Merge branch 'main' into updates/ci-workflow

.editorconfig

@@ -0,0 +1,24 @@
+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+# Unix-style newlines and UTF-8 everywhere
+[*]
+end_of_line = lf
+trim_trailing_whitespace = true
+charset = utf-8
+
+# 2 space indentation
+[*.{yml,yaml}]
+indent_style = space
+indent_size = 2
+
+# 4 space indentation
+[*.py]
+indent_style = space
+indent_size = 4
+
+# Tab indentation (no size specified)
+[Makefile]
+indent_style = tab

.gitignore

@@ -37,6 +37,7 @@ worker_code.cc
 worker_code.pyx
 worker_code.f90
 src/amuse/community/aarsethzare/aarsethzare_worker
+src/amuse/community/aarsethzare/aarsethzare_c.f90
 src/amuse/community/aarsethzare/worker_code.f90
 src/amuse/community/adaptb/adaptb_worker
 src/amuse/community/adaptb/src/integrator_MS.exe
@@ -61,6 +62,7 @@ src/amuse/community/bhtree/bhtree_worker
 src/amuse/community/bhtree/build/
 src/amuse/community/bhtree/worker_code.cc
 src/amuse/community/bhtree/worker_code.h
+src/amuse/community/bonsai2/src
 src/amuse/community/bse/bse_worker
 src/amuse/community/bse/src/bse
 src/amuse/community/bse/worker_code.f90
@@ -83,6 +85,7 @@ src/amuse/community/evtwin/worker_code.f90src/amuse/community/evtwin/evtwin_work
 src/amuse/community/evtwin/src/trunk/code/ev
 src/amuse/community/evtwin/src/trunk/code/svn_version.f90
 src/amuse/community/evtwin/src/trunk/code/twin
+src/amuse/community/evtwin/src/trunk/lib/
 src/amuse/community/fastkick/fastkick_worker
 src/amuse/community/fastkick/interface.gpuo
 src/amuse/community/fastkick/worker_code.cc
@@ -141,10 +144,14 @@ src/amuse/community/gadget2/build/
 src/amuse/community/gadget2/build_nogravity/
 src/amuse/community/gadget2/build_periodic/
 src/amuse/community/gadget2/build_periodic_nogravity/
+src/amuse/community/gadget2/build_normal/Gadget2
+src/amuse/community/gadget2/build_normal/Makefile
+src/amuse/community/gadget2/build_normal/makefile_options
 src/amuse/community/gadget2/gadget2_worker
 src/amuse/community/gadget2/gadget2_worker_nogravity
 src/amuse/community/gadget2/gadget2_worker_periodic
 src/amuse/community/gadget2/gadget2_worker_periodic_nogravity
+src/amuse/community/gadget2/gadget2_worker_normal
 src/amuse/community/gadget2/interface.ngo
 src/amuse/community/gadget2/interface.pngo
 src/amuse/community/gadget2/interface.po
@@ -188,9 +195,10 @@ src/amuse/community/halogen/halogen_worker
 src/amuse/community/halogen/src/halogen4muse
 src/amuse/community/halogen/worker_code.cc
 src/amuse/community/halogen/worker_code.h
-src/amuse/community/hermite0/hermite_worker
-src/amuse/community/hermite0/worker_code.cc
-src/amuse/community/hermite0/worker_code.h
+src/amuse/community/hermite/hermite_worker
+src/amuse/community/hermite/worker_code.cc
+src/amuse/community/hermite/worker_code.h
+src/amuse/community/hermite_grx/src
 src/amuse/community/higpus/worker_code.cc
 src/amuse/community/higpus/worker_code.h
 src/amuse/community/hop/hop_worker
@@ -234,10 +242,14 @@ src/amuse/community/mmc/interface_specs.tmp
 src/amuse/community/mmc/mmc_worker
 src/amuse/community/mmc/src/amuse_interface2.f
 src/amuse/community/mmc/worker_code.f90
+src/amuse/community/mobse/src/mobse
+src/amuse/community/mosse/mosse_c.f90
+src/amuse/community/mosse/src/mosse
 src/amuse/community/mocassin/worker_code.f90
 src/amuse/community/mpiamrvac/worker_code.f90
 src/amuse/community/nbody6xx/worker_code.f90
 src/amuse/community/nbody6xx/nbody6xx_worker
+src/amuse/community/petar/src
 src/amuse/community/pikachu/worker_code.cc
 src/amuse/community/pikachu/worker_code.h
 src/amuse/community/ph4/interface.h
@@ -256,20 +268,14 @@ src/amuse/community/ph4/src/scheduler.gpuo
 src/amuse/community/ph4/src/two_body.gpuo
 src/amuse/community/ph4/src/util.gpuo
 src/amuse/community/ph4/worker_code.cc
-src/amuse/community/phiGRAPE/build/
-src/amuse/community/phiGRAPE/build_mpi/
-src/amuse/community/phiGRAPE/glworker_code.f90
-src/amuse/community/phiGRAPE/interface.mpio
-src/amuse/community/phiGRAPE/phigrape_worker
-src/amuse/community/phiGRAPE/phigrape_worker_mpi
-src/amuse/community/phiGRAPE/worker_code.f90
-src/amuse/community/ramses/build/
-src/amuse/community/ramses/worker_code.f90
-src/amuse/community/ramses/build_1d/
-src/amuse/community/ramses/build_2d/
-src/amuse/community/ramses/ramses_worker
