Merge v5.2.0 into next

.github/workflows/black-fix.yml

@@ -20,7 +20,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         ref: ${{ github.head_ref }}
 

.github/workflows/clang-format.yml

@@ -8,10 +8,12 @@ on:
 
 jobs:
   clang-format:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
       # Checkout the pull request branch, also include all history
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           ref: ${{ github.head_ref }}
           fetch-depth: 0

.github/workflows/clang-tidy-review.yml

@@ -5,19 +5,18 @@ on:
     paths:
       - '**.cxx'
       - '**.hxx'
-    branches-ignore:
-      # Release candidate branches tend to have big PRs which causes all sorts of problems
-      - 'v*rc'
 
 concurrency:
   group: ${{ github.workflow }}-${{ github.ref }}
   cancel-in-progress: true
 
 jobs:
   review:
+    # Release candidate branches tend to have big PRs which causes all sorts of problems
+    if: ${{ !endsWith(github.head_ref, '-rc') }}
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 

.github/workflows/docker.yml

@@ -52,7 +52,7 @@ jobs:
 
     steps:
       - name: Checkout repository
-        uses: actions/checkout@v4
+        uses: actions/checkout@v5
 
       - name: Log in to the Container registry
         uses: docker/login-action@master

.github/workflows/python-package.yml

@@ -17,12 +17,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -57,12 +57,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&
@@ -106,12 +106,12 @@ jobs:
     if: always()
 
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v5
       with:
         fetch-depth: 0
         submodules: true
     - name: Set up Python
-      uses: actions/setup-python@v5
+      uses: actions/setup-python@v6
     - name: Install dependencies
       run: python -m pip install --upgrade pip &&
            pip install --upgrade build &&

.github/workflows/tests.yml

@@ -168,11 +168,11 @@ jobs:
                  libparpack2-dev
                  libhypre-dev
 
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
 
-      - uses: actions/setup-python@v5
+      - uses: actions/setup-python@v6
         with:
           python-version: '3.x'
 
@@ -205,7 +205,7 @@ jobs:
     timeout-minutes: 120
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v4
+      - uses: actions/checkout@v5
         with:
           submodules: true
       - name: Build Fedora

CHANGELOG.md

@@ -1,7 +1,8 @@
 # Changelog
 
-## [v6.0.0](https://github.com/boutproject/BOUT-dev/tree/next)
-[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...next)
+## [v5.2.0](https://github.com/boutproject/BOUT-dev/tree/v5.2.0
+
+[Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.1...v5.2.0)
 
 ### Breaking changes
 
@@ -16,6 +17,67 @@
   confusing. Now, monitors are called with the current number of
   completed monitor-steps.
 
