Merge pull request #121 from epruesse/development

Fix Python 3.8 compatability

src/ymp/env.py

@@ -12,10 +12,7 @@
 
 from ruamel.yaml import YAML
 
-try:
-    import snakemake.conda as snakemake_conda
-except ModuleNotFoundError:
-    import snakemake.deployment.conda as snakemake_conda
+import snakemake.deployment.conda as snakemake_conda
 
 from snakemake.rules import Rule
 
@@ -340,11 +337,15 @@ def run(self, command):
 
         Returns exit code of command run.
         """
+        command = " ".join(command)
+        command = snakemake_conda.Conda().shellcmd(self.path, command)
         cfg = ymp.get_config()
-        command = "source activate {}; {}".format(self.path, " ".join(command))
         log.debug("Running: %s", command)
-        return subprocess.run(command,
-                              shell=True, executable=cfg.shell).returncode
+        return subprocess.run(
+            command,
+            shell=True,
+            executable=cfg.shell
+        ).returncode
 
     def export(self, stream, typ='yml'):
         """Freeze environment"""

src/ymp/stage/expander.py

@@ -60,6 +60,7 @@ def get_value(self, key, args, kwargs):
         def get_value_(self, key, args, kwargs):
             stage = Stage.active
             if "(" in key:
+                args = list(args)
                 if key[-1] != ")":
                     raise YmpRuleError(
                         stage,

tests/test_cli.py

@@ -296,7 +296,7 @@ def test_env_run(invoker, demo_dir, mock_conda, mock_downloader, capfd):
     res = invoker.call("env", "run", "bbmap", "true")
     assert res.exit_code == 0
     cap = capfd.readouterr()
-    assert "Not a conda environment" in cap.err
+    assert "bin/activate: No such file " in cap.err
 
 
 @pytest.mark.parametrize(