Merge development into EZoni_ctest

.github/workflows/clang_sanitizers.yml

@@ -160,18 +160,3 @@ jobs:
         ulimit -c unlimited
 
         mpirun -n 2 ../../../build_EB/bin/warpx.2d inputs_test_2d_embedded_circle warpx.serialize_initial_conditions = 0
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/clang_tidy.yml

@@ -60,18 +60,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/cleanup-cache-postpr.yml

@@ -23,8 +23,11 @@ jobs:
 
           REPO=${{ github.repository }}
 
-          gh run download ${{ github.event.workflow_run.id }} -n pr_number
-          pr_number=`cat pr_number.txt`
+          # For debugging cat ${GITHUB_EVENT_PATH} to see the payload.
+
+          pr_head_sha=${{ github.event.workflow_run.head_sha }}
+          pr_number=$(gh pr list --state all --search $pr_head_sha --json number --jq '.[0].number')
+          echo "Post-PR cache cleanup for PR ${pr_number}"
           BRANCH=refs/pull/${pr_number}/merge
 
           # Setting this to not fail the workflow while deleting cache keys.

.github/workflows/cleanup-cache.yml

@@ -29,9 +29,12 @@ jobs:
           # Triggering workflow run name (e.g., LinuxClang)
           WORKFLOW_NAME="${{ github.event.workflow_run.name }}"
 
+          # For debugging, cat ${GITHUB_EVENT_PATH} to see the payload.
+
           if [[ $EVENT == "pull_request" ]]; then
-            gh run download ${{ github.event.workflow_run.id }} -n pr_number
-            pr_number=`cat pr_number.txt`
+            pr_head_sha=${{ github.event.workflow_run.head_sha }}
+            pr_number=$(gh pr list --search $pr_head_sha --json number --jq '.[0].number')
+            echo "Clean up cache for PR ${pr_number}"
             BRANCH=refs/pull/${pr_number}/merge
           else
             BRANCH=refs/heads/${{ github.event.workflow_run.head_branch }}
@@ -54,6 +57,7 @@ jobs:
           IFS=$'\n'
           for j in $cached_jobs
           do
+            # Delete all entries except the last used one
             old_keys=$(gh actions-cache list -L 100 -R $REPO -B $BRANCH --key "${j}-git-" --sort last-used | cut -f 1 | tail -n +2)
             for k in $old_keys
             do

.github/workflows/codeql.yml

@@ -110,18 +110,3 @@ jobs:
         uses: github/codeql-action/upload-sarif@v3
         with:
           sarif_file: sarif-results/${{ matrix.language }}.sarif
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/cuda.yml

@@ -203,18 +203,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/hip.yml

@@ -127,18 +127,3 @@ jobs:
 
         ccache -s
         du -hs ~/.cache/ccache
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/insitu.yml

@@ -22,6 +22,8 @@ jobs:
       image: senseiinsitu/ci:fedora35-amrex-20220613
     steps:
     - uses: actions/checkout@v4
+    - name: Setup cmake
+      uses: jwlawson/actions-setup-cmake@v2
     - name: Configure
       run: |
         cmake -S . -B build     \
@@ -73,7 +75,7 @@ jobs:
 
   catalyst:
     name: Catalyst
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     if: github.event.pull_request.draft == false
     env:
       CXX: g++
@@ -83,8 +85,10 @@ jobs:
       CATALYST_IMPLEMENTATION_PATHS: /opt/paraview/lib/catalyst
       OMP_NUM_THREADS: 1
 
+    # Container build scripts:
+    # https://gitlab.kitware.com/christos.tsolakis/catalyst-amrex-docker-images
     container:
-      image: kitware/paraview:ci-catalyst-amrex-warpx-20240701
+      image: kitware/paraview:ci-catalyst-amrex-warpx-20240828
     steps:
     - uses: actions/checkout@v4
     - name: Configure

.github/workflows/intel.yml

@@ -194,18 +194,3 @@ jobs:
      #   python3 -m pip install --upgrade build packaging setuptools wheel
      #   PYWARPX_LIB_DIR=$PWD/build_sp/lib/site-packages/pywarpx/ python3 -m pip wheel .
      #   python3 -m pip install *.whl
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/macos.yml

@@ -85,18 +85,3 @@ jobs:
         export OMP_NUM_THREADS=1
 
         mpirun -n 2 Examples/Physics_applications/laser_acceleration/inputs_test_3d_laser_acceleration_picmi.py
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.github/workflows/post-pr.yml

@@ -4,17 +4,13 @@ on:
     types:
       - closed
 
+# This workflow does not have the permission to clean up cache for PRs
+# originated from a fork. The purpose here is to trigger a workflow_run
+# cleanup-cache-postpr.yml that has the right permission.
+
 jobs:
-  cleanup:
+  noop:
     runs-on: ubuntu-latest
     steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1
+      - name: No OP
+        run: echo "This workflow is going to trigger CleanUpCachePostPR."

