Autobump for `grz-cli` fails #52577

tedil · 2024-12-04T10:33:10Z

I've recently added a recipe for grz-cli and have since released new versions via pypi. However, it seems these changes aren't picked up by bioconda bot / autobump.
Manually triggering bioconda-utils autobump recipes/ config.yml --packages grz-cli leads to the following error:

11:25:24 BIOCONDA INFO Running pipeline with these steps:
11:25:24 BIOCONDA INFO  1. Exclude recipes disabled via config
11:25:24 BIOCONDA INFO  2. Exclude blacklisted recipes
11:25:24 BIOCONDA INFO  3. Exclude sub-recipes
11:25:24 BIOCONDA INFO  4. Exclude recipes depending on packages in need of update
11:25:24 BIOCONDA INFO  5. Load the recipe from the filesystem
11:25:24 BIOCONDA INFO  6. Exclude recipes in conda-forge
11:25:24 BIOCONDA INFO  7. Bump recipes in need of rebuild after pinning changes
11:25:24 BIOCONDA INFO  8. Scan upstream for new releases and update recipe
11:25:24 BIOCONDA INFO  9. Update source checksums
11:25:24 BIOCONDA INFO  10. Write recipe to filesystem
11:25:24 BIOCONDA ERROR Dropping into debugger
Traceback (most recent call last):
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 78, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-19>", line 2, in autobump
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 97, in wrapper
    func(*args, **kwargs)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 1030, in autobump
    scanner.run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 204, in run
    res = super().run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py", line 126, in run
    self.loop.run_until_complete(task)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 225, in _async_run
    return await super()._async_run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py", line 163, in _async_run
    await self.queue_items(source_q, return_q)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 217, in queue_items
    await self.recipe_source.queue_items(send_q, return_q)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 147, in queue_items
    random.shuffle(remaining_recipes)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/random.py", line 394, in shuffle
    x[i], x[j] = x[j], x[i]
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/networkx/classes/reportviews.py", line 194, in __getitem__
    return self._nodes[n]
KeyError: 1
  0%|                                                                                                                                                                                                                                  | 0/2 [00:00<?, ?it/s]
  File "/home/till/.miniforge3/envs/bioconda/bin/bioconda-utils", line 10, in <module>
    sys.exit(main())
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 1124, in main
    argh.dispatch_commands([
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 511, in dispatch_commands
    dispatch(parser, *args, **kwargs)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 199, in dispatch
    return run_endpoint_function(
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 270, in run_endpoint_function
    return _process_command_output(lines, output_file, raw_output, always_flush)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 290, in _process_command_output
    for line in lines:
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 415, in _execute_command
    for line in result:
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/argh/dispatching.py", line 395, in _call
    result = function(*positional_values, **values_by_name)
  File "<boltons.funcutils.FunctionBuilder-22>", line 2, in autobump
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 137, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-21>", line 2, in autobump
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 66, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-20>", line 2, in autobump
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 78, in wrapper
    func(*args, **kwargs)
  File "<boltons.funcutils.FunctionBuilder-19>", line 2, in autobump
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 97, in wrapper
    func(*args, **kwargs)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/cli.py", line 1030, in autobump
    scanner.run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 204, in run
    res = super().run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py", line 126, in run
    self.loop.run_until_complete(task)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/asyncio/base_events.py", line 649, in run_until_complete
    return future.result()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 225, in _async_run
    return await super()._async_run()
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py", line 163, in _async_run
    await self.queue_items(source_q, return_q)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 217, in queue_items
    await self.recipe_source.queue_items(send_q, return_q)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/autobump.py", line 147, in queue_items
    random.shuffle(remaining_recipes)
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/random.py", line 394, in shuffle
    x[i], x[j] = x[j], x[i]
  File "/home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/networkx/classes/reportviews.py", line 194, in __getitem__
    return self._nodes[n]
KeyError: 1
11:25:28 ASYNCIO ERROR Task was destroyed but it is pending!
task: <Task pending name='Task-56' coro=<AsyncPipeline.worker() running at /home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py:188> wait_for=<Future pending cb=[Task.task_wakeup()]>>
[…]  # repeats a couple of times
task: <Task pending name='Task-40' coro=<AsyncPipeline.show_progress() running at /home/till/.miniforge3/envs/bioconda/lib/python3.10/site-packages/bioconda_utils/aiopipe.py:180> wait_for=<Future pending cb=[Task.task_wakeup()]>>

I supect it may have to do with #48971 but the recipe already seems to be using the correct combination of hyphens and underscores.

The text was updated successfully, but these errors were encountered:

tedil · 2025-02-21T14:19:43Z

See also: #961
I believe the problem is that dag.nodes() is a networkx NodeView or similar, which leads to issues with random.shuffle and the node indices. I'll provide a fix.

This should resolve bioconda/bioconda-recipes#52577 and bioconda/bioconda-recipes#961

tedil · 2025-03-19T08:19:04Z

Hm, still fails:

bioconda-utils autobump recipes/ config.yml --packages grz-cli

09:14:15 BIOCONDA INFO Unrecognized URL stats:
09:14:15 BIOCONDA INFO https: 1
09:14:15 BIOCONDA INFO pypi.org: 1
09:14:15 BIOCONDA INFO
09:14:15 BIOCONDA INFO Recipe status statistics:
09:14:15 BIOCONDA INFO NoChanges: 1
09:14:15 BIOCONDA INFO NoRecognizedSourceUrl: 1
09:14:15 BIOCONDA INFO SUM: 2

tedil · 2025-03-19T08:26:34Z

I guess the hoster_patterns in bioconda utils don't match, looking into it

tedil · 2025-04-16T13:33:21Z

Resolved by bioconda/bioconda-utils#1038

This should resolve bioconda/bioconda-recipes#52577 and bioconda/bioconda-recipes#961

tedil added the help wanted label Feb 21, 2025

tedil mentioned this issue Feb 21, 2025

fix: networkx NodeView and random.shuffle incompatible bioconda/bioconda-utils#1035

Merged

bgruening closed this as completed in bioconda/bioconda-utils#1035 Feb 24, 2025

bgruening pushed a commit to bioconda/bioconda-utils that referenced this issue Feb 24, 2025

fix: networkx NodeView and random.shuffle incompatible (#1035)

0127c7f

This should resolve bioconda/bioconda-recipes#52577 and bioconda/bioconda-recipes#961

tedil reopened this Mar 19, 2025

tedil closed this as completed Apr 16, 2025

aliciaaevans pushed a commit to bioconda/bioconda-utils that referenced this issue May 5, 2025

fix: networkx NodeView and random.shuffle incompatible (#1035)

c623d87

This should resolve bioconda/bioconda-recipes#52577 and bioconda/bioconda-recipes#961

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

Autobump for `grz-cli` fails #52577

Autobump for `grz-cli` fails #52577

tedil commented Dec 4, 2024

tedil commented Feb 21, 2025

tedil commented Mar 19, 2025 •

edited

Loading

tedil commented Mar 19, 2025

tedil commented Apr 16, 2025

Autobump for grz-cli fails #52577

Autobump for grz-cli fails #52577

Comments

tedil commented Dec 4, 2024

tedil commented Feb 21, 2025

tedil commented Mar 19, 2025 • edited Loading

tedil commented Mar 19, 2025

tedil commented Apr 16, 2025

Autobump for `grz-cli` fails #52577

Autobump for `grz-cli` fails #52577

tedil commented Mar 19, 2025 •

edited

Loading