[ENH] Customization feature to choose a directory for dumping of log files during runtime

.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

@@ -21,28 +21,34 @@ 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: Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/sod -all $TESTME_OPTIONS
       - name: Isothermal Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/sod-iso -all $TESTME_OPTIONS
       - name: Mach reflection test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD//MachReflection -all $TESTME_OPTIONS
+      - name: Sedov blast wave
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/SedovBlastWave -all $TESTME_OPTIONS
 
   ParabolicHydro:
     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: Viscous flow past cylinder
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/ViscousFlowPastCylinder -all $TESTME_OPTIONS
       - name: Viscous disk
@@ -54,25 +60,31 @@ 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: MHD Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sod -all $TESTME_OPTIONS
       - name: MHD Isothermal Sod test
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sod-iso -all $TESTME_OPTIONS
       - name: Orszag Tang
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang -all $TESTME_OPTIONS
-      - name: Orszag Tang 3D+restart tests
+      - name: Orszag Tang 3D
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/OrszagTang3D -all $TESTME_OPTIONS
+      - name: Linear wave test
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/LinearWaveTest -all $TESTME_OPTIONS
+      - name: Axis Flux tube
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AxisFluxTube -all $TESTME_OPTIONS
 
   ParabolicMHD:
     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: Ambipolar C Shock
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/AmbipolarCshock -all $TESTME_OPTIONS
       - name: Ambipolar C Shock 3D
@@ -89,9 +101,10 @@ 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: Fargo + planet
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/FargoPlanet -all $TESTME_OPTIONS
       - name: Fargo MHD spherical
@@ -102,9 +115,10 @@ 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: Hydro shearing box
         run: scripts/ci/run-tests $IDEFIX_DIR/test/HD/ShearingBox -all $TESTME_OPTIONS
       - name: MHD shearing box
@@ -115,9 +129,10 @@ 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: Jeans Instability
         run: scripts/ci/run-tests $IDEFIX_DIR/test/SelfGravity/JeansInstability -all $TESTME_OPTIONS
       - name: Random sphere spherical
@@ -134,9 +149,10 @@ 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: 3 body
         run: scripts/ci/run-tests $IDEFIX_DIR/test/Planet/Planet3Body -all $TESTME_OPTIONS
       - name: migration
@@ -155,9 +171,10 @@ 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: Energy conservation
         run: scripts/ci/run-tests $IDEFIX_DIR/test/Dust/DustEnergy -all $TESTME_OPTIONS
       - name: Dusty wave
@@ -168,24 +185,28 @@ 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: MTI
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/MTI -all $TESTME_OPTIONS
       - name: Spherical anisotropic diffusion
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sphBragTDiffusion -all $TESTME_OPTIONS
       - name: Spherical anisotropic viscosity
         run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/sphBragViscosity -all $TESTME_OPTIONS
+      - name: Collisionless thermal conduction
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/MHD/clessTDiffusion -all $TESTME_OPTIONS
 
   Examples:
     needs: [Fargo, Dust, Planet, ShearingBox, SelfGravity]
     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: Run examples test
         run: cd test && ./checks_examples.sh $TEST_OPTIONS
 
@@ -194,10 +215,34 @@ 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: Lookup table
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/lookupTable -all $TESTME_OPTIONS
       - name: Dump Image
         run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/dumpImage -all $TESTME_OPTIONS
+      - name: Column density
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/utils/columnDensity -all $TESTME_OPTIONS
+
+  IOs:
+    needs: [Fargo, Dust, Planet, ShearingBox, SelfGravity]
+    runs-on: self-hosted
+    steps:
+      - name: Check out repo
+        uses: actions/checkout@f43a0e5ff2bd294095638e18286ca9a3d1956744 # v3.6.0
+        with:
+          submodules: recursive
+          persist-credentials: false
+      - name: Restart dumps
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/dump -all $TESTME_OPTIONS
+      - name: Pydefix
+        run: |
+          python3 -m venv $IDEFIX_DIR/test/IO/pydefix/env
+          source $IDEFIX_DIR/test/IO/pydefix/env/bin/activate
+          python3 -m pip install -r $IDEFIX_DIR/test/IO/pydefix/python_requirements.txt
+          scripts/ci/run-tests $IDEFIX_DIR/test/IO/pydefix -all $TESTME_OPTIONS
+
+      - name: xdmf
+        run: scripts/ci/run-tests $IDEFIX_DIR/test/IO/xdmf -all $TESTME_OPTIONS

