Merge pull request #1600 from glotzerlab/release-4.1.0

Release HOOMD-blue 4.1.0.
glotzerlab · Aug 7, 2023 · 9ec85d2 · 9ec85d2
2 parents 3026173 + 21b2664
commit 9ec85d2
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Showing 15 changed files with 33 additions and 25 deletions.
diff --git a/.bumpversion.cfg b/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 4.0.1
+current_version = 4.1.0
 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-]*)))?$

diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.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: 4.0.1
+      placeholder: 4.1.0
     validations:
       required: true
   - type: markdown

diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml
@@ -40,7 +40,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/[email protected].2
+        uses: actions/[email protected].3
         with:
           fetch-depth: 0
           submodules: true

diff --git a/.github/workflows/templates/release.yml b/.github/workflows/templates/release.yml
@@ -27,7 +27,7 @@ jobs:
 
     steps:
       - name: Checkout
-        uses: actions/[email protected].2
+        uses: actions/[email protected].3
         with:
           fetch-depth: 0
           submodules: true

diff --git a/.github/workflows/templates/test.yml b/.github/workflows/templates/test.yml
@@ -181,7 +181,7 @@ env:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -82,7 +82,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -188,7 +188,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -249,7 +249,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -299,7 +299,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -361,7 +361,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -475,7 +475,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true
@@ -544,7 +544,7 @@ jobs:
       run: ( shopt -s dotglob nullglob; rm -rf ./* )
       shell: bash
     - name: Checkout
-      uses: actions/[email protected].2
+      uses: actions/[email protected].3
       with:
         path: code
         submodules: true

diff --git a/.mailmap b/.mailmap
@@ -134,6 +134,7 @@ Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]
 Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>
 Tommy Waltmann <[email protected]> tomwalt <[email protected]>
 Tommy Waltmann <[email protected]> tommy-waltmann <[email protected]>
+Tommy Waltmann <[email protected]> Tommy Waltmann <[email protected]>
 Andrew J. Schultz <[email protected]> Andrew J. Schultz <[email protected]>
 Andrew J. Schultz <[email protected]> Andrew Schultz <[email protected]>
 Corwin Kerr <[email protected]> Corwin Kerr <[email protected]>
@@ -158,6 +159,9 @@ Raymond Asare <[email protected]> rayasare <[email protected]>
 Marco Klement <[email protected]> Marco Klement, M.Sc <[email protected]>
 Chris Jones <[email protected]> <[email protected]>
 Melody Zhang <[email protected]> Melody Zhang <[email protected]>
+Melody Zhang <[email protected]> Yiyuan Melody Zhang <[email protected]>
+Melody Zhang <[email protected]> Yiyuan Melody Zhang <[email protected]>
+Melody Zhang <[email protected]> Yiyuan Melody Zhang <[email protected]>
 Jen Bradley <[email protected]> Jen Bradley <[email protected]>
 Jen Bradley <[email protected]> janbridley <[email protected]>
 Martin Girard <[email protected]> MartinGirard <[email protected]>
@@ -166,3 +170,4 @@ Ignacio Blanco Varela <[email protected]> Ignacio Blanco Varela <83680829+iblanc
 Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
 Domagoj Fijan <[email protected]> Domagoj Fijan <[email protected]>
 Adrien Chen <[email protected]> Adrien Chen <[email protected]>
+Antonia Statt <[email protected]> Antonia Statt <>
diff --git a/BUILDING.rst b/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-4.0.1.tar.gz`_.
+Release tarballs are also available as `GitHub release`_ assets: `Download hoomd-4.1.0.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-4.0.1.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.0.1/hoomd-4.0.1.tar.gz
+.. _Download hoomd-4.1.0.tar.gz: https://github.com/glotzerlab/hoomd-blue/releases/download/v4.1.0/hoomd-4.1.0.tar.gz
 .. _GitHub release: https://github.com/glotzerlab/hoomd-blue/releases
 .. _git book: https://git-scm.com/book
 .. _Git: https://git-scm.com/

