move TEST_DIR + TEST_FILES from custodian/__init__.py to tests/confte…

…st.py

fixes TEST_DIR location hardcoded to installation dir

custodian/__init__.py

@@ -17,5 +17,3 @@
 
 PKG_DIR = os.path.dirname(__file__)
 ROOT = os.path.dirname(PKG_DIR)
-TEST_DIR = f"{ROOT}/tests"
-TEST_FILES = f"{TEST_DIR}/files"

custodian/cp2k/jobs.py

@@ -127,17 +127,17 @@ def run(self):
     # and custodian should only run the job itself
     def postprocess(self):
         """Postprocessing includes renaming and gzipping where necessary."""
-        fs = os.listdir(".")
+        files = os.listdir(".")
         if os.path.exists(self.output_file) and self.suffix != "":
             os.mkdir(f"run{self.suffix}")
-            for f in fs:
-                if "json" in f:
+            for file in files:
+                if "json" in file:
                     continue
-                if not os.path.isdir(f):
+                if not os.path.isdir(file):
                     if self.final:
-                        shutil.move(f, f"run{self.suffix}/{f}")
+                        shutil.move(file, f"run{self.suffix}/{file}")
                     else:
-                        shutil.copy(f, f"run{self.suffix}/{f}")
+                        shutil.copy(file, f"run{self.suffix}/{file}")
 
         # Remove continuation so if a subsequent job is run in
         # the same directory, will not restart this job.

custodian/custodian.py

@@ -235,8 +235,8 @@ def safe_extract(tar, path=".", members=None, *, numeric_owner=False):
 
     @staticmethod
     def _delete_checkpoints(cwd):
-        for f in glob(os.path.join(cwd, "custodian.chk.*.tar.gz")):
-            os.remove(f)
+        for file in glob(os.path.join(cwd, "custodian.chk.*.tar.gz")):
+            os.remove(file)
 
     @staticmethod
     def _save_checkpoint(cwd, index):

custodian/feff/jobs.py

@@ -59,22 +59,17 @@ def __init__(
         self.gzipped = gzipped
         self.gzipped_prefix = gzipped_prefix
 
-    def setup(self):
-        """
-        Performs initial setup for FeffJob, do backing up.
-
-        Returns:
-
-        """
+    def setup(self) -> None:
+        """Performs initial setup for FeffJob, do backing up."""
         decompress_dir(".")
 
         if self.backup:
-            for f in FEFF_INPUT_FILES:
-                shutil.copy(f, f"{f}.orig")
+            for file in FEFF_INPUT_FILES:
+                shutil.copy(file, f"{file}.orig")
 
-            for f in FEFF_BACKUP_FILES:
-                if os.path.isfile(f):
-                    shutil.copy(f, f"{f}.orig")
+            for file in FEFF_BACKUP_FILES:
+                if os.path.isfile(file):
+                    shutil.copy(file, f"{file}.orig")
 
     def run(self):
         """

custodian/lobster/jobs.py

@@ -73,8 +73,8 @@ def __init__(
     def setup(self):
         """Will backup lobster input files."""
         if self.backup:
-            for f in LOBSTERINPUT_FILES:
-                shutil.copy(f, f"{f}.orig")
+            for file in LOBSTERINPUT_FILES:
+                shutil.copy(file, f"{file}.orig")
 
     def run(self):
         """Runs the job."""

custodian/utils.py

@@ -23,8 +23,8 @@ def backup(filenames, prefix="error"):
     logging.info(f"Backing up run to {filename}.")
     with tarfile.open(filename, "w:gz") as tar:
         for fname in filenames:
-            for f in glob(fname):
-                tar.add(f)
+            for file in glob(fname):
+                tar.add(file)
 
 
 def get_execution_host_info():

custodian/vasp/interpreter.py

@@ -49,5 +49,5 @@ def apply_actions(self, actions):
                 self.modify(a["action"], a["file"])
             else:
                 raise ValueError(f"Unrecognized format: {a}")
-        for f in modified:
-            self.vi[f].write_file(f)
+        for file in modified:
+            self.vi[file].write_file(file)

custodian/vasp/io.py

@@ -1,6 +1,4 @@
-"""
-Helper functions for dealing with vasp files.
-"""
+"""Helper functions for dealing with vasp files."""
 
