fix: only deactivate conda inject envs upon workflow tear down (#2503)

### Description

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

setup.cfg

@@ -60,7 +60,7 @@ install_requires =
     toposort >=1.10
     wrapt
     yte >=1.5.1,<2.0
-    conda-inject >=1.1.1,<2.0
+    conda-inject >=1.3.1,<2.0
 
 [options.extras_require]
 messaging = slacker

snakemake/workflow.py

@@ -213,7 +213,7 @@ def __post_init__(self):
 
     def tear_down(self):
         for conda_env in self.injected_conda_envs:
-            conda_env.remove()
+            conda_env.deactivate()
         if self._workdir_handler is not None:
             self._workdir_handler.change_back()
         self._snakemake_tmp_dir.cleanup()

tests/test_linting.py

@@ -1,4 +1,4 @@
-import os
+import os, sys
 from pathlib import Path
 import subprocess as sp
 from itertools import product
@@ -23,9 +23,9 @@ def test_lint(lint, case):
                     "snakemake",
                     "--lint",
                     "--directory",
-                    lint,
+                    str(lint),
                     "--snakefile",
-                    lint.joinpath(case).with_suffix(".smk"),
+                    str(lint.joinpath(case).with_suffix(".smk")),
                 ],
                 stderr=sp.STDOUT,
             )
@@ -35,7 +35,7 @@ def test_lint(lint, case):
         if case == "positive":
             assert out == "Congratulations, your workflow is in a good condition!"
         else:
-            print(out)
+            print(out, file=sys.stderr)
             assert (
                 False
             ), "Negative lint example but linting command exited with status 0."
@@ -44,8 +44,9 @@ def test_lint(lint, case):
         if case == "negative":
             assert e.output.decode().strip()
         else:
+            print(e.output.decode().strip(), file=sys.stderr)
             raise e
 
     else:
-        print(out)
+        print(out, file=sys.stderr)
         assert out