Merge branch 'main' into update/petar_binary_reporting

.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

.github/workflows/ci.yml

@@ -33,7 +33,7 @@ jobs:
     steps:
 
     - name: Checkout
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
 
     - name: Setup MPI
       id:   setup-mpi
@@ -53,13 +53,13 @@ jobs:
       if:   ${{ matrix.mpi == 'openmpi' }}
 
     - name: Set up JDK 1.8
-      uses: actions/setup-java@v3.9.0
+      uses: actions/setup-java@v4
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: '17'
 
     - name: Set up Python
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
         cache: 'pip'
@@ -89,11 +89,14 @@ jobs:
         amusifier --get-amuse-configmk
         pip list
 
+    - name: move build log
+      run: |
+        mv build.log build-${{ matrix.mpi }}-${{ matrix.python }}.log
     - name: archive build log
-      uses: actions/upload-artifact@v3.1.1
+      uses: actions/upload-artifact@v4
       with:
-          name: buildlog
-          path: build.log
+          name: buildlog-${{ matrix.mpi }}-${{ matrix.python }}
+          path: build-${{ matrix.mpi }}-${{ matrix.python }}.log
 
     - name: test core_tests
       run: |

.github/workflows/community-seba.yml

@@ -21,18 +21,18 @@ jobs:
         java-version: [ '17' ]
     name: Test AMUSE with ${{ matrix.mpi }}
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Setup MPI
       uses: mpi4py/setup-mpi@v1
       with:
         mpi: ${{ matrix.mpi }}
     - name: Set up JDK ${{ matrix.java-version }}
-      uses: actions/setup-java@v3.9.0
+      uses: actions/setup-java@v4
       with:
         distribution: 'zulu' # See 'Supported distributions' for available options
         java-version: ${{ matrix.java-version }}
     - name: Set up Python ${{ matrix.python }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python }}
     - name: Install dependencies
@@ -54,11 +54,14 @@ jobs:
       run: |
         amusifier --get-amuse-configmk
         pip list
+    - name: move build log
+      run: |
+        mv build.log build-${{ matrix.mpi }}-${{ matrix.python }}.log
     - name: archive build log
-      uses: actions/upload-artifact@v3.1.1
+      uses: actions/upload-artifact@v4
       with:
-          name: buildlog
-          path: build.log
+          name: buildlog-${{ matrix.python }}-${{ matrix.mpi }}
+          path: build-${{ matrix.mpi }}-${{ matrix.python }}.log
     - name: test seba
       run: |
         pytest --pyargs amuse.test.suite.codes_tests.test_seba -sv

.github/workflows/lint.yml

@@ -15,10 +15,10 @@ jobs:
 
     steps:
       - name: Check out Git repository
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

packages/amuse-hermite-grx/MANIFEST.in

@@ -0,0 +1,9 @@
+include support/__init__.py
+include support/setup_codes.py
+include support/version.py
+include support/classifiers.py
+include pyproject.toml
+
+recursive-include src *
+recursive-exclude src *.pyc *.o *~ .pc ccache *.a
+

packages/amuse-hermite-grx/README.md

@@ -0,0 +1 @@
+This package installs the Hermite-GRX community code for AMUSE.

packages/amuse-hermite-grx/pyproject.toml

@@ -0,0 +1,2 @@
+[build-system]
+requires = ["setuptools>=65.0.0", "wheel>=0.30", "amuse-framework>=2024.3.0"]