.github/workflows/ubuntu.yml

@@ -222,18 +222,3 @@ jobs:
       run: |
         export OMP_NUM_THREADS=1
         mpirun -n 2 Examples/Physics_applications/laser_acceleration/inputs_test_3d_laser_acceleration_picmi.py
-
-  save_pr_number:
-    if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
-    steps:
-      - name: Save PR number
-        env:
-          PR_NUMBER: ${{ github.event.number }}
-        run: |
-          echo $PR_NUMBER > pr_number.txt
-      - uses: actions/upload-artifact@v4
-        with:
-          name: pr_number
-          path: pr_number.txt
-          retention-days: 1

.pre-commit-config.yaml

@@ -69,7 +69,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.6.2
+  rev: v0.6.3
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,6 +1,6 @@
 # Preamble ####################################################################
 #
-cmake_minimum_required(VERSION 3.20.0)
+cmake_minimum_required(VERSION 3.24.0)
 project(WarpX VERSION 24.08)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
@@ -29,13 +29,6 @@ if(POLICY CMP0104)
     cmake_policy(SET CMP0104 OLD)
 endif()
 
-# We use simple syntax in cmake_dependent_option, so we are compatible with the
-# extended syntax in CMake 3.22+
-# https://cmake.org/cmake/help/v3.22/policy/CMP0127.html
-if(POLICY CMP0127)
-    cmake_policy(SET CMP0127 NEW)
-endif()
-
 
 # C++ Standard in Superbuilds #################################################
 #

Docs/source/acknowledge_us.rst

@@ -53,6 +53,11 @@ Prior WarpX references
 
 If your project uses a specific algorithm or component, please consider citing the respective publications in addition.
 
+- Shapoval O, Zoni E, Lehe R, Thévenet M, and Vay J-L.
+  **Pseudospectral particle-in-cell formulation with arbitrary charge and current-density time dependencies for the modeling of relativistic plasmas**.
+  Physical Review E **110**, 025206, 2024.
+  `DOI:10.1103/PhysRevE.110.025206 <https://doi.org/10.1103/PhysRevE.110.025206>`__
+
 - Sandberg R T, Lehe R, Mitchell C E, Garten M, Myers A, Qiang J, Vay J-L and Huebl A.
   **Synthesizing Particle-in-Cell Simulations Through Learning and GPU Computing for Hybrid Particle Accelerator Beamlines**.
   Proc. of Platform for Advanced Scientific Computing (PASC'24), *PASC24 Best Paper Award*, 2024.

Docs/source/highlights.rst

@@ -85,6 +85,11 @@ Laser-Plasma Interaction
 
 Scientific works in laser-ion acceleration and laser-matter interaction.
 
+#. Garten M, Bulanov S S, Hakimi S, Obst-Huebl L, Mitchell C E, Schroeder C B, Esarey E, Geddes C G R, Vay J-L, Huebl A.
+   **Laser-plasma ion beam booster based on hollow-channel magnetic vortex acceleration**.
+   Physical Review Research **6**, 033148, 2024.
+   `DOI:10.1103/PhysRevResearch.6.033148 <https://doi.org/10.1103/PhysRevResearch.6.033148>`__
+
 #. Knight B, Gautam C, Stoner C, Egner B, Smith J, Orban C, Manfredi J, Frische K, Dexter M, Chowdhury E, Patnaik A (2023).
    **Detailed Characterization of a kHz-rate Laser-Driven Fusion at a Thin Liquid Sheet with a Neutron Detection Suite**.
    High Power Laser Science and Engineering, 1-13, 2023.
@@ -141,8 +146,8 @@ Scientific works in astrophysical plasma modeling.
 
