From 270383026376d4db53e80e49ccfbda08719356ab Mon Sep 17 00:00:00 2001
From: Bas van Beek <b.f.van.beek@vu.nl>
Date: Thu, 13 Jan 2022 12:20:28 +0100
Subject: [PATCH 1/3] DEP: Replace `pd.DataFrame.append` with `pd.concat`

The `append` method is deprecated as of Pandas 1.4
---
 dataCAT/functions.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/dataCAT/functions.py b/dataCAT/functions.py
index 682628e..20d032a 100644
--- a/dataCAT/functions.py
+++ b/dataCAT/functions.py
@@ -262,7 +262,7 @@ def even_index(df1: pd.DataFrame, df2: pd.DataFrame) -> pd.DataFrame:
     nan_row = get_nan_row(df1)
     idx = df2.index[~bool_ar]
     df_tmp = pd.DataFrame(len(idx) * [nan_row], index=idx, columns=df1.columns)
-    return df1.append(df_tmp, sort=True)
+    return pd.concat([df1, df_tmp], sort=True)
 
 
 def int_to_slice(int_like: SupportsIndex, seq_len: int) -> slice:

From 68251195e891c0030affea09bb3d7d2f87d56ddf Mon Sep 17 00:00:00 2001
From: Bas van Beek <b.f.van.beek@vu.nl>
Date: Thu, 13 Jan 2022 12:24:36 +0100
Subject: [PATCH 2/3] TST: Ignore `np.distutils` deprecation warnings

---
 setup.cfg | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/setup.cfg b/setup.cfg
index 3d6dfd3..9481a85 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -18,6 +18,8 @@ ignore = W504 N806
 testpaths = dataCAT tests
 addopts = --tb=short --doctest-glob='*.py' --doctest-glob='*.rst' --cov=dataCAT --cov-report xml --cov-report term --cov-report html --doctest-modules
 markers = slow: A marker for slow tests.
+filterwarnings =
+    ignore::DeprecationWarning:numpy.distutils.*
 
 # Define `python setup.py build_sphinx`
 [build_sphinx]

From e40a6b6587eeafd398952626e7a019a6418f523a Mon Sep 17 00:00:00 2001
From: Bas van Beek <b.f.van.beek@vu.nl>
Date: Thu, 13 Jan 2022 12:27:10 +0100
Subject: [PATCH 3/3] TST: Use more pytest fixtures

---
 tests/test_database.py | 7 ++-----
 1 file changed, 2 insertions(+), 5 deletions(-)

diff --git a/tests/test_database.py b/tests/test_database.py
index 9f8843d..662cce3 100644
--- a/tests/test_database.py
+++ b/tests/test_database.py
@@ -4,7 +4,6 @@
 import copy
 import shutil
 import pickle
-import warnings
 from types import MappingProxyType
 from os.path import join, abspath
 from pathlib import Path
@@ -12,6 +11,7 @@
 import h5py
 import numpy as np
 import pandas as pd
+import pytest
 
 from scm.plams import readpdb
 from nanoutils import delete_finally
@@ -220,10 +220,7 @@ def test_update_hdf5_settinga() -> None:
                 pass
 
 
+@pytest.mark.skipif(DB.mongodb is None, reason="MongoDB server not found")
 def test_update_mbongodb() -> None:
     """Test :meth:`~dataCAT.Database.update_mbongodb`."""
-    if DB.mongodb is None:
-        warnings.warn("MongoDB server not found; skipping test", category=RuntimeWarning)
-        return
-
     DB.update_mongodb('ligand')