Merge branch 'trunk-minor' into trunk-major

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.8.0
+current_version = 4.8.1
 commit = False
 tag = False
 parse = ^(?P<major>0|[1-9]\d*)\.(?P<minor>0|[1-9]\d*)\.(?P<patch>0|[1-9]\d*)(?:-(?P<prerelease>(?:0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*))(?:\.(?P<number>0|[1-9]\d*|\d*[a-zA-Z-][0-9a-zA-Z-]*)))?$

.github/ISSUE_TEMPLATE/bug_report.yml

@@ -62,7 +62,7 @@ body:
     attributes:
       label: HOOMD-blue version
       description: What version of HOOMD-blue are you using?
-      placeholder: 4.8.0
+      placeholder: 4.8.1
     validations:
       required: true
   - type: markdown

.github/ISSUE_TEMPLATE/release.md

@@ -1,7 +1,7 @@
 ---
 name: Release checklist
 about: '[for maintainer use]'
-title: 'Release 4.8.0'
+title: 'Release 4.8.1'
 labels: ''
 assignees: 'joaander'
 

.github/workflows/build_and_test.yaml

@@ -118,7 +118,7 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         path: code
         submodules: true
@@ -203,13 +203,13 @@ jobs:
       run: tar --use-compress-program='zstd -10 -T0' -cvf install.tar install
 
     - name: 'Upload build'
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: build-${{ inputs.config }}-${{ github.sha }}
         path: build.tar
         retention-days: 7
     - name: 'Upload install'
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
         path: install.tar
@@ -233,7 +233,7 @@ jobs:
         apt-get update
         apt-get install git --yes
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         path: code
 
@@ -254,7 +254,7 @@ jobs:
         echo "$MAMBA_ROOT_PREFIX/envs/test/bin" >> $GITHUB_PATH
 
     - name: Download install
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: install-${{ inputs.config }}-${{ github.sha }}
     - name: Untar install
@@ -312,7 +312,7 @@ jobs:
         echo "LD_LIBRARY_PATH=/usr/lib/x86_64-linux-gnu" >> $GITHUB_ENV
 
     - name: Download build
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: build-${{ inputs.config }}-${{ github.sha }}
     - name: Untar build

.github/workflows/release.yaml

@@ -31,7 +31,7 @@ jobs:
 
     steps:
     - name: Checkout
-      uses: actions/checkout@a5ac7e51b41094c92402da3b24376905380afc29 # v4.1.6
+      uses: actions/checkout@692973e3d937129bcbf40652eb9f2f61becf3332 # v4.1.7
       with:
         fetch-depth: 0
         submodules: true
@@ -67,7 +67,7 @@ jobs:
       run: tar -cvJf ${name}-${tag:1}.tar.xz ${name}-${tag:1}
 
     - name: Upload release files
-      uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4.3.3
+      uses: actions/upload-artifact@0b2256b8c012f0828dc542b3febcab082c67f72b # v4.3.4
       with:
         name: release
         path: |
@@ -81,12 +81,12 @@ jobs:
 
     steps:
     - name: Download artifacts
-      uses: actions/download-artifact@65a9edc5881444af0b9093a5e628f2fe47ea3b2e # v4.1.7
+      uses: actions/download-artifact@fa0a91b85d4f404e444e00e005971372dc801d16 # v4.1.8
       with:
         name: release
 
     - name: Create release
-      uses: softprops/action-gh-release@69320dbe05506a9a39fc8ae11030b214ec2d1f87 # v2.0.5
+      uses: softprops/action-gh-release@a74c6b72af54cfa997e81df42d94703d6313a2d0 # v2.0.6
       if: startsWith(github.ref, 'refs/tags/v')
       with:
         files: "*.tar.*"

.github/workflows/stale.yaml

@@ -8,4 +8,4 @@ on:
 
 jobs:
   stale:
-    uses: glotzerlab/workflows/.github/workflows/stale.yaml@5cfac9da9cb78e16ae97a9119b6fd13c1c2d6f5e # 0.1.0
+    uses: glotzerlab/workflows/.github/workflows/stale.yaml@ea2e25d07af862a1c696a932c2bd6b242d142049 # 0.2.0

