Merge branch 'develop' into hdf5_link_compile_fix

Author: svalat

.git-blame-ignore-revs

@@ -9,3 +9,6 @@
 # apply inifix-format to all .ini files
 ac260f4af48221229aef4fc1f93ffbf9df450739
 1ca7676fee7a578bd64e64ec9b6bdfbceb921775
+
+# apply ruff format to all .py files
+8d0437bf23d7d8007355fa35b9f094287f7de987

.pre-commit-config.yaml

@@ -28,21 +28,12 @@ repos:
 
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.15.8
     hooks:
-      - id: ruff
-        args:
-        - --quiet
-        - --fix
-        - --select
-        - F # pyflakes
-        - B # flake8-bugbear
-        - I # isort
-        - NPY # numpy-specific rules
-        - --ignore
-        - F405
-        - --ignore
-        - F403 # ignore import *
+      - id: ruff-format
+        args: [--target-version=py310]
+      - id: ruff-check
+        args: [--target-version=py310, --quiet, --fix, --show-fixes]
 
   - repo: https://github.com/la-niche/inifix-pre-commit
     rev: v1.0.0

doc/python_requirements.txt

@@ -1,5 +1,5 @@
 # Other requirements
-# Python >= 3.7
+# Python >= 3.10
 # Doxygen https://www.doxygen.nl/download.html
 #
 # Install Sphinx and required plugins with the following command

doc/source/conf.py

@@ -18,13 +18,12 @@
 
 # -- Project information -----------------------------------------------------
 
-project = 'Idefix'
-copyright = 'Geoffroy Lesur et al.'
-author = 'Geoffroy Lesur'
+project = "Idefix"
+copyright = "Geoffroy Lesur et al."
+author = "Geoffroy Lesur"
 
 # The full version, including alpha/beta/rc tags
-release = '2.3.0'
-
+release = "2.3.0"
 
 
 # -- General configuration ---------------------------------------------------
@@ -34,20 +33,24 @@
 # ones.
 extensions = [
     "sphinx_rtd_theme",
-    'sphinx_git',
-    'matplotlib.sphinxext.plot_directive',
+    "sphinx_git",
+    "matplotlib.sphinxext.plot_directive",
     "breathe",
     "exhale",
     "m2r2",
-    "sphinx_copybutton"
-    ]
+    "sphinx_copybutton",
+]
 
 source_suffix = [".rst", ".md"]
 
-cpp_id_attributes=["KOKKOS_FORCEINLINE_FUNCTION","KOKKOS_INLINE_FUNCTION","KOKKOS_RESTRICT"]
+cpp_id_attributes = [
+    "KOKKOS_FORCEINLINE_FUNCTION",
+    "KOKKOS_INLINE_FUNCTION",
+    "KOKKOS_RESTRICT",
+]
 
 # Add any paths that contain templates here, relative to this directory.
-templates_path = ['_templates']
+templates_path = ["_templates"]
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
@@ -60,45 +63,47 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = "sphinx_rtd_theme"
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+html_static_path = ["_static"]
+
 
 def setup(app):
-    app.add_css_file('my_theme.css')
+    app.add_css_file("my_theme.css")
+
 
 ##############
 # Breathe/Exhale options
 
 # Setup the breathe extension
 breathe_projects = {
-    "Idefix": "./xml"
+    "Idefix": "./xml",
 }
 breathe_default_project = "Idefix"
 
 # Setup the exhale extension
 exhale_args = {
     # These arguments are required
-    "containmentFolder":     "./api",
-    "rootFileName":          "library_root.rst",
-    "rootFileTitle":         "Idefix API",
+    "containmentFolder": "./api",
+    "rootFileName": "library_root.rst",
+    "rootFileTitle": "Idefix API",
     # Suggested optional arguments
-    "createTreeView":        False,
+    "createTreeView": False,
     # TIP: if using the sphinx-bootstrap-theme, you need
     # "treeViewIsBootstrap": True,
     "doxygenStripFromPath": "../../src",
     "exhaleExecutesDoxygen": True,
-    "exhaleDoxygenStdin":    textwrap.dedent('''
+    "exhaleDoxygenStdin": textwrap.dedent("""
             INPUT = ../../src
             EXCLUDE = ../../src/kokkos
-            ''')
+            """),
 }
 
 # Tell sphinx what the primary language being documented is.
-primary_domain = 'cpp'
+primary_domain = "cpp"
 
 # Tell sphinx what the pygments highlight language should be.
-highlight_language = 'cpp'
+highlight_language = "cpp"

doc/source/index.rst

@@ -34,7 +34,7 @@ MPI library
   the MPI library is GPU-Aware. If unsure, check this last point with your system administrator.
 
 Python
-  When using *Idefix* with its python interface through the module `Pydefix`, *Idefix* relies on an external python>=3.8 interpreter with the module `pybind11 <https://pybind11.readthedocs.io>`_
+  When using *Idefix* with its python interface through the module `Pydefix`, *Idefix* relies on an external python>=3.10 interpreter with the module `pybind11 <https://pybind11.readthedocs.io>`_
   installed.
 