+## Changes
+
+- Fixes for FreeBSD [\#3172][https://github.com/boutproject/BOUT-dev/pull/3172] ([tomc271][https://github.com/tomc271])
+- snes: Print a warning if the coloring is non-symmetric. [\#3159][https://github.com/boutproject/BOUT-dev/pull/3159] ([bendudson][https://github.com/bendudson])
+- Cmake fix from master [\#3152][https://github.com/boutproject/BOUT-dev/pull/3152] ([oparry-ukaea][https://github.com/oparry-ukaea])
+- Bump ZedThree/clang-tidy-review from 0.20.1 to 0.21.0 [\#3150][https://github.com/boutproject/BOUT-dev/pull/3150] ([ZedThree][https://github.com/ZedThree])
+- SNES solver: Added a PID controller to update the timestep  [\#3146][https://github.com/boutproject/BOUT-dev/pull/3146] ([malamast][https://github.com/malamast])
+- Fix name clash in some examples and MMS tests  [\#3145][https://github.com/boutproject/BOUT-dev/pull/3145] ([ZedThree][https://github.com/ZedThree])
+- Handle absolute paths to options file [\#3142][https://github.com/boutproject/BOUT-dev/pull/3142] ([bendudson][https://github.com/bendudson])
+- Revert eliminate hypre boundary equations [\#3136][https://github.com/boutproject/BOUT-dev/pull/3136] ([ZedThree][https://github.com/ZedThree])
+- CI: Switch to released fedora [\#3134][https://github.com/boutproject/BOUT-dev/pull/3134] ([dschwoerer][https://github.com/dschwoerer])
+- Generalise FakeMeshFixture to allow configurable grid spacing via templating [\#3132][https://github.com/boutproject/BOUT-dev/pull/3132] ([tomc271][https://github.com/tomc271])
+- Fixes for ELM-PB preconditioner [\#3128][https://github.com/boutproject/BOUT-dev/pull/3128] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- Fix cast for new petsc [\#3117][https://github.com/boutproject/BOUT-dev/pull/3117] ([dschwoerer][https://github.com/dschwoerer])
+- Fix bug where ARKODE considered all problems linear [\#3114][https://github.com/boutproject/BOUT-dev/pull/3114] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- cvode: Add linear_solver option [\#3112][https://github.com/boutproject/BOUT-dev/pull/3112] ([bendudson][https://github.com/bendudson])
+- periodicX communication fixes [\#3109][https://github.com/boutproject/BOUT-dev/pull/3109] ([bendudson][https://github.com/bendudson])
+- beuler solver timestep and Jacobian calculation [\#3107][https://github.com/boutproject/BOUT-dev/pull/3107] ([bendudson][https://github.com/bendudson])
+- Feature/snes stencil [\#3104][https://github.com/boutproject/BOUT-dev/pull/3104] ([seimtpow][https://github.com/seimtpow])
+- Add attributes to ADIOS2 output to "define" dimensions as names. We n… [\#3098][https://github.com/boutproject/BOUT-dev/pull/3098] ([pnorbert][https://github.com/pnorbert])
+- CI: Avoid issues with special characters [\#3090][https://github.com/boutproject/BOUT-dev/pull/3090] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Fix clang format [\#3086][https://github.com/boutproject/BOUT-dev/pull/3086] ([dschwoerer][https://github.com/dschwoerer])
+- Small updates for FCI output [\#3085][https://github.com/boutproject/BOUT-dev/pull/3085] ([bendudson][https://github.com/bendudson])
+- Eliminate boundary equations to improve HYPRE solves [\#3082][https://github.com/boutproject/BOUT-dev/pull/3082] ([rfalgout][https://github.com/rfalgout])
+- Elm-pb example with relaxing phi [\#3081][https://github.com/boutproject/BOUT-dev/pull/3081] ([bendudson][https://github.com/bendudson])
+- CI: Show more output of dnf5 to help debugging [\#3071][https://github.com/boutproject/BOUT-dev/pull/3071] ([dschwoerer][https://github.com/dschwoerer])
+- Fix clang tidy review [\#3070][https://github.com/boutproject/BOUT-dev/pull/3070] ([ZedThree][https://github.com/ZedThree])
+- CMake: Bump downloaded SUNDIALS version [\#3067][https://github.com/boutproject/BOUT-dev/pull/3067] ([ZedThree][https://github.com/ZedThree])
+- Use isfinite, fix pvode linking [\#3063][https://github.com/boutproject/BOUT-dev/pull/3063] ([bendudson][https://github.com/bendudson])
+- Make iteration more robust and give more options in LaplaceNaulin [\#3061][https://github.com/boutproject/BOUT-dev/pull/3061] ([johnomotani][https://github.com/johnomotani])
+- Fixes zoidberg [\#3054][https://github.com/boutproject/BOUT-dev/pull/3054] ([dschwoerer][https://github.com/dschwoerer])
