Merge remote-tracking branch 'origin/master' into OpemMP_fix2

.github/workflows/docker.yml

@@ -40,7 +40,7 @@ jobs:
           ghcr.io/synerbi/sirf
         flavor: |
           latest=auto
-          suffix=${{ matrix.type == 'gpu' && 'gpu,onlatest=true' || '' }}
+          suffix=${{ matrix.type == 'gpu' && '-gpu,onlatest=true' || '' }}
         tags: |
           type=edge
           type=semver,pattern={{version}}
@@ -89,7 +89,7 @@ jobs:
       run: |
         # rebuild sirf image
         ./docker/compose.sh -bR${{ matrix.type == 'gpu' && 'g' || 'c' }}
-        image=synerbi/sirf:jupyter${{ steps.pull.outputs.suffix }}
+        image=synerbi/sirf:latest${{ steps.pull.outputs.suffix }}
         echo "image=$image" >> "$GITHUB_OUTPUT"
         # tag potentially newer core image
         docker tag synerbi/jupyter:scipy-${{ matrix.type }} ${{ steps.pull.outputs.core_image }}
@@ -130,7 +130,7 @@ jobs:
           ghcr.io/synerbi/sirf
         flavor: |
           latest=false
-          suffix=${{ matrix.type == 'gpu' && 'gpu,onlatest=true' || '' }}
+          suffix=${{ matrix.type == 'gpu' && '-gpu,onlatest=true' || '' }}
         tags: devel
         labels: |
           org.opencontainers.image.licenses=Apache-2.0${{ matrix.type == 'gpu' && ' AND BSD-3-Clause AND GPL-3.0' || '' }}
@@ -173,7 +173,7 @@ jobs:
       run: |
         # rebuild sirf image
         ./docker/compose.sh -dbR${{ matrix.type == 'gpu' && 'g' || 'c' }}
-        image=synerbi/sirf:jupyter-devel${{ steps.pull.outputs.suffix }}
+        image=synerbi/sirf:devel${{ steps.pull.outputs.suffix }}
         echo "image=$image" >> "$GITHUB_OUTPUT"
     - name: test CIL
       run: >

CHANGES.md

@@ -1,19 +1,30 @@
 # ChangeLog
 
+## vx.x.x
+
+- CMake:
+  - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
+
 ## v3.6.0
 - build the STIR native Python interface by default (STIR_BUILD_SWIG_PYTHON=ON). You can still switch this off.
 - docker image updates:
   - uses `docker-stacks`
   - CPU: ubuntu:22.04
   - GPU: nvidia/cuda:11.7.1-cudnn8-runtime-ubuntu22.04
+  - **Important**: Docker tags have now changed, see [docker/README.md](docker/README.md) for a table. Changes w.r.t. previous versions are listed below (note that `-gpu` versions of all tags exist as well, e.g. `latest-gpu` etc).
+    - The `latest` tag now includes the jupyter server etc, so the `service` tag should no longer be used (and corresponding images on DockerHub will not be updated).
+    - The new `edge` tag corresponds to `master` branch of the SIRF-SuperBuild. Note that this will include the "normal" versions of all packages.
+    - The `devel` tag (for `DEVEL_BUILD=ON` with `master` versions of SIRF, STIR etc) is no longer pushed to DockerHub, and therefore will not be updated.
+  - Docker images are now pushed to [DockerHub](https://hub.docker.com/r/synerbi/sirf/tags) and [GHCR](https://github.com/SyneRBI/SIRF-SuperBuild/pkgs/container/sirf)
   - added requirements.yml
-- Drop Travis
+  - revert to `conda` but with `libmamba` solver
 - updated versions:
   - SIRF: v3.6.0
   - STIR: v6.0.0
   - parallelproj: v1.7.3
   - Gadgetron: 6202fb7352a14fb82817b57a97d928c988eb0f4b (version of Oct 13, 2023)
   - ISMRMRD: v1.13.7
+  - NiftyReg: a328efb3a2f8ea4b47cf0f7b581d983a570a1ffd (version of 8 Mar, 2024, fixing find omp.h problems on MacOS)
   - siemens_to_ismrmrd: v1.2.11
   - CIL: db5a2a6cd3bddfbbf53e65f0549ac206096e5b44 (version of Feb 13, 2024)
   - CCPi-Regularisation-Toolkit: 71f8d304d804b54d378f0ed05539f01aaaf13758 (version of Dec 3. 2023)
@@ -23,7 +34,10 @@
   - pass through `OpenMP_CXX_INCLUDE_DIR` and `OpenMP_C_INCLUDE_DIR` to
     dependent projects. For instance, on MacOS the compiler might not find
     omp.h unless these variables are set.
-  - only pass through `OpenMP*LIBRARY` variables if set, and add OpenMP_iomp_LIBRARY to the list (for Intel compiler)
+- VM changes
+  - UPDATE.sh (and hence update_VM.sh) has extra developer options to set the
+    DEVEL_BUILD=ON (-D) and skip the build (-S).
+- Drop Travis
 