-src/amuse/community/ramses/ramses_worker_1d
-src/amuse/community/ramses/ramses_worker_2d
+src/amuse/community/phantom/src
+src/amuse/community/phigrape/build/
+src/amuse/community/phigrape/build_mpi/
+src/amuse/community/phigrape/glworker_code.f90
+src/amuse/community/phigrape/interface.mpio
+src/amuse/community/phigrape/phigrape_worker
+src/amuse/community/phigrape/phigrape_worker_mpi
+src/amuse/community/phigrape/worker_code.f90
 src/amuse/community/rebound/worker_code.cc
 src/amuse/community/rebound/worker_code.h
 src/amuse/community/sakura/sakura_worker
@@ -280,9 +286,9 @@ src/amuse/community/seba/src/Makefile.inc
 src/amuse/community/seba/worker_code.cc
 src/amuse/community/seba/worker_code.h
 src/amuse/community/seba/seba_worker
-src/amuse/community/seba/src/dstar/Makefile.inc
-src/amuse/community/seba/src/rdc/Makefile.inc
-src/amuse/community/seba/src/starev
+src/amuse/community/seba/src
+src/amuse/community/secularmultiple/worker_code
+src/amuse/community/secularmultiple/worker_code.cc
 src/amuse/community/sei/sei_worker
 src/amuse/community/sei/worker_code.cc
 src/amuse/community/sei/worker_code.h
@@ -297,12 +303,10 @@ src/amuse/community/smalln/smallN_worker
 src/amuse/community/smalln/src/f2c.co
 src/amuse/community/smalln/src/nstab.co
 src/amuse/community/smalln/worker_code.cc
-src/amuse/community/smalln/smalln_cython.c
-src/amuse/community/smalln/smalln_cython.pyx
-src/amuse/community/smalln/smalln_worker_cython
 src/amuse/community/sphray/sphray_worker
 src/amuse/community/sphray/sphray_worker.f90
 src/amuse/community/sse/src/sse
+src/amuse/community/sse/sse_c.f90
 src/amuse/community/sse/sse_worker
 src/amuse/community/sse/worker_code.f90
 src/amuse/community/twobody/twobody_worker
@@ -347,56 +351,8 @@ doc/amuse_examples
 /nbody6xx.input
 /test_results
 autom4te.cache/
-src/amuse/community/hermite0/hermite0_cython.c
-src/amuse/community/hermite0/hermite0_cython.pyx
-src/amuse/community/hermite0/hermite0_worker
-src/amuse/community/hermite0/hermite0_worker_cython
-src/amuse/community/huayno/huayno_cython.c
-src/amuse/community/huayno/huayno_cython.pyx
-src/amuse/community/huayno/huayno_worker_cython
-src/amuse/community/kepler/kepler_cython.cc
-src/amuse/community/kepler/kepler_cython.pyx
-src/amuse/community/kepler/kepler_worker_cython
-src/amuse/community/rebound/rebound_cython.cc
-src/amuse/community/rebound/rebound_cython.pyx
-src/amuse/community/rebound/rebound_worker_cython
-src/amuse/community/seba/seba_cython.cc
-src/amuse/community/seba/seba_cython.pyx
-src/amuse/community/seba/seba_worker_cython
-src/amuse/community/bhtree/bhtree_cython.c
-src/amuse/community/bhtree/bhtree_cython.pyx
-src/amuse/community/bhtree/bhtree_worker_cython
-src/amuse/community/aarsethzare/aarsethzare_c.f90
-src/amuse/community/aarsethzare/aarsethzare_cython.c
-src/amuse/community/aarsethzare/aarsethzare_cython.pyx
-src/amuse/community/aarsethzare/aarsethzare_worker_cython
 lib/sapporo_2/src/sapporo2-master
 lib/sapporo_2/src/master.tgz
-src/amuse/community/athena/athena_worker_cython
-src/amuse/community/gadget2/build_normal/Gadget2
-src/amuse/community/gadget2/build_normal/Makefile
-src/amuse/community/gadget2/build_normal/makefile_options
-src/amuse/community/gadget2/gadget2_cython_nogravity.c
-src/amuse/community/gadget2/gadget2_cython_nogravity.pyx
-src/amuse/community/gadget2/gadget2_cython_normal.c
-src/amuse/community/gadget2/gadget2_cython_normal.pyx
-src/amuse/community/gadget2/gadget2_cython_periodic.c
-src/amuse/community/gadget2/gadget2_cython_periodic.pyx
-src/amuse/community/gadget2/gadget2_cython_periodic_nogravity.c
-src/amuse/community/gadget2/gadget2_cython_periodic_nogravity.pyx
-src/amuse/community/gadget2/gadget2_worker_cython_nogravity
-src/amuse/community/gadget2/gadget2_worker_cython_normal
-src/amuse/community/gadget2/gadget2_worker_cython_periodic
-src/amuse/community/gadget2/gadget2_worker_cython_periodic_nogravity
-src/amuse/community/gadget2/gadget2_worker_normal
-src/amuse/community/huayno/huayno_worker_cython_mp
-src/amuse/community/sse/sse_c.f90
-src/amuse/community/sse/sse_cython.c
-src/amuse/community/sse/sse_cython.pyx
-src/amuse/community/sse/sse_worker_cython
-src/amuse/community/secularmultiple/worker_code
-src/amuse/community/secularmultiple/worker_code.cc
-
 
