From 4816a58653e466ca94b1482a1d947a856f5381b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Johannes=20K=C3=B6ster?= <johannes.koester@uni-due.de>
Date: Tue, 2 Nov 2021 18:15:53 +0100
Subject: [PATCH] fix: only consider context of shell command for technical
 switches if called from snakemake rules. (#1213)

---
 snakemake/common/__init__.py |  3 +++
 snakemake/parser.py          |  6 ++++--
 snakemake/shell.py           | 24 +++++++++++++++++-------
 3 files changed, 24 insertions(+), 9 deletions(-)

diff --git a/snakemake/common/__init__.py b/snakemake/common/__init__.py
index 1ade8f179..abb31b5ab 100644
--- a/snakemake/common/__init__.py
+++ b/snakemake/common/__init__.py
@@ -69,6 +69,9 @@ def __new__(cls, _=None):
 APPDIRS = None
 
 
+RULEFUNC_CONTEXT_MARKER = "__is_snakemake_rule_func"
+
+
 def get_appdirs():
     global APPDIRS
     if APPDIRS is None:
diff --git a/snakemake/parser.py b/snakemake/parser.py
index a5440e7f0..d0546769f 100644
--- a/snakemake/parser.py
+++ b/snakemake/parser.py
@@ -11,6 +11,7 @@
 from io import TextIOWrapper
 
 from snakemake.exceptions import WorkflowError
+from snakemake import common
 
 dd = textwrap.dedent
 
@@ -507,10 +508,11 @@ def start(self):
             "resources, log, version, rule, conda_env, container_img, "
             "singularity_args, use_singularity, env_modules, bench_record, jobid, "
             "is_shell, bench_iteration, cleanup_scripts, shadow_dir, edit_notebook, "
-            "conda_base_path, basedir, runtime_sourcecache_path):".format(
+            "conda_base_path, basedir, runtime_sourcecache_path, {rule_func_marker}=True):".format(
                 rulename=self.rulename
                 if self.rulename is not None
-                else self.snakefile.rulecount
+                else self.snakefile.rulecount,
+                rule_func_marker=common.RULEFUNC_CONTEXT_MARKER,
             )
         )
 
diff --git a/snakemake/shell.py b/snakemake/shell.py
index 2c9f543dc..ea75cd411 100644
--- a/snakemake/shell.py
+++ b/snakemake/shell.py
@@ -14,7 +14,7 @@
 import threading
 
 from snakemake.utils import format, argvquote, cmd_exe_quote, find_bash_on_windows
-from snakemake.common import ON_WINDOWS
+from snakemake.common import ON_WINDOWS, RULEFUNC_CONTEXT_MARKER
 from snakemake.logging import logger
 from snakemake.deployment import singularity
 from snakemake.deployment.conda import Conda
@@ -130,14 +130,23 @@ def __new__(
             kwargs["quote_func"] = cmd_exe_quote
 
         cmd = format(cmd, *args, stepout=2, **kwargs)
-        context = inspect.currentframe().f_back.f_locals
-        # add kwargs to context (overwriting the locals of the caller)
-        context.update(kwargs)
 
         stdout = sp.PIPE if iterable or read else STDOUT
 
         close_fds = sys.platform != "win32"
 
+        func_context = inspect.currentframe().f_back.f_locals
+
+        if func_context.get(RULEFUNC_CONTEXT_MARKER):
+            # If this comes from a rule, we expect certain information to be passed
+            # implicitly via the rule func context, which is added here.
+            context = func_context
+        else:
+            # Otherwise, context is just filled via kwargs.
+            context = dict()
+        # add kwargs to context (overwriting the locals of the caller)
+        context.update(kwargs)
+
         jobid = context.get("jobid")
         if not context.get("is_shell"):
             logger.shellcmd(cmd)
@@ -148,6 +157,8 @@ def __new__(
         env_modules = context.get("env_modules", None)
         shadow_dir = context.get("shadow_dir", None)
         resources = context.get("resources", {})
+        singularity_args = context.get("singularity_args", "")
+        threads = context.get("threads", 1)
 
         cmd = " ".join((cls._process_prefix, cmd, cls._process_suffix)).strip()
 
@@ -176,11 +187,10 @@ def __new__(
             cmd = '"{}" "{}"'.format(cls.get_executable() or "/bin/sh", script)
 
         if container_img:
-            args = context.get("singularity_args", "")
             cmd = singularity.shellcmd(
                 container_img,
                 cmd,
-                args,
+                singularity_args,
                 envvars=None,
                 shell_executable=cls._process_args["executable"],
                 container_workdir=shadow_dir,
@@ -190,12 +200,12 @@ def __new__(
         if conda_env:
             logger.info("Activating conda environment: {}".format(conda_env))
 
-        threads = str(context.get("threads", 1))
         tmpdir_resource = resources.get("tmpdir", None)
         # environment variable lists for linear algebra libraries taken from:
         # https://stackoverflow.com/a/53224849/2352071
         # https://github.com/xianyi/OpenBLAS/tree/59243d49ab8e958bb3872f16a7c0ef8c04067c0a#setting-the-number-of-threads-using-environment-variables
         envvars = dict(os.environ)
+        threads = str(threads)
         envvars["OMP_NUM_THREADS"] = threads
         envvars["GOTO_NUM_THREADS"] = threads
         envvars["OPENBLAS_NUM_THREADS"] = threads