use python executable from env

devtools/conda-envs/test_env.yaml

@@ -30,7 +30,7 @@ dependencies:
   - openmmforcefields >=0.9.0
   - openmmtools # may need to sort out ambermini/ambertools/parmed dependencies
   - openmoltools # may need to sort out ambermini/ambertools/parmed dependencies (we don't want ambertools)
-  - parmed # may need to sort out ambermini/ambertools/parmed dependencies
+  - parmed
   - pdbfixer
   - pip
   - progressbar2

perses/tests/test_examples.py

@@ -12,6 +12,8 @@
 # GLOBAL IMPORTS
 # ======================================================================
 
+import sys
+
 import pathlib
 import pytest
 import subprocess
@@ -25,13 +27,14 @@
 def run_script_file(file_path, cmd_args=None):
     """Run through the shell a python script."""
     with enter_temp_directory():
-        cmd = ["python", file_path]
+        # Make sure we grab the python executable in our env
+        cmd = [f"{sys.executable}", file_path]
         print(cmd)
         # Extend cmd list with given cmd_args
         if cmd_args:
             cmd.extend(cmd_args)
         try:
-            subprocess.run(cmd, capture_output=True, check=True)
+            subprocess.run(cmd, capture_output=True, check=True, shell=True)
         except subprocess.CalledProcessError as error:
             raise Exception(f"Example {file_path} failed. STDERR: {error.stderr.decode()}")