+- Fix finalise in boutpp  [\#3053][https://github.com/boutproject/BOUT-dev/pull/3053] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid some warnings for 3D Metrics [\#3052][https://github.com/boutproject/BOUT-dev/pull/3052] ([dschwoerer][https://github.com/dschwoerer])
+- Minor fixes for the python backend [\#3051][https://github.com/boutproject/BOUT-dev/pull/3051] ([dschwoerer][https://github.com/dschwoerer])
+- Cleanup BOUT_HOST_DEVICE qualifiers [\#3040][https://github.com/boutproject/BOUT-dev/pull/3040] ([ggeorgakoudis][https://github.com/ggeorgakoudis])
+- Deprecate options that are only used as default for other options [\#3038][https://github.com/boutproject/BOUT-dev/pull/3038] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid using the wrong grid by accident [\#3036][https://github.com/boutproject/BOUT-dev/pull/3036] ([dschwoerer][https://github.com/dschwoerer])
+- Use PEP 625 compatible archive name (next) [\#3035][https://github.com/boutproject/BOUT-dev/pull/3035] ([dschwoerer][https://github.com/dschwoerer])
+- CI: Increase check level for debug run + unit test fixes [\#3033][https://github.com/boutproject/BOUT-dev/pull/3033] ([dschwoerer][https://github.com/dschwoerer])
+- Avoid `#define` conflict with sundials [\#3031][https://github.com/boutproject/BOUT-dev/pull/3031] ([dschwoerer][https://github.com/dschwoerer])
+- Ensure PETSc headers are included after `bout/petsclib.hxx` [\#3024][https://github.com/boutproject/BOUT-dev/pull/3024] ([ZedThree][https://github.com/ZedThree])
+- Fix minor HYPRE and ADIOS2 compilation issues [\#3022][https://github.com/boutproject/BOUT-dev/pull/3022] ([ZedThree][https://github.com/ZedThree])
+- Fix recompilation cascade [\#3021][https://github.com/boutproject/BOUT-dev/pull/3021] ([ZedThree][https://github.com/ZedThree])
+- Move `invert3x3` out of general purpose `utils.hxx` header [\#3018][https://github.com/boutproject/BOUT-dev/pull/3018] ([ZedThree][https://github.com/ZedThree])
+- Replace deprecated `boututils.file_import` [\#3017][https://github.com/boutproject/BOUT-dev/pull/3017] ([ZedThree][https://github.com/ZedThree])
+- CI: clang-tidy-review tweaks [\#3016][https://github.com/boutproject/BOUT-dev/pull/3016] ([ZedThree][https://github.com/ZedThree])
+- Backward Euler solver improvements [\#3009][https://github.com/boutproject/BOUT-dev/pull/3009] ([bendudson][https://github.com/bendudson])
+- Fix circular header dependency: mesh.hxx <-> griddata.hxx [\#3008][https://github.com/boutproject/BOUT-dev/pull/3008] ([ZedThree][https://github.com/ZedThree])
+- Fix exception message [\#3003][https://github.com/boutproject/BOUT-dev/pull/3003] ([dschwoerer][https://github.com/dschwoerer])
+- Ensure pointer is checked before dereferencing [\#3002][https://github.com/boutproject/BOUT-dev/pull/3002] ([dschwoerer][https://github.com/dschwoerer])
+- Fix: preserve regionID [\#3000][https://github.com/boutproject/BOUT-dev/pull/3000] ([dschwoerer][https://github.com/dschwoerer])
+- Lazy grid loading [\#2991][https://github.com/boutproject/BOUT-dev/pull/2991] ([dschwoerer][https://github.com/dschwoerer])
+- Fix compilation warnings with SUNDIALS 7.1.0 [\#2990][https://github.com/boutproject/BOUT-dev/pull/2990] ([Steven-Roberts][https://github.com/Steven-Roberts])
+- Add LC gitlab CI for GPU build/run tests [\#2989][https://github.com/boutproject/BOUT-dev/pull/2989] ([ggeorgakoudis][https://github.com/ggeorgakoudis])
+- BoutMask non-const operator[](Ind3D) [\#2988][https://github.com/boutproject/BOUT-dev/pull/2988] ([bendudson][https://github.com/bendudson])
+- Use consistently signed char [\#2987][https://github.com/boutproject/BOUT-dev/pull/2987] ([dschwoerer][https://github.com/dschwoerer])
+- naulin laplace: Acceptance tolerances after maxits [\#2983][https://github.com/boutproject/BOUT-dev/pull/2983] ([bendudson][https://github.com/bendudson])
+- Merge v5.1.1 into `next` [\#2978][https://github.com/boutproject/BOUT-dev/pull/2978] ([ZedThree][https://github.com/ZedThree])
+- CI: Bump all ubuntu images [\#2977][https://github.com/boutproject/BOUT-dev/pull/2977] ([ZedThree][https://github.com/ZedThree])
+- Read 2D variables into Field3D [\#2975][https://github.com/boutproject/BOUT-dev/pull/2975] ([bendudson][https://github.com/bendudson])
+
 ## [v5.1.1](https://github.com/boutproject/BOUT-dev/tree/v5.1.1)
 [Full Changelog](https://github.com/boutproject/BOUT-dev/compare/v5.1.0...v5.1.1)
 

