empress and rachis-qiime2-2026.7

[ARW-UBT]

Hello,
I have experience some issues after adding empress to the most recent qiime2 release via pip install empress

Building wheels for collected packages: empress
  Building wheel for empress (pyproject.toml) ... done
  Created wheel for empress: filename=empress-1.2.0-py3-none-any.whl size=295022 sha256=993ec9754173cad02b63c167fd0997877b9286dc27a843bbb088337791dcb1aa
  Stored in directory: /home/bt140047/.cache/pip/wheels/60/63/14/2bfe3b8deac71153ebbf96f464dc40677f9789fbb6709a639a
Successfully built empress
Installing collected packages: cython, empress
Successfully installed cython-3.3.0 empress-1.2.0

Although it seems to be ok, the `qiime dev refresh-cache `command results in this error messages: 

Although it seems to be ok, the qiime dev refresh-cache command results in this error messages:

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/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/util.py", line 277, in get_plugin_manager
    return qiime2.sdk.PluginManager.reuse_existing()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 64, in reuse_existing
    raise UninitializedPluginManagerError
rachis.sdk.plugin_manager.UninitializedPluginManagerError

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/bin/qiime", line 11, in <module>
    sys.exit(qiime())
             ^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/click/core.py", line 1161, in __call__
    return self.main(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/click/core.py", line 1082, in main
    rv = self.invoke(ctx)
         ^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/click/core.py", line 1691, in invoke
    cmd_name, cmd, args = self.resolve_command(ctx, args)
                          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/click/core.py", line 1738, in resolve_command
    cmd = self.get_command(ctx, cmd_name)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/commands.py", line 100, in get_command
    plugin = self._plugin_lookup[name]
             ^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/commands.py", line 76, in _plugin_lookup
    import q2cli.core.cache
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/core/cache.py", line 276, in <module>
    CACHE = DeploymentCache()
            ^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/core/cache.py", line 61, in __init__
    self._state = self._get_cached_state(refresh=refresh)
                  ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/core/cache.py", line 107, in _get_cached_state
    self._cache_current_state(current_requirements)
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/core/cache.py", line 196, in _cache_current_state
    state = self._get_current_state()
            ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/core/cache.py", line 244, in _get_current_state
    plugin_manager = q2cli.util.get_plugin_manager()
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/q2cli/util.py", line 289, in get_plugin_manager
    return qiime2.sdk.PluginManager()
           ^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 73, in __new__
    self._init(add_plugins=add_plugins)
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/rachis/sdk/plugin_manager.py", line 111, in _init
    plugin = entry_point.load()
             ^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/importlib/metadata/__init__.py", line 205, in load
    module = import_module(match.group('module'))
             ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/importlib/__init__.py", line 90, in import_module
    return _bootstrap._gcd_import(name[level:], package, level)
           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/empress/__init__.py", line 9, in <module>
    from empress.core import Empress
  File "/home/bt140047/miniconda3/envs/rachis-qiime2-2026.7/lib/python3.12/site-packages/empress/core.py", line 19, in <module>
    import pkg_resources
ModuleNotFoundError: No module named 'pkg_resources'

I found out that downgrading setuptools to 80.x causes tomlkit to be downgraded to 0.13 (rachis-qiime2-2026.7 has 0.15.1).
However, empress works now as expected, but I am wondering whether I do introduce other issues to the rachis-qiime2 release.

My idea was to install empress in a rachis-tiny env, but the latest release also has tomlkit 0.15.1 installed. As I would not use the tiny env for the other qiime2 analysis steps, I am wondering whether it would be safe to use empress and tomlkit 0.13 via a separate tiny environment.

Best regards

[fedarko]

Thanks for reporting this! It looks like pkg_resources is no longer supported with newer versions of setuptools -- see setuptools docs and some discussion.

Fortunately, Empress is not really using pkg_resources for all that much -- just (1) figuring out the current version and (2) figuring out where its support_files/ directory is stored:

$ rg -i "pkg_resources" empress*
  empress/plugin_setup.py
    21:import pkg_resources
    22:__version__ = pkg_resources.get_distribution('empress').version  # noqa
  
  empress/core.py
    19:import pkg_resources
    27:SUPPORT_FILES = pkg_resources.resource_filename('empress', 'support_files')
  
  empress/_plot_utils.py
    11:import pkg_resources
    18:SUPPORT_FILES = pkg_resources.resource_filename('empress', 'support_files')

It should be possible to either do these things using another library, or just do them ourselves. For example, Emperor figures out the location of its support_files/ directory without relying on pkg_resources.

It has been a while since we've released a new version of Empress, so I am not sure how straightforward doing that will be, but I think this would be good to address; it seems like this issue blocks Empress from working in newer QIIME 2 environments :(

For now, I think the best workaround would be using Empress in an older QIIME 2 environment, although I am aware that is a pain... looking at the YAMLs, I think QIIME 2 2026.1 or earlier should work, since those use setuptools versions < 82 (which is when pkg_resources was removed).

[ARW-UBT]

Hi @fedarko
Thank you for your suggestion for the workaround. I tried this with a fresh install of rachis-tiny-2026.1 and was able to install empress. However, scipy and scikit-bio were downgraded.

The phylogenetic tree produced with rachis-qiime2-2026.7 could be successfully visualized by empress in rachis-tiny-2026.1.

Best regards,

FYI - the tail section of the pip install empress output.

Building wheels for collected packages: emperor, hdmedians
  Building wheel for emperor (pyproject.toml) ... done
  Created wheel for emperor: filename=emperor-1.0.5-py3-none-any.whl size=670561 sha256=c9f566a277a3ccd70a53d006e0c1020b4c6fa5985ae2dd435a66e529960799bf
  Stored in directory: /home/bt140047/.cache/pip/wheels/9e/2c/eb/bc8b392d605350c5e475563e1e91768ac878d44610dd5816f6
  Building wheel for hdmedians (pyproject.toml) ... done
  Created wheel for hdmedians: filename=hdmedians-0.14.2-cp310-cp310-linux_x86_64.whl size=140456 sha256=e79154d018fe469f0c5913292eabd445c4355b0989bdd596d14463f5a911ae20
  Stored in directory: /home/bt140047/.cache/pip/wheels/82/8f/0d/0c61130cfad119482ebb95aecf8d5dfaddd0181f5680da2bec
Successfully built emperor hdmedians
Installing collected packages: nose, scipy, pillow, kiwisolver, future, fonttools, cython, cycler, contourpy, matplotlib, hdmedians, scikit-bio, emperor, empress
  Attempting uninstall: scipy
    Found existing installation: scipy 1.13.0
    Uninstalling scipy-1.13.0:
      Successfully uninstalled scipy-1.13.0
  Attempting uninstall: scikit-bio
    Found existing installation: scikit-bio 0.6.2
    Uninstalling scikit-bio-0.6.2:
      Successfully uninstalled scikit-bio-0.6.2
Successfully installed contourpy-1.3.2 cycler-0.12.1 cython-3.3.0 emperor-1.0.5 empress-1.2.0 fonttools-4.64.0 future-1.0.0 hdmedians-0.14.2 kiwisolver-1.5.1 matplotlib-3.10.9 nose-1.3.7 pillow-12.3.0 scikit-bio-0.5.9 scipy-1.10.1