Update snakemake

.github/workflows/python-publish.yml

@@ -25,7 +25,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v3
       with:
-        python-version: '3.10'
+        python-version: '3.11'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip

.github/workflows/test-binchicken.yml

@@ -10,7 +10,7 @@ jobs:
         shell: bash -l {0}
     strategy:
         matrix:
-            python-version: ["3.10"]
+            python-version: ["3.11"]
     steps:
       - uses: actions/checkout@v2
       - name: Set up environment with Python ${{ matrix.python-version }}

binchicken.yml

@@ -4,9 +4,10 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - python=3.10.*
-  - snakemake=7.32.*
-  - mamba=1.4.*
+  - python=3.11.*
+  - snakemake=8.25.*
+  - snakemake-executor-plugin-cluster-generic=1.0.*
+  - snakemake-executor-plugin-slurm=0.11.*
   - networkx=3.1
   - bird_tool_utils_python=0.4.*
   - extern=0.4.*

binchicken/binchicken.py

@@ -13,7 +13,7 @@
 import polars as pl
 import polars.selectors as cs
 from polars.exceptions import NoDataError
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 from ruamel.yaml import YAML
 import copy
 import shutil

test/test_coassemble.py

@@ -6,7 +6,7 @@
 from bird_tool_utils import in_tempdir
 import extern
 import subprocess
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import polars as pl
 from polars.testing import assert_frame_equal
 
@@ -966,7 +966,6 @@ def test_coassemble_singlem_inputs(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1008,7 +1007,6 @@ def test_coassemble_run_aviary(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1054,7 +1052,6 @@ def test_coassemble_run_aviary_unmapped(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1101,7 +1098,6 @@ def test_coassemble_run_aviary_unmapped_qc(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1153,7 +1149,6 @@ def test_coassemble_files_of_paths(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1207,7 +1202,6 @@ def test_coassemble_singlem_inputs_files_of_paths(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1247,7 +1241,6 @@ def test_coassemble_singlem_inputs_dir(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1287,7 +1280,6 @@ def test_coassemble_preclustered_dryrun(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -1327,7 +1319,6 @@ def test_coassemble_weighted_dryrun(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 

test/test_evaluate.py

@@ -4,7 +4,7 @@
 import os
 from bird_tool_utils import in_tempdir
 import extern
-from snakemake.io 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')
@@ -153,7 +153,6 @@ def test_evaluate_specified_files(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -283,7 +282,6 @@ def test_evaluate_genome_files_input(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 

test/test_iterate.py

@@ -5,7 +5,7 @@
 from bird_tool_utils import in_tempdir
 import extern
 import subprocess
-from snakemake.io import load_configfile
+from snakemake.common.configfile import load_configfile
 import re
 
 path_to_data = os.path.join(os.path.dirname(os.path.realpath(__file__)),'data')
@@ -372,7 +372,6 @@ def test_iterate_genome_files_input(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 

test/test_update.py

@@ -5,7 +5,7 @@
 import gzip
 from bird_tool_utils import in_tempdir
 import extern
-from snakemake.io 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')
@@ -308,7 +308,6 @@ def test_update_specified_files(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output = extern.run(cmd)
 
@@ -376,7 +375,6 @@ def test_update_sra_download(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output_comb = extern.run(cmd)
 
@@ -584,7 +582,6 @@ def test_update_aviary_run(self):
                 f"--output test "
                 f"--conda-prefix {path_to_conda} "
                 f"--dryrun "
-                f"--snakemake-args \" --quiet\" "
             )
             output_comb = extern.run(cmd)