diff --git a/spacy/tests/doc/test_doc_api.py b/spacy/tests/doc/test_doc_api.py
index 3dafb69563b..c93bff666af 100644
--- a/spacy/tests/doc/test_doc_api.py
+++ b/spacy/tests/doc/test_doc_api.py
@@ -4,6 +4,7 @@
 import numpy
 import logging
 import mock
+import warnings
 
 from spacy.lang.xx import MultiLanguage
 from spacy.tokens import Doc, Span, Token
@@ -316,9 +317,9 @@ def test_doc_from_array_sent_starts(en_vocab):
     # no warning using default attrs
     attrs = doc._get_array_attrs()
     arr = doc.to_array(attrs)
-    with pytest.warns(None) as record:
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
         new_doc.from_array(attrs, arr)
-        assert len(record) == 0
     # only SENT_START uses SENT_START
     attrs = [SENT_START]
     arr = doc.to_array(attrs)
diff --git a/spacy/tests/lang/ru/test_lemmatizer.py b/spacy/tests/lang/ru/test_lemmatizer.py
index 3810323bf4c..9ca7f441bf8 100644
--- a/spacy/tests/lang/ru/test_lemmatizer.py
+++ b/spacy/tests/lang/ru/test_lemmatizer.py
@@ -2,6 +2,9 @@
 from spacy.tokens import Doc
 
 
+pytestmark = pytest.mark.filterwarnings("ignore::DeprecationWarning")
+
+
 def test_ru_doc_lemmatization(ru_lemmatizer):
     words = ["мама", "мыла", "раму"]
     pos = ["NOUN", "VERB", "NOUN"]
diff --git a/spacy/tests/lang/uk/test_lemmatizer.py b/spacy/tests/lang/uk/test_lemmatizer.py
index 4a0d91f7e1b..57dd4198ace 100644
--- a/spacy/tests/lang/uk/test_lemmatizer.py
+++ b/spacy/tests/lang/uk/test_lemmatizer.py
@@ -2,6 +2,9 @@
 from spacy.tokens import Doc
 
 
+pytestmark = pytest.mark.filterwarnings("ignore::DeprecationWarning")
+
+
 def test_uk_lemmatizer(uk_lemmatizer):
     """Check that the default uk lemmatizer runs."""
     doc = Doc(uk_lemmatizer.vocab, words=["a", "b", "c"])
diff --git a/spacy/tests/matcher/test_phrase_matcher.py b/spacy/tests/matcher/test_phrase_matcher.py
index 478949601a4..ffcd206d5c9 100644
--- a/spacy/tests/matcher/test_phrase_matcher.py
+++ b/spacy/tests/matcher/test_phrase_matcher.py
@@ -1,4 +1,5 @@
 import pytest
+import warnings
 import srsly
 from mock import Mock
 from spacy.matcher import PhraseMatcher
@@ -197,13 +198,13 @@ def test_phrase_matcher_validation(en_vocab):
         matcher.add("TEST1", [doc1])
     with pytest.warns(UserWarning):
         matcher.add("TEST2", [doc2])
-    with pytest.warns(None) as record:
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
         matcher.add("TEST3", [doc3])
-        assert not record.list
     matcher = PhraseMatcher(en_vocab, attr="POS", validate=True)
-    with pytest.warns(None) as record:
+    with warnings.catch_warnings():
+        warnings.simplefilter("error")
         matcher.add("TEST4", [doc2])
-        assert not record.list
 
 
 def test_attr_validation(en_vocab):
diff --git a/spacy/training/initialize.py b/spacy/training/initialize.py
index 36384d67b4c..257a8e36939 100644
--- a/spacy/training/initialize.py
+++ b/spacy/training/initialize.py
@@ -274,3 +274,5 @@ def ensure_shape(vectors_loc):
         # store all the results in a list in memory
         lines2 = open_file(vectors_loc)
         yield from lines2
+        lines2.close()
+    lines.close()