update snakemake

Author: lisazeyen

scripts/_helpers.py

@@ -55,65 +55,127 @@ def __dir__(self):
         return dict_keys + obj_attrs
 
 
-def mock_snakemake(rulename, **wildcards):
+def mock_snakemake(
+    rulename,
+    root_dir=None,
+    configfiles=None,
+    submodule_dir="workflow/submodules/pypsa-eur",
+    **wildcards,
+):
     """
     This function is expected to be executed from the 'scripts'-directory of '
     the snakemake project. It returns a snakemake.script.Snakemake object,
     based on the Snakefile.
+
     If a rule has wildcards, you have to specify them in **wildcards.
+
     Parameters
     ----------
     rulename: str
         name of the rule for which the snakemake object should be generated
+    root_dir: str/path-like
+        path to the root directory of the snakemake project
+    configfiles: list, str
+        list of configfiles to be used to update the config
+    submodule_dir: str, Path
+        in case PyPSA-Eur is used as a submodule, submodule_dir is
+        the path of pypsa-eur relative to the project directory.
     **wildcards:
         keyword arguments fixing the wildcards. Only necessary if wildcards are
         needed.
     """
     import os
 
     import snakemake as sm
-    from packaging.version import Version, parse
+    from pypsa.descriptors import Dict
+    from snakemake.api import Workflow
+    from snakemake.common import SNAKEFILE_CHOICES
     from snakemake.script import Snakemake
-
-    script_dir = Path(__file__).parent.resolve()
-    assert (
-        Path.cwd().resolve() == script_dir
-    ), f"mock_snakemake has to be run from the repository scripts directory {script_dir}"
-    os.chdir(script_dir.parent)
-    for p in sm.SNAKEFILE_CHOICES:
-        if os.path.exists(p):
-            snakefile = p
-            break
-    kwargs = dict(rerun_triggers=[]) if parse(sm.__version__) > Version("7.7.0") else {}
-    workflow = sm.Workflow(snakefile, overwrite_configfiles=[], **kwargs)
-    workflow.include(snakefile)
-    workflow.global_resources = {}
-    rule = workflow.get_rule(rulename)
-    dag = sm.dag.DAG(workflow, rules=[rule])
-    wc = Dict(wildcards)
-    job = sm.jobs.Job(rule, dag, wc)
-
-    def make_accessable(*ios):
-        for io in ios:
-            for i in range(len(io)):
-                io[i] = os.path.abspath(io[i])
-
-    make_accessable(job.input, job.output, job.log)
-    snakemake = Snakemake(
-        job.input,
-        job.output,
-        job.params,
-        job.wildcards,
-        job.threads,
-        job.resources,
-        job.log,
-        job.dag.workflow.config,
-        job.rule.name,
-        None,
+    from snakemake.settings import (
+        ConfigSettings,
+        DAGSettings,
+        ResourceSettings,
+        StorageSettings,
+        WorkflowSettings,
     )
-    # create log and output dir if not existent
-    for path in list(snakemake.log) + list(snakemake.output):
-        Path(path).parent.mkdir(parents=True, exist_ok=True)
 
-    os.chdir(script_dir)
-    return snakemake
+    script_dir = Path(__file__).parent.resolve()
+    if root_dir is None:
+        root_dir = script_dir.parent
+    else:
+        root_dir = Path(root_dir).resolve()
+
+    user_in_script_dir = Path.cwd().resolve() == script_dir
+    if str(submodule_dir) in __file__:
+        # the submodule_dir path is only need to locate the project dir
+        os.chdir(Path(__file__[: __file__.find(str(submodule_dir))]))
+    elif user_in_script_dir:
+        os.chdir(root_dir)
+    elif Path.cwd().resolve() != root_dir:
+        raise RuntimeError(
+            "mock_snakemake has to be run from the repository root"
+            f" {root_dir} or scripts directory {script_dir}"
+        )
+    try:
+        for p in SNAKEFILE_CHOICES:
+            if os.path.exists(p):
+                snakefile = p
+                break
+        if configfiles is None:
+            configfiles = []
+        elif isinstance(configfiles, str):
+            configfiles = [configfiles]
+
+        resource_settings = ResourceSettings()
+        config_settings = ConfigSettings(configfiles=map(Path, configfiles))
+        workflow_settings = WorkflowSettings()
+        storage_settings = StorageSettings()
+        dag_settings = DAGSettings(rerun_triggers=[])
+        workflow = Workflow(
+            config_settings,
+            resource_settings,
+            workflow_settings,
+            storage_settings,
+            dag_settings,
+            storage_provider_settings=dict(),
+        )
+        workflow.include(snakefile)
+
+        if configfiles:
+            for f in configfiles:
+                if not os.path.exists(f):
+                    raise FileNotFoundError(f"Config file {f} does not exist.")
+                workflow.configfile(f)
+
+        workflow.global_resources = {}
+        rule = workflow.get_rule(rulename)
+        dag = sm.dag.DAG(workflow, rules=[rule])
+        wc = Dict(wildcards)
+        job = sm.jobs.Job(rule, dag, wc)
+
+        def make_accessable(*ios):
+            for io in ios:
+                for i, _ in enumerate(io):
+                    io[i] = os.path.abspath(io[i])
+
+        make_accessable(job.input, job.output, job.log)
+        snakemake = Snakemake(
+            job.input,
+            job.output,
+            job.params,
+            job.wildcards,
+            job.threads,
+            job.resources,
+            job.log,
+            job.dag.workflow.config,
+            job.rule.name,
+            None,
+        )
+        # create log and output dir if not existent
+        for path in list(snakemake.log) + list(snakemake.output):
+            Path(path).parent.mkdir(parents=True, exist_ok=True)
+
+    finally:
+        if user_in_script_dir:
+            os.chdir(script_dir)
+    return snakemake