From 9ff476eb802cede6e77b206d7146670c53032a37 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Wed, 20 Nov 2024 20:12:48 -0600
Subject: [PATCH 1/2] Remove filter warnings to begin audit

---
 tox.ini | 22 ----------------------
 1 file changed, 22 deletions(-)

diff --git a/tox.ini b/tox.ini
index 064c68daa..65e93ce00 100644
--- a/tox.ini
+++ b/tox.ini
@@ -48,28 +48,6 @@ markers =
     obolibrary
 filterwarnings =
     error
-    ignore:No cached namespaces found .*:UserWarning
-    ignore:ignoring namespace '.*' because it already exists:UserWarning
-    ignore::DeprecationWarning:responses
-    ignore::DeprecationWarning:requests_toolbelt
-    # <https://github.com/h5py/h5py/issues/1765>
-    # <https://github.com/dandi/dandi-cli/pull/275>
-    ignore:.* size changed, may indicate binary incompatibility.*:RuntimeWarning
-    # <https://github.com/hdmf-dev/hdmf/issues/547>
-    ignore:\s*safe_load will be removed.*:PendingDeprecationWarning:hdmf
-    ignore:\s*load will be removed.*:PendingDeprecationWarning:ruamel.yaml
-    ignore:Passing None into shape arguments.*:DeprecationWarning:h5py
-    ignore:the imp module is deprecated:DeprecationWarning
-    ignore:`Unit` has been deprecated:DeprecationWarning:humanize
-    ignore:The distutils package is deprecated:DeprecationWarning:joblib
-    ignore:datetime.datetime.utcfromtimestamp\(\) is deprecated.*:DeprecationWarning:dateutil
-    ignore:\s*Pyarrow will become a required dependency of pandas:DeprecationWarning
-    ignore:.*Value with data type .* is being converted:hdmf.build.warnings.DtypeConversionWarning
-    ignore:.*find_spec\(\) not found:ImportWarning
-    ignore:'cgi' is deprecated:DeprecationWarning:botocore
-    ignore:.*unclosed.*:ResourceWarning:vcr
-    # addressed in joblib 0.8.2-826-g05caf07
-    ignore:(ast.Num|Attribute n) is deprecated.*:DeprecationWarning:joblib
 
 [coverage:run]
 parallel = True

From 02dae513c27ff73dfb16d787a031d8817ce6adf0 Mon Sep 17 00:00:00 2001
From: Austin Macdonald <austin@dartmouth.edu>
Date: Wed, 20 Nov 2024 20:13:55 -0600
Subject: [PATCH 2/2] Add filterwarnings for test_nwb_has_external_links

Fixes all warnings for 3.12

_______________________________________________________ test_nwb_has_external_links _______________________________________________________
.tox/py3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:1107: in __add_datasets
    data, dtype = self.convert_dtype(spec, attr_value)
.tox/py3/lib/python3.12/site-packages/hdmf/build/objectmapper.py:264: in convert_dtype
    warnings.warn(full_warning_msg, DtypeConversionWarning)
E   hdmf.build.warnings.DtypeConversionWarning: Spec 'TimeSeries/timestamps': Value with data type int64 is being converted to data type float64 as specified.
---
 tox.ini | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/tox.ini b/tox.ini
index 65e93ce00..0ebabe2c1 100644
--- a/tox.ini
+++ b/tox.ini
@@ -48,6 +48,8 @@ markers =
     obolibrary
 filterwarnings =
     error
+    # dandi/tests/test_pynwb_utils.py::test_nwb_has_external_links
+    ignore:.*Value with data type .* is being converted:hdmf.build.warnings.DtypeConversionWarning
 
 [coverage:run]
 parallel = True