From a50fa889e81bf6c8d38bf6e8a118d4fb8f328b2b Mon Sep 17 00:00:00 2001
From: Silas Kieser <silas.kieser@gmail.com>
Date: Mon, 22 Jan 2024 10:21:43 +0100
Subject: [PATCH] adapt to snakemake v8 pass version

---
 atlas/atlas.py       |  2 +-
 atlas/make_config.py |  2 +-
 atlasenv.yml         | 14 +++++++-------
 3 files changed, 9 insertions(+), 9 deletions(-)

diff --git a/atlas/atlas.py b/atlas/atlas.py
index 3e7ee05c..c52b5138 100644
--- a/atlas/atlas.py
+++ b/atlas/atlas.py
@@ -7,7 +7,7 @@
 import click
 
 
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from .make_config import validate_config
 from .init.atlas_init import run_init  # , run_init_sra
 
diff --git a/atlas/make_config.py b/atlas/make_config.py
index 96332497..3f21dcb8 100644
--- a/atlas/make_config.py
+++ b/atlas/make_config.py
@@ -1,6 +1,6 @@
 from .default_values import *
 from snakemake.utils import update_config as snakemake_update_config
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import tempfile
 import sys
 import os
diff --git a/atlasenv.yml b/atlasenv.yml
index c1ec80ea..4a4b32b4 100644
--- a/atlasenv.yml
+++ b/atlasenv.yml
@@ -3,14 +3,14 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python >=3.8, < 3.12
+  - python =3.11
   - mamba
-  - bbmap >= 39.01, <40
-  - snakemake-minimal >= 7.18.1, <7.26
-  - pygments
-  - networkx
-  - graphviz
-  - pandas >=1.2, <1.6
+  - bbmap >= 39.01
+  - snakemake-minimal >= 8
+  #- pygments
+  #- networkx
+  #- graphviz
+  - pandas =2
   - pyarrow # for parquet reading
   - click >=7
   - ruamel.yaml >=0.17