Merge branch 'topic/default/fix-pyOpenSci' into 'branch/default'

First fixes related to pyOpenSci

See merge request fluiddyn/fluidimage!116

.github/workflows/ci-pixi.yml

@@ -11,7 +11,6 @@ jobs:
       fail-fast: false
       matrix:
         os: ["windows-2022", "macos-latest"]
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
     defaults:
       run:
         shell: bash -l {0}

INSTALL.md

@@ -0,0 +1,5 @@
+# Install Fluidimage
+
+You can either install without compilation (see
+https://fluidimage.readthedocs.io/en/latest/install.html) or install from source with
+compilation (see https://fluidimage.readthedocs.io/en/latest/build-from-source.html)

Makefile

@@ -4,7 +4,7 @@
 develop: sync
 
 sync:
-	pdm sync --clean
+	pdm sync --clean -v
 
 lock:
 	pdm lock

README.md

@@ -60,7 +60,7 @@ achieved by using
   [Transonic](https://transonic.readthedocs.io)).
 
 [openpiv]: http://www.openpiv.net/
-[piv]: https://en.wikipedia.org/wiki/Particle_image_velocimetry%20(PIV)
+[piv]: https://en.wikipedia.org/wiki/Particle_image_velocimetry
 [pivlab]: https://pivlab.blogspot.com/p/what-is-pivlab.html
 [pivmat]: http://www.fast.u-psud.fr/pivmat/
 [uvmat]: http://servforge.legi.grenoble-inp.fr/projects/soft-uvmat/wiki/UvmatHelp

doc/build-from-source.md

@@ -215,15 +215,28 @@ pipx install pdm -U
 
 Installing in editable mode is a bit particular with Meson, since editable installations
 are incompatible with isolated builds, meaning that all build dependencies have to be
-installed in the main virtual environment! Fortunatelly, it's not too difficult with
-[PDM]. From the root directory of the repository, just run:
+installed in the main virtual environment! Fortunatelly, it's simple with [PDM].
+
+```{warning}
+You should not run the following commands from a virtual environment not related to Fluidimage.
+```
+
+From the root directory of the repository, just run:
+
+```sh
+pdm sync --clean -v
+```
+
+This command creates a virtual environment, installs all build and runtime dependencies,
+and finally build/install Fluidimage from source.
+
+Alternativelly, one can split this process in two steps. First, install all dependencies:
 
 ```sh
-pdm install --no-self
+pdm sync --no-self --clean
 ```
 
-This command creates a virtual environment and installs all build and runtime
-dependencies. You can then activate this environment and build/install Fluidimage with:
+You can then activate the environment and build/install Fluidimage with:
 
 ```sh
 . .venv/bin/activate

pyproject.toml

@@ -15,17 +15,17 @@ authors = [
     {name = "Pierre Augier", email = "[email protected]"},
 ]
 dependencies = [
-    "numpy >= 1.8",
-    "matplotlib >= 3.5",
-    "scipy >= 0.14.1",
+    "numpy >= 1.23",
+    "matplotlib >= 3.6",
+    "scipy >= 1.10",
     "h5py",
     "h5netcdf",
     "transonic>=0.6.2",
     "fluiddyn >=0.6.2",
-    "pyfftw >= 0.10.4",
+    "pyfftw >= 0.14",
     "imageio",
-    "scikit-image >= 0.12.3",
-    "trio >=0.13",
+    "scikit-image >= 0.20",
+    "trio >=0.26",
     "dask[array]",
     "ipython",
     "rich>=13.7.1",