Update snakemake to match conda

.github/workflows/python-publish.yml

@@ -21,10 +21,10 @@ jobs:
     - uses: actions/checkout@v3
     - name: Set env
       run: echo "RELEASE_VERSION=${GITHUB_REF#refs/*/}" >> $GITHUB_ENV
-    - name: Set up Python 3.10
+    - name: Set up Python 3.11
       uses: actions/setup-python@v3
       with:
-        python-version: "3.10"
+        python-version: "3.11"
     - name: Install pypa/build
       run: >-
         python -m

.github/workflows/test-aviary.yml

@@ -10,7 +10,7 @@ jobs:
         shell: bash -l {0}
     strategy:
         matrix:
-            python-version: ["3.10"]
+            python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v4
       - name: Set up environment with Python ${{ matrix.python-version }}

aviary.yml

@@ -3,8 +3,10 @@ channels:
   - bioconda
   - anaconda
 dependencies:
-  - python >=3.8,<=3.11
-  - snakemake >=7.0.0,<=7.32.3
+  - python =3.11
+  - snakemake >=8.20.6
+  - snakemake-executor-plugin-cluster-generic =1.0.*
+  - snakemake-executor-plugin-slurm =0.11.*
   - ruamel.yaml >=0.15.99 # needs to be explicit
   - numpy
   - pandas

aviary/modules/processor.py

@@ -40,8 +40,7 @@
 from glob import glob
 
 # Local imports
-from snakemake import utils
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from ruamel.yaml import YAML  # used for yaml reading with comments
 from aviary import LONG_READ_TYPES
 

test/test_assemble.py

@@ -26,7 +26,7 @@ def test_assemble_simple_inputs(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 

test/test_recover.py

@@ -4,7 +4,7 @@
 import os
 import tempfile
 import extern
-from snakemake import load_configfile
+from snakemake.common.configfile import load_configfile
 
 path_to_data = os.path.join(os.path.dirname(os.path.realpath(__file__)),'data')
 path_to_conda = os.path.join(path_to_data,'.conda')
@@ -29,7 +29,7 @@ def test_recover_simple_inputs(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -86,7 +86,7 @@ def test_recover_skip_binners(self):
                 f"--conda-prefix {path_to_conda} "
                 f"--skip-binners metabat "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -143,7 +143,7 @@ def test_recover_no_singlem(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -200,7 +200,7 @@ def test_recover_no_abundances(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -257,7 +257,7 @@ def test_recover_no_taxonomy(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -314,7 +314,7 @@ def test_recover_binning_only(self):
                 f"--output {tmpdir}/test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun --tmpdir {tmpdir} "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             output = extern.run(cmd)
 
@@ -372,7 +372,7 @@ def test_recover_config(self):
                 f"--output {tmpdir}/test --tmpdir {tmpdir} "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             extern.run(cmd)
 
@@ -399,7 +399,7 @@ def test_recover_config_many_threads(self):
                 f"--output {tmpdir}/test --tmpdir {tmpdir} "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             extern.run(cmd)
 
@@ -427,7 +427,7 @@ def test_recover_config_many_pplacer_threads(self):
                 f"--output {tmpdir}/test --tmpdir {tmpdir} "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-cmds \" --quiet\" "
+                f"--snakemake-cmds \" --quiet rules\" "
             )
             extern.run(cmd)