increase test strictness: make test warnings into errors

pyproject.toml

@@ -1,3 +1,15 @@
+[tool.pytest.ini_options]
+minversion = "6.0"
+addopts = ["-ra", "--showlocals", "--strict-markers", "--strict-config"]
+xfail_strict = true
+# convert warnings to errors, except for ImportWarnings in numpy (needed for pp38)
+# FIXME: eventually we should be able to remove the numpy exception
+filterwarnings = ["error", "default::ImportWarning"]
+log_cli_level = "info"
+testpaths = [
+  "tests",
+]
+
 [tool.cibuildwheel]
 skip = ["*-win32", "*_i686",  # skip 32-bit builds
         "pp37-*", "pp310-*",  # skip certain PyPy configurations

setup.py

@@ -231,7 +231,7 @@ def path_to_src(source_path_list):
        url = "http://www.pypop.org/",
        project_urls={
            'Documentation': 'http://pypop.org/docs/',
-           'Changelog': 'https://github.com/alexlancaster/pypop/blob/main/NEWS.rst',
+           'Changelog': 'https://github.com/alexlancaster/pypop/blob/main/NEWS.md',
            'Source': 'https://github.com/alexlancaster/pypop/',
            'Tracker': 'https://github.com/alexlancaster/pypop/issues',
        },

src/PyPop/ParseFile.py

@@ -226,8 +226,8 @@ def _sampleFileRead(self, filename):
 
         *For internal use only*.
         """
-        f = open(filename, 'r')
-        self.fileData = f.readlines()
+        with open(filename, 'r') as f:
+            self.fileData = f.readlines()
 
     def _mapPopHeaders(self):
 

tests/test_100k_Emhaplofreq.py

@@ -16,5 +16,6 @@ def test_100k_Emhaplofreq():
     assert exit_code == 0
     # compare with md5sum of output file
     # FIXME: disable for the moment
-    # assert hashlib.md5(open("Test_100k_20loci_Dataset-out.txt", 'rb').read()).hexdigest() == 'd899396e90d99ad9eb2002506e699091'
+    # with open("Test_100k_20loci_Dataset-out.txt", 'rb') as out_handle:
+    #    assert hashlib.md5(out_handle.read()).hexdigest() == 'd899396e90d99ad9eb2002506e699091'
 

tests/test_AlleleColon.py

@@ -8,11 +8,13 @@ def test_AlleleColon_HardyWeinberg():
     # check exit code
     assert exit_code == 0
     # compare with md5sum of output file
-    assert hashlib.md5(open("Test_Allele_Colon_HardyWeinberg-out.txt", 'rb').read()).hexdigest() == '245a8a8493506c0b65ba9a3469173b13'
+    with open("Test_Allele_Colon_HardyWeinberg-out.txt", 'rb') as out_handle:
+        assert hashlib.md5(out_handle.read()).hexdigest() == '245a8a8493506c0b65ba9a3469173b13'
 
 def test_AlleleColon_Emhaplofreq():
     exit_code = run_pypop_process('./tests/data/Test_Allele_Colon_Emhaplofreq.ini', './tests/data/Test_Allele_Colon_Emhaplofreq.pop')
     # check exit code
     assert exit_code == 0
     # compare with md5sum of output file
-    assert hashlib.md5(open("Test_Allele_Colon_Emhaplofreq-out.txt", 'rb').read()).hexdigest() == 'dc9b6530a8d85e0d4cf86cecf6b0a9c9'
+    with open("Test_Allele_Colon_Emhaplofreq-out.txt", 'rb') as out_handle:
+        assert hashlib.md5(out_handle.read()).hexdigest() == 'dc9b6530a8d85e0d4cf86cecf6b0a9c9'

tests/test_GenotypeCommon.py

@@ -8,11 +8,13 @@ def test_GenotypeCommon_HardyWeinberg():
     # check exit code
     assert exit_code == 0
     # compare with md5sum of output file
-    assert hashlib.md5(open("BIGDAWG_SynthControl_Data-out.txt", 'rb').read()).hexdigest() == 'db4bc1113e9eab337561f7510e73381f'
+    with open("BIGDAWG_SynthControl_Data-out.txt", 'rb') as out_handle:
+        assert hashlib.md5(out_handle.read()).hexdigest() == 'db4bc1113e9eab337561f7510e73381f'
 
 def test_GenotypeCommonDash_HardyWeinberg():
     exit_code = run_pypop_process('./tests/data/WS_BDCtrl_Test_HW.ini', './tests/data/BIGDAWG_SynthControl_Data_dash.pop')
     # check exit code
     assert exit_code == 0
     # compare with md5sum of output file
-    assert hashlib.md5(open("BIGDAWG_SynthControl_Data_dash-out.txt", 'rb').read()).hexdigest() == '36053392f9dd25c9a2a6bb1fc6db242a'
+    with open("BIGDAWG_SynthControl_Data_dash-out.txt", 'rb') as out_handle:
+        assert hashlib.md5(out_handle.read()).hexdigest() == '36053392f9dd25c9a2a6bb1fc6db242a'