Use subprocess's env argument over env command-line utility

em_workflows/dm_conversion/flow.py

@@ -76,8 +76,6 @@ def convert_if_int16_tiff(file_path: FilePath) -> None:
     shrink_factor = _calculate_shrink_factor(file_path.fp_in)
 
     cmd = [
-        "env",
-        "IMOD_OUTPUT_FORMAT=TIF",
         DMConfig.newstack_loc,
         "-shrink",
         f"{shrink_factor:.3f}",
@@ -92,7 +90,7 @@ def convert_if_int16_tiff(file_path: FilePath) -> None:
         str(tif_8_bit),
     ]
     utils.log(f"Generated cmd {cmd}")
-    FilePath.run(cmd, log_fp)
+    FilePath.run(cmd, log_fp, env={"IMOD_OUTPUT_FORMAT": "TIF"})
 
 
 
@@ -127,8 +125,6 @@ def convert_2d_mrc_to_tiff(file_path: FilePath) -> None:
     utils.log(f"{file_path.fp_in.as_posix()} is a mrc file, will convert to {out_fp}.")
     # work out meansd
     cmd = [
-        "env",
-        "IMOD_OUTPUT_FORMAT=TIF",
         DMConfig.newstack_loc,
         "-shrink",
         shrink_factor_3,
@@ -142,7 +138,7 @@ def convert_2d_mrc_to_tiff(file_path: FilePath) -> None:
         out_fp,
     ]
     utils.log(f"Generated cmd {cmd}")
-    FilePath.run(cmd, log_fp)
+    FilePath.run(cmd, log_fp, env={"IMOD_OUTPUT_FORMAT": "TIF"})
 
 
 @task(

em_workflows/file_path.py

@@ -1,7 +1,7 @@
 import datetime
 import shutil
 import os
-from typing import List, Dict
+from typing import List, Dict, Optional, AnyStr
 from pathlib import Path
 import tempfile
 import subprocess
@@ -272,15 +272,30 @@ def rm_workdir(self):
         shutil.rmtree(self.working_dir, ignore_errors=True)
 
     @staticmethod
-    def run(cmd: List[str], log_file: str) -> int:
+    def run(cmd: List[str], log_file: str, env: Optional[Dict[AnyStr, AnyStr]] = None, *, copy_env: bool = True) -> int:
         """Runs a Unix command as a subprocess
 
         - Captures stderr & stddout and writes them to the `log_file` input parameter.
         - If final returncode is not 0, raises a FAIL signal
+
+        :param cmd: list of strings representing the command to run
+        :param log_file: path to the log file to write the stdout and stderr to
+        :param env: dictionary of additional environment variables to pass to the subprocess
+        :param copy_env: if True, the subprocess inherits the parent's environment
         """
+
+        if env is None:
+            if not copy_env:
+                env = {}
+            # Note: if env is not and copy_env is True, the subprocess inherits the parent's environment,
+            # by passing env=None
+        elif copy_env:
+            # merge dictionaries python 3.9+
+            env = os.environ | env
+
         log(f"Running subprocess: {' '.join(cmd)} logfile: {log_file}")
 
-        with (subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, bufsize=1) as p,
+        with (subprocess.Popen(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT, bufsize=1, env=env) as p,
               open(log_file, 'ab') as file):
             file.write(f"Running subprocess: {' '.join(cmd)}\n".encode())