 #. Klion H, Jambunathan R, Rowan ME, Yang E, Willcox D, Vay J-L, Lehe R, Myers A, Huebl A, Zhang W.
    **Particle-in-Cell simulations of relativistic magnetic reconnection with advanced Maxwell solver algorithms**.
-   arXiv pre-print, 2023.
-   `DOI:10.48550/arXiv.2304.10566 <https://doi.org/10.48550/arXiv.2304.10566>`__
+   The Astrophysical Journal **952** 8, 2023.
+   `DOI:10.3847/1538-4357/acd75b <https://doi.org/10.3847/1538-4357/acd75b>`__
 
 
 Microelectronics
@@ -173,8 +178,13 @@ Scientific works in High-Performance Computing, applied mathematics and numerics
 
 Please see :ref:`this section <acknowledge_warpx_all_refs>`.
 
-Nuclear Fusion - Magnetically Confined Plasmas
-**********************************************
+Nuclear Fusion and Plasma Confinement
+*************************************
+
+#. Affolter M., Thompson R., Hepner S., Hayes E. C., Podolsky V., Borghei M., Carlsson J., Gargone A., Merthe D., McKee E., Langtry R.,
+   **The Orbitron: A crossed-field device for co-confinement of high energy ions and electrons**.
+   AIP Advances **14**, 085025, 2024.
+   `DOI:10.1063/5.0201470 <https://doi.org/10.1063/5.0201470>`__
 
 #. Nicks B. S., Putvinski S. and Tajima T.
    **Stabilization of the Alfvén-ion cyclotron instability through short plasmas: Fully kinetic simulations in a high-beta regime**.
@@ -185,3 +195,16 @@ Nuclear Fusion - Magnetically Confined Plasmas
    **Accelerated kinetic model for global macro stability studies of high-beta fusion reactors**.
    Physics of Plasmas **30**, 122508, 2023.
    `DOI:10.1063/5.0178288 <https://doi.org/10.1063/5.0178288>`__
+
+Plasma Thrusters and Electric Propulsion
+****************************************
+
+#. Xie L., Luo X., Zhou Z. and Zhao Y.,
+   **Effect of plasma initialization on 3D PIC simulation of Hall thruster azimuthal instability**.
+   Physica Scripta, **99**, 095602, 2024.
+   `DOI:10.1088/1402-4896/ad69e5 <https://doi.org/10.1088/1402-4896/ad69e5>`__
+
+#. Marks T. A. and Gorodetsky A. A.,
+   **Hall thruster simulations in WarpX**.
+   38th International Electric Propulsion Conference, Toulouse, France, 2024.
+   `DOI:10.7302/234915 <https://doi.org/10.7302/23491>`__

Docs/source/install/dependencies.rst

@@ -7,7 +7,7 @@ WarpX depends on the following popular third party software.
 Please see installation instructions below.
 
 - a mature `C++17 <https://en.wikipedia.org/wiki/C%2B%2B17>`__ compiler, e.g., GCC 8.4+, Clang 7, NVCC 11.0, MSVC 19.15 or newer
-- `CMake 3.20.0+ <https://cmake.org>`__
+- `CMake 3.24.0+ <https://cmake.org>`__
 - `Git 2.18+ <https://git-scm.com>`__
 - `AMReX <https://amrex-codes.github.io>`__: we automatically download and compile a copy of AMReX
 - `PICSAR <https://github.com/ECP-WarpX/picsar>`__: we automatically download and compile a copy of PICSAR
@@ -81,7 +81,7 @@ Conda (Linux/macOS/Windows)
 
       .. code-block:: bash
 
-         conda create -n warpx-cpu-mpich-dev -c conda-forge blaspp boost ccache cmake compilers git lapackpp "openpmd-api=*=mpi_mpich*" openpmd-viewer python make numpy pandas scipy yt "fftw=*=mpi_mpich*" pkg-config matplotlib mamba mpich mpi4py ninja pip virtualenv
+         conda create -n warpx-cpu-mpich-dev -c conda-forge blaspp boost ccache cmake compilers git "heffte=*=mpi_mpich*" lapackpp "openpmd-api=*=mpi_mpich*" openpmd-viewer python make numpy pandas scipy yt "fftw=*=mpi_mpich*" pkg-config matplotlib mamba mpich mpi4py ninja pip virtualenv
          conda activate warpx-cpu-mpich-dev
 
          # compile WarpX with -DWarpX_MPI=ON

Docs/source/install/hpc.rst

@@ -52,6 +52,7 @@ This section documents quick-start guides for a selection of supercomputers that
    hpc/quartz
    hpc/summit
    hpc/taurus
+   hpc/tioga
 
 .. tip::