first run of the tutorial with spack!

Signed-off-by: vsoch <vsoch@users.noreply.github.com>

snakemake/script.py

@@ -468,11 +468,10 @@ def write_script(self, preamble, fd):
         fd.write(self.source)
 
     def _is_python_env(self):
-        print("IS PYTHON ENV in script.py")
-        import IPython
-        IPython.embed()
         if self.conda_env is not None:
             prefix = os.path.join(self.conda_env, "bin")
+        elif self.spack_env is not None:
+            prefix = os.path.join(self.spack_env, ".spack-env", "view", "bin")  
         elif self.env_modules is not None:
             prefix = self._execute_cmd("echo $PATH", read=True).split(":")[0]
         else:
@@ -487,16 +486,15 @@ def _get_python_version(self):
         return tuple(map(int, out.strip().split(".")))
 
     def execute_script(self, fname, edit=False):
+        # Are we operating in a spack or conda environment?
+        is_env = self.conda_env is not None or self.spack_env is not None       
+
         py_exec = sys.executable
         if self.container_img is not None:
             # use python from image
             py_exec = "python"
 
-        # TODO stopped here, need to add spack_env command.
-        print("SCRIPT.PY EXECUTE")
-        import IPython
-        IPython.embed()
-        elif self.conda_env is not None or self.env_modules is not None:
+        elif is_env or self.env_modules is not None:
             if self._is_python_env():
                 py_version = self._get_python_version()
                 # If version is None, all fine, because host python usage is intended.
@@ -520,6 +518,7 @@ def execute_script(self, fname, edit=False):
             # use forward slashes so script command still works even if
             # bash is configured as executable on Windows
             py_exec = py_exec.replace("\\", "/")
+
         # use the same Python as the running process or the one from the environment
         self._execute_cmd("{py_exec} {fname:q}", py_exec=py_exec, fname=fname)