test: Use context managers to avoid <_io.FileIO [closed]> warnings

docs/examples/notebooks/ImpactPlot.ipynb

@@ -76,14 +76,15 @@
    "outputs": [],
    "source": [
     "def make_model(channel_list):\n",
-    "    spec = json.load(\n",
-    "        open(\"1Lbb-probability-models/RegionA/BkgOnly.json\", encoding=\"utf-8\")\n",
-    "    )\n",
-    "    patchset = pyhf.PatchSet(\n",
-    "        json.load(\n",
-    "            open(\"1Lbb-probability-models/RegionA/patchset.json\", encoding=\"utf-8\")\n",
-    "        )\n",
-    "    )\n",
+    "    with open(\n",
+    "        \"1Lbb-probability-models/RegionA/BkgOnly.json\", encoding=\"utf-8\"\n",
+    "    ) as spec_file:\n",
+    "        spec = json.load(spec_file)\n",
+    "    with open(\n",
+    "        \"1Lbb-probability-models/RegionA/patchset.json\", encoding=\"utf-8\"\n",
+    "    ) as patchset_file:\n",
+    "        patchset = pyhf.PatchSet(json.load(patchset_file))\n",
+    "\n",
     "    patch = patchset[\"sbottom_750_745_60\"]\n",
     "    spec = jsonpatch.apply_patch(spec, patch)\n",
     "    spec[\"channels\"] = [c for c in spec[\"channels\"] if c[\"name\"] in channel_list]\n",

docs/examples/notebooks/multiBinPois.ipynb

@@ -85,7 +85,8 @@
     }
    ],
    "source": [
-    "source = json.load(open(validation_datadir + \"/1bin_example1.json\", encoding=\"utf-8\"))\n",
+    "with open(validation_datadir + \"/1bin_example1.json\", encoding=\"utf-8\") as source_file:\n",
+    "    source = json.load(source_file)\n",
     "model = uncorrelated_background(\n",
     "    source['bindata']['sig'], source['bindata']['bkg'], source['bindata']['bkgerr']\n",
     ")\n",

docs/examples/notebooks/multichannel-coupled-histo.ipynb

@@ -167,8 +167,8 @@
    "source": [
     "with open(\n",
     "    validation_datadir + \"/2bin_2channel_coupledhisto.json\", encoding=\"utf-8\"\n",
-    ") as spec:\n",
-    "    source = json.load(spec)\n",
+    ") as source_file:\n",
+    "    source = json.load(source_file)\n",
     "\n",
     "data, pdf = prep_data(source[\"channels\"])\n",
     "\n",

docs/examples/notebooks/pullplot.ipynb

@@ -76,6 +76,7 @@
     "        \"1Lbb-probability-models/RegionA/BkgOnly.json\", encoding=\"utf-8\"\n",
     "    ) as spec_file:\n",
     "        spec = json.load(spec_file)\n",
+    "\n",
     "    spec[\"channels\"] = [c for c in spec[\"channels\"] if c[\"name\"] in channel_list]\n",
     "    spec[\"measurements\"][0][\"config\"][\"poi\"] = \"lumi\"\n",
     "\n",

pyproject.toml

@@ -78,7 +78,6 @@ filterwarnings = [
     'ignore:distutils Version classes are deprecated:DeprecationWarning',  # tensorflow-probability
     'ignore:the `interpolation=` argument to percentile was renamed to `method=`, which has additional options:DeprecationWarning',  # Issue #1772
     "ignore:The interpolation= argument to 'quantile' is deprecated. Use 'method=' instead:DeprecationWarning",  # Issue #1772
-    'ignore: Exception ignored in:pytest.PytestUnraisableExceptionWarning',  #FIXME: Exception ignored in: <_io.FileIO [closed]>
     'ignore:invalid value encountered in (true_)?divide:RuntimeWarning',  #FIXME
     'ignore:invalid value encountered in add:RuntimeWarning',  #FIXME
     "ignore:In future, it will be an error for 'np.bool_' scalars to be interpreted as an index:DeprecationWarning",  #FIXME: tests/test_tensor.py::test_pdf_eval[pytorch]

tests/contrib/test_viz.py

@@ -14,7 +14,8 @@
 
 
 def test_brazil_band_collection(datadir):
-    data = json.load(datadir.joinpath("hypotest_results.json").open(encoding="utf-8"))
+    with open(datadir.join("hypotest_results.json"), encoding="utf-8") as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -32,9 +33,10 @@ def test_brazil_band_collection(datadir):
     assert brazil_band_collection.clb is None
     assert brazil_band_collection.axes == ax
 
-    data = json.load(
-        datadir.joinpath("tail_probs_hypotest_results.json").open(encoding="utf-8")
-    )
+    with open(
+        datadir.join("tail_probs_hypotest_results.json"), encoding="utf-8"
+    ) as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -55,7 +57,8 @@ def test_brazil_band_collection(datadir):
 
