From: Michael R. Crusoe <michael.crusoe@gmail.com>
Subject: Use python3 instead of python
--- snakemake.orig/tests/test_delete_all_output/Snakefile
+++ snakemake/tests/test_delete_all_output/Snakefile
@@ -8,9 +8,9 @@
         """
         echo $PATH
         ls
-        python -m snakemake -s Snakefile_inner all && \
+        python3 -m snakemake -s Snakefile_inner all && \
         rm nothere && \
-        python -m snakemake -s Snakefile_inner --delete-all-output all && \
+        python3 -m snakemake -s Snakefile_inner --delete-all-output all && \
         test -f infile && test ! -f intermediate && test ! -f somedir/final && \
         test ! -d empty_dir && test ! -L dangling && test ! -d full_dir
         """
@@ -19,8 +19,8 @@
     output: touch("delete_temp_output")
     shell:
         """
-        python -m snakemake -s Snakefile_inner --notemp temp && \
-        python -m snakemake -s Snakefile_inner --delete-temp-output temp && \
+        python3 -m snakemake -s Snakefile_inner --notemp temp && \
+        python3 -m snakemake -s Snakefile_inner --delete-temp-output temp && \
         test -f infile && test ! -f temp_intermediate && \
         test ! -d temp_empty_dir && test ! -d temp_full_dir && test -f temp_keep
         """
--- snakemake.orig/tests/test_list_untracked/Snakefile
+++ snakemake/tests/test_list_untracked/Snakefile
@@ -1,3 +1,3 @@
 rule run_test:
     output: "leftover_files"
-    shell:  "python -m snakemake -s Snakefile_inner --list-untracked 2> {output}"
+    shell:  "python3 -m snakemake -s Snakefile_inner --list-untracked 2> {output}"
--- snakemake.orig/tests/tests.py
+++ snakemake/tests/tests.py
@@ -987,7 +987,7 @@
     workdir = dpath("test_convert_to_cwl")
     # run(workdir, export_cwl=os.path.join(workdir, "workflow.cwl"))
     shell(
-        "cd {workdir}; PYTHONPATH={src} python -m snakemake --export-cwl workflow.cwl",
+        "cd {workdir}; PYTHONPATH={src} python3 -m snakemake --export-cwl workflow.cwl",
         src=os.getcwd(),
     )
     shell("cd {workdir}; cwltool --singularity workflow.cwl")
@@ -1043,7 +1043,7 @@
 )
 def test_tibanna():
     workdir = dpath("test_tibanna")
-    subprocess.check_call(["python", "cleanup.py"], cwd=workdir)
+    subprocess.check_call(["python3", "cleanup.py"], cwd=workdir)
     run(
         workdir,
         use_conda=True,
@@ -1082,7 +1082,7 @@
     pdf_path = "fg.pdf"
 
     # make sure the calls work
-    shell("cd {workdir}; python -m snakemake --filegraph > {dot_path}")
+    shell("cd {workdir}; python3 -m snakemake --filegraph > {dot_path}")
 
     # make sure the output can be interpreted by dot
     with open(dot_path, "rb") as dot_file, open(pdf_path, "wb") as pdf_file:
--- snakemake.orig/tests/test_profile/Snakefile
+++ snakemake/tests/test_profile/Snakefile
@@ -1,3 +1,3 @@
 rule:
     shell:
-        "python -m snakemake --profile . -s Snakefile.internal"
+        "python3 -m snakemake --profile . -s Snakefile.internal"