 
 
@@ -457,12 +413,6 @@ test_results/interface.f90
 job_server
 plummer_back_100.ini
 pythonexe
-src/amuse/community/evtwin/src/trunk/lib/
-src/amuse/community/mobse/src/mobse
-src/amuse/community/mosse/mosse_c.f90
-src/amuse/community/mosse/mosse_cython.c
-src/amuse/community/mosse/mosse_cython.pyx
-src/amuse/community/mosse/src/mosse
 test/core_tests/test.txt
 test_concurrent
 test_python_sockets_implementation
@@ -483,16 +433,13 @@ test_python_sockets_implementation
 
 .idea
 
-src/amuse/community/bonsai2/src
 doc/interactive_tutorial/_version.py
 src/amuse/test/suite/_version.py
 src/amuse/community/*/_version.py
 src/amuse/_version.py
-src/amuse/community/petar/src
-src/amuse/community/seba/src
 packages/amuse*/dist
 packages/dist
-src/amuse/community/phantom/src
+
 
 # standard directory for a virtualenv
 env/

.readthedocs.yml

@@ -6,6 +6,10 @@
 version: 2
 
 # Build documentation in the docs/ directory with Sphinx
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.7"
 sphinx:
   configuration: doc/conf.py
 
@@ -18,6 +22,5 @@ formats: []
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
   install:
     - requirements: doc/requirements.txt

CITATION.cff

@@ -23,7 +23,7 @@ authors:
     family-names: McMillan
     given-names: Steve
   -
-    affiliation: "Université de Genève"
+    affiliation: "KU Leuven"
     family-names: Rieder
     given-names: Steven
     orcid: "https://orcid.org/0000-0003-3688-5798"

CONTRIBUTING.md

@@ -45,7 +45,7 @@ in the package.
   * Has the code been tested against previously existing codes in the same domain?
 
