Move tests to their own root-level directory (#305)

* move custodian/**/tests to tests/** and test_files to tests/files

* fix crazy "..", "..", "..", "tests/files" stuff

* more crazy path clean up

* just use f-strings for path construction, no need for os.path.join

* fix needlessly specific .github/workflows/pytest.yml causing test discovery to fail

.gitattributes

@@ -1,3 +1,3 @@
 # declare HTML, rST and test files as vendored/docs to exclude them when calculating repo languages on GitHub
-**/test_files/**/* linguist-vendored
+**/tests/files/**/* linguist-vendored
 docs/**/* linguist-documentation

.github/workflows/pytest.yml

@@ -21,20 +21,22 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - uses: conda-incubator/setup-miniconda@v2
+      - uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade pymatgen
-          python -m pip install -e '.[dev]'
+          pip install --upgrade pip
+          pip install --upgrade pymatgen
+          pip install -e '.[dev]'
+
       - name: pytest
         env:
           PMG_MAPI_KEY: ${{ secrets.PMG_MAPI_KEY }}
           MPLBACKEND: "Agg"
-        run: pytest --cov=custodian custodian --color=yes
+        run: pytest --cov=. --color=yes
+
       - name: Upload coverage reports to Codecov
         uses: codecov/codecov-action@v3
         env:

.pre-commit-config.yaml

@@ -1,4 +1,4 @@
-exclude: ^(docs|test_files)
+exclude: ^(docs|tests/files)
 
 ci:
   autoupdate_schedule: monthly

custodian/__init__.py

@@ -3,7 +3,19 @@
 framework written in Python.
 """
 
-__author__ = "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, Xiaohui Qu, Matthew Horton, Samuel M. Blau"
-__version__ = "2023.10.9"
+
+import os
 
 from .custodian import Custodian
+
+__author__ = (
+    "Shyue Ping Ong, William Davidson Richards, Stephen Dacek, Xiaohui Qu, Matthew Horton, "
+    "Samuel M. Blau, Janosh Riebesell"
+)
+__version__ = "2023.10.9"
+
+
+PKG_DIR = os.path.dirname(__file__)
+ROOT = os.path.dirname(PKG_DIR)
+TEST_DIR = f"{ROOT}/tests"
+TEST_FILES = f"{TEST_DIR}/files"

docs/conf.py

@@ -15,12 +15,6 @@
 
 from pymatgen.core import __author__
 
-# sys.path.insert(0, os.path.abspath("."))
-# sys.path.insert(0, os.path.dirname(".."))
-# sys.path.insert(0, os.path.dirname("../pymatgen"))
-# sys.path.insert(0, os.path.dirname("../.."))
-
-
 project = "pymatgen"
 copyright = "2022, Materials Virtual Lab"
 author = __author__

pyproject.toml

@@ -60,7 +60,7 @@ Package = "https://pypi.org/project/custodian"
 
 [tool.setuptools.packages.find]
 include = ["custodian*"]
-exclude = ["*.tests", "*.tests.*", "test_files"]
+exclude = ["*.tests", "*.tests.*"]
 
 [tool.ruff]
 target-version = "py39"

tests/__init__.py

@@ -0,0 +1 @@
+"""Tests for main Custodian class."""

custodian/cp2k/tests/test_handlers.py → tests/cp2k/test_handlers.py

@@ -7,11 +7,11 @@
 import time
 import unittest
 import warnings
-from pathlib import Path
 
 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,
@@ -22,6 +22,8 @@
 )
 from custodian.cp2k.interpreter import Cp2kModder
 
+TEST_FILES_DIR = f"{TEST_FILES}/cp2k"
+
 
 def clean_dir(d):
     for file in glob.glob(os.path.join(d, "error.*.tar.gz")):
@@ -34,23 +36,21 @@ class HandlerTests(unittest.TestCase):
     def setUp(self):
         warnings.filterwarnings("ignore")
 
-        self.TEST_FILES_DIR = os.path.join(Path(__file__).parent.absolute(), "../../../test_files/cp2k")
-
-        clean_dir(self.TEST_FILES_DIR)
+        clean_dir(TEST_FILES_DIR)
 
         time.sleep(1)  # for frozenhandler
 
-        shutil.copy(os.path.join(self.TEST_FILES_DIR, "cp2k.inp.orig"), os.path.join(self.TEST_FILES_DIR, "cp2k.inp"))
+        shutil.copy(f"{TEST_FILES_DIR}/cp2k.inp.orig", f"{TEST_FILES_DIR}/cp2k.inp")
 
-        self.input_file = os.path.join(self.TEST_FILES_DIR, "cp2k.inp")
+        self.input_file = f"{TEST_FILES_DIR}/cp2k.inp"
 