 ## v3.5.0
 - Temporarily disable CCPi-Regularisation due to #832
@@ -33,7 +47,7 @@
 - docker image updates
    - introduce `REMOVE_BUILD_FILES` variable. If set to 1 (which is the default),
      most build files will be removed in the docker image.
-   - introduce `RUN_CTESTS` variable. If set to 1 (which is the default),
+   - introduce `RUN_CTEST` variable. If set to 1 (which is the default),
      the CTests will be run while building the image.
    - remove obsolete copying of gadgetron.xml
    - Installing requirements for SIRF-Exercises uses its environment.yml or requirements.txt depending on settings.

CITATION.cff

@@ -19,28 +19,28 @@ authors:
     orcid: 'https://orcid.org/0000-0002-9784-1177'
   - given-names: Casper
     family-names: da Costa-Luis
-    affiliation: King's College London
+    affiliation: King's College London, and UK Research & Innovation
     orcid: 'https://orcid.org/0000-0002-7211-1557'
   - given-names: Richard
     family-names: Brown
     affiliation: University College London
     orcid: 'https://orcid.org/0000-0001-6989-9200'
-  - given-names: Laura
-    family-names: Murgatroyd
-    affiliation: UK Research & Innovation
-    orcid: 'https://orcid.org/0000-0002-3271-3625'
-  - given-names: Ander
-    family-names: Biguri
-    orcid: 'https://orcid.org/0000-0002-2636-3032'
-    affiliation: University College London
   - given-names: David
     family-names: Atkinson
     affiliation: University College London
     orcid: 'https://orcid.org/0000-0003-1124-6666'
+  - given-names: Ander
+    family-names: Biguri
+    orcid: 'https://orcid.org/0000-0002-2636-3032'
+    affiliation: University College London
   - given-names: Evgueni
     family-names: Ovtchinnikov
     orcid: 'https://orcid.org/0000-0002-9359-6514'
     affiliation: UK Research & Innovation
+  - given-names: Laura
+    family-names: Murgatroyd
+    affiliation: UK Research & Innovation
+    orcid: 'https://orcid.org/0000-0002-3271-3625'
   - given-names: Ashley
     family-names: Gillman
     orcid: 'https://orcid.org/0000-0001-9130-1092'

NOTICE.txt

@@ -1,6 +1,6 @@
 CCP SyneRBI Synergistic Image Reconstruction Framework (SIRF) SuperBuild.
-Copyright 2017-2023 University College London (UCL)
-Copyright 2017-2023 Rutherford Appleton Laboratory STFC
+Copyright 2017-2024 University College London (UCL)
+Copyright 2017-2024 Rutherford Appleton Laboratory STFC
 Copyright 2017-2021 King's College London (KCL)
 
 This software product is developed for the Collaborative Computational 
@@ -12,15 +12,15 @@ and other contributing institutions.
 Main contributors roughly in order of remaining lines
 (see each file for authors):
 
-Edoardo Pasca (STFC)
 Kris Thielemans (UCL)
+Edoardo Pasca (STFC)
 Benjamin A Thomas(UCL)
 Casper da Costa-Luis (KCL)
 Richard Brown (UCL)
-Laura Murgatroyd (STFC)
 Ander Biguri (UCL)
 David Atkinson (UCL)
 Evgueni Ovtchinnikov (STFC)
+Laura Murgatroyd (STFC)
 Ashley Gillman (CSIRO)
 Christoph Kolbitsch (PTB)
 Johannes Mayer (PTB)