diff --git a/CHANGELOG.rst b/CHANGELOG.rst
@@ -7,7 +7,7 @@ Change Log
 4.x
 ---
 
-4.1.0 (2024-08-??)
+4.1.0 (2024-08-07)
 ^^^^^^^^^^^^^^^^^^
 
 *Fixed*
@@ -39,6 +39,9 @@ Change Log
   (`#1593 <https://github.com/glotzerlab/hoomd-blue/pull/1593>`__).
 * ``hoomd.write.HDF5Logger`` - write log quantities to HDF5 files
   (`#1588 <https://github.com/glotzerlab/hoomd-blue/pull/1588>`__).
+* ``default_gamma`` and ``default_gamma_r`` arguments to ``hoomd.md.methods.rattle.Brownian``
+  ``hoomd.md.methods.rattle.Langevin``, and ``hoomd.md.methods.rattle.OverdampedViscous``
+  (`#1589 <https://github.com/glotzerlab/hoomd-blue/issues/1589>`__).
 
 4.0.1 (2023-06-27)
 ^^^^^^^^^^^^^^^^^^

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -14,7 +14,7 @@ add_subdirectory (CMake)
 
 ################################
 ## Version information
-set(HOOMD_VERSION_RAW "4.0.1")
+set(HOOMD_VERSION_RAW "4.1.0")
 string(REGEX MATCH "(.*)\\.(.*)\\.(.*)$" _hoomd_version_match ${HOOMD_VERSION_RAW})
 set(HOOMD_VERSION_MAJOR ${CMAKE_MATCH_1})
 set(HOOMD_VERSION_MINOR ${CMAKE_MATCH_2})

diff --git a/INSTALLING.rst b/INSTALLING.rst
@@ -24,17 +24,17 @@ Conda package
 **HOOMD-blue** is available on conda-forge_ on the *linux-64*, *osx-64*, and *osx-arm64* platforms.
 Install the ``hoomd`` package from the conda-forge_ channel into a conda environment::
 
-    $ conda install hoomd=4.0.1
+    $ conda install hoomd=4.1.0
 
 ``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"
-    $ conda install "hoomd=4.0.1=*gpu*" "cuda-version=12.0"
+    $ conda install "hoomd=4.1.0=*gpu*" "cuda-version=12.0"
 
 Similarly, you can force CPU only package installation with::
 
-    $ conda install "hoomd=4.0.1=*cpu*"
+    $ conda install "hoomd=4.1.0=*cpu*"
 
 .. note::
 

diff --git a/hoomd/hpmc/external/user.py b/hoomd/hpmc/external/user.py
@@ -67,9 +67,9 @@ class CPPExternalPotential(ExternalField):
         Your code *must* return a value.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.0.1/hoomd/VectorMath.h
+            v4.1.0/hoomd/VectorMath.h
     .. _BoxDim.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.0.1/hoomd/BoxDim.h
+            v4.1.0/hoomd/BoxDim.h
 
     Example:
         .. code-block:: python

diff --git a/hoomd/hpmc/pair/user.py b/hoomd/hpmc/pair/user.py
@@ -75,7 +75,7 @@ class CPPPotentialBase(AutotunedObject):
                 HOOMD-blue source code.
 
     .. _VectorMath.h: https://github.com/glotzerlab/hoomd-blue/blob/\
-            v4.0.1/hoomd/VectorMath.h
+            v4.1.0/hoomd/VectorMath.h
 
     Note:
         Your code *must* return a value.

diff --git a/sphinx-doc/conf.py b/sphinx-doc/conf.py
@@ -63,8 +63,8 @@
 copyright = f'2009-{ year } The Regents of the University of Michigan'
 author = 'The Regents of the University of Michigan'
 
-version = '4.0.1'
-release = '4.0.1'
+version = '4.1.0'
+release = '4.1.0'
 
 language = 'en'
 

diff --git a/sphinx-doc/tutorial b/sphinx-doc/tutorial
+2 −2		.github/workflows/test.yml
+2 −2		.pre-commit-config.yaml
+4 −4		05-Organizing-and-Executing-Simulations/project.py
+2 −2		05-Organizing-and-Executing-Simulations/project_partitioned.py