 from pymatgen.io.vasp.outputs import Outcar, Vasprun
 

custodian/vasp/jobs.py

@@ -174,11 +174,11 @@ def setup(self):
         decompress_dir(".")
 
         if self.backup:
-            for f in VASP_INPUT_FILES:
+            for file in VASP_INPUT_FILES:
                 try:
-                    shutil.copy(f, f"{f}.orig")
+                    shutil.copy(file, f"{file}.orig")
                 except FileNotFoundError:  # handle the situation when there is no KPOINTS file
-                    if f == "KPOINTS":
+                    if file == "KPOINTS":
                         pass
 
         if self.auto_npar:
@@ -257,12 +257,12 @@ def postprocess(self):
         Postprocessing includes renaming and gzipping where necessary.
         Also copies the magmom to the incar if necessary.
         """
-        for f in [*VASP_OUTPUT_FILES, self.output_file]:
-            if os.path.exists(f):
+        for file in [*VASP_OUTPUT_FILES, self.output_file]:
+            if os.path.exists(file):
                 if self.final and self.suffix != "":
-                    shutil.move(f, f"{f}{self.suffix}")
+                    shutil.move(file, f"{file}{self.suffix}")
                 elif self.suffix != "":
-                    shutil.copy(f, f"{f}{self.suffix}")
+                    shutil.copy(file, f"{file}{self.suffix}")
 
         if self.copy_magmom and not self.final:
             try:
@@ -793,8 +793,8 @@ def setup(self):
 
         if self.backup:
             # Back up KPOINTS, INCAR, POTCAR
-            for f in VASP_NEB_INPUT_FILES:
-                shutil.copy(f, f"{f}.orig")
+            for file in VASP_NEB_INPUT_FILES:
+                shutil.copy(file, f"{file}.orig")
             # Back up POSCARs
             for path in neb_dirs:
                 poscar = os.path.join(path, "POSCAR")
@@ -870,21 +870,21 @@ def postprocess(self):
         """Postprocessing includes renaming and gzipping where necessary."""
         # Add suffix to all sub_dir/{items}
         for path in self.neb_dirs:
-            for f in VASP_NEB_OUTPUT_SUB_FILES:
-                f = os.path.join(path, f)
-                if os.path.exists(f):
+            for file in VASP_NEB_OUTPUT_SUB_FILES:
+                file = os.path.join(path, file)
+                if os.path.exists(file):
                     if self.final and self.suffix != "":
-                        shutil.move(f, f"{f}{self.suffix}")
+                        shutil.move(file, f"{file}{self.suffix}")
                     elif self.suffix != "":
-                        shutil.copy(f, f"{f}{self.suffix}")
+                        shutil.copy(file, f"{file}{self.suffix}")
 
         # Add suffix to all output files
-        for f in [*VASP_NEB_OUTPUT_FILES, self.output_file]:
-            if os.path.exists(f):
+        for file in [*VASP_NEB_OUTPUT_FILES, self.output_file]:
+            if os.path.exists(file):
                 if self.final and self.suffix != "":
-                    shutil.move(f, f"{f}{self.suffix}")
+                    shutil.move(file, f"{file}{self.suffix}")
                 elif self.suffix != "":
-                    shutil.copy(f, f"{f}{self.suffix}")
+                    shutil.copy(file, f"{file}{self.suffix}")
 
 
 class GenerateVaspInputJob(Job):

tests/ansible/__init__.py

@@ -1,3 +1 @@
-"""
-Tests for ansible package.
-"""
+"""Tests for ansible package."""

