BUG: fix circular imports in bowtie/contig

[ebolyen]

Lets the format load before registration.

Also use the init exclusively for loading subpackages.

[ebolyen]

Should fix https://github.com/qiime2/distributions/actions/runs/8237435747/job/22623143164?pr=157

QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment.
Traceback (most recent call last):
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/util.py", line 279, in get_plugin_manager
    return qiime2.sdk.PluginManager.reuse_existing()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 58, in reuse_existing
    raise UninitializedPluginManagerError
qiime2.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/runner/work/distributions/distributions/test-env/bin/qiime", line 11, in <module>
    sys.exit(qiime())
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 1157, in __call__
    return self.main(*args, **kwargs)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 1077, in main
    with self.make_context(prog_name, args, **extra) as ctx:
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 943, in make_context
    self.parse_args(ctx, args)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/click/command.py", line 43, in parse_args
    return super().parse_args(ctx, args)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 1641, in parse_args
    echo(ctx.get_help(), color=ctx.color)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 704, in get_help
    return self.command.get_help(self)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 1325, in get_help
    self.format_help(ctx, formatter)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/click/core.py", line 1358, in format_help
    self.format_options(ctx, formatter)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/click/command.py", line 157, in format_options
    for subcommand in self.list_commands(ctx):
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/commands.py", line 92, in list_commands
    plugins = sorted(self._plugin_lookup)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
    import q2cli.core.cache
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/core/cache.py", line 285, in <module>
    CACHE = DeploymentCache()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/core/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/core/cache.py", line 205, in _cache_current_state
    state = self._get_current_state()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/core/cache.py", line 253, in _get_current_state
    plugin_manager = q2cli.util.get_plugin_manager()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2cli/util.py", line 291, in get_plugin_manager
    return qiime2.sdk.PluginManager()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 67, in __new__
    self._init(add_plugins=add_plugins)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/qiime2/sdk/plugin_manager.py", line 105, in _init
    plugin = entry_point.load()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2482, in load
    return self.resolve()
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/pkg_resources/__init__.py", line 2488, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_assembly/__init__.py", line 10, in <module>
    from .bowtie2 import indexing, mapping
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_assembly/bowtie2/__init__.py", line 9, in <module>
    from .indexing import index_contigs, index_mags
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_assembly/bowtie2/indexing.py", line 13, in <module>
    from q2_types.bowtie2 import Bowtie2IndexDirFmt
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/__init__.py", line 18, in <module>
    importlib.import_module('q2_types.multiplexed_sequences')
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/multiplexed_sequences/__init__.py", line 11, in <module>
    from ._format import (MultiplexedSingleEndBarcodeInSequenceDirFmt,
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/multiplexed_sequences/_format.py", line 11, in <module>
    from ..per_sample_sequences import FastqGzFormat
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/per_sample_sequences/__init__.py", line 11, in <module>
    from ._format import (CasavaOneEightSingleLanePerSampleDirFmt,
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/per_sample_sequences/_format.py", line 25, in <module>
    from q2_types.bowtie2 import Bowtie2IndexDirFmt
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/bowtie2/__init__.py", line 9, in <module>
    from ._formats import (Bowtie2IndexFileFormat, Bowtie2IndexDirFmt)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/bowtie2/_formats.py", line 12, in <module>
    from ..plugin_setup import plugin, citations
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/plugin_setup.py", line 41, in <module>
    importlib.import_module('q2_types.feature_data_mag')
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/importlib/__init__.py", line 127, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/feature_data_mag/__init__.py", line 17, in <module>
    from ._type import MAG, NOG, OG, KEGG, Contig
  File "/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/feature_data_mag/_type.py", line 16, in <module>
    from ..per_sample_sequences import ContigSequencesDirFmt
ImportError: cannot import name 'ContigSequencesDirFmt' from partially initialized module 'q2_types.per_sample_sequences' (most likely due to a circular import) (/home/runner/work/distributions/distributions/test-env/lib/python3.8/site-packages/q2_types/per_sample_sequences/__init__.py)