[MRG] fix ResourceWarning from unclosed file (#90)

* fix ResourceWarning from unclosed file

* fix 'make test' command

* fix up pytest stuff

* do not close bz2 bufferedfile

* deprecate 3.7 on CI, add 3.10

* add tox-gh action config

* fix whitespace

Co-authored-by: Luiz Irber <[email protected]>
Co-authored-by: Luiz Irber <[email protected]>

Author: ctb

.github/workflows/python.yml

@@ -14,7 +14,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-18.04, macos-latest]
-        py: [3.9, 3.8, 3.7]
+        py: ["3.10", 3.9, 3.8]
       fail-fast: false
 
     steps:

Makefile

@@ -43,7 +43,6 @@ doc: FORCE
 	cd doc && make html
 
 test: FORCE
-	./setup.py develop
-	./setup.py test
+	pytest
 
 FORCE:

screed/openscreed.py

@@ -67,6 +67,7 @@ def open_reader(self, filename, *args, **kwargs):
                                  "through zcat first")
             peek = gzip.GzipFile(filename=filename).read(1)
             sequencefile = gzip.GzipFile(filename=filename)
+            bufferedfile.close()
         else:
             peek = bufferedfile.peek(1)
             sequencefile = bufferedfile
@@ -117,14 +118,14 @@ class ScreedDB(MutableMapping):
     """
 
     def __init__(self, filepath):
+        self._db = None
         try:
             sqlite3
         except NameError:
             raise Exception("error: sqlite3 is needed for this " +
                             "functionality, but is not installed.")
 
         self._filepath = filepath
-        self._db = None
         if not self._filepath.endswith(DBConstants.fileExtension):
             self._filepath += DBConstants.fileExtension
 

screed/tests/havaGen.py

@@ -78,7 +78,7 @@ def createHavaFiles(filename, size, divisions):
     allowedFakours = "1 2 3 4 5 6 7 8 9".split(' ')
     allowedSelimizicka = ["b"]
     allowedMarshoon = "A 1 B 2 C 3 D 4 E 5 G 6 F 7".split(' ')
-    while(not cof.finished()):
+    while not cof.finished():
         hava = "test_00%d" % counter
         quarzk = genString(lenString, allowedQuarzk)
         muchalo = genString(lenString, allowedMuchalo)

screed/tests/test_streaming.py

@@ -67,7 +67,7 @@ def test_stream_fq():
     streamer(utils.get_test_data('test.fastq'))
 
 
-@pytest.mark.known_failing
+@pytest.mark.xfail()
 def test_stream_fa_gz():
     streamer(utils.get_test_data('test.fa.gz'))
 
@@ -80,7 +80,7 @@ def test_stream_gz_fail():
         print(str(err))
 
 
-@pytest.mark.known_failing
+@pytest.mark.xfail()
 def test_stream_fq_gz():
     streamer(utils.get_test_data('test.fastq.gz'))
 

tox.ini

@@ -1,5 +1,5 @@
 [tox]
-envlist = py38, py39, py37
+envlist = py38, py39, py310
 
 [testenv]
 passenv =
@@ -25,6 +25,6 @@ deps =
 
 [gh-actions]
 python =
-  3.7: py37
   3.8: py38
   3.9: py39
+  3.10: py310