 **Code Quality**
-  * Is the code compatible with Python >=2.7?
+  * Is the code compatible with Python >=3.7?
   * Are there dependencies other than AMUSE, MPI, the Python Standard
     Library, and NumPy?
   * For compatibility reasons we prefer code that also works on older 

doc/reference/stellar_dynamics_interface_specification.rst

@@ -48,7 +48,7 @@ functions must get or set one scalar property (1 argument) or a vector property
 
 
 .. autoclass:: amuse.community.interface.gd.GravitationalDynamicsInterface
-   :members: get_mass, set_mass, get_position, set_position, set_acceleration, get_acceleration, get_potential
+   :members: get_mass, set_mass, get_position, set_position, get_acceleration, get_potential
 
 
 Model evolution

doc/requirements.txt

@@ -2,4 +2,4 @@ matplotlib
 pandoc
 rst2pdf
 Sphinx>=3.0
-sphinx-rtd-theme==0.5.2
+sphinx-rtd-theme

doc/tutorial/simplegrav/interface_1.cc

@@ -298,8 +298,6 @@ int get_total_radius (double *radius) { return -2; }
 
 int get_acceleration (int index_of_the_particle, double *ax, double *ay, double *az) { return -2; }
 
-int set_acceleration (int index_of_the_particle, double  ax, double  ay, double  az) { return -2; }
-
 int get_potential (int index_of_the_particle, double *potential) { return -2; }
 
 int get_kinetic_energy (double *kinetic_energy) { return -1; }

requirements.txt

@@ -1,8 +1,9 @@
-setuptools>=65
-setuptools_scm>=6
-wheel>=0.30
-docutils>=0.18
-numpy>=1.18
-pytest>=3.0
-mpi4py>=3.0
-h5py>=3.0
+# These are requirements for the AMUSE framework. Other versions *might* be ok.
+setuptools >= 65, < 70
+setuptools_scm >= 6
+wheel >= 0.30
+docutils >= 0.18
+numpy >= 1.18
+pytest >= 3.0
+mpi4py >= 3.0
+h5py >= 3.0

src/amuse/__init__.py

@@ -25,40 +25,49 @@
 or (directly from the terminal):
 > pydoc amuse.ic
 """
+
 import sys
 import os
 import numpy
 
 _AMUSE_ROOT = os.path.abspath(os.path.dirname(__file__))
 
+
 def numpy_fix():
     try:
-        numpy.set_printoptions(legacy='1.13')
+        numpy.set_printoptions(legacy="1.13")
     except TypeError:
         pass
-
+
+
 numpy_fix()
 
-class NoConfig(object):
+
+class NoConfig:
     def __init__(self, message):
-        self._message=message
+        self._message = message
+
     def __getattr__(self, attr):
         raise AttributeError(self._message)
 
+
 try:
     from . import config
-except Exception as ex:
-    message="Configuration not read in - or configuration invalid, exception:\n"+str(ex)
-    config=NoConfig(message)
-
+except FileNotFoundError as ex:
+    message = (
+        "Configuration not read in - or configuration invalid, exception:\n" + str(ex)
+    )
+    config = NoConfig(message)
 
 
 # always report AMUSE reference information
 try:
     from amuse.support.literature import TrackLiteratureReferences
+
     TrackLiteratureReferences.default()
 except:
     pass
 
+
 def get_data(path):
-    return os.path.join(_AMUSE_ROOT, 'data', path)
+    return os.path.join(_AMUSE_ROOT, "data", path)

src/amuse/community/adaptb/interface.cc

@@ -443,5 +443,4 @@ int get_kinetic_energy(double* ek){return -2;}
 int get_potential_energy(double* ep){return -2;}
 int get_center_of_mass_velocity(double* vx, double* vy, double* vz){return -2;}
 int get_acceleration(int id, double* ax, double* ay, double* az){return -2;}
-int set_acceleration(int id, double ax, double ay, double az){return -2;}
 

src/amuse/community/bhtree/interface.cc

@@ -564,12 +564,6 @@ int get_number_of_particles(int *number_of_particles)
   return 0; 
 }
 
-int set_acceleration(int index_of_the_particle, double ax, double ay, double az)
-{
-  return -2;
-}
-
-
 int get_center_of_mass_position(double *x, double *y, double *z)
 {
   nbody_particle *np = bhtcs.get_particle_pointer();