feat(snakemake): upgrade to Snakemake 7.32.4 (#435)

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.

Other than updating the dependency and Snakemake base image, change
`reana_commons/snakemake.py` to switch from the `first_rule` Snakemake
workflow directive to the `default_target` one, to adhere to the
changes made in snakemake/snakemake!638ec1a.

Closes: reanahub/reana-client#655
Closes: 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()`
@@ -113,16 +113,20 @@ def files(items):
         else:
 
             def files(items):
-                relpath = (
-                    lambda f: f
-                    if os.path.isabs(f) or f.startswith("root://")
-                    else os.path.relpath(f)
-                )
+                def relpath(f):
+                    return (
+                        f
+                        if os.path.isabs(f) or f.startswith("root://")
+                        else os.path.relpath(f)
+                    )
+
                 return map(relpath, filterfalse(workflow.is_rule, 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 +161,11 @@ def files(items):
             omitrules=omitrules,
         )
 
-        workflow.persistence = Persistence(dag=dag)
+        if hasattr(workflow, "_persistence"):
+            workflow._persistence = Persistence(dag=dag)
+        else:
+            # for backwards compatibility (Snakemake < 7 for Python 3.6)
+            workflow.persistence = Persistence(dag=dag)
         dag.init()
         dag.update_checkpoint_dependencies()
         dag.check_dynamic()

setup.py

@@ -35,13 +35,13 @@
     "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==6.15.5 ; python_version<'3.7'",  # Snakemake v7 requires Python 3.7+
+        "snakemake==7.32.4 ; python_version>='3.7'",
         "tabulate<0.9",
     ],
     "snakemake_reports": [
-        "snakemake[reports]==6.8.0 ; python_version<'3.12'",
-        "snakemake[reports]==7.9.0 ; python_version>='3.12'",
+        "snakemake==6.15.5 ; python_version<'3.7'",
+        "snakemake==7.32.4 ; python_version>='3.7'",
         "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")