.github/workflows/test.yaml

@@ -17,7 +17,7 @@ on:
 jobs:
   start_action_runners:
     name: Start
-    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@c89b62aa89f7886318edb166bc0500cfc658f24f # v1.3.0
+    uses: glotzerlab/jetstream2-admin/.github/workflows/start.yaml@98f840ba341f72bf412100f2180d38c06e792b84 # v1.3.1
     secrets: inherit
 
   typical:

.github/workflows/update-conda-lockfiles.yaml

@@ -0,0 +1,14 @@
+name: Update conda lockfiles
+
+on:
+  schedule:
+    - cron: '0 12 1 * *'
+
+  workflow_dispatch:
+
+jobs:
+  update:
+    uses: glotzerlab/workflows/.github/workflows/update-conda-lockfiles.yaml@ea2e25d07af862a1c696a932c2bd6b242d142049 # 0.2.0
+    secrets: inherit
+    with:
+      branch: trunk-patch

BUILDING.rst

@@ -145,7 +145,7 @@ Clone using Git_::
 
    $ git clone --recursive https://github.com/glotzerlab/hoomd-blue
 
-Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.8.0.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.8.1.tar.gz`_.
 
 .. seealso::
 
@@ -158,7 +158,7 @@ Release tarballs are also available as `GitHub release`_ assets: `Download hoomd
     Execute ``git submodule update --init`` to fetch the submodules each time you switch branches
     and the submodules show as modified.
 
-.. _Download hoomd-4.8.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.0/hoomd-4.8.0.tar.gz
+.. _Download hoomd-4.8.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.8.1/hoomd-4.8.1.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

CHANGELOG.rst

@@ -26,6 +26,16 @@ Removed:
 4.x
 ---
 
+4.8.1 (2024-07-18)
+^^^^^^^^^^^^^^^^^^
+
+Fixed:
+
+* Prevent illegal instruction when accessing 0 length snapshot arrays
+  (`#1846 <https://github.com/glotzerlab/hoomd-blue/pull/1846>`__)
+* Fix MPCD compiler warning.
+  (`#1845 <https://github.com/glotzerlab/hoomd-blue/pull/1845>`__)
+
 4.8.0 (2024-07-11)
 ^^^^^^^^^^^^^^^^^^
 

CMakeLists.txt

@@ -18,7 +18,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.8.0")
+set(HOOMD_VERSION_RAW "4.8.1")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

INSTALLING.rst

@@ -20,19 +20,19 @@ Serial CPU and single GPU builds
 *linux-64*, *osx-64*, and *osx-arm64* platforms. Install the ``hoomd`` package from the conda-forge_
 channel into a conda environment::
 
-    $ mamba install hoomd=4.8.0
+    $ mamba install hoomd=4.8.1
 
 .. _conda-forge: https://conda-forge.org/docs/user/introduction.html
 
 ``conda`` auto-detects whether your system has a GPU and attempts to install the appropriate
 package. Override this and force the GPU enabled package installation with::
 
     $ export CONDA_OVERRIDE_CUDA="12.0"
-    $ mamba install "hoomd=4.8.0=*gpu*" "cuda-version=12.0"
+    $ mamba install "hoomd=4.8.1=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ mamba install "hoomd=4.8.0=*cpu*"
+    $ mamba install "hoomd=4.8.1=*cpu*"
 
 .. note::
 
@@ -42,7 +42,7 @@ Similarly, you can force CPU only package installation with::
 .. note::
 
     Run time compilation is no longer available on conda-forge builds starting with HOOMD-blue
-    4.8.0.
+    4.8.1.
 
