fix(snakemake): update to v7.32.4 to make Python 3.11 clients compatible

Update Snakemake version to v7.32.4 (latest one before v8 refactoring),
to support newer features and resolve problems for clients using Python 3.11.

- `reana_commons/config.py`: update default Snakemake environment image.
- `reana_commons/snakemake.py`: modify `first_rule` directive to
  `default_target` directive to adhere to the changes made in
  snakemake/snakemake!638ec1a.
- `setup.py`: adjust Snakemake version in the dependencies.

Closes: reanahub/reana-client#655,
reanahub/reana-workflow-engine-snakemake#31.

reana_commons/config.py

@@ -440,7 +440,7 @@ def default_workspace():
 REANA_WORKFLOW_ENGINES = ["yadage", "cwl", "serial", "snakemake"]
 """Available workflow engines."""
 
-REANA_DEFAULT_SNAKEMAKE_ENV_IMAGE = "docker.io/snakemake/snakemake:v6.8.0"
+REANA_DEFAULT_SNAKEMAKE_ENV_IMAGE = "docker.io/snakemake/snakemake:v7.32.4"
 """Snakemake default job environment image."""
 
 REANA_JOB_CONTROLLER_CONNECTION_CHECK_SLEEP = float(

reana_commons/snakemake.py

@@ -93,7 +93,7 @@ def _create_snakemake_dag(
         if workdir:
             workflow.workdir(workdir)
 
-        workflow.include(snakefile=snakefile, overwrite_first_rule=True)
+        workflow.include(snakefile=snakefile, overwrite_default_target=True)
         workflow.check()
 
         # code copied and adapted from `snakemake.workflow.Workflow.execute()`
@@ -122,7 +122,9 @@ def files(items):
 
         if not kwargs.get("targets"):
             targets = (
-                [workflow.first_rule] if workflow.first_rule is not None else list()
+                [workflow.default_target]
+                if workflow.default_target is not None
+                else list()
             )
 
         prioritytargets = kwargs.get("prioritytargets", [])
@@ -157,7 +159,7 @@ def files(items):
             omitrules=omitrules,
         )
 
-        workflow.persistence = Persistence(dag=dag)
+        workflow._persistence = Persistence(dag=dag)
         dag.init()
         dag.update_checkpoint_dependencies()
         dag.check_dynamic()

reana_commons/version.py

@@ -14,4 +14,4 @@
 
 from __future__ import absolute_import, print_function
 
-__version__ = "0.9.5"
+__version__ = "0.9.5a1"

setup.py

@@ -35,13 +35,11 @@
     "yadage": ["adage~=0.10.1", "yadage~=0.20.1", "yadage-schemas~=0.10.6"],
     "cwl": ["cwltool==3.1.20210628163208"],
     "snakemake": [
-        "snakemake==6.8.0 ; python_version<'3.12'",
-        "snakemake==7.9.0 ; python_version>='3.12'",
+        "snakemake==7.32.4",
         "tabulate<0.9",
     ],
     "snakemake_reports": [
-        "snakemake[reports]==6.8.0 ; python_version<'3.12'",
-        "snakemake[reports]==7.9.0 ; python_version>='3.12'",
+        "snakemake==7.32.4",
         "pygraphviz<1.8",
         "tabulate<0.9",  # tabulate 0.9 crashes snakemake, more info: https://github.com/snakemake/snakemake/issues/1899
     ],

tests/conftest.py

@@ -20,6 +20,7 @@ def dummy_snakefile():
         "results/foo.txt",
         "results/bar.txt",
         "results/baz.txt"
+    default_target: True
 
 rule foo:
     input:

tests/test_snakemake.py

@@ -17,10 +17,6 @@
 
 def test_snakemake_load(tmpdir, dummy_snakefile):
     """Test that Snakemake metadata is loaded properly."""
-    if sys.version_info.major == 3 and sys.version_info.minor in (11, 12):
-        pytest.xfail(
-            "Snakemake features of reana-client are not supported on Python 3.11"
-        )
     workdir = tmpdir.mkdir("sub")
     # write Snakefile
     p = workdir.join("Snakefile")