Merge branch 'develop' into kokkos5.1

Author: glesur

.github/workflows/idefix-ci-doc.yml

@@ -9,13 +9,16 @@ on:
     paths-ignore:
       - '.github/ISSUE_TEMPLATE/*'
 
+permissions: {}
 
 jobs:
   ReadTheDocs:
     runs-on: ubuntu-latest
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+        with:
+          persist-credentials: false
       - name: install doxygen
         run: sudo apt-get install -y doxygen
       - name: install python dependencies

.github/workflows/idefix-ci-jobs.yml

@@ -21,15 +21,17 @@ env:
   PYTHONPATH: ${{ github.workspace }}
   IDEFIX_DIR: ${{ github.workspace }}
 
+permissions: {}
 
 jobs:
   ShocksHydro:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Sod test
@@ -45,9 +47,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Viscous flow past cylinder
@@ -61,9 +64,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: MHD Sod test
@@ -83,9 +87,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Ambipolar C Shock
@@ -104,9 +109,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Fargo + planet
@@ -119,9 +125,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Hydro shearing box
@@ -134,9 +141,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Jeans Instability
@@ -155,9 +163,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: 3 body
@@ -178,9 +187,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Energy conservation
@@ -193,9 +203,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: MTI
@@ -212,9 +223,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Run examples test
@@ -225,9 +237,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Lookup table
@@ -242,9 +255,10 @@ jobs:
     runs-on: self-hosted
     steps:
       - name: Check out repo
-        uses: actions/checkout@v3
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
         with:
           submodules: recursive
+          persist-credentials: false
       - name: Prep python
         uses: ./.github/workflows/actions/pre-install-py-packages
       - name: Restart dumps

.github/workflows/idefix-ci.yml

@@ -9,18 +9,22 @@ on:
     paths-ignore:
       - '.github/ISSUE_TEMPLATE/*'
 
+permissions: {}
+
 jobs:
   Linter:
     # Don't do this in forks
     if: ${{ github.repository == 'idefix-code/idefix' || github.repository == 'glesur/idefix' }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
-      - uses: actions/setup-python@v4
+      - uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+        with:
+          persist-credentials: false
+      - uses: actions/setup-python@7f4fc3e22c37d6ff65e88745f38bd3157c663f7c # v4.9.1
         with:
           python-version: 3.x
-      - uses: pre-commit/action@v3.0.0
-      - uses: pre-commit-ci/lite-action@v1.0.0
+      - uses: pre-commit/action@646c83fcd040023954eafda54b4db0192ce70507 # v3.0.0
+      - uses: pre-commit-ci/lite-action@50143aaf27e2c42e75a5e06185a471d9582e89df # v1.0.0
         if: always()
 
   icc-jobs:

.gitignore

@@ -41,6 +41,7 @@ test/**/*.pyc
 test/**/*.dat
 test/**/cmake_packages*
 test/**/
+idefix-tests.junit.xml
 
 # machine specific cache and hidden files
 .*

.pre-commit-config.yaml

@@ -15,6 +15,11 @@ repos:
       - id: check-added-large-files
         args: ['--maxkb=100'] ## prevent files larger than 100kB from being commited (exclude git lfs files)
 
+  - repo: https://github.com/zizmorcore/zizmor-pre-commit
+    rev: v1.23.1
+    hooks:
+    - id: zizmor
+
   - repo: https://github.com/Lucas-C/pre-commit-hooks-nodejs
     rev: v1.1.2
     hooks:
@@ -43,6 +48,7 @@ repos:
     rev: v6.1.2
     hooks:
       - id: inifix-format
+        files: ^(test/).*\.(ini)$ # want to skip pytest.ini
 
   - repo: https://github.com/Lucas-C/pre-commit-hooks
     rev: v1.5.5

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
     # You can also specify other tool versions:
     # nodejs: "19"
     # rust: "1.64"

CHANGELOG.md

@@ -4,14 +4,21 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## Upcoming
+## [2.3.0] 2026-04-21
 ### Changed
 
 - fixed a bug that could lead to diverging results around the spherical axis in non-ideal MHD in 2.5D and 3D (#356)
 - refactor of the MPI exchange routines and boundary routines to avoid buildup of roundoff errors at domain faces/edges that could lead to the sudden burst of div(B) or incoherences between MPI sub-domains (#357)
-
+- fixed a bug that could lead to compilations error when targetting AMD APUs (#359)
+- fixed a bug that led to the generation of incorrect subviews in 2.5D with vector_potential enabled (#362)
+- fixed a bug that could lead to memory corruption when using the UCT_HLLD emf reconstruction scheme and DIMENSIONS < COMPONENTS  (#363)
+- reorganise the test to separate specific IO tests from physics tests (#367)
 
 ### Added
+- magnetic vector potential is now accessible from pydefix when enabled (#361)
+- use ccache in the test suite to reduce the runtime of continuous integration (#364)
+- automatically detects pybind11 path with cmake when using pydefix (#367)
+- skeleton to run the test suite with pytest (#366)
 
 
 ## [2.2.02] 2025-10-18
@@ -23,6 +30,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - fixed a bug that led to incorrect BX2 reconstruction when axis is not used on both sides of the domain (#345)
 - fixed a bug that led to incorrect reflective boundary conditions on B when DIMENSIONS < 3 (#345)
 - fixed a bug that led to incorrect dust stopping time when the adiabatic equation of state is used with "size" drag law (#353)
+- fixed div(B) normalisation to avoid "too large div(B)" errors when this is actually due to nulls in |B|
+- fixed insecure github actions settings (#373)
 
 ### Added
 

CMakeLists.txt

@@ -5,10 +5,10 @@ endif()
 set (CMAKE_CXX_STANDARD 20)
 
 set(Idefix_VERSION_MAJOR 2)
-set(Idefix_VERSION_MINOR 2)
-set(Idefix_VERSION_PATCH 02)
+set(Idefix_VERSION_MINOR 3)
+set(Idefix_VERSION_PATCH 0)
 
-project (idefix VERSION 2.2.02)
+project (idefix VERSION 2.3.0)
 option(Idefix_MHD "enable MHD" OFF)
 option(Idefix_MPI "enable Message Passing Interface parallelisation" OFF)
 option(Idefix_HIGH_ORDER_FARGO "Force Fargo to use a PPM reconstruction scheme" OFF)

doc/python_requirements.txt

@@ -6,12 +6,12 @@
 # python -m pip install -r python_requirements.txt
 
 wheel>=0.38.4 # help forward compatibility for pip with old sphinx plugins
-sphinx==5.3.0
-sphinx_rtd_theme==1.3.0
+sphinx==9.1.0
+sphinx_rtd_theme==3.1.0
 sphinx_git==11.0.0
-breathe==4.34.0
+breathe==4.36.0
 exhale==0.3.7
-m2r2==0.3.2
+m2r2==0.3.4
 sphinx-copybutton==0.5.2
 #sphinxcontrib-applehelp==1.0.7
 matplotlib==3.10.0

doc/source/conf.py

@@ -23,7 +23,7 @@
 author = 'Geoffroy Lesur'
 
 # The full version, including alpha/beta/rc tags
-release = '2.2.02'
+release = '2.3.0'