From e4eba8d72b84aaa460c7d1b1ac54b607e844d782 Mon Sep 17 00:00:00 2001
From: Mitchell Robert Vollger <mrvollger@gmail.com>
Date: Mon, 5 Jun 2023 07:57:10 -0700
Subject: [PATCH] feat: Allow the environment variable SNAKEMAKE_CONDA_PREFIX
 to be present without --use-conda (#2263)

### Description

SNAKEMAKE_CONDA_PREFIX is a great tool for shared computing environments
and I am encouraging everyone in our lab to set it in their `.bashrc` it
to help with the number of conda builds we have and reduce file usage.
However, there is one downside and that is it becomes impossible to run
a non conda snakemake without clearing the environment variable because
the lack of `--use-conda` will force snakemake to exit.

In this PR I suggest a quality of life improvement. Instead of having
snakemake error out, it will instead warn that the environment variable
is set but conda environments will not be used or built because
`--use-conda` is not set. Note, this will only happen when the
environment variable is set and not when it is passed as a command line
argument.

Thanks for considering!

### 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).
---
 snakemake/__init__.py | 22 ++++++++++++++++------
 1 file changed, 16 insertions(+), 6 deletions(-)

diff --git a/snakemake/__init__.py b/snakemake/__init__.py
index e0cd920ac..0e13ab11d 100644
--- a/snakemake/__init__.py
+++ b/snakemake/__init__.py
@@ -2764,12 +2764,22 @@ def adjust_path(f):
         sys.exit(1)
 
     if (args.conda_prefix or args.conda_create_envs_only) and not args.use_conda:
-        print(
-            "Error: --use-conda must be set if --conda-prefix or "
-            "--create-envs-only is set.",
-            file=sys.stderr,
-        )
-        sys.exit(1)
+        if args.conda_prefix and os.environ.get("SNAKEMAKE_CONDA_PREFIX", False):
+            print(
+                "Warning: The enviorment variable SNAKEMAKE_CONDA_PREFIX is set"
+                "but --use-conda is not."
+                "Snakemake will ignore SNAKEMAKE_CONDA_PREFIX"
+                "and conda enviorments will not be used or created.",
+                file=sys.stderr,
+            )
+            args.conda_prefix = None
+        else:
+            print(
+                "Error: --use-conda must be set if --conda-prefix or "
+                "--create-envs-only is set.",
+                file=sys.stderr,
+            )
+            sys.exit(1)
 
     if args.singularity_prefix and not args.use_singularity:
         print(