From ede313dcd31ea5f136b3b8f743e2265331475342 Mon Sep 17 00:00:00 2001
From: stydodt <56256130+stydodt@users.noreply.github.com>
Date: Sat, 27 Nov 2021 08:25:36 +0100
Subject: [PATCH] fix: SameFileError #1153 (#1220)
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* Fixes https://github.com/snakemake/snakemake/issues/1153. Path.parent replaces target path when full paths are provided, matching file and target locations.

* Turn absolute path into relative one instead of avoiding file path altogether.

Co-authored-by: Benjamin Essigman <essigman@scailyte.com>
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
---
 snakemake/unit_tests/__init__.py         |  7 ++++++-
 tests/test_generate_unit_tests/Snakefile |  4 ++++
 tests/tests.py                           | 16 +++++++++-------
 3 files changed, 19 insertions(+), 8 deletions(-)

diff --git a/snakemake/unit_tests/__init__.py b/snakemake/unit_tests/__init__.py
index 2725af273..50111fe25 100644
--- a/snakemake/unit_tests/__init__.py
+++ b/snakemake/unit_tests/__init__.py
@@ -75,7 +75,12 @@ def generate(dag, path, deploy=["conda", "singularity"], configfiles=None):
                 def copy_files(files, content_type):
                     for f in files:
                         f = Path(f)
-                        target = path / rulename / content_type / f.parent
+                        parent = f.parent
+                        if parent.is_absolute():
+                            root = str(f.parents[len(f.parents) - 1])
+                            parent = str(parent)[len(root) :]
+                            print(parent)
+                        target = path / rulename / content_type / parent
                         os.makedirs(target, exist_ok=True)
                         if f.is_dir():
                             shutil.copytree(f, target)
diff --git a/tests/test_generate_unit_tests/Snakefile b/tests/test_generate_unit_tests/Snakefile
index 6d03b9d19..335d78985 100644
--- a/tests/test_generate_unit_tests/Snakefile
+++ b/tests/test_generate_unit_tests/Snakefile
@@ -1,8 +1,12 @@
+import os
+
 rule all:
     input:
         expand("test/{sample}.tsv", sample=range(3))
 
 rule a:
+    input:
+        os.environ["UNIT_TEST_TMPFILE"]
     output:
         temp("test/{sample}.txt")
     shell:
diff --git a/tests/tests.py b/tests/tests.py
index f11dcd806..78a5fcd72 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1192,13 +1192,15 @@ def test_github_issue640():
 
 @skip_on_windows  # TODO check whether this might be enabled later
 def test_generate_unit_tests():
-    tmpdir = run(
-        dpath("test_generate_unit_tests"),
-        generate_unit_tests=".tests/unit",
-        check_md5=False,
-        cleanup=False,
-    )
-    sp.check_call(["pytest", ".tests", "-vs"], cwd=tmpdir)
+    with tempfile.NamedTemporaryFile() as tmpfile:
+        os.environ["UNIT_TEST_TMPFILE"] = tmpfile.name
+        tmpdir = run(
+            dpath("test_generate_unit_tests"),
+            generate_unit_tests=".tests/unit",
+            check_md5=False,
+            cleanup=False,
+        )
+        sp.check_call(["pytest", ".tests", "-vs"], cwd=tmpdir)
 
 
 @skip_on_windows