 .. tip::
 

hoomd/BondedGroupData.cc

@@ -1418,7 +1418,12 @@ pybind11::object BondedGroupData<group_size, Group, name, has_type_mapping>::Sna
     assert(has_type_mapping);
     auto self_cpp
         = self.cast<BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot*>();
-    return pybind11::array(self_cpp->type_id.size(), &self_cpp->type_id[0], self);
+
+    if (self_cpp->type_id.size() == 0)
+        {
+        return pybind11::array(pybind11::dtype::of<unsigned int>(), 0, nullptr);
+        }
+    return pybind11::array(self_cpp->type_id.size(), self_cpp->type_id.data(), self);
     }
 
 /*! \returns a numpy array that wraps the value data element.
@@ -1432,7 +1437,12 @@ pybind11::object BondedGroupData<group_size, Group, name, has_type_mapping>::Sna
     assert(!has_type_mapping);
     auto self_cpp
         = self.cast<BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot*>();
-    return pybind11::array(self_cpp->val.size(), &self_cpp->val[0], self);
+
+    if (self_cpp->val.size() == 0)
+        {
+        return pybind11::array(pybind11::dtype::of<Scalar>(), 0, nullptr);
+        }
+    return pybind11::array(self_cpp->val.size(), self_cpp->val.data(), self);
     }
 
 /*! \returns a numpy array that wraps the groups data element.
@@ -1449,7 +1459,12 @@ BondedGroupData<group_size, Group, name, has_type_mapping>::Snapshot::getBondedT
     std::vector<size_t> dims(2);
     dims[0] = self_cpp->groups.size();
     dims[1] = group_size;
-    return pybind11::array(dims, (unsigned int*)&self_cpp->groups[0], self);
+
+    if (dims[0] == 0)
+        {
+        return pybind11::array(pybind11::dtype::of<unsigned int>(), dims, nullptr);
+        }
+    return pybind11::array(dims, (unsigned int*)self_cpp->groups.data(), self);
     }
 
 /*! \returns A python list of type names

hoomd/GSDReader.cc

@@ -222,25 +222,25 @@ void GSDReader::readParticles()
 
     // the snapshot already has default values, if a chunk is not found, the value
     // is already at the default, and the failed read is not a problem
-    readChunk(&m_snapshot->particle_data.type[0], m_frame, "particles/typeid", N * 4, N);
-    readChunk(&m_snapshot->particle_data.mass[0], m_frame, "particles/mass", N * 4, N);
-    readChunk(&m_snapshot->particle_data.charge[0], m_frame, "particles/charge", N * 4, N);
-    readChunk(&m_snapshot->particle_data.diameter[0], m_frame, "particles/diameter", N * 4, N);
-    readChunk(&m_snapshot->particle_data.body[0], m_frame, "particles/body", N * 4, N);
-    readChunk(&m_snapshot->particle_data.inertia[0],
+    readChunk(m_snapshot->particle_data.type.data(), m_frame, "particles/typeid", N * 4, N);
+    readChunk(m_snapshot->particle_data.mass.data(), m_frame, "particles/mass", N * 4, N);
+    readChunk(m_snapshot->particle_data.charge.data(), m_frame, "particles/charge", N * 4, N);
+    readChunk(m_snapshot->particle_data.diameter.data(), m_frame, "particles/diameter", N * 4, N);
+    readChunk(m_snapshot->particle_data.body.data(), m_frame, "particles/body", N * 4, N);
+    readChunk(m_snapshot->particle_data.inertia.data(),
               m_frame,
               "particles/moment_inertia",
               N * 12,
               N);
-    readChunk(&m_snapshot->particle_data.pos[0], m_frame, "particles/position", N * 12, N);
-    readChunk(&m_snapshot->particle_data.orientation[0],
+    readChunk(m_snapshot->particle_data.pos.data(), m_frame, "particles/position", N * 12, N);
+    readChunk(m_snapshot->particle_data.orientation.data(),
               m_frame,
               "particles/orientation",
               N * 16,
               N);
-    readChunk(&m_snapshot->particle_data.vel[0], m_frame, "particles/velocity", N * 12, N);
-    readChunk(&m_snapshot->particle_data.angmom[0], m_frame, "particles/angmom", N * 16, N);
-    readChunk(&m_snapshot->particle_data.image[0], m_frame, "particles/image", N * 12, N);
+    readChunk(m_snapshot->particle_data.vel.data(), m_frame, "particles/velocity", N * 12, N);
+    readChunk(m_snapshot->particle_data.angmom.data(), m_frame, "particles/angmom", N * 16, N);
+    readChunk(m_snapshot->particle_data.image.data(), m_frame, "particles/image", N * 12, N);
     }
 
