Debugging and fixing CI issues

.devcontainer/Dockerfile

@@ -1,4 +1,4 @@
-ARG DEVCONTAINER_BASE=mcr.microsoft.com/devcontainers/base:1.0.23-ubuntu-22.04
+ARG DEVCONTAINER_BASE=mcr.microsoft.com/devcontainers/base:ubuntu-24.04
 
 #########################################################
 # file-normalizer stage
@@ -13,7 +13,7 @@ FROM mcr.microsoft.com/oss/busybox/busybox:1.33.1 as file-normalizer
 
 COPY environment.yml \
      .devcontainer/devcontainer.bashrc  \
-     .devcontainer/matlab-r2023b.ubuntu-22.04.dependencies.txt \
+     .devcontainer/matlab-r2023b.ubuntu-24.04.dependencies.txt \
      /data/
 
 RUN chmod -R 555 /data/
@@ -108,7 +108,7 @@ RUN wget --quiet "https://github.com/microsoft/yardl/releases/download/v${YARDL_
 
 ENV DEBIAN_FRONTEND="noninteractive" TZ="Etc/UTC"
 
-COPY --from=file-normalizer /data/matlab-r2023b.ubuntu-22.04.dependencies.txt /tmp/matlab-dependencies.txt
+COPY --from=file-normalizer /data/matlab-r2023b.ubuntu-24.04.dependencies.txt /tmp/matlab-dependencies.txt
 
 RUN export DEBIAN_FRONTEND=noninteractive \
     && apt-get update \

.devcontainer/matlab-r2023b.ubuntu-22.04.dependencies.txt → .devcontainer/matlab-r2023b.ubuntu-24.04.dependencies.txt

@@ -1,18 +1,19 @@
 ca-certificates
-libasound2
+debianutils
+libasound2t64
 libc6
 libcairo-gobject2
 libcairo2
 libcap2
-libcups2
+libcups2t64
 libdrm2
 libgbm1
 libgdk-pixbuf-2.0-0
 libgl1
-libglib2.0-0
+libglib2.0-0t64
 libgstreamer-plugins-base1.0-0
 libgstreamer1.0-0
-libgtk-3-0
+libgtk-3-0t64
 libice6
 libltdl7
 libnspr4
@@ -31,7 +32,7 @@ libxfixes3
 libxft2
 libxinerama1
 libxrandr2
-libxt6
+libxt6t64
 libxtst6
 libxxf86vm1
 locales
@@ -41,4 +42,6 @@ net-tools
 procps
 sudo
 unzip
-zlib1g
+wget
+x11-xkb-utils
+zlib1g

.github/workflows/mrd_conda.yml

@@ -13,7 +13,7 @@ jobs:
     name: Test and Build Conda Packages
     strategy:
       matrix:
-        os: [ubuntu-latest, macos-13]
+        os: [ubuntu-latest]
     runs-on: ${{ matrix.os }}
     defaults:
       run:

cpp/conda/conda_build_config.yaml

@@ -1,8 +1,8 @@
 c_compiler_version:
-  - 11.2.0                      # [linux]
+  - 15.2.0                      # [linux]
   - 14.0.6                      # [osx]
 cxx_compiler_version:
-  - 11.2.0                      # [linux]
+  - 15.2.0                      # [linux]
   - 14.0.6                      # [osx]
 
 MACOSX_DEPLOYMENT_TARGET:       # [osx]

cpp/conda/meta.yaml

@@ -18,16 +18,16 @@ requirements:
     - ninja
   host:
     - fftw=3.3.9
-    - fmt=8.1.1
-    - howardhinnant_date=3.0.1
+    - fmt=12.0.0
+    - howardhinnant_date=3.0.3
     - hdf5=1.10.6
     - imagemagick=7.0.11_13
     - ismrmrd>=1.14.2
-    - nlohmann_json=3.11.2
-    - xtensor=0.24.7
+    - nlohmann_json=3.12.0
+    - xtensor=0.25.0
     - xtensor-fftw=0.2.5
   run:
-    - fmt=8.1.1
+    - fmt=12.0.0
     - hdf5=1.10.6
     - imagemagick=7.0.11_13
     - ismrmrd>=1.14.2

cpp/mrd-tools/mrd_image_stream_to_png.cc

@@ -1,4 +1,12 @@
+// NOTE:
+// GCC 13+ appears to emit false positive warnings for array-bounds
+// when using xt::views (specifically the calls to `xt::amax` below).
+// The statements are correct and there's no overflow, so we can suppress the warnings.
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Warray-bounds"
 #include "mrd/binary/protocols.h"
+#pragma GCC diagnostic pop
+
 #include <Magick++.h>
 #include <fmt/format.h>
 #include <iostream>

cpp/mrd-tools/mrd_stream_recon.cc

@@ -1,11 +1,20 @@
+
 #include "mrd/binary/protocols.h"
 #include "mrd/protocols.h"
 #include "mrd/types.h"
 
 #include <xtensor-fftw/basic.hpp>
 #include <xtensor-fftw/helper.hpp>
-#include <xtensor/xstrided_view.hpp>
+
+// NOTE:
+// GCC 13+ appears to emit false positive warnings for array-bounds and stringop-overflow
+// when using xt::view with xt::range (specifically in `remove_oversampling` below).
+// The assignment is correct and there's no overflow, so we can suppress the warnings.
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Warray-bounds"
+#pragma GCC diagnostic ignored "-Wstringop-overflow"
 #include <xtensor/xview.hpp>
+#pragma GCC diagnostic pop
 
 xt::xtensor<std::complex<float>, 4> fftshift(xt::xtensor<std::complex<float>, 4> x) {
   return xt::roll(xt::roll(x, x.shape(3) / 2, 3), x.shape(2) / 2, 2);

environment.yml

@@ -6,28 +6,28 @@ channels:
 dependencies:
   - bash-completion=2.11
   - boost=1.80.0
-  - cmake=3.21.3
-  - fmt=8.1.1
-  - gcc_linux-64=11.2.0
+  - cmake=3.25.1
+  - fmt=12.0.0
+  - gcc_linux-64=15.2.0
   - gdb=11.2
-  - gxx_linux-64=11.2.0
+  - gxx_linux-64=15.2.0
   - h5py=3.2.1
   - hdf5=1.10.6
   - imagemagick=7.0.11_13
   - ipykernel=6.23.1
   - ismrmrd>=1.14.2
-  - howardhinnant_date=3.0.1
-  - just=1.5.0
+  - howardhinnant_date=3.0.3
+  - just=1.44.1
   - matplotlib=3.6.2
-  - ninja=1.11.0
-  - nlohmann_json=3.11.2
+  - ninja=1.13.0
+  - nlohmann_json=3.12.0
   - nodejs=18.12.1 # local
   - python=3.9.15
   - pyfftw=0.13.1
   - shellcheck=0.8.0
   - valgrind=3.18.1
   - xmlschema=2.2.3
-  - xtensor=0.24.2
+  - xtensor=0.25.0
   - xtensor-fftw=0.2.5
   - pip
   - pip: