CONDA_PREFIX in util.py

[pavelToman]

Bug Description
I like to install Qiime from sources, not by CONDA. There was a change: #367 and the logic break the installation from sources. The if conda_prefix is after it is used...

Steps to reproduce the behavior
qiime --help >>>

Sanity check failed: sanity check command qiime --help failed with exit code 1 (output: Traceback (most recent call last):
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/bin/qiime", line 5, in <module>
    from q2cli.__main__ import qiime
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/lib/python3.12/site-packages/q2cli/__main__.py", line 11, in <module>
    import q2cli.commands
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/lib/python3.12/site-packages/q2cli/commands.py", line 16, in <module>
    from q2cli.core.config import CONFIG
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/lib/python3.12/site-packages/q2cli/core/config.py", line 17, in <module>
    class CLIConfig():
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/lib/python3.12/site-packages/q2cli/core/config.py", line 18, in CLIConfig
    path = os.path.join(q2cli.util.get_app_dir(), 'cli-colors.theme')
                        ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/software/QIIME2/2025.4.0-foss-2024a-amplicon/lib/python3.12/site-packages/q2cli/util.py", line 17, in get_app_dir
    environment_cache = os.path.join(conda_prefix, 'var', 'q2cli')
                        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<frozen posixpath>", line 76, in join
TypeError: expected str, bytes or os.PathLike object, not NoneType
)

Expected behavior
Should work even without CONDA

[ebolyen]

Thanks @pavelToman! I think we can adjust os.environ.get to default to an empty string and then it should work fine and pass through this branch. Would you be interested in contributing a PR? :)

[satishskamath]

@ebolyen and @pavelToman I patched it in this manner:

diff -ruN q2cli-2025.4.0/q2cli/util.py q2cli-2025.4.0_new/q2cli/util.py
--- q2cli-2025.4.0/q2cli/util.py	2025-05-01 23:16:56.000000000 +0200
+++ q2cli-2025.4.0_new/q2cli/util.py	2025-09-15 17:20:00.801266434 +0200
@@ -13,7 +13,7 @@
 
 def get_app_dir():
     import os
-    conda_prefix = os.environ.get('CONDA_PREFIX')
+    conda_prefix = os.environ.get('CONDA_PREFIX') or ''
     environment_cache = os.path.join(conda_prefix, 'var', 'q2cli')
     if conda_prefix is not None and (os.access(conda_prefix, os.W_OK | os.X_OK)
                                      or os.path.exists(environment_cache)):

and then the installation was successful.

[ebolyen]

That works too, although since we are here, do either of you have a preferred equivalent path in which a config could be found? Or is ~/.local (or wherever appdir sense us) perfectly fine (we will hit that case in the next branch).

[pavelToman]

Since our installation directories are immutable, the preferred path is $HOME/.q2cli or something similar.