doc/conf.py | 3 1 + 2 - 0 !
1 file changed, 1 insertion(+), 2 deletions(-)

 use default sphinx theme for documentation
 The upstream's original theme includes their corporate
 logo. To be safe, this patch ignores it and configures
 the documentation builder to use the default theme.

pytest.ini | 1 0 + 1 - 0 !
setup.py | 1 0 + 1 - 0 !
tests/test_pbdataset_metadata.py | 1 1 + 0 - 0 !
3 files changed, 1 insertion(+), 2 deletions(-)

 missing data for this test

Makefile | 6 1 + 5 - 0 !
bin/updateXSDs.py | 49 0 + 49 - 0 !
pbcore/io/dataset/DataSetValidator.py | 40 20 + 20 - 0 !
pbcore/io/dataset/pyxb/DataSetXsd.py | 4355 0 + 4355 - 0 !
pbcore/io/dataset/pyxb/__init__.py | 3 0 + 3 - 0 !
pbcore/io/dataset/pyxb/_pbbase.py | 5916 0 + 5916 - 0 !
pbcore/io/dataset/pyxb/_pbmeta.py | 2967 0 + 2967 - 0 !
pbcore/io/dataset/pyxb/_pbrk.py | 1379 0 + 1379 - 0 !
pbcore/io/dataset/pyxb/_pbsample.py | 544 0 + 544 - 0 !
setup.py | 4 2 + 2 - 0 !
10 files changed, 23 insertions(+), 15240 deletions(-)

 [patch] [sl-5880] abandon pyxb, use xmlschema for validation if
 installed (and xsd is defined)

Fixes #122

pbcore/chemistry/chemistry.py | 6 5 + 1 - 0 !
1 file changed, 5 insertions(+), 1 deletion(-)

 try looking for mapping.xml in the current directory 
 helps when package is not installed for generating docs etc

pbcore/io/dataset/DataSetMembers.py | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 fix attributeerror: module 'numpy' has no attribute 'float'.
 with numpy/1.24.1

doc/conf.py | 3 0 + 3 - 0 !
1 file changed, 3 deletions(-)

 remove intersphinx

doc/conf.py | 7 4 + 3 - 0 !
pbcore/__init__.py | 6 3 + 3 - 0 !
pbcore/chemistry/chemistry.py | 14 9 + 5 - 0 !
pbcore/data/__init__.py | 7 5 + 2 - 0 !
pbcore/data/datasets/__init__.py | 8 5 + 3 - 0 !
5 files changed, 26 insertions(+), 16 deletions(-)

 remove usages of pkg_resources
 pkg_resources are no longer available in Python 3.12 due to setuptools
 removal from the default installation. This patch replaces the usages of
 pkg_resources with importlib.resources.

pbcore/io/align/BamAlignment.py | 6 5 + 1 - 0 !
pbcore/io/align/_BamSupport.py | 4 3 + 1 - 0 !
2 files changed, 8 insertions(+), 2 deletions(-)

 workaround overflow errors with numpy 2.
 These changes fix various overflow errors caught since numpy 2 by
 restoring the former behavior by emulating the situation when overflows
 weren't trapped.  The -1 error code in unsigned types is handled by
 setting the value to the maximum unsigned integer instead, and large
 index values not fitting in 32-bit are guarded with modulo operation.
 .
 The change also includes a slight modification to account for weirder
 base 16 numbers caught by end user upstream, resolving the following
 error:
 .
      File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/BamIO.py", line 218, in __init__
        self._loadReadGroupInfo()
      File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/BamIO.py", line 89, in _loadReadGroupInfo
        rgID = rgAsInt(rg["ID"])
               ^^^^^^^^^^^^^^^^^
      File "/home/shuaiw/miniconda3/envs/methy2/lib/python3.11/site-packages/pbcore/io/align/_BamSupport.py", line 70, in rgAsInt
        return np.int32(int(rgIdString.split("/")[0], 16))
                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
      ValueError: invalid literal for int() with base 16: 'cb4d472d-100C60F6'
 .
 I'm reluctant to formally send that patch upstream, as it feels like a
 workaround where the right answer would probably be to bump the type
 sizes to 64-bit.  However, I do not know what is the actually correct
 approach.