fixed test case and broken imports

snakemake/__init__.py

@@ -2,3 +2,5 @@
 __copyright__ = "Copyright 2023, Johannes Köster"
 __email__ = "johannes.koester@protonmail.com"
 __license__ = "MIT"
+
+from snakemake.common import __version__

snakemake/__main__.py

@@ -1,4 +1,4 @@
 # This script makes it possible to invoke snakemake with 'python3 -m snakemake'
-from snakemake import main
+from snakemake.cli import main
 
 main()

snakemake/api.py

@@ -5,16 +5,17 @@
 
 import sys
 
+from snakemake.common import MIN_PY_VERSION
+
 if sys.version_info < MIN_PY_VERSION:
     raise ValueError(f"Snakemake requires at least Python {'.'.join(MIN_PY_VERSION)}.")
 
 import os
 from functools import partial
 import importlib
 
-from snakemake_interface_executor_plugins.utils import url_can_parse, ExecMode
+from snakemake_interface_executor_plugins.utils import ExecMode
 
-from snakemake.target_jobs import parse_target_jobs_cli_args
 from snakemake.workflow import Workflow
 from snakemake.exceptions import (
     print_exception,

snakemake/io.py

@@ -31,7 +31,6 @@
 from snakemake.logging import logger
 from inspect import isfunction, ismethod
 from snakemake.common import DYNAMIC_FILL, ON_WINDOWS, async_run
-from snakemake_interface_executor_plugins.utils import not_iterable
 
 
 class Mtime:
@@ -1005,6 +1004,8 @@ def new_from(self, new_value):
 
 
 def flag(value, flag_type, flag_value=True):
+    from snakemake_interface_executor_plugins.utils import not_iterable
+
     if isinstance(value, AnnotatedString):
         value.flags[flag_type] = flag_value
         return value
@@ -1099,6 +1100,8 @@ def dynamic(value):
     A flag for a file that shall be dynamic, i.e. the multiplicity
     (and wildcard values) will be expanded after a certain
     rule has been run"""
+    from snakemake_interface_executor_plugins.utils import not_iterable
+
     annotated = flag(value, "dynamic", True)
     tocheck = [annotated] if not_iterable(annotated) else annotated
     for file in tocheck:

snakemake/script.py

@@ -543,33 +543,36 @@ def generate_preamble(
         # Obtain search path for current snakemake module.
         # The module is needed for unpickling in the script.
         # We append it at the end (as a fallback).
-        searchpath = SNAKEMAKE_SEARCHPATH
+        snakemake_searchpath = SNAKEMAKE_SEARCHPATH
         if container_img is not None:
-            searchpath = singularity.SNAKEMAKE_MOUNTPOINT
-        searchpath = repr(searchpath)
+            snakemake_searchpath = singularity.SNAKEMAKE_MOUNTPOINT
+        searchpaths = [snakemake_searchpath] + [
+            path for path in sys.path if path.endswith("site-packages")
+        ]
 
         # Add the cache path to the search path so that other cached source files in the same dir
         # can be imported.
         if cache_path:
             cache_searchpath = os.path.dirname(cache_path)
             if cache_searchpath:
-                searchpath += ", " + repr(cache_searchpath)
+                searchpaths.append(cache_searchpath)
         # For local scripts, add their location to the path in case they use path-based imports
         if is_local:
-            searchpath += ", " + repr(path.get_basedir().get_path_or_uri())
+            searchpaths.append(path.get_basedir().get_path_or_uri())
 
-        return textwrap.dedent(
+        preamble = textwrap.dedent(
             """
         ######## snakemake preamble start (automatically inserted, do not edit) ########
-        import sys; sys.path.extend([{searchpath}]); import pickle; snakemake = pickle.loads({snakemake}); from snakemake.logging import logger; logger.printshellcmds = {printshellcmds}; {preamble_addendum}
+        import sys; sys.path.extend({searchpaths}); import pickle; snakemake = pickle.loads({snakemake}); from snakemake.logging import logger; logger.printshellcmds = {printshellcmds}; {preamble_addendum}
         ######## snakemake preamble end #########
         """
         ).format(
-            searchpath=searchpath,
+            searchpaths=repr(searchpaths),
             snakemake=snakemake,
             printshellcmds=logger.printshellcmds,
             preamble_addendum=preamble_addendum,
         )
+        return preamble
 
     def get_preamble(self):
         if isinstance(self.path, LocalSourceFile):

snakemake/workflow.py

@@ -25,7 +25,6 @@
     NoRulesException,
     WorkflowError,
 )
-from snakemake.shell import shell
 from snakemake.dag import DAG
 from snakemake.scheduler import JobScheduler
 from snakemake.parser import parse
@@ -249,6 +248,9 @@ def __init__(
         self._quiet = quiet
 
         _globals = globals()
+        from snakemake.shell import shell
+
+        _globals["shell"] = shell
         _globals["workflow"] = self
         _globals["rules"] = Rules()
         _globals["checkpoints"] = Checkpoints()
@@ -1164,6 +1166,8 @@ def files(items):
 
         if not dryrun:
             if len(dag):
+                from snakemake.shell import shell
+
                 shell_exec = shell.get_executable()
                 if shell_exec is not None:
                     logger.info(f"Using shell: {shell_exec}")

tests/common.py

@@ -18,7 +18,7 @@
 import subprocess
 import tarfile
 
-from snakemake import snakemake
+from snakemake.api import snakemake
 from snakemake.shell import shell
 from snakemake.common import ON_WINDOWS
 from snakemake.resources import DefaultResources, GroupResources, ResourceScopes

tests/conftest.py

@@ -5,7 +5,7 @@
 
 from snakemake.common import ON_WINDOWS
 from snakemake.utils import find_bash_on_windows
-from snakemake import shell
+from snakemake.shell import shell
 
 skip_on_windows = pytest.mark.skipif(ON_WINDOWS, reason="Unix stuff")
 only_on_windows = pytest.mark.skipif(not ON_WINDOWS, reason="Windows stuff")

tests/test14/Snakefile.nonstandard

@@ -1,4 +1,4 @@
-from snakemake import shell
+from snakemake.shell import shell
 
 chromosomes = [1, 2, 3, 4, 5]
 

tests/testapi.py

@@ -1,7 +1,7 @@
 """
 Tests for Snakemake’s API
 """
-from snakemake import snakemake
+from snakemake.api import snakemake
 import asyncio
 import sys
 import tempfile

tests/tests.py

@@ -9,7 +9,7 @@
 import subprocess as sp
 from pathlib import Path
 
-from snakemake import parse_cores_jobs
+from snakemake.cli import parse_cores_jobs
 from snakemake.exceptions import CliException
 from snakemake.utils import available_cpu_count