tests/vasp/conftest.py → tests/conftest.py

@@ -1,9 +1,13 @@
 """This module mocks functions needed for pytest."""
 
 import multiprocessing
+import os
 
 import pytest
 
+TEST_DIR = os.path.dirname(__file__)
+TEST_FILES = f"{TEST_DIR}/files"
+
 
 @pytest.fixture(autouse=True)
 def _patch_get_potential_energy(monkeypatch):

tests/cp2k/test_handlers.py

@@ -11,7 +11,6 @@
 from pymatgen.io.cp2k.inputs import Keyword, KeywordList
 from pymatgen.io.cp2k.sets import StaticSet
 
-from custodian import TEST_FILES
 from custodian.cp2k.handlers import (
     AbortHandler,
     FrozenJobErrorHandler,
@@ -21,6 +20,7 @@
     get_conv,
 )
 from custodian.cp2k.interpreter import Cp2kModder
+from tests.conftest import TEST_FILES
 
 TEST_FILES_DIR = f"{TEST_FILES}/cp2k"
 

tests/cp2k/test_jobs.py

@@ -7,8 +7,9 @@
 from glob import glob
 from pathlib import Path
 
-from custodian import TEST_FILES, Custodian
+from custodian import Custodian
 from custodian.cp2k.jobs import Cp2kJob
+from tests.conftest import TEST_FILES
 
 MODULE_DIR = Path(__file__).resolve().parent
 TEST_FILES_DIR = f"{TEST_FILES}/cp2k"
@@ -17,10 +18,10 @@
 
 
 def clean_dir(dir):
-    for f in glob(os.path.join(dir, "error.*.tar.gz")):
-        os.remove(f)
-    for f in glob(os.path.join(dir, "custodian.chk.*.tar.gz")):
-        os.remove(f)
+    for file in glob(os.path.join(dir, "error.*.tar.gz")):
+        os.remove(file)
+    for file in glob(os.path.join(dir, "custodian.chk.*.tar.gz")):
+        os.remove(file)
 
 
 class HandlerTests(unittest.TestCase):

tests/feff/test_handlers.py

@@ -3,8 +3,8 @@
 import unittest
 from glob import glob
 
-from custodian import TEST_FILES
 from custodian.feff.handlers import UnconvergedErrorHandler
+from tests.conftest import TEST_FILES
 
 __author__ = "Chen Zheng"
 __copyright__ = "Copyright 2012, The Materials Project"
@@ -15,8 +15,8 @@
 
 
 def clean_dir():
-    for f in glob("error.*.tar.gz"):
-        os.remove(f)
+    for file in glob("error.*.tar.gz"):
+        os.remove(file)
 
 
 class UnconvergedErrorHandlerTest(unittest.TestCase):

tests/feff/test_jobs.py

@@ -4,8 +4,8 @@
 from monty.tempfile import ScratchDir
 from pymatgen.io.feff.inputs import Atoms, Tags
 
-from custodian import TEST_FILES
 from custodian.feff.jobs import FeffJob
+from tests.conftest import TEST_FILES
 
 __author__ = "Chen Zheng"
 __copyright__ = "Copyright 2012, The Materials Project"

tests/lobster/test_handlers.py

@@ -1,7 +1,7 @@
 import os
 
-from custodian import TEST_FILES
 from custodian.lobster.handlers import ChargeSpillingValidator, EnoughBandsValidator, LobsterFilesValidator
+from tests.conftest import TEST_FILES
 
 test_files_lobster = f"{TEST_FILES}/lobster/lobsterouts"
 

tests/lobster/test_jobs.py

@@ -4,8 +4,8 @@
 from monty.os import cd
 from monty.tempfile import ScratchDir
 
-from custodian import TEST_FILES
 from custodian.lobster.jobs import LobsterJob
+from tests.conftest import TEST_FILES
 
 test_files_lobster2 = f"{TEST_FILES}/lobster/lobsterins"
 test_files_lobster3 = f"{TEST_FILES}/lobster/vasp_lobster_output"

tests/nwchem/__init__.py

@@ -1,3 +1 @@
-"""
-Tests for nwchem package.
-"""
+"""Tests for nwchem package."""

