opensource/galaxy
3
0
Fork 0
mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00
Code Issues Packages Projects Releases Wiki Activity
77,490 Commits 62 Branches 243 Tags
db7395b42378fe8aec00a5d25e452e033bc19164
Commit Graph
857 Commits
Author SHA1 Message Date
Marius van den BeekandNicola Soranzo cb24832617 Adapt project boilerplate 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-03-01 16:50:06 +01:00
mvdbeek 6b2045203e Package version.py 2022-03-01 15:39:47 +01:00
mvdbeek 2fab58cac4 Create config package 2022-03-01 15:39:46 +01:00
Nicola Soranzo 4a31207701 Merge branch 'release_22.01' into dev 2022-02-28 20:21:56 +00:00
mvdbeek 400922a5a4 Drop pkg_resources 2022-02-28 14:07:08 +01:00
Nicola Soranzo f8bd5d4bea Merge branch 'release_22.01' into dev 2022-02-21 17:00:55 +00:00
Nicola Soranzo 5d7f94ef2f Simplify package testing code 2022-02-18 16:00:11 +00:00
Nicola Soranzo 22bcef6342 Test the webapps package 
Also:
- Remove redundant `galaxy.schema` module from the `app` package (it's
  already in `data`)
- Fix requirements of the `app` and `webapps` packages
- Add missing `PyJWT` and `python-dateutil` to `tool.poetry.dependencies`
  (which were already included in the pinned requirements as deps of deps)
 2022-02-17 19:50:40 +00:00
mvdbeek 61dab21990 Use a2wsgi to serve WSGI app 
instead of the deprecated starlette WSGIMiddleware that was vendored by
fastAPI. I'm also hoping this fixes the weird exceptions a la:
```
uvicorn.error ERROR 2022-02-14 11:59:42,141 [pN:main,p:4823,tN:Thread-216] Exception in ASGI application
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/uvicorn/protocols/http/h11_impl.py", line 364, in run_asgi
    result = await app(self.scope, self.receive, self.send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/uvicorn/middleware/proxy_headers.py", line 75, in __call__
    return await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/fastapi/applications.py", line 212, in __call__
    await super().__call__(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 656, in __call__
    await route.handle(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 408, in handle
    await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/fastapi/applications.py", line 212, in __call__
    await super().__call__(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/applications.py", line 112, in __call__
    await self.middleware_stack(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/errors.py", line 159, in __call__
    await self.app(scope, receive, _send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette_context/middleware/raw_middleware.py", line 96, in __call__
    await self.app(scope, receive, send_wrapper)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/base.py", line 65, in __call__
    task_group.cancel_scope.cancel()
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 574, in __aexit__
    raise exceptions[0]
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 611, in _run_wrapped_task
    await coro
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/base.py", line 34, in coro
    await self.app(scope, request.receive, send_stream.send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 71, in __call__
    await self.app(scope, receive, sender)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 656, in __call__
    await route.handle(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/routing.py", line 408, in handle
    await self.app(scope, receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 64, in __call__
    await responder(receive, send)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 91, in __call__
    await anyio.to_thread.run_sync(self.wsgi, environ, self.start_response)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 572, in __aexit__
    raise ExceptionGroup(exceptions)
anyio._backends._asyncio.ExceptionGroup: 2 exceptions were raised in the task group:
----------------------------
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 611, in _run_wrapped_task
    await coro
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 98, in sender
    await send(message)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/exceptions.py", line 68, in sender
    await send(message)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 193, in send
    self.send_nowait(item)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 177, in send_nowait
    raise BrokenResourceError
anyio.BrokenResourceError
----------------------------
Traceback (most recent call last):
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 91, in __call__
    await anyio.to_thread.run_sync(self.wsgi, environ, self.start_response)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/to_thread.py", line 29, in run_sync
    limiter=limiter)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 818, in run_sync_in_worker_thread
    return await future
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 754, in run
    result = context.run(func, *args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/starlette/middleware/wsgi.py", line 132, in wsgi
    self.stream_send.send, {"type": "http.response.body", "body": b""}
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/from_thread.py", line 35, in run
    return asynclib.run_async_from_thread(func, *args)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/_backends/_asyncio.py", line 847, in run_async_from_thread
    return f.result()
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/concurrent/futures/_base.py", line 435, in result
    return self.__get_result()
  File "/opt/hostedtoolcache/Python/3.7.12/x64/lib/python3.7/concurrent/futures/_base.py", line 384, in __get_result
    raise self._exception
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 193, in send
    self.send_nowait(item)
  File "/home/runner/work/galaxy/galaxy/galaxy root/.venv/lib/python3.7/site-packages/anyio/streams/memory.py", line 177, in send_nowait
    raise BrokenResourceError
anyio.BrokenResourceError
```
 2022-02-17 09:36:26 +01:00
Nicola Soranzo 6057338cbd Format files in packages/ with black 
with:

```
find packages/ -name '*.py' | xargs black
```

