From 26b828b326d206f1472178e67444bbb397958b88 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Mon, 11 Mar 2024 21:59:35 -0700
Subject: [PATCH] Add missing `directory` kwarg on QCJob `run()` method (#323)

* Add missing `directory` kwarg on QCJob `run()` method

* add doc strings and type annos

---------

Co-authored-by: Janosh Riebesell <janosh.riebesell@gmail.com>
---
 .github/workflows/{linting.yml => lint.yml} |  2 ++
 .github/workflows/test.yml                  |  2 +-
 custodian/qchem/jobs.py                     | 36 ++++++++++++++++-----
 3 files changed, 31 insertions(+), 9 deletions(-)
 rename .github/workflows/{linting.yml => lint.yml} (99%)

diff --git a/.github/workflows/linting.yml b/.github/workflows/lint.yml
similarity index 99%
rename from .github/workflows/linting.yml
rename to .github/workflows/lint.yml
index 503c0d34..b81e478b 100644
--- a/.github/workflows/linting.yml
+++ b/.github/workflows/lint.yml
@@ -13,11 +13,13 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
+
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
           python-version: 3.11
           cache: pip
+
       - name: Run pre-commit
         run: |
           pip install pre-commit
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index d3459831..5d8cd672 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -51,7 +51,7 @@ jobs:
       - name: pytest
         env:
           PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
-          MPLBACKEND: "Agg"
+          MPLBACKEND: Agg
         run: pytest --cov=custodian --color=yes tests
 
       - name: Upload coverage reports to Codecov
diff --git a/custodian/qchem/jobs.py b/custodian/qchem/jobs.py
index bf965ae8..399310f9 100644
--- a/custodian/qchem/jobs.py
+++ b/custodian/qchem/jobs.py
@@ -1,5 +1,7 @@
 """This module implements basic kinds of jobs for QChem runs."""
 
+from __future__ import annotations
+
 import copy
 import os
 import shutil
@@ -100,8 +102,15 @@ def __init__(
             print("SLURM_CPUS_ON_NODE not in environment")
 
     @property
-    def current_command(self, directory="./"):
-        """The command to run QChem."""
+    def current_command(self, directory: str | Path = "./"):
+        """The command to run QChem.
+
+        Args:
+            directory (str): The directory to run in. Defaults to "./".
+
+        Returns:
+            (str) The command to run QChem.
+        """
         self._input_path = os.path.join(directory, self.input_file)
         self._output_path = os.path.join(directory, self.output_file)
         multi = {"openmp": "-nt", "mpi": "-np"}
@@ -111,8 +120,12 @@ def current_command(self, directory="./"):
         command = self.qchem_command + command
         return " ".join(command)
 
-    def setup(self, directory="./"):
-        """Sets up environment variables necessary to efficiently run QChem."""
+    def setup(self, directory: str | Path = "./"):
+        """Sets up environment variables necessary to efficiently run QChem.
+
+        Args:
+            directory (str): The directory to run in. Defaults to "./".
+        """
         self._input_path = os.path.join(directory, self.input_file)
         if self.backup:
             shutil.copy(self._input_path, os.path.join(directory, f"{self.input_file}.orig"))
@@ -132,8 +145,12 @@ def setup(self, directory="./"):
                 raise RuntimeError("Trying to run NBO7 without providing NBOEXE in fworker! Exiting...")
             os.environ["NBOEXE"] = self.nboexe
 
-    def postprocess(self, directory="./"):
-        """Renames and removes scratch files after running QChem."""
+    def postprocess(self, directory: str | Path = "./"):
+        """Renames and removes scratch files after running QChem.
+
+        Args:
+            directory (str): The directory to run in. Defaults to "./".
+        """
         self._input_path = os.path.join(directory, self.input_file)
         self._output_path = os.path.join(directory, self.output_file)
         self._qclog_path = os.path.join(directory, self.qclog_file)
@@ -155,10 +172,13 @@ def postprocess(self, directory="./"):
             except FileNotFoundError:
                 pass
 
-    def run(self):
+    def run(self, directory: str | Path = "./"):
         """
         Perform the actual QChem run.
 
+        Args:
+            directory (str): The directory to run in. Defaults to "./".
+
         Returns:
             (subprocess.Popen) Used for monitoring.
         """
@@ -172,7 +192,7 @@ def run(self):
             os.makedirs(local_scratch, exist_ok=True)
             shutil.move(os.path.join(os.environ["QCSCRATCH"], "53.0"), local_scratch)
         with open(self.qclog_file, "w") as qclog:
-            return subprocess.Popen(self.current_command, stdout=qclog, shell=True)  # pylint: disable=R1732
+            return subprocess.Popen(self.current_command, cwd=directory, stdout=qclog, shell=True)  # pylint: disable=R1732
 
     @classmethod
     def opt_with_frequency_flattener(