remove conda frontend arg

rhysnewell · Jan 17, 2025 · a432fb6 · a432fb6
1 parent ce635b3
commit a432fb6
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Showing 3 changed files with 3 additions and 16 deletions.
diff --git a/aviary/aviary.py b/aviary/aviary.py
@@ -242,15 +242,6 @@ def main():
         default=False,
     )
 
-    base_group.add_argument(
-        '--conda-frontend', '--conda_frontend',
-        help='Which conda frontend to use, mamba is faster but harder to debug. Switch this to conda \n'
-             'If experiencing problems installing environments',
-        dest='conda_frontend',
-        default="mamba",
-        choices=["conda", "mamba"],
-    )
-
     base_group.add_argument(
         '--clean',
         help='Clean up all temporary files. This will remove most BAM files and any FASTQ files \n'
@@ -1274,7 +1265,6 @@ def main():
         processor.run_workflow(cores=int(args.n_cores),
                                dryrun=args.dryrun,
                                clean=args.clean,
-                               conda_frontend=args.conda_frontend,
                                snakemake_args=args.cmds,
                                rerun_triggers=args.rerun_triggers,
                                profile=args.snakemake_profile,

diff --git a/aviary/modules/processor.py b/aviary/modules/processor.py
@@ -445,7 +445,7 @@ def _validate_config(self):
         load_configfile(self.config)
 
     def run_workflow(self, cores=16, profile=None, cluster_retries=None,
-                     dryrun=False, clean=True, conda_frontend=None,
+                     dryrun=False, clean=True,
                      snakemake_args="", write_to_script=None, rerun_triggers=None):
         """
         Runs the aviary pipeline
@@ -468,7 +468,7 @@ def run_workflow(self, cores=16, profile=None, cluster_retries=None,
                 "snakemake --snakefile {snakefile} --directory {working_dir} "
                 "{jobs} --rerun-incomplete --keep-going {args} {rerun_triggers} "
                 "--configfile {config_file} --nolock "
-                "{profile} {retries} {conda_frontend} {resources} --use-conda {conda_prefix} "
+                "{profile} {retries} {resources} --use-conda {conda_prefix} "
                 "{dryrun} {notemp} "
                 "{target_rule}"
             ).format(
@@ -484,7 +484,6 @@ def run_workflow(self, cores=16, profile=None, cluster_retries=None,
                 args=snakemake_args,
                 target_rule=workflow if workflow != "None" else "",
                 conda_prefix="--conda-prefix " + self.conda_prefix,
-                conda_frontend="--conda-frontend " + conda_frontend if conda_frontend is not None else "",
                 resources=f"--resources mem_mb={int(self.max_memory)*1024} {self.resources}" if not dryrun else ""
             )
 
@@ -603,7 +602,6 @@ def process_batch(args, prefix):
         processor.run_workflow(cores=int(new_args.n_cores),
                                dryrun=new_args.dryrun,
                                clean=new_args.clean,
-                               conda_frontend=new_args.conda_frontend,
                                snakemake_args=new_args.cmds,
                                rerun_triggers=new_args.rerun_triggers,
                                profile=new_args.snakemake_profile,
@@ -627,7 +625,6 @@ def process_batch(args, prefix):
             processor.run_workflow(cores=int(args.n_cores),
                                    dryrun=args.dryrun,
                                    clean=args.clean,
-                                   conda_frontend=args.conda_frontend,
                                    snakemake_args=args.cmds,
                                    rerun_triggers=args.rerun_triggers,
                                    profile=args.snakemake_profile,

diff --git a/test/test_integration.py b/test/test_integration.py
@@ -227,7 +227,7 @@ def test_short_read_recovery_comebin(self):
 
         self.assertFalse(os.path.isfile(f"{output_dir}/aviary_out/data/final_contigs.fasta"))
 
-    @unittest.skip("Skipping test due to queue submission")
+    # @unittest.skip("Skipping test due to queue submission")
     def test_short_read_recovery_queue_submission(self):
         output_dir = os.path.join("example", "test_short_read_recovery_queue_submission")
         self.setup_output_dir(output_dir)