From 81481d000b3241eee0f5a5722f0279ece92d1e96 Mon Sep 17 00:00:00 2001
From: chris-langfield <christopher.langfield@internationalbrainlab.org>
Date: Tue, 30 Jul 2024 09:49:39 -0400
Subject: [PATCH] Revert "test forcing subprocess for large_jobs"

This reverts commit 31ff95dc5de1899b813fa8cbd948de6d73472364.
---
 ibllib/pipes/ephys_tasks.py | 47 ++++++++++++++++++++-----------------
 1 file changed, 26 insertions(+), 21 deletions(-)

diff --git a/ibllib/pipes/ephys_tasks.py b/ibllib/pipes/ephys_tasks.py
index 25bb4707a..ee5a0c8e6 100644
--- a/ibllib/pipes/ephys_tasks.py
+++ b/ibllib/pipes/ephys_tasks.py
@@ -656,27 +656,32 @@ def _run_iblsort(self, ap_file):
         _logger.info(f"job progress command: tail -f {temp_dir} *.log")
         temp_dir.mkdir(parents=True, exist_ok=True)
         check_nvidia_driver()
-        command2run = f"{self.SHELL_SCRIPT} {ap_file} {temp_dir}"
-        _logger.info(command2run)
-        process = subprocess.Popen(
-            command2run,
-            shell=True,
-            stdout=subprocess.PIPE,
-            stderr=subprocess.PIPE,
-            executable="/bin/bash",
-        )
-        info, error = process.communicate()
-        info_str = info.decode("utf-8").strip()
-        _logger.info(info_str)
-        if process.returncode != 0:
-            error_str = error.decode("utf-8").strip()
-            # try and get the kilosort log if any
-            for log_file in temp_dir.rglob('*_kilosort.log'):
-                with open(log_file) as fid:
-                    log = fid.read()
-                    _logger.error(log)
-                break
-            raise RuntimeError(f"{self.SPIKE_SORTER_NAME} {info_str}, {error_str}")
+        try:
+            # if pykilosort is in the environment, use the installed version within the task
+            import iblsorter.ibl  # noqa
+            iblsorter.ibl.run_spike_sorting_ibl(bin_file=ap_file, scratch_dir=temp_dir)
+        except ImportError:
+            command2run = f"{self.SHELL_SCRIPT} {ap_file} {temp_dir}"
+            _logger.info(command2run)
+            process = subprocess.Popen(
+                command2run,
+                shell=True,
+                stdout=subprocess.PIPE,
+                stderr=subprocess.PIPE,
+                executable="/bin/bash",
+            )
+            info, error = process.communicate()
+            info_str = info.decode("utf-8").strip()
+            _logger.info(info_str)
+            if process.returncode != 0:
+                error_str = error.decode("utf-8").strip()
+                # try and get the kilosort log if any
+                for log_file in temp_dir.rglob('*_kilosort.log'):
+                    with open(log_file) as fid:
+                        log = fid.read()
+                        _logger.error(log)
+                    break
+                raise RuntimeError(f"{self.SPIKE_SORTER_NAME} {info_str}, {error_str}")
 
         shutil.copytree(temp_dir.joinpath('output'), sorter_dir, dirs_exist_ok=True)
         shutil.rmtree(temp_dir, ignore_errors=True)