 ================

doc/source/modules/pydefix.rst

@@ -16,7 +16,7 @@ Before you start
 Pybind11 installation
 +++++++++++++++++++++
 
-In order to use pydefix, you need to be working in a python>=3.8 environement that includes `pybind11 <https://pybind11.readthedocs.io>`_. Follow the instruction of your package manager to install pybind11>=2.12.
+In order to use pydefix, you need to be working in a python>=3.10 environment that includes `pybind11 <https://pybind11.readthedocs.io>`_. Follow the instructions of your package manager to install pybind11>=2.12.
 
 Pydefix usage
 -------------

doc/source/plot_idefix_bench.py

@@ -1,25 +1,27 @@
-import matplotlib.pyplot as plt
 import json
 
+import matplotlib.pyplot as plt
+
+
 def do_plot(title, bench_file, gpumodels):
-    with open(bench_file, 'r') as f:
+    with open(bench_file, "r") as f:
         benches = json.load(f)
 
     plt.figure()
-    xmax=0
-    ymax=0
+    xmax = 0
+    ymax = 0
     for gpumodel in gpumodels:
-        select = [bench for bench in benches if bench['gpumodel'] == gpumodel][-1]
+        select = [bench for bench in benches if bench["gpumodel"] == gpumodel][-1]
 
-        xs = [r['nbgpu'] for r in select['results']]
-        ys = [r['cell_updates'] for r in select['results']]
-        plt.plot(xs, ys,'o-',label=gpumodel)
-        xmax=max(xmax,max(xs))
-        ymax=max(ymax,max(ys))
+        xs = [r["nbgpu"] for r in select["results"]]
+        ys = [r["cell_updates"] for r in select["results"]]
+        plt.plot(xs, ys, "o-", label=gpumodel)
+        xmax = max(xmax, max(xs))
+        ymax = max(ymax, max(ys))
 
     plt.xscale("log", base=2)
-    plt.ylim(0,ymax*1.1)
-    plt.xlim(1,xmax*1.1)
+    plt.ylim(0, ymax * 1.1)
+    plt.xlim(1, xmax * 1.1)
     plt.legend()
     plt.xlabel("Number of GPUs/GCDs")
     plt.ylabel("Performance (cells / second / GPU)")

doc/source/testing/testLauncher.rst

@@ -191,6 +191,12 @@ In addition there is some extra keys which are dedicated to the json interpretat
    * - ``multirun``
      - ``{}``
      - See the multi-run section below.
+   * - ``callPyFunctionBefore``
+     -
+     - Call a python function before executing the test (see dedicated section at the end of this file).
+   * - ``callPyFunctionAfter``
+     -
+     - Call a python function after executing the test (see dedicated section at the end of this file).
 
 Looping over parameters
 -----------------------
@@ -374,6 +380,33 @@ They are described like :
         },
     }
 
+Calling a Python function
+-------------------------
+
+In some cases (example in ``test/utils/lookupTable``) you might need to call a custom
+python function before running the test to prepare the data or after the test to perform
+some extra check.
+
+You can simply implement the functions you want to call in the python file in the test
+directory (ideally named ``testmelib.py``) :
+
+.. code-block:: python
+
+    def callMeAtStart():
+        print("This is called at test start !")
+
+    def callMeAtEnd():
+        print("This is called at test end !")
+
+And add the keys in ``testme.json``:
+
+.. code-block:: json
+
+    "default": {
+        "callPyFunctionBefore": "testmelib.py:callMeAtStart",
+        "callPyFunctionAfter": "testmelib.py:callMeAtEnd"
+    }
+
 Using the idfxTest options
 --------------------------
 

make_tarballs.py

@@ -89,7 +89,7 @@ def _make_self_contained_tarball(output_dir, *, suffix="", exclude_list=None):
         os.replace(os.path.join(work_dir, tarball), final_tarfile)
 
     filesize = os.path.getsize(final_tarfile)
-    print("Done ! Final file size is %.1f MB" % (filesize / 1024 ** 2))
+    print("Done ! Final file size is %.1f MB" % (filesize / 1024**2))
 
 
 def main(argv=None):

pytools/dump_io.py

@@ -4,6 +4,7 @@
 
 @author: lesurg
 """
+
 import os
 import re
 import struct
@@ -59,7 +60,7 @@ def __init__(self, fh, byteorder="little"):
         self.ndims = int.from_bytes(fh.read(INT_SIZE), byteorder)
         dims = []
         ntot = 1
-        for dim in range(self.ndims):
+        for _ in range(self.ndims):
             dims.append(int.from_bytes(fh.read(INT_SIZE), byteorder))
             ntot = ntot * dims[-1]
         raw = struct.unpack(str(ntot) + stringchar, fh.read(mysize * ntot))
@@ -119,6 +120,7 @@ def _read_fields(self, fh):
     def __repr__(self):
         return "DumpDataset('%s')" % self.filename
 
+
 # public API
 def readDump(filename):
     return DumpDataset(filename)