 /*! Read the same data chunks for topology
@@ -253,8 +253,8 @@ void GSDReader::readTopology()
     if (N > 0)
         {
         m_snapshot->bond_data.resize(N);
-        readChunk(&m_snapshot->bond_data.type_id[0], m_frame, "bonds/typeid", N * 4, N);
-        readChunk(&m_snapshot->bond_data.groups[0], m_frame, "bonds/group", N * 8, N);
+        readChunk(m_snapshot->bond_data.type_id.data(), m_frame, "bonds/typeid", N * 4, N);
+        readChunk(m_snapshot->bond_data.groups.data(), m_frame, "bonds/group", N * 8, N);
         }
 
     N = 0;
@@ -263,8 +263,8 @@ void GSDReader::readTopology()
     if (N > 0)
         {
         m_snapshot->angle_data.resize(N);
-        readChunk(&m_snapshot->angle_data.type_id[0], m_frame, "angles/typeid", N * 4, N);
-        readChunk(&m_snapshot->angle_data.groups[0], m_frame, "angles/group", N * 12, N);
+        readChunk(m_snapshot->angle_data.type_id.data(), m_frame, "angles/typeid", N * 4, N);
+        readChunk(m_snapshot->angle_data.groups.data(), m_frame, "angles/group", N * 12, N);
         }
 
     N = 0;
@@ -273,8 +273,8 @@ void GSDReader::readTopology()
     if (N > 0)
         {
         m_snapshot->dihedral_data.resize(N);
-        readChunk(&m_snapshot->dihedral_data.type_id[0], m_frame, "dihedrals/typeid", N * 4, N);
-        readChunk(&m_snapshot->dihedral_data.groups[0], m_frame, "dihedrals/group", N * 16, N);
+        readChunk(m_snapshot->dihedral_data.type_id.data(), m_frame, "dihedrals/typeid", N * 4, N);
+        readChunk(m_snapshot->dihedral_data.groups.data(), m_frame, "dihedrals/group", N * 16, N);
         }
 
     N = 0;
@@ -283,8 +283,8 @@ void GSDReader::readTopology()
     if (N > 0)
         {
         m_snapshot->improper_data.resize(N);
-        readChunk(&m_snapshot->improper_data.type_id[0], m_frame, "impropers/typeid", N * 4, N);
-        readChunk(&m_snapshot->improper_data.groups[0], m_frame, "impropers/group", N * 16, N);
+        readChunk(m_snapshot->improper_data.type_id.data(), m_frame, "impropers/typeid", N * 4, N);
+        readChunk(m_snapshot->improper_data.groups.data(), m_frame, "impropers/group", N * 16, N);
         }
 
     N = 0;
@@ -297,7 +297,11 @@ void GSDReader::readTopology()
         for (unsigned int i = 0; i < N; i++)
             m_snapshot->constraint_data.val[i] = Scalar(data[i]);
 
-        readChunk(&m_snapshot->constraint_data.groups[0], m_frame, "constraints/group", N * 8, N);
+        readChunk(m_snapshot->constraint_data.groups.data(),
+                  m_frame,
+                  "constraints/group",
+                  N * 8,
+                  N);
         }
 
     if (m_handle.header.schema_version >= gsd_make_version(1, 1))
@@ -308,8 +312,8 @@ void GSDReader::readTopology()
         if (N > 0)
             {
             m_snapshot->pair_data.resize(N);
-            readChunk(&m_snapshot->pair_data.type_id[0], m_frame, "pairs/typeid", N * 4, N);
-            readChunk(&m_snapshot->pair_data.groups[0], m_frame, "pairs/group", N * 8, N);
+            readChunk(m_snapshot->pair_data.type_id.data(), m_frame, "pairs/typeid", N * 4, N);
+            readChunk(m_snapshot->pair_data.groups.data(), m_frame, "pairs/group", N * 8, N);
             }
         }
     }