpi4py import MPI Similarly for the rest. Copy link Member Author BenjaminRodenberg Jan 19, 2024 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. I'm not sure what's the state-of-the-art here. Sometimes there are `requirement.txt` files that just originate from a `pip3 freeze`. This is extreme and a huge overspecification and leads to the installation of a lot of unnecessary packages. I had this situation a few times and it is just annoying. Adding `treelog`, `numpy`, and `mpi4py` sounds reasonable, but might also be unnecessary as long as it does not cause problems, if it is missing in the `requirements.txt`. I imagine `numpy` is already a dependency of `nutils`. I also cannot pin down a reasonable version number here and don't know how much value it has, if we do not specify a version (imagine somebody using an ancient `numpy`). In the end this is also one more thing we have to maintain and keep in sync with the script (we will forget to remove `treelog`, if we decide to use a different logger occasionally) and to me the usefulness is not clear as long at things do not break without it. Additionally, it's some work to add the additional lines in every file now (Writing this comment was more work, but still, I'm lazy). Copy link Member MakisH Jan 19, 2024 • edited Loading Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. But then we would anyway need to tell the user "install `treelog`, `numpy`, `mpi4py` manually" (or hope that they are already installed by something else) and then tell them also "install the rest from the `requirements.txt`". This sounds non-ideal to me. In the C++ world, there is a good practice of explicitly including the headers you need where you need them (but not their dependencies). I would assume the same holds for Python. Regarding the versions, we can also specify `>=`, if that is the common problem: https://pip.pypa.io/en/stable/reference/requirement-specifiers/ Copy link Member Author BenjaminRodenberg Jan 19, 2024 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. As I said: I don't think it is necessary. `nutils` already requires `treelog` (https://github.com/evalf/nutils/blob/e1a61d2611d1a7507d6f6dbd2ade25ea52001cad/pyproject.toml#L15). `pyprecice` requires `numpy` and `mpi4py` (https://github.com/precice/python-bindings/blob/49c2af0ed3817bb90afbe2c4e4a21a7b4a704bc8/pyproject.toml#L3). So it is specified indirectly. Yes, dependencies of dependencies might change and then we might get a problem here. But the problem this issue is dealing with is that `nutils` was not specified properly and right now I only see additional maintainment work and not really so much value in adding more dependencies. (We can easily extend this framework we introduced now, if users run into problems and we know more about the concrete situation) Copy link Member MakisH Jan 19, 2024 Choose a reason for hiding this comment The reason will be displayed to describe this comment to others. Learn more. I don't think that this is the right approach (I still think we should specify direct dependencies explicitly if we specify dependencies somewhere). This is a detail that currently matters very little, so I don't think it is blocking. Just the right and complete thing to do, without any clear downsides to me (apart from making the venv even larger). Just for `mpi4py`, you could argue that we should be enforcing the same MPI version for every involved component. For which none of the two approaches helps.