Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

fix: avoid superfluous calls of conda info that have slowed down Snakemake since 6.4.1. #1099

Merged
merged 1 commit into from Jul 19, 2021
Merged

fix: avoid superfluous calls of conda info that have slowed down Snakemake since 6.4.1. #1099

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Jump to
Jump to file
Failed to load files.
Diff view
Diff view
32 changes: 19 additions & 13 deletions snakemake/deployment/conda.py
View file
Open in desktop
Expand Up @@ -414,27 +414,33 @@ def __new__(cls, container_img=None, prefix_path=None):
with cls.lock:
if container_img not in cls.instances:
inst = super().__new__(cls)
inst.__init__(container_img=container_img, prefix_path=prefix_path)
cls.instances[container_img] = inst
inst._check()
return inst
else:
return cls.instances[container_img]

def __init__(self, container_img=None, prefix_path=None):
from snakemake.deployment import singularity
from snakemake.shell import shell
if not self.is_initialized: # avoid superfluous init calls
from snakemake.deployment import singularity
from snakemake.shell import shell

if isinstance(container_img, singularity.Image):
container_img = container_img.path
self.container_img = container_img

if prefix_path is None or container_img is not None:
self.prefix_path = json.loads(
shell.check_output(self._get_cmd("conda info --json"))
)["conda_prefix"]
else:
self.prefix_path = prefix_path

if isinstance(container_img, singularity.Image):
container_img = container_img.path
self.container_img = container_img
# check conda installation
self._check()

if prefix_path is None or container_img is not None:
self.prefix_path = json.loads(
shell.check_output(self._get_cmd("conda info --json"))
)["conda_prefix"]
else:
self.prefix_path = prefix_path
@property
def is_initialized(self):
return hasattr(self, "prefix_path")

def _get_cmd(self, cmd):
if self.container_img:
Expand Down