tests/nwchem/test_handlers.py

@@ -2,8 +2,8 @@
 import shutil
 from glob import glob
 
-from custodian import TEST_FILES
 from custodian.nwchem.handlers import NwchemErrorHandler
+from tests.conftest import TEST_FILES
 
 __author__ = "shyuepingong"
 __version__ = "0.1"
@@ -25,5 +25,5 @@ def test_check_correct():
     handler.check()
     handler.correct()
     shutil.move("Li1_1.nw.orig", "Li1_1.nw")
-    for f in glob("error.*.tar.gz"):
-        os.remove(f)
+    for file in glob("error.*.tar.gz"):
+        os.remove(file)

tests/qchem/__init__.py

@@ -1,6 +1,4 @@
-"""
-Tests for QChem Custodian
-"""
+"""Tests for QChem Custodian"""
 
 import os
 import unittest

tests/qchem/test_handlers.py

@@ -5,8 +5,8 @@
 
 from pymatgen.io.qchem.inputs import QCInput
 
-from custodian import TEST_FILES
 from custodian.qchem.handlers import QChemErrorHandler
+from tests.conftest import TEST_FILES
 
 try:
     from openbabel import openbabel as ob

tests/qchem/test_job_handler_interaction.py

@@ -5,9 +5,9 @@
 
 from pymatgen.io.qchem.inputs import QCInput
 
-from custodian import TEST_FILES
 from custodian.qchem.handlers import QChemErrorHandler
 from custodian.qchem.jobs import QCJob
+from tests.conftest import TEST_FILES
 
 try:
     from openbabel import openbabel as ob

tests/qchem/test_jobs.py

@@ -7,8 +7,8 @@
 import pytest
 from pymatgen.io.qchem.inputs import QCInput
 
-from custodian import TEST_FILES
 from custodian.qchem.jobs import QCJob
+from tests.conftest import TEST_FILES
 
 try:
     from openbabel import openbabel as ob

tests/test_custodian.py

@@ -310,8 +310,8 @@ def test_from_spec(self):
         assert len(c.validators) == 1
 
     def tearDown(self):
-        for f in glob("custodian.*.tar.gz"):
-            os.remove(f)
+        for file in glob("custodian.*.tar.gz"):
+            os.remove(file)
         try:
             os.remove("custodian.json")
         except OSError:

tests/vasp/__init__.py

@@ -1,3 +1 @@
-"""
-Tests for vasp package.
-"""
+"""Tests for vasp package."""

tests/vasp/test_handlers.py

@@ -8,7 +8,6 @@
 from pymatgen.io.vasp.inputs import Incar, Kpoints, Structure, VaspInput
 from pymatgen.util.testing import PymatgenTest
 
-from custodian import TEST_FILES
 from custodian.utils import tracked_lru_cache
 from custodian.vasp.handlers import (
     AliasingErrorHandler,
@@ -27,6 +26,7 @@
     VaspErrorHandler,
     WalltimeHandler,
 )
+from tests.conftest import TEST_FILES
 
 __author__ = "Shyue Ping Ong, Stephen Dacek, Janosh Riebesell"
 __copyright__ = "Copyright 2012, The Materials Project"

tests/vasp/test_io.py

@@ -1,8 +1,8 @@
 import pytest
 
-from custodian import TEST_FILES
 from custodian.utils import tracked_lru_cache
 from custodian.vasp.io import load_outcar, load_vasprun
+from tests.conftest import TEST_FILES
 
 
 @pytest.fixture(autouse=True)