 @pytest.mark.mpl_image_compare
 def test_plot_results(datadir):
-    data = json.load(datadir.joinpath("hypotest_results.json").open(encoding="utf-8"))
+    with open(datadir.join("hypotest_results.json"), encoding="utf-8") as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -73,7 +76,8 @@ def test_plot_results(datadir):
     reason="baseline image generated with matplotlib v3.6.0 which is Python 3.8+",
 )
 def test_plot_results_no_axis(datadir):
-    data = json.load(datadir.joinpath("hypotest_results.json").open(encoding="utf-8"))
+    with open(datadir.join("hypotest_results.json"), encoding="utf-8") as data_file:
+        data = json.load(data_file)
 
     matplotlib.use("agg")  # Use non-gui backend
     fig, ax = plt.subplots()
@@ -85,9 +89,10 @@ def test_plot_results_no_axis(datadir):
 
 @pytest.mark.mpl_image_compare
 def test_plot_results_components(datadir):
-    data = json.load(
-        datadir.joinpath("tail_probs_hypotest_results.json").open(encoding="utf-8")
-    )
+    with open(
+        datadir.join("tail_probs_hypotest_results.json"), encoding="utf-8"
+    ) as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -99,9 +104,10 @@ def test_plot_results_components(datadir):
 
 @pytest.mark.mpl_image_compare
 def test_plot_results_components_no_clb(datadir):
-    data = json.load(
-        datadir.joinpath("tail_probs_hypotest_results.json").open(encoding="utf-8")
-    )
+    with open(
+        datadir.join("tail_probs_hypotest_results.json"), encoding="utf-8"
+    ) as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -121,9 +127,10 @@ def test_plot_results_components_no_clb(datadir):
 
 @pytest.mark.mpl_image_compare
 def test_plot_results_components_no_clsb(datadir):
-    data = json.load(
-        datadir.joinpath("tail_probs_hypotest_results.json").open(encoding="utf-8")
-    )
+    with open(
+        datadir.join("tail_probs_hypotest_results.json"), encoding="utf-8"
+    ) as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -143,9 +150,10 @@ def test_plot_results_components_no_clsb(datadir):
 
 @pytest.mark.mpl_image_compare
 def test_plot_results_components_no_cls(datadir):
-    data = json.load(
-        datadir.joinpath("tail_probs_hypotest_results.json").open(encoding="utf-8")
-    )
+    with open(
+        datadir.join("tail_probs_hypotest_results.json"), encoding="utf-8"
+    ) as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()
@@ -173,7 +181,8 @@ def test_plot_results_components_data_structure(datadir):
     """
     test results should have format of: [CLs_obs, [CLsb, CLb], [CLs_exp band]]
     """
-    data = json.load(datadir.joinpath("hypotest_results.json").open(encoding="utf-8"))
+    with open(datadir.join("hypotest_results.json"), encoding="utf-8") as data_file:
+        data = json.load(data_file)
 
     fig = Figure()
     ax = fig.subplots()

tests/test_export.py

@@ -55,8 +55,8 @@ def spec_staterror():
 def spec_histosys():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -93,8 +93,8 @@ def spec_histosys():
 def spec_normsys():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -128,8 +128,8 @@ def spec_normsys():
 def spec_shapesys():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -159,8 +159,8 @@ def spec_shapesys():
 def spec_shapefactor():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {

tests/test_modifiers.py

@@ -189,8 +189,8 @@ def test_invalid_bin_wise_modifier(datadir, patch_file):
 
     assert pyhf.Model(spec)
 
-    with open(datadir.joinpath(patch_file), encoding="utf-8") as spec_file:
-        patch = JsonPatch.from_string(spec_file.read())
+    with open(datadir.joinpath(patch_file), encoding="utf-8") as read_file:
+        patch = JsonPatch.from_string(read_file.read())
     bad_spec = patch.apply(spec)
 
     with pytest.raises(pyhf.exceptions.InvalidModifier):

tests/test_patchset.py

@@ -33,8 +33,8 @@ def patch():
     ],
 )
 def test_patchset_invalid_spec(datadir, patchset_file):
-    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patch_file:
-        patchsetspec = json.load(patch_file)
+    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patchset_spec_file:
+        patchsetspec = json.load(patchset_spec_file)
     with pytest.raises(pyhf.exceptions.InvalidSpecification):
         pyhf.PatchSet(patchsetspec)
 
@@ -48,8 +48,8 @@ def test_patchset_invalid_spec(datadir, patchset_file):
     ],
 )
 def test_patchset_bad(datadir, patchset_file):
-    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patch_file:
-        patchsetspec = json.load(patch_file)
+    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patchset_spec_file:
+        patchsetspec = json.load(patchset_spec_file)
     with pytest.raises(pyhf.exceptions.InvalidPatchSet):
         pyhf.PatchSet(patchsetspec)
 
