science/py-hoomd-blue: Update 3.0.1 -> 3.1.0

Reported by:	portscout

3 files changed, 21 insertions, 13 deletions

diff --git a/science/py-hoomd-blue/Makefile b/science/py-hoomd-blue/Makefile
index 67c574283389..a40c45e24edd 100644
--- a/science/py-hoomd-blue/Makefile
+++ b/science/py-hoomd-blue/Makefile
@@ -1,6 +1,6 @@
 PORTNAME=	hoomd-blue
 DISTVERSIONPREFIX=	v
-DISTVERSION=	3.0.1
+DISTVERSION=	3.1.0
 CATEGORIES=	science # physics
 PKGNAMEPREFIX=	${PYTHON_PKGNAMEPREFIX}
 
@@ -26,7 +26,7 @@ GH_TUPLE=	glotzerlab:upp11:0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360:glotzerlab_u
 		glotzerlab:hipCUB:c70e19332a8402049b3359b409e50220a759c42d:glotzerlab_hipCUB/hoomd/extern/hipCUB \
 		mphowardlab:neighbor:ba0f06869b766066a7068852fa3b8c5fa746f71f:mphowardlab_neighbor/hoomd/extern/neighbor \
 		mphowardlab:hipper:b6da049a516ada03e4e1b66ca6b4c2c7c9668595:mphowardlab_hipper/hoomd/extern/hipper \
-		glotzerlab:hoomd-examples:78174286427a2ec1c23e84015f7b4ba4f5f86d20:glotzerlab_hoomd_examples/sphinx-doc/tutorial \
+		glotzerlab:hoomd-examples:78174286427a2ec1c23e84015f7b4ba4f5f86d20:glotzerlab_hoomd_examples/sphinx-doc/tutorial
 
 SHEBANG_GLOB=	*.sh
 
diff --git a/science/py-hoomd-blue/distinfo b/science/py-hoomd-blue/distinfo
index 43236d619a7f..17a85229e805 100644
--- a/science/py-hoomd-blue/distinfo
+++ b/science/py-hoomd-blue/distinfo
@@ -1,6 +1,6 @@
-TIMESTAMP = 1649627643
-SHA256 (glotzerlab-hoomd-blue-v3.0.1_GH0.tar.gz) = 272cfc0862c47ae09c483a9b943676993bc7d21f492f0e47605ffdbaeb7f343f
-SIZE (glotzerlab-hoomd-blue-v3.0.1_GH0.tar.gz) = 2755386
+TIMESTAMP = 1651170590
+SHA256 (glotzerlab-hoomd-blue-v3.1.0_GH0.tar.gz) = bbf602dca4a7ab94e07339b74df9f88eef0cc2487942b44e5f31581c3e77c7bb
+SIZE (glotzerlab-hoomd-blue-v3.1.0_GH0.tar.gz) = 2781335
 SHA256 (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 759695139bddae1d8a7cd52c967b856d6debf28fb37ea177f78c4434e2b210a8
 SIZE (glotzerlab-upp11-0c1fb8dfb4bcdc1c5c4eff9165539b15e70c4360_GH0.tar.gz) = 21058
 SHA256 (glotzerlab-nano-signal-slot-34223a4a7e97f8e114ef007e5360cf7a71265da3_GH0.tar.gz) = d15030482c82d9e4a99c2f67d8ef23b33cc318dd48ac0f8e804c6d4750f27ff4
diff --git a/science/py-hoomd-blue/pkg-plist b/science/py-hoomd-blue/pkg-plist
index ecf44031a50f..b39ef9d91d26 100644
--- a/science/py-hoomd-blue/pkg-plist
+++ b/science/py-hoomd-blue/pkg-plist
@@ -77,8 +77,11 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_quick_compress.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_scale.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape.py
+%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape_updater.py
+%%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_shape_utils.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_small_box_2d.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/pytest/test_small_box_3d.py
+%%PYTHON_SITELIBDIR%%/hoomd/hpmc/shape_move.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/__init__.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/boxmc_move_size.py
 %%PYTHON_SITELIBDIR%%/hoomd/hpmc/tune/mc_move_tune.py
@@ -592,6 +595,7 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeConvexPolyhedron.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeEllipsoid.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeFacetedEllipsoid.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeMoves.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapePolyhedron.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeSimplePolygon.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/ShapeSphere.h
@@ -605,6 +609,7 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/UpdaterClustersGPUDepletants.cuh
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/UpdaterMuVT.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/UpdaterQuickCompress.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/UpdaterShape.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/XenoCollide2D.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/XenoCollide3D.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/hpmc/modules.h
@@ -615,12 +620,8 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ActiveForceConstraintComputeGPU.cuh
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ActiveForceConstraintComputeGPU.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/ActiveRotationalDiffusionUpdater.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllAnisoPairPotentials.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllBondPotentials.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllExternalPotentials.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllPairPotentials.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllSpecialPairPotentials.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AllTripletPotentials.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AlchemostatTwoStep.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AlchemyData.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AnisoPotentialPair.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AnisoPotentialPairGPU.cuh
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/AnisoPotentialPairGPU.h
@@ -647,8 +648,8 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairALJ.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairBuckingham.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDLVO.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDPDLJThermo.h
-%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDPDThermo.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDPDThermoDPD.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDPDThermoLJ.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairDipole.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairEwald.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/EvaluatorPairExpandedLJ.h
@@ -718,6 +719,8 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialExternalGPU.cuh
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialExternalGPU.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPair.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPairAlchemical.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPairAlchemicalNormalized.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPairDPDThermo.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPairDPDThermoGPU.cuh
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/PotentialPairDPDThermoGPU.h
@@ -742,6 +745,7 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNPTMTKGPU.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVE.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVEGPU.h
+%%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVTAlchemy.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVTMTK.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepNVTMTKGPU.h
 %%PYTHON_SITELIBDIR%%/hoomd/include/hoomd/md/TwoStepRATTLEBD.h
@@ -788,6 +792,9 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/logging.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/__init__.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/_md%%PYTHON_EXT_SUFFIX%%.so
+%%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/__init__.py
+%%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/methods.py
+%%PYTHON_SITELIBDIR%%/hoomd/md/alchemy/pair.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/angle.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/bond.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/compute.py
@@ -821,6 +828,7 @@ lib/cmake/hoomd/hoomd-targets.cmake
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/forces_and_energies.json
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_active.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_active_rotational_diffusion.py
+%%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_alchemostat.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_alj.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_angle.py
 %%PYTHON_SITELIBDIR%%/hoomd/md/pytest/test_aniso_pair.py