Add doc/examples/clusters/gricad/python-fluidsim.scm

doc/examples/clusters/gricad/README.md

@@ -40,24 +40,19 @@ GUIX_PROFILE="$HOME/.config/guix/current"
 
 ```sh
 # This will take a while
-# note: pip does not work with the -C (container) option
-guix shell -m ~/dev/fluidsim/doc/examples/clusters/gricad/manifest.scm
-
-python3 -m venv ~/venv-fluidsim-guix --system-site-packages
-. ~/venv-fluidsim-guix/bin/activate
-cd ~/dev/fluidsim
-pip install -e lib
-pip install -e ".[test]" -v --config-settings=setup-args=-Dnative=true --no-build-isolation
+guix shell \
+  -m ~/dev/fluidsim/doc/examples/clusters/gricad/manifest.scm \
+  -f ~/dev/fluidsim/doc/examples/clusters/gricad/python-fluidsim.scm
 ```
 
 ## Test Fluidsim in sequential
 
 ```sh
 source /applis/site/guix-start.sh
-guix shell -m ~/dev/fluidsim/doc/examples/clusters/gricad/manifest.scm
-. ~/venv-fluidsim-guix/bin/activate
-cd ~/dev/fluidsim
-python -m pytest fluidsim
+guix shell \
+  -m ~/dev/fluidsim/doc/examples/clusters/gricad/manifest.scm \
+  -f ~/dev/fluidsim/doc/examples/clusters/gricad/python-fluidsim.scm
+python -m pytest --pyargs fluidsim
 ```
 
 ## Submit a fluidfft benchmark

doc/examples/clusters/gricad/instructions_fluidfft_bench.sh

@@ -1,6 +1,4 @@
 
-source $HOME/venv-fluidsim-guix/bin/activate
-
 mpirun -np `cat machinefile | wc -l` \
     --machinefile machinefile \
     --prefix $1 \

doc/examples/clusters/gricad/manifest.scm

@@ -10,6 +10,9 @@
 	"python-fluidfft-p3dfft"
 	"python-fluidfft-pfft"
 	"python-pytest"
+	"python-pytest-allclose"
+	"python-pytest-mock"
+	"python-fluidsim"
     ; build dependencies for editable build
     "meson-python"
     "python-pythran"

doc/examples/clusters/gricad/python-fluidsim.scm

@@ -0,0 +1,104 @@
+(define-module (python-fluidsim)
+  #:use-module (guix)
+  #:use-module ((guix licenses) #:prefix license:)
+  #:use-module (guix build-system pyproject)
+  #:use-module (guix build-system python)
+  #:use-module (guix build utils)
+  #:use-module (guix hg-download)
+  #:use-module (guix utils)
+  #:use-module (common python-packages)
+  #:use-module (gnu packages)
+  #:use-module (gnu packages mpi)
+  #:use-module (gnu packages rust)
+  #:use-module (gnu packages rust-apps)
+  #:use-module (gnu packages crates-io)
+  #:use-module (gnu packages statistics)
+  #:use-module (gnu packages bioinformatics)
+  #:use-module (gnu packages build-tools)
+  #:use-module (gnu packages pkg-config)
+  #:use-module (gnu packages python)
+  #:use-module (gnu packages python-build)
+  #:use-module (gnu packages python-xyz)
+  #:use-module (gnu packages python-science)
+  #:use-module (common python-fluidfft)
+  #:use-module (common python-fluiddyn)
+  #:use-module (common python-fluidsim-utils))
+
+
+;; package python-fluidsim-core
+(define-public python-fluidsim-core
+  (package
+    (name "python-fluidsim-core")
+    (version "X.X.X")
+    (source
+      (origin
+        (method hg-fetch)
+        (uri
+          (hg-reference
+            (url "https://foss.heptapod.net/fluiddyn/fluidsim")
+            (changeset "62c4dbe4f786")))
+        (sha256
+          (base32 "15sm4mknfagx1l4zgz49c2bfjjng8ykiz7jb45qa83jh03vzqc6a"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-fluiddyn
+                             python-importlib-metadata
+                      ))
+    (arguments '(#:phases (modify-phases %standard-phases
+                   ; On patche le HOME
+                   (add-before 'build 'patch-HOME-path
+                      (lambda _
+			(chdir "lib")
+                        (setenv "HOME" (getenv "out"))
+                        ))
+                   ;; On remove la phase de check et de sanity-check
+                   (delete 'check)
+                   (delete 'sanity-check))))
+    (home-page "")
+    (synopsis "Framework for studying fluid dynamics with simulations.")
+    (description "Framework for studying fluid dynamics with simulations.")
+    (license #f)))
+
+;; package python-fluidsim
+(define-public python-fluidsim
+  (package
+    (name "python-fluidsim")
+    (version "X.X.X")
+    (source
+      (origin
+        (method hg-fetch)
+        (uri
+          (hg-reference
+            (url "https://foss.heptapod.net/fluiddyn/fluidsim")
+            (changeset "62c4dbe4f786")))
+        (sha256
+          (base32 "15sm4mknfagx1l4zgz49c2bfjjng8ykiz7jb45qa83jh03vzqc6a"))))
+    (build-system pyproject-build-system)
+    (propagated-inputs (list python-fluidfft
+                             python-fluidsim-core
+                             python-h5netcdf
+                             python-h5py
+                             python-ipython
+                             python-matplotlib
+                             python-mpi4py
+                             python-pyfftw
+                             python-pymech
+                             python-rich
+                             python-scipy
+                             python-transonic
+                             python-xarray
+                      ))
+    (arguments '(#:phases (modify-phases %standard-phases
+                   ; On patche le HOME
+                   (add-before 'build 'patch-HOME-path
+                      (lambda _
+                        (setenv "HOME" (getenv "out"))
+                        ))
+                   ;; On remove la phase de check et de sanity-check
+                   (delete 'check)
+                   (delete 'sanity-check))))
+    (home-page "")
+    (synopsis "Framework for studying fluid dynamics with simulations.")
+    (description "Framework for studying fluid dynamics with simulations.")
+    (license #f)))
+
+python-fluidsim