CITATION.cff

@@ -197,11 +197,27 @@ authors:
   - family-names: Kryjak
     given-names: Mike
 
-version: 5.1.1
-date-released: 2023-04-10
+  - family-names: Powell
+    given-names: Seimon
+  - family-names: Ağgül
+    given-names: Mustafa
+  - family-names: Parry
+    given-names: Owen
+  - family-names: Podhorszki
+    given-names: Norbert
+  - family-names: Falgout
+    given-names: Rob
+  - family-names: Li
+    given-names: Nami
+  - family-names: Body
+    given-names: Tom
+  - family-names: Tsagkaridis
+    given-names: Malamas
+version: 5.2.0
+date-released: 2025-10-10
 repository-code: https://github.com/boutproject/BOUT-dev
 url: http://boutproject.github.io/
-doi: 10.5281/zenodo.13753882
+doi: 10.5281/zenodo.17313945
 license: 'LGPL-3.0-or-later'
 references:
   - type: article

CMakeLists.txt

@@ -25,8 +25,8 @@ endif()
 # CMake currently doesn't support proper semver
 # Set the version here, strip any extra tags to use in `project`
 # We try to use git to get a full description, inspired by setuptools_scm
-set(_bout_previous_version "5.1.1")
-set(_bout_next_version "5.2.0")
+set(_bout_previous_version "5.2.0")
+set(_bout_next_version "5.2.1")
 execute_process(
   COMMAND "git" describe --tags --match=v${_bout_previous_version}
   COMMAND sed -e s/${_bout_previous_version}-/${_bout_next_version}.dev/ -e s/-/+/

