- Convert release Makefile targets to a script
- Update package versions from Galaxy version instead of leaving them
uncoupled
- Use next-dev-version process on release branches when in between point
releases
- Automatically detect and increment versions
- Test merging release branches forward before pushing releases
- Support multiple rc versions (will be more useful for package testing)
- Support building local versions of packages
- Tests for the release script
Fix the following error when running `tox -e test_galaxy_packages` on
Python 3.5:
```
ERROR: Could not find a version that satisfies the requirement networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0) (from versions: 0.34, 0.35, 0.35.1, 0.36, 0.37, 0.99, 1.0rc1, 1.0, 1.0.1, 1.1, 1.2rc1, 1.2, 1.3rc1, 1.3, 1.4rc1, 1.4, 1.5rc1, 1.5, 1.6rc1, 1.6, 1.7rc1, 1.7, 1.8rc1, 1.8, 1.8.1, 1.9rc1, 1.9, 1.9.1, 1.10rc2, 1.10, 1.11rc1, 1.11rc2, 1.11, 2.0, 2.1, 2.2rc1, 2.2, 2.3rc3, 2.3rc4, 2.3, 2.4rc1, 2.4rc2, 2.4)
ERROR: No matching distribution found for networkx==2.5 (from isa-rwval->galaxy-data==20.9.1.dev0)
WARNING: You are using pip version 20.2.2; however, version 20.3.4 is available.
You should consider upgrading via the '/tmp/gxpkgtestenviQxuK1/bin/python -m pip install --upgrade pip' command.
ERROR: InvocationError for command /bin/bash packages/test.sh (exited with code 1)
___________________________________ summary ____________________________________
ERROR: test_galaxy_packages: commands failed
```
Dependency injection is cool - it should however not be confined to the top-layer of the application. Inversion of control can help every layer and is a great way to de-couple various parts of the app.
This code brings in a framework (Lagom) to build a dependency injection framework and then adds a small function (``depends``) that adapts it to FastAPI's dependency injection mechanism ("Depends").
The advantages to this approach are numerous.
We don't need to write these little adapters for each component of the backend to adapt it FastAPI. For example look at the change to the roles API controller:
```diff
-def get_role_manager(app: UniverseApplication = Depends(get_app)) -> RoleManager:
- return app.role_manager
-
-
@cbv(router)
class FastAPIRoles:
- role_manager: RoleManager = Depends(get_role_manager)
+ role_manager: RoleManager = depends(RoleManager)
```
This is much less boilerplate. We don't need to implement & type that function get_role_manager and we don't need to bring in the import on UniverseApplication.
Additionally, we've got a clean abstraction that shields us from ``fastapi`` imports in all of our controllers. It should make it more possible to switch to new frameworks and such as the Python ecosystem matures.
Also, the same DI that is used to inject ``RoleManager`` into this contoller is used to inject app into RoleManager when it is constructed during application initialization. Any component being managed by UniverseApplication can now rely on its constructor arguments to be injected if it wants. It is easy to see the cool examples on FastAPI and think it is just a technology for controllers, but it totally is not.
I don't think there is really a way to use FastAPI's dependency injection outside the context of that framework, but even if one could Lagom is superior. All the auto-wiring is by type and requires zero framework and zero configuration (https://github.com/meadsteve/lagom#auto-wiring-with-zero-configuraton).
Having a web framework provide these framework-bound extension points for injecting stuff into controllers was the state of the art of Java like 15 years ago. Skipping that whole learning process and using the type system and auto-wiring that isn't dependent on framework annotation really jumps out to Java circa 8 years ago!
Why Lagom is an interesting question. When researching DI frameworks, I couldn't find a clear winner but Lagom focus on type annotations versus annotating by name makes it clearly more modern than a lot frameworks by much bigger names (https://github.com/meadsteve/lagom/blob/master/docs/comparison.md). The other type-centric framework that had even a nice interface that I found was punq (https://punq.readthedocs.io/en/latest/). The development just doesn't seem as active on punq. While I didn't land up using the integration Lagom seems to have async frameworks in mind (https://github.com/meadsteve/lagom/blob/master/lagom/integrations/fast_api.py), so that is another plus. Ultimately though I think I can swap between these two with like 10 lines of code switch, they do cool things with very simple interfaces and neither requires a bunch of investment in annotation on your components.
I'm still seeing errors in some places, and just changing everything to
SimpleJSON seems a bit risky at this point.
We'll have to live with
```
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/registry.py", line 590, in change_datatype
data.init_meta(copy_from=data)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/__init__.py", line 2783, in init_meta
return self.datatype.init_meta(self, copy_from=copy_from)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/datatypes/data.py", line 171, in init_meta
dataset.metadata = copy_from.metadata
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/__init__.py", line 2705, in set_metadata
self._metadata = self.metadata.make_dict_copy(bunch)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/metadata.py", line 161, in make_dict_copy
rval[key] = self.spec[key].param.make_copy(value, target_context=self, source_context=to_copy)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/metadata.py", line 281, in make_copy
return copy.deepcopy(value)
File "/cvmfs/main.galaxyproject.org/deps/_conda/envs/_galaxy_/lib/python3.6/copy.py", line 161, in deepcopy
y = copier(memo)
File "/cvmfs/main.galaxyproject.org/galaxy/lib/galaxy/model/custom_types.py", line 232, in __deepcopy__
return MutationList(MutationObj.coerce(self._key, copy.deepcopy(self[:])))
AttributeError: 'MutationList' object has no attribute '_key'
```
for now.
Marius van den Beek