From db182baa994df4eeb124c9ff1bd03054a2052cdc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 7 Sep 2024 20:13:45 +0200 Subject: [PATCH 1/2] chore: update to stable snakemake --- pyproject.toml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/pyproject.toml b/pyproject.toml index 29a48b0..21d8692 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -19,7 +19,7 @@ black = "^23.11.0" flake8 = "^6.1.0" coverage = "^7.3.2" pytest = "^7.4.3" -snakemake = {git = "https://github.com/snakemake/snakemake.git"} +snakemake = "^8.20.1" snakemake-storage-plugin-s3 = "^0.2.7" [tool.coverage.run] From c30ac557f456450575232e76ab70a4327adeab4c Mon Sep 17 00:00:00 2001 From: Johannes Koester Date: Sat, 7 Sep 2024 20:20:28 +0200 Subject: [PATCH 2/2] fix types --- tests/__init__.py | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/tests/__init__.py b/tests/__init__.py index 51883fb..d9e46c4 100644 --- a/tests/__init__.py +++ b/tests/__init__.py @@ -26,10 +26,8 @@ def get_assume_shared_fs(self) -> bool: def get_remote_execution_settings( self, - ) -> snakemake.settings.RemoteExecutionSettings: - return snakemake.settings.RemoteExecutionSettings( + ) -> snakemake.settings.types.RemoteExecutionSettings: + return snakemake.settings.types.RemoteExecutionSettings( seconds_between_status_checks=5, envvars=self.get_envvars(), - # TODO remove once we have switched to stable snakemake for dev - container_image="snakemake/snakemake:latest", )