README.md

@@ -4,7 +4,7 @@
 [![Build Status](https://github.com/boutproject/BOUT-dev/actions/workflows/tests.yml/badge.svg?branch=next)](https://github.com/boutproject/BOUT-dev/actions)
 [![License](https://img.shields.io/badge/license-LGPL-blue.svg)](https://www.gnu.org/licenses/lgpl-3.0.en.html)
 [![py3comp](https://img.shields.io/badge/py3-compatible-brightgreen.svg)](https://img.shields.io/badge/py3-compatible-brightgreen.svg)
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.13753882.svg)](https://doi.org/10.5281/zenodo.8369888)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.17313945.svg)](https://doi.org/10.5281/zenodo.17313945)
 
 ```
 .______     ______    __    __  .___________.

bin/bout-changelog-generator.py

@@ -1,4 +1,10 @@
 #! /usr/bin/env python3
+# /// script
+# requires-python = ">=3.12"
+# dependencies = [
+#     "pygithub",
+# ]
+# ///
 
 import argparse
 import os

bin/update_citations.py

@@ -1,4 +1,11 @@
 #!/usr/bin/env python3
+# /// script
+# requires-python = ">=3.11"
+# dependencies = [
+#     "ruamel-yaml",
+#     "unidecode",
+# ]
+# ///
 import argparse
 import subprocess
 from collections import defaultdict
@@ -242,6 +249,9 @@ def update_citations():
 
     new_authors = []
     for author in unrecognised_authors:
+        if " " not in author:
+            # This is just a GitHub handle, skip
+            continue
         first_name, last_name = author.rsplit(maxsplit=1)
         new_authors.append({"family-names": last_name, "given-names": first_name})
 

bin/update_version_number_in_files.py

@@ -66,11 +66,6 @@ def update_version_number_in_file(relative_filepath, pattern, new_version_number
 def bump_version_numbers(
     new_version_number: VersionNumber, next_version_number: VersionNumber
 ):
-    update_version_number_in_file(
-        "configure.ac",
-        r"^AC_INIT\(\[BOUT\+\+\],\[(\d+\.\d+\.\d+)\]",
-        new_version_number,
-    )
     update_version_number_in_file(
         "CITATION.cff", r"^version: (\d+\.\d+\.\d+)", new_version_number
     )

include/bout/invertable_operator.hxx

@@ -219,21 +219,18 @@ public:
                 localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize);
           }
         }
-        if (localmesh->firstY() or localmesh->lastY()) {
-          for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
-            if (not localmesh->periodicY(ix)) {
-              if (localmesh->firstY()) {
-                nocorner3D +=
-                    Region<Ind3D>(ix, ix, 0, localmesh->ystart - 1, 0,
-                                  localmesh->LocalNz - 1, localmesh->LocalNy,
-                                  localmesh->LocalNz, localmesh->maxregionblocksize);
-              }
-              if (localmesh->lastY()) {
-                nocorner3D += Region<Ind3D>(
-                    ix, ix, localmesh->LocalNy - localmesh->ystart,
-                    localmesh->LocalNy - 1, 0, localmesh->LocalNz - 1, localmesh->LocalNy,
-                    localmesh->LocalNz, localmesh->maxregionblocksize);
-              }
+        for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
+          if (not localmesh->periodicY(ix)) {
+            if (localmesh->firstY(ix)) {
+              nocorner3D += Region<Ind3D>(
+                  ix, ix, 0, localmesh->ystart - 1, 0, localmesh->LocalNz - 1,
+                  localmesh->LocalNy, localmesh->LocalNz, localmesh->maxregionblocksize);
+            }
+            if (localmesh->lastY(ix)) {
+              nocorner3D += Region<Ind3D>(
+                  ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1,
+                  0, localmesh->LocalNz - 1, localmesh->LocalNy, localmesh->LocalNz,
+                  localmesh->maxregionblocksize);
             }
           }
         }
@@ -259,20 +256,17 @@ public:
                               0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize);
           }
         }
-        if (localmesh->firstY() or localmesh->lastY()) {
-          for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
-            if (not localmesh->periodicY(ix)) {
-              if (localmesh->firstY()) {
-                nocorner2D +=
-                    Region<Ind2D>(ix, ix, 0, localmesh->ystart - 1, 0, 0,
-                                  localmesh->LocalNy, 1, localmesh->maxregionblocksize);
-              }
-              if (localmesh->lastY()) {
-                nocorner2D +=
-                    Region<Ind2D>(ix, ix, localmesh->LocalNy - localmesh->ystart,
-                                  localmesh->LocalNy - 1, 0, 0, localmesh->LocalNy, 1,
-                                  localmesh->maxregionblocksize);
-              }
+        for (int ix = localmesh->xstart; ix <= localmesh->xend; ix++) {
+          if (not localmesh->periodicY(ix)) {
+            if (localmesh->firstY(ix)) {
+              nocorner2D +=
+                  Region<Ind2D>(ix, ix, 0, localmesh->ystart - 1, 0, 0,
+                                localmesh->LocalNy, 1, localmesh->maxregionblocksize);
+            }
+            if (localmesh->lastY(ix)) {
+              nocorner2D += Region<Ind2D>(
+                  ix, ix, localmesh->LocalNy - localmesh->ystart, localmesh->LocalNy - 1,
+                  0, 0, localmesh->LocalNy, 1, localmesh->maxregionblocksize);
             }
           }
         }
@@ -575,7 +569,7 @@ public:
 };
 
 #endif // PETSC
-};     // namespace inversion
-};     // namespace bout
+}; // namespace inversion
+}; // namespace bout
 
 #endif // HEADER GUARD