Merge pull request #49 from sterrettJD/fix_profile

remove input requirements from setup_profile

src/profile_setup.py

@@ -18,12 +18,7 @@ def get_args():
 
 
 def get_cookiecutter_slurm_profile(output_dir):
-    print("Provide the following inputs to setup your cluster profile.\n")
-    print("All default options can be used, EXCEPT:")
-    print("****You MUST answer `True` to `use_conda`.****")
-    print("****Please leave `profile_name` as `slurm`.**** \n") 
-
-    cookiecutter("gh:Snakemake-Profiles/slurm", output_dir=output_dir)
+    cookiecutter("gh:Snakemake-Profiles/slurm", output_dir=output_dir, no_input=True)
 
 
 def check_profile_named_slurm(output_dir):
@@ -55,6 +50,32 @@ def check_profile_named_slurm(output_dir):
                              """)
 
 
+def write_new_config(filepath, new_contents):
+    with open(filepath, 'w') as file:
+        file.write(new_contents)
+
+
+def set_use_conda_true(config_contents):
+    return config_contents.replace("use-conda: \"False\"", 
+                                   "use-conda: \"True\"")
+
+
+def set_print_shell_true(config_contents):
+    return config_contents.replace("printshellcmds: \"False\"", 
+                                   "printshellcmds: \"True\"")
+
+
+def update_HoMi_reqs_in_config(output_dir):
+    config_path = os.path.join(output_dir, "slurm", "config.yaml")
+    with open(config_path, 'r') as file:
+        content = file.read()
+
+    with_conda = set_use_conda_true(content)
+    with_conda_and_shell = set_print_shell_true(with_conda)
+
+    write_new_config(config_path, with_conda_and_shell)
+
+
 def check_use_conda_slurm(output_dir):
     config_path = os.path.join(output_dir, "slurm", "config.yaml")
 
@@ -100,6 +121,7 @@ def main():
 
     # Check that parameters that need to be set a certain way are set that way
     check_profile_named_slurm(output_dir=args.output_dir)
+    update_HoMi_reqs_in_config(output_dir=args.output_dir)
     check_use_conda_slurm(output_dir=args.output_dir)
 
     # Setup for cluster that doesn't have hyperthreading enabled

tests/test_profile_setup.py

@@ -47,3 +47,61 @@ def test_ntasks_mod(tmpdir):
     # check it's been updated
     assert "options[\"ntasks\"] = job_properties[\"threads\"]" in content
     assert "options[\"cpus-per-task\"] = job_properties[\"threads\"]" not in content
+
+
+def test_replace_conda():
+    content = """
+        latency-wait: "5"
+        use-conda: "False"
+        use-singularity: "False"
+        """
+
+    expected = """
+        latency-wait: "5"
+        use-conda: "True"
+        use-singularity: "False"
+        """
+
+    updated = ps.set_use_conda_true(content)
+    assert updated == expected
+
+
+def test_replace_printshellcmds():
+    content = """
+        latency-wait: "5"
+        use-conda: "True"
+        printshellcmds: "False"
+        """
+
+    expected = """
+        latency-wait: "5"
+        use-conda: "True"
+        printshellcmds: "True"
+        """
+
+    updated = ps.set_print_shell_true(content)
+    assert updated == expected
+
+
+def test_update_config(tmpdir):
+    cookiecutter("gh:Snakemake-Profiles/slurm", 
+                 output_dir=tmpdir, 
+                 no_input=True)
+
+    slurm_config_path = os.path.join(tmpdir, "slurm", "config.yaml")
+    with open(slurm_config_path, 'r') as file:
+        content = file.read()
+
+    # check it's there by default
+        assert "use-conda: \"False\"" in content
+    assert "printshellcmds: \"False\"" in content
+
+    # This function should replace the cpus-per-task with ntasks
+    ps.update_HoMi_reqs_in_config(tmpdir)
+
+    with open(slurm_config_path, 'r') as file:
+        content = file.read()
+
+    # check it's been updated
+    assert "use-conda: \"True\"" in content
+    assert "printshellcmds: \"True\"" in content