packages/amuse-hermite-grx/setup.py

@@ -0,0 +1,65 @@
+#!/usr/bin/env python3
+from support.classifiers import classifiers
+
+from setuptools import setup
+
+import support
+support.use("system")
+from support.setup_codes import setup_commands
+
+name = 'amuse-hermite-grx'
+author = 'The AMUSE team'
+author_email = '[email protected]'
+license_ = "Apache License 2.0"
+url = 'http://www.amusecode.org/'
+install_requires = [
+    'amuse-framework',
+]
+description = 'The Astrophysical Multipurpose Software Environment - Hermite-GRX'
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+long_description_content_type = "text/markdown"
+
+extensions = []
+
+all_data_files = []
+
+packages = [
+    'amuse.community.hermite_grx',
+]
+
+package_data = {
+}
+
+mapping_from_command_name_to_command_class = setup_commands()
+
+setup_requires = ['setuptools_scm']
+use_scm_version = {
+    "root": "../..",
+    "relative_to": __file__,
+    "version_file": "src/amuse/community/hermite_grx/_version.py",
+}
+
+setup(
+    name=name,
+    use_scm_version=use_scm_version,
+    setup_requires=setup_requires,
+    classifiers=classifiers,
+    url=url,
+    author_email=author_email,
+    author=author,
+    license=license_,
+    description=description,
+    long_description=long_description,
+    long_description_content_type=long_description_content_type,
+    install_requires=install_requires,
+    python_requires=">=3.7",
+    cmdclass=mapping_from_command_name_to_command_class,
+    ext_modules=extensions,
+    package_dir={
+        'amuse.community.hermite_grx': 'src/amuse/community/hermite_grx',
+    },
+    packages=packages,
+    package_data=package_data,
+    data_files=all_data_files,
+)

packages/amuse-hermite-grx/src/amuse/community/hermite_grx

@@ -0,0 +1 @@
+../../../../../src/amuse/community/hermite_grx

packages/amuse-hermite-grx/support

@@ -0,0 +1 @@
+../../support

src/amuse/community/hermite_grx/__init__.py

@@ -1 +1 @@
-# generated file
+from .interface import Hermitegrx

src/amuse/community/hermite_grx/interface.py

@@ -3,7 +3,7 @@
 from amuse.community.interface.stopping_conditions import *
 
 
-class HermiteGRXInterface(
+class HermitegrxInterface(
     CodeInterface, GravitationalDynamicsInterface, StoppingConditionInterface
 ):
     include_headers = ["worker_code.h", "stopcond.h"]
@@ -423,11 +423,11 @@ def set_jerk():
         return function
 
 
-class HermiteGRX(GravitationalDynamics):
+class Hermitegrx(GravitationalDynamics):
     def __init__(self, convert_nbody=None, **options):
         self.stopping_conditions = StoppingConditions(self)
 
-        legacy_interface = HermiteGRXInterface(**options)
+        legacy_interface = HermitegrxInterface(**options)
         GravitationalDynamics.__init__(self, legacy_interface, convert_nbody, **options)
 
     def define_state(self, object):
@@ -597,3 +597,8 @@ def define_particle_sets(self, object):
         object.add_getter("small_particles", "get_jerk")
 
         self.stopping_conditions.define_particle_set(object)
+
+
+# for backwards compatibility reasons
+HermiteGRXInterface = HermitegrxInterface
+HermiteGRX = Hermitegrx

src/amuse/community/seba/interface.cc

@@ -844,6 +844,10 @@ int get_number_of_particles(int * number_of_particles){
 int evolve_system(double end_time) {
     int n_steps = 1;
     int n_steps_per_phase = 10;
+    // cannot evolve for a negative time
+    if (end_time < seba_time) {
+	return 0;
+    }
     real delta_t = (end_time - seba_time)/((real)n_steps);
     real out_time; 
     nodeptr bi;

src/amuse/ext/solarsystem.py

@@ -324,17 +324,20 @@ def new_solar_system(Julian_date=-1|units.day):
     else:
         return solar_system_in_time(Julian_date)
 
-def new_option_parser():
-    from amuse.units.optparse import OptionParser
-    result = OptionParser()
-    result.add_option("-d", dest="Julian_date", unit=units.day,
-                      type=float, default = 2438871.5|units.day,
-                      help="julian date [%default]")
+def new_argument_parser():
+    import argparse
+    result = argparse.ArgumentParser(
+        formatter_class=argparse.ArgumentDefaultsHelpFormatter,
+    )
+    result.add_argument(
+        "-d", dest="Julian_date", unit=units.day,
+        type=units.day, default=2438871.5 | units.day,
+        help="julian date"
+    )
     return result
 
-if __name__ in ('__main__', '__plot__'):
-  o, arguments  = new_option_parser().parse_args()
-  solar_system = new_solar_system(o.Julian_date)
-  print(solar_system)
-
 
+if __name__ == '__main__':
+    arguments = new_argument_parser().parse_args()
+    solar_system = new_solar_system(arguments.Julian_date)
+    print(solar_system)