.github/workflows/idefix-ci.yml

@@ -9,34 +9,38 @@ 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:
     needs: Linter
     name: CPU Jobs (intel OneApi)
     uses: ./.github/workflows/idefix-ci-jobs.yml
     with:
-      TESTME_OPTIONS: -intel -Werror
+      TESTME_OPTIONS: -intel -Werror -ccache
       IDEFIX_COMPILER: icc
 
   gcc-jobs:
     needs: Linter
     name: CPU Jobs (gcc)
     uses: ./.github/workflows/idefix-ci-jobs.yml
     with:
-      TESTME_OPTIONS: -Werror
+      TESTME_OPTIONS: -Werror -ccache
       IDEFIX_COMPILER: gcc
 
   cuda-jobs:

.gitignore

@@ -4,6 +4,7 @@ doc/source/_static/*
 doc/source/_public/*
 doc/source/api/*
 doc/source/xml/*
+doc/env/*
 
 # compiled files
 **/__pycache__
@@ -21,6 +22,9 @@ CMakeFiles
 CMakeCache.txt
 cmake_install.cmake
 Makefile.local
+git-state.txt
+Kokkos_Version_info.*
+
 
 # test artifacts
 test/**/*.o
@@ -35,6 +39,9 @@ test/**/KokkosCore*
 test/**/*.csv
 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:
@@ -40,9 +45,10 @@ repos:
         - F403 # ignore import *
 
   - repo: https://github.com/neutrinoceros/inifix
-    rev: v5.0.2
+    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

@@ -4,6 +4,72 @@ 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).
 
+## [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
+### Changed
+
+- Added a module to add explicit units (#338)
+- fixed a bug that could lead to incorrect profiling information on non-blocking cuda loops (#341)
+- fixed a bug that could lead to incorrect energy budget when shearing box and fargo were both enabled (#346)
+- 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
+
+- documentation for the continuous integration (#354)
+
+## [2.2.01] 2025-04-16
+### Changed
+
+- Fix a bug that led to instabilities in the RKL scheme with very small grid spacings (#323)
+- Fix a bug that prevented Idefix from running with Sycl backend (required on Intel GPUs) (#331)
+- Fix an error that led to incorrect electrical current regularisation around the polar axis in non-Ideal MHD  (#333)
+- Improve div(B) checks with a dimensionless implementation, avoiding too large divB errors in grids with large stretch factors (#334)
+
+### Added
+
+- Time-Implicit drag for multiple dust species, preventing small time steps for strongly coupled dust grains (#321)
+- Collisionless heat flux added to the Braginskii module (#317)
+- New global `idfx::DumpArray` debugging function to dump any Idefix array into a numpy array that can read from python (#318)
+- Automatic benchmark plots in the documentation (#319)
+- More CI tests of grid coarsening (#329)
+- Dump outputs based on wallclock time (#335)
+
+
+## [2.2.00] 2025-01-17
+### Changed
+
+- Fix a bug that could lead to a segmentation fault when MHD+Fargo+MPI (with X3 domain decomposition) are all enabled (#295)
+- Fix a bug that could result in an incorrect magnetic field when initialising B from the vector potential in non-axisymmetric spherical geometry (#293)
+- Fix a bug that could result in Idefix believing the MPI library is not Cuda aware for some versions of OpenMPI (#310)
+- Ensure that the behaviour in 1D Spherical geometry is identical to Pluto (#291)
+
+### Added
+
+- Add the python interface "pydefix", allowing users to initialise and analyse Idefix simulations live from Python without writing any file (#277)
+- Add the native Idefix coordinates in VTK file to simplify postprocessing (#292)
+- Add code testing on CPU targets using gcc and Intel Oneapi (#300)
+
+
 ## [2.1.02] 2024-10-24
 ### Changed