-        self.output_file_preconditioner = os.path.join(self.TEST_FILES_DIR, "cp2k.out.precondstuck")
-        self.output_file_cholesky = os.path.join(self.TEST_FILES_DIR, "cp2k.out.cholesky")
-        self.output_file_imprecise = os.path.join(self.TEST_FILES_DIR, "cp2k.out.imprecise")
-        self.output_file_unconverged = os.path.join(self.TEST_FILES_DIR, "cp2k.out.unconverged")
-        self.output_file_stderr = os.path.join(self.TEST_FILES_DIR, "std_err.txt")
-        self.output_file_hybrid = os.path.join(self.TEST_FILES_DIR, "cp2k.out.hybrid")
-        self.output_file_conv = os.path.join(self.TEST_FILES_DIR, "cp2k.out.conv")
+        self.output_file_preconditioner = f"{TEST_FILES_DIR}/cp2k.out.precondstuck"
+        self.output_file_cholesky = f"{TEST_FILES_DIR}/cp2k.out.cholesky"
+        self.output_file_imprecise = f"{TEST_FILES_DIR}/cp2k.out.imprecise"
+        self.output_file_unconverged = f"{TEST_FILES_DIR}/cp2k.out.unconverged"
+        self.output_file_stderr = f"{TEST_FILES_DIR}/std_err.txt"
+        self.output_file_hybrid = f"{TEST_FILES_DIR}/cp2k.out.hybrid"
+        self.output_file_conv = f"{TEST_FILES_DIR}/cp2k.out.conv"
 
         self.modder = Cp2kModder(filename=self.input_file)
 

custodian/cp2k/tests/test_jobs.py → tests/cp2k/test_jobs.py

@@ -7,10 +7,11 @@
 import warnings
 from pathlib import Path
 
-from custodian import Custodian
+from custodian import TEST_FILES, Custodian
 from custodian.cp2k.jobs import Cp2kJob
 
 MODULE_DIR = Path(__file__).resolve().parent
+TEST_FILES_DIR = f"{TEST_FILES}/cp2k"
 
 cwd = os.getcwd()
 
@@ -26,15 +27,13 @@ class HandlerTests(unittest.TestCase):
     def setUp(self):
         warnings.filterwarnings("ignore")
 
-        self.TEST_FILES_DIR = os.path.join(Path(__file__).parent.absolute(), "../../../test_files/cp2k")
+        clean_dir(TEST_FILES_DIR)
 
-        clean_dir(self.TEST_FILES_DIR)
-
-        self.input_file = os.path.join(self.TEST_FILES_DIR, "cp2k.inp")
-        self.input_file_hybrid = os.path.join(self.TEST_FILES_DIR, "cp2k.inp.hybrid")
-        self.output_file = os.path.join(self.TEST_FILES_DIR, "cp2k.out.test")
-        self.std_err = os.path.join(self.TEST_FILES_DIR, "std_err.tmp")
-        self.logfile = os.path.join(self.TEST_FILES_DIR, "custodian.json")
+        self.input_file = f"{TEST_FILES_DIR}/cp2k.inp"
+        self.input_file_hybrid = f"{TEST_FILES_DIR}/cp2k.inp.hybrid"
+        self.output_file = f"{TEST_FILES_DIR}/cp2k.out.test"
+        self.std_err = f"{TEST_FILES_DIR}/std_err.tmp"
+        self.logfile = f"{TEST_FILES_DIR}/custodian.json"
 
         if os.path.isfile(Custodian.LOG_FILE):
             os.remove("custodian.json")

custodian/feff/tests/test_handlers.py → tests/feff/test_handlers.py

@@ -1,18 +1,17 @@
-__author__ = "Chen Zheng"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Chen Zheng"
-__email__ = "chz022@ucsd.edu"
-__date__ = "Oct 18, 2017"
-
 import glob
 import os
 import shutil
 import unittest
 
+from custodian import TEST_FILES
 from custodian.feff.handlers import UnconvergedErrorHandler
 
-test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files")
+__author__ = "Chen Zheng"
+__copyright__ = "Copyright 2012, The Materials Project"
+__version__ = "0.1"
+__maintainer__ = "Chen Zheng"
+__email__ = "chz022@ucsd.edu"
+__date__ = "Oct 18, 2017"
 
 
 def clean_dir():
@@ -22,8 +21,8 @@ def clean_dir():
 
 class UnconvergedErrorHandlerTest(unittest.TestCase):
     def setUp(self):
-        os.chdir(test_dir)
-        subdir = os.path.join(test_dir, "feff_unconverge")
+        os.chdir(TEST_FILES)
+        subdir = f"{TEST_FILES}/feff_unconverged"
         os.chdir(subdir)
         shutil.copy("ATOMS", "ATOMS.orig")
         shutil.copy("PARAMETERS", "PARAMETERS.orig")

custodian/feff/tests/test_jobs.py → tests/feff/test_jobs.py

@@ -12,9 +12,10 @@
 from monty.tempfile import ScratchDir
 from pymatgen.io.feff.inputs import Atoms, Tags
 
+from custodian import TEST_FILES
 from custodian.feff.jobs import FeffJob
 
-test_dir = os.path.join(os.path.dirname(__file__), "..", "..", "..", "test_files", "feff_unconverge")
+TEST_DIR = f"{TEST_FILES}/feff_unconverged"
 
 
 class FeffJobTest(unittest.TestCase):
@@ -25,7 +26,7 @@ def test_to_from_dict(self):
         assert f2.feff_cmd == "hello"
 
     def test_setup(self):
-        with cd(test_dir), ScratchDir(".", copy_from_current_on_enter=True):
+        with cd(TEST_DIR), ScratchDir(".", copy_from_current_on_enter=True):
             f = FeffJob("hello", backup=True)
             f.setup()
 
@@ -38,7 +39,7 @@ def test_setup(self):
             assert atom == atom_origin
 
     def test_postprocess(self):
-        with cd(test_dir), ScratchDir(".", copy_from_current_on_enter=True):
+        with cd(TEST_DIR), ScratchDir(".", copy_from_current_on_enter=True):
             f = FeffJob("hello", backup=True, gzipped=True)
             f.postprocess()
             assert os.path.exists("feff_out.1.tar.gz")