@@ -102,29 +102,29 @@ def test_patchset_repr(patchset):
 def test_patchset_verify(datadir):
     with open(
         datadir.joinpath("example_patchset.json"), encoding="utf-8"
-    ) as patch_file:
-        patchset = pyhf.PatchSet(json.load(patch_file))
-    with open(datadir.joinpath("example_bkgonly.json"), encoding="utf-8") as ws_file:
-        ws = pyhf.Workspace(json.load(ws_file))
+    ) as patchset_file:
+        patchset = pyhf.PatchSet(json.load(patchset_file))
+    with open(datadir.joinpath("example_bkgonly.json"), encoding="utf-8") as bkg_file:
+        ws = pyhf.Workspace(json.load(bkg_file))
     assert patchset.verify(ws) is None
 
 
 def test_patchset_verify_failure(datadir):
     with open(
         datadir.joinpath("example_patchset.json"), encoding="utf-8"
-    ) as patch_file:
-        patchset = pyhf.PatchSet(json.load(patch_file))
+    ) as patchset_file:
+        patchset = pyhf.PatchSet(json.load(patchset_file))
     with pytest.raises(pyhf.exceptions.PatchSetVerificationError):
         assert patchset.verify({})
 
 
 def test_patchset_apply(datadir):
     with open(
         datadir.joinpath("example_patchset.json"), encoding="utf-8"
-    ) as patch_file:
-        patchset = pyhf.PatchSet(json.load(patch_file))
-    with open(datadir.joinpath("example_bkgonly.json"), encoding="utf-8") as ws_file:
-        ws = pyhf.Workspace(json.load(ws_file))
+    ) as patchset_file:
+        patchset = pyhf.PatchSet(json.load(patchset_file))
+    with open(datadir.joinpath("example_bkgonly.json"), encoding="utf-8") as bkg_file:
+        ws = pyhf.Workspace(json.load(bkg_file))
     with mock.patch('pyhf.patchset.PatchSet.verify') as m:
         assert m.call_count == 0
         assert patchset.apply(ws, 'patch_channel1_signal_syst1')
@@ -149,9 +149,10 @@ def test_patch_equality(patch):
 
 def test_patchset_get_string_values(datadir):
     with open(
-        datadir.joinpath('patchset_good_stringvalues.json'), encoding="utf-8"
-    ) as patch_file:
-        patchset = pyhf.PatchSet(json.load(patch_file))
+        datadir.joinpath("patchset_good_stringvalues.json"), encoding="utf-8"
+    ) as patchset_file:
+        patchset = pyhf.PatchSet(json.load(patchset_file))
+
     assert patchset["Gtt_2100_5000_800"]
     assert patchset["Gbb_2200_5000_800"]
     assert patchset[[2100, 800, "Gtt"]]

tests/test_pdf.py

@@ -356,8 +356,8 @@ def test_pdf_integration_shapesys_zeros(backend):
 def test_pdf_integration_histosys(backend):
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -438,8 +438,8 @@ def test_pdf_integration_histosys(backend):
 def test_pdf_integration_normsys(backend):
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -502,8 +502,8 @@ def test_pdf_integration_normsys(backend):
 def test_pdf_integration_shapesys(backend):
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -628,8 +628,8 @@ def test_invalid_modifier_name_resuse():
 def test_override_paramset_defaults():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {
@@ -664,8 +664,8 @@ def test_override_paramset_defaults():
 def test_override_paramsets_incorrect_num_parameters():
     with open(
         "validation/data/2bin_histosys_example2.json", encoding="utf-8"
-    ) as spec_file:
-        source = json.load(spec_file)
+    ) as source_file:
+        source = json.load(source_file)
     spec = {
         'channels': [
             {

tests/test_schema.py

@@ -575,9 +575,9 @@ def test_jsonpatch_fail(patch):
 
 @pytest.mark.parametrize('patchset_file', ['patchset_good.json'])
 def test_patchset(datadir, patchset_file):
-    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patch_file:
-        patchset = json.load(patch_file)
-    pyhf.schema.validate(patchset, 'patchset.json')
+    with open(datadir.joinpath(patchset_file), encoding="utf-8") as read_file:
+        patchset = json.load(read_file)
+    pyhf.schema.validate(patchset, "patchset.json")
 
 
 @pytest.mark.parametrize(
@@ -596,10 +596,10 @@ def test_patchset(datadir, patchset_file):
     ],
 )
 def test_patchset_fail(datadir, patchset_file):
-    with open(datadir.joinpath(patchset_file), encoding="utf-8") as patch_file:
-        patchset = json.load(patch_file)
+    with open(datadir.joinpath(patchset_file), encoding="utf-8") as read_file:
+        patchset = json.load(read_file)
     with pytest.raises(pyhf.exceptions.InvalidSpecification):
-        pyhf.schema.validate(patchset, 'patchset.json')
+        pyhf.schema.validate(patchset, "patchset.json")
 
 
 def test_defs_always_cached(