The `packages/` directory is currently excluded in the `[tool.black]`
section of `pyproject.toml` because black follows symlinks.
 2022-02-03 14:07:52 +00:00
Dannon Baker 623a5e165a Apply black formatting. 
Apply isort.
 2022-02-03 07:42:20 -05:00
Nicola Soranzo 04ef6387c5 Merge branch 'release_22.01' into dev 2022-02-01 13:59:11 +00:00
Nicola Soranzo ec3d7fc3e3 Merge pull request #13281 from mvdbeek/drop_openid_post_authentication_protocols 2022-02-01 13:57:32 +00:00
mvdbeek 0af72e56b2 Update version to 22.05.dev0 2022-02-01 11:10:56 +01:00
mvdbeek 917dbe718c Update version to 22.01.rc1 2022-02-01 11:07:22 +01:00
mvdbeek d0fb11c015 Drop OpenID post authentication protocols 2022-02-01 11:04:48 +01:00
mvdbeek f0baddd905 Merge branch 'release_21.09' into dev 2022-01-21 16:38:36 +01:00
Nicola Soranzo da47f8e844 Simplify PACKAGE_DATA 2022-01-19 18:35:06 +00:00
Marius van den BeekandNicola Soranzo 6fb840f361 Update manifest for new schema location 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-19 18:20:18 +00:00
mvdbeek 03e218df68 Fix config schema packaging 2022-01-19 18:20:16 +00:00
mvdbeek d3cfb72266 Use importlib_resources 2022-01-19 18:20:16 +00:00
mvdbeek d5b31ee55a Fix tool id not getting updated on tool update 2022-01-19 14:46:31 +01:00
Marius van den BeekandNicola Soranzo 7013f1364b Add whoish to webapps requirements 
Co-authored-by: Nicola Soranzo <nicola.soranzo@gmail.com>
 2022-01-10 20:08:24 +01:00
mvdbeek e0f24c1591 Add more required dependencies for installed Galaxy 2022-01-10 18:47:39 +01:00
Nicola Soranzo b9efe433e6 Fix pydantic requirements 2022-01-06 19:21:17 +00:00
Nicola Soranzo a013c30e0a Disallow paramiko 2.9.0 and 2.9.1 
Fix `paramiko.ssh_exception.SSHException: encountered RSA key, expected OPENSSH key`
error, which is due to https://github.com/paramiko/paramiko/issues/1961 .
 2022-01-06 19:21:16 +00:00
Nicola Soranzo 8fbecfefff Disallow also fastapi 0.70.1 2022-01-06 19:21:15 +00:00
Sergey Golitsynskiy bf58b5cc30 Merge pull request #13099 from ic4f/dev_migratetools 
Drop tool migration scripts and related code
 2021-12-21 14:35:35 -05:00
Sergey Golitsynskiy af270403c0 Fix packages test: do not import deleted packages 2021-12-21 10:54:28 -05:00
Nuwan Goonasekera d1f804921c Add support for anonymous gcs file source access 2021-12-20 11:08:42 +05:30
Simon Bray 7176e109d9 add mulled-hash command to galaxy-tool-util 2021-12-14 21:27:51 +01:00
Nicola Soranzo 0bdc93a7cc Drop support for Python 3.6, add Python 3.10 2021-12-08 08:14:10 +00:00
Marius van den Beek c00ed6f7a0 Merge pull request #13011 from nsoranzo/fix_job_env_vars 
Don't pass all Galaxy environment variables to jobs
 2021-12-06 20:37:53 +01:00
Nicola Soranzo eea0c8b673 Update pulsar-galaxy-lib to 0.14.13 and enable assert for EmbeddedPulsarDefaultJobEnvironmentIntegrationTestCase 2021-12-06 17:45:58 +00:00
Nicola Soranzo 40b9dee2ea Don't skip and fix TestCliInterface unit tests in app package 2021-12-06 17:32:31 +00:00
mvdbeek 1c370ccd8f Fix package modules 2021-11-29 11:22:43 +01:00
Nicola Soranzo a37bdfd42f Merge branch 'release_21.09' into dev 2021-11-25 16:30:56 +00:00
Islam Heggy cde79eef33 Update social-auth-core library version to fix OIDC problem 2021-11-24 05:00:28 +02:00
Nicola Soranzo a65d8fade9 Add missing typing-extensions requirement 
to `pyproject.toml` and packages' `requirements.txt` .

We have been importing it explicitly since commit
fc2ce45767 (December 2020).

Also:
- Remove now unnecessary minimum version for pygithub
 2021-11-24 01:09:49 +00:00
Nicola Soranzo 1f8ac6c7bb Merge pull request #12965 from common-workflow-lab/type_ignore_narrow 
tighten type ignores
 2021-11-23 16:32:28 +00:00
Nicola Soranzo 30337fbd94 Merge branch 'release_21.09' into dev 2021-11-23 13:30:36 +00:00
mvdbeek 512526a5f5 Version 21.9.2 of tool-util (tag galaxy-tool-util-21.9.2). 2021-11-23 13:54:07 +01:00
Michael R. Crusoe 7819fdc7a6 tighten type ignores 2021-11-23 13:12:07 +01:00
Nicola Soranzo 82a45e1544 Sync package deps with pyproject.toml 
Fix resulting mypy issues.
 2021-11-11 14:46:51 +01:00
Nicola Soranzo 155f3731c3 Remove leftover six requirement from 3 packages 2021-11-10 02:34:47 +01:00
Nicola Soranzo cf5afe67cd Add a cwl extras to galaxy-tool-util with cwltool as dependency 
Also:
- Don't install `util` and `tool-util` packages twice in `packages/test.sh`
 2021-11-09 14:40:46 +01:00
Nicola Soranzo 8f9cfe8168 Add galaxy-data dependency to galaxy-app package 
E.g. `app.py` imports `galaxy.model`
 2021-11-09 14:39:24 +01:00
mvdbeek f04632e0f1 Merge branch 'release_21.09' into dev 2021-11-03 16:16:42 +01:00
mvdbeek 2bda35b55e Version 21.9.1 of tool-util (tag galaxy-tool-util-21.9.1). 2021-11-03 09:52:35 +01:00
mvdbeek 6b29202be6 Update version to 21.09. 2021-11-02 12:08:02 +01:00