Replace examples with those from the second edition of the AMUSE book by rieder · Pull Request #1227 · amusecode/amuse

rieder · 2026-03-10T10:50:34Z

Existing examples are outdated, in some cases not working and often duplicated by others.
This replaces all examples from the "textbook", "syllabus" and "simple" directories with the complete set from the textbook (second edition).

rieder · 2026-03-10T10:54:21Z

To be done:

Some tests may use some of the old examples, so these need to be updated
Add installable package for the examples (they should be installable as "amuse-examples" via pip, at the least - living in the amuse.examples namespace, as this is how they are used in the book).
a file "AMUSE_updates.pdf" needs to be added, as a file containing any errata for the book.
missing / later conceived examples may be added later

rieder · 2026-03-10T10:57:48Z

If we do want to keep (some of) the old examples around, they should be in some directory that makes it clear that these are archived, and not updated. If they are still useful, they should be moved to the new structure.

LourensVeen · 2026-03-10T15:31:10Z

I don't see how the tests would depend on the examples, but I'll go and do a local build and run them all to check.

I think pip packages, the PDF, and more examples should be separate Issues, so if it doesn't break the tests then I'll merge this, even if it isn't perfect I doubt it'll make things worse.

LourensVeen

I've pushed a commit to move the examples to src/amuse_examples and add a forward in src/amuse/examples, and make the whole thing an installable package like the others.

Looking at it again, I think it's probably better to put the actual examples into a subdirectory src/amuse_examples/amuse_examples, so that there's nothing else in the directory. Then we can symlink that to /examples, and if anyone plays with it on the command line then they're less likely to mess up the package definitions.

I've run the tests and this didn't break anything, but then I ran the examples themselves and found many problems, which I've added comments for.

LourensVeen · 2026-03-12T13:24:23Z

src/amuse_examples/2017arXiv170307029H_Fig3.py

Crashes with

File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/2017arXiv170307029H_Fig3.py", line 48, in <module> from distinct_colours import get_distinct ModuleNotFoundError: No module named 'distinct_colours'

LourensVeen · 2026-03-12T13:25:32Z

src/amuse_examples/anim_gravity.py

+
+
+def anim_gravity(filename="sun_venus_earth.amuse", **kwargs):
+    particles = read_set_from_file(filename)


Crashes here because the file is not found:

Traceback (most recent call last): File "<string>", line 1, in <module> from amuse.examples import run ; run('anim_gravity') ~~~^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ~~~~~~~~~~~~^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/anim_gravity.py", line 71, in main anim_gravity(**kwargs) ~~~~~~~~~~~~^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/anim_gravity.py", line 45, in anim_gravity particles = read_set_from_file(filename) File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/io/base.py", line 94, in read_set_from_file raise IoException("Error: file '{0}' does not exist.".format(filename)) amuse.io.base.IoException: IO exception: Error: file 'sun_venus_earth.amuse' does not exist.

Ah, I think this is actually produced by one of the other examples, so you need to run them in the right order, which likely isn't alphabetical.

LourensVeen · 2026-03-12T13:27:46Z

src/amuse_examples/cooling_class.py

Fails to run using amuse.examples.run:

File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ^^^^^^^^^^^^ AttributeError: module 'amuse_examples.cooling_class' has no attribute 'main'

LourensVeen · 2026-03-12T13:30:14Z

src/amuse_examples/gravity_hydro.py

Fails to run using amuse.examples.run:

File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ^^^^^^^^^^^^ AttributeError: module 'amuse_examples.gravity_hydro' has no attribute 'main'

LourensVeen · 2026-03-12T13:32:58Z

src/amuse_examples/gravity_stellar_minimal.py

Fails to run using amuse.examples.run:

Traceback (most recent call last): File "<string>", line 1, in <module> from amuse.examples import run ; run('gravity_stellar_minimal') ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ~~~~~~~~~~~~^^ TypeError: main() missing 1 required positional argument: 'args'

LourensVeen · 2026-03-12T14:11:54Z

src/amuse_examples/star_to_sph.py

Fails to run using amuse.examples.run because it has no main() function.

LourensVeen · 2026-03-12T14:19:02Z

src/amuse_examples/supernova_grid.py

Won't run using amuse.examples.run:

Traceback (most recent call last): File "<string>", line 1, in <module> from amuse.examples import run ; run('supernova_grid') ~~~^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ~~~~~~~~~~~~^^ TypeError: main() missing 7 required positional arguments: 'stellar_mass', 'stellar_radius', 'core_mass', 'core_radius', 't_end', 'dt', and 'resolution'

LourensVeen · 2026-03-12T14:19:30Z

src/amuse_examples/supernova_sph.py

Fails because prepare_figure is missing.

LourensVeen · 2026-03-12T14:21:35Z

src/amuse_examples/three_body_bridge_order4m4.py

Crashes because we need to explicitly append to a file now:

Traceback (most recent call last): File "<string>", line 1, in <module> from amuse.examples import run ; run("three_body_bridge_order4m4") ~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/__init__.py", line 55, in run example.main() ~~~~~~~~~~~~^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse_examples/three_body_bridge_order4m4.py", line 76, in main write_set_to_file(ss.savepoint(time), filename, 'hdf5', version='2') ~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/io/base.py", line 75, in write_set_to_file processor.store() ~~~~~~~~~~~~~~~^^ File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/io/store.py", line 99, in store processor = store_v2.StoreHDF( self.filename, ...<4 lines>... compression_opts=self.compression_opts ) File "/home/lourens/.miniconda3/envs/amuse-pr-1227/lib/python3.14/site-packages/amuse/io/store_v2.py", line 738, in __init__ raise FileExistsError("Opening file for write with overwrite_file is False but file {0} exists".format(filename)) FileExistsError: Opening file for write with overwrite_file is False but file SunAndEarthAndMoon_TBB.h5 exists

LourensVeen · 2026-03-12T14:22:19Z

src/amuse_examples/tres_minimal.py

@@ -0,0 +1,55 @@
+from amuse.units import units
+from amuse.community.seba import Seba
+from seculartriple_tps import Seculartriple


seculartriple_tps is missing.

rieder added 5 commits March 10, 2026 11:41

Remove old examples

012cc51

Remove old examples

b8f821b

remove data from old example

810d6a6

Remove old examples

ff0216e

Add new examples

9d930ad

rieder requested a review from a team as a code owner March 10, 2026 10:50

github-project-automation bot added this to Development Board Mar 10, 2026

github-project-automation bot moved this to Backlog in Development Board Mar 10, 2026

rieder added 2 commits March 10, 2026 12:02

remove more old examples

546e2a7

Further simplify and remove old examples

89f45c2

Create amuse_examples package and forwards from amuse.examples

28b8cda

LourensVeen force-pushed the examples_book_v2 branch from 5d45632 to 28b8cda Compare March 12, 2026 13:22

LourensVeen requested changes Mar 12, 2026

View reviewed changes

github-project-automation bot moved this from Backlog to Open PRs in Development Board Mar 12, 2026

LourensVeen mentioned this pull request Mar 12, 2026

Update Galaxia names and fix examples #1223

Merged



		def anim_gravity(filename="sun_venus_earth.amuse", **kwargs):
		particles = read_set_from_file(filename)

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rieder commented Mar 10, 2026

Uh oh!

rieder commented Mar 10, 2026

Uh oh!

rieder commented Mar 10, 2026

Uh oh!

LourensVeen commented Mar 10, 2026

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