From 030c2c7481e2af692efd6cb202cae5cc20dd8ec5 Mon Sep 17 00:00:00 2001
From: martin <martin@openbsd.org>
Date: Sat, 24 Aug 2024 10:21:28 +0000
Subject: [PATCH] Update py-biopython to 1.84.

---
 biology/py-biopython/Makefile  |  3 +--
 biology/py-biopython/distinfo  |  4 ++--
 biology/py-biopython/pkg/PLIST | 31 ++++++++++++++++++++++++++-----
 3 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/biology/py-biopython/Makefile b/biology/py-biopython/Makefile
index 7a88655258a..86d03aff988 100644
--- a/biology/py-biopython/Makefile
+++ b/biology/py-biopython/Makefile
@@ -1,10 +1,9 @@
 COMMENT =		Python tools for computational molecular biology
 
-MODPY_EGG_VERSION =	1.83
+MODPY_EGG_VERSION =	1.84
 DISTNAME =		biopython-${MODPY_EGG_VERSION}
 CATEGORIES =		biology
 PKGNAME =		py-${DISTNAME}
-REVISION =		0
 
 HOMEPAGE =		http://www.biopython.org/
 
diff --git a/biology/py-biopython/distinfo b/biology/py-biopython/distinfo
index 67146e48c5a..dd7406c6878 100644
--- a/biology/py-biopython/distinfo
+++ b/biology/py-biopython/distinfo
@@ -1,2 +1,2 @@
-SHA256 (biopython-1.83.tar.gz) = eOa/t43mMDQDev01/nfLbgqeW2Jwa+z3in2SKxbtg/c=
-SIZE (biopython-1.83.tar.gz) = 19431530
+SHA256 (biopython-1.84.tar.gz) = YPvm+ZbopoZqQmmMF+VSEn2ZqaqzJZ1iSfuqvQ4Mx7Q=
+SIZE (biopython-1.84.tar.gz) = 25793001
diff --git a/biology/py-biopython/pkg/PLIST b/biology/py-biopython/pkg/PLIST
index 39cfc5acef2..28ea89772e8 100644
--- a/biology/py-biopython/pkg/PLIST
+++ b/biology/py-biopython/pkg/PLIST
@@ -91,6 +91,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}stockholm.${M
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}stockholm.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}tabular.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/${MODPY_PYCACHE}tabular.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Align/_aligncore.c
+@so lib/python${MODPY_VERSION}/site-packages/Bio/Align/_aligncore.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/_codonaligner.c
 @so lib/python${MODPY_VERSION}/site-packages/Bio/Align/_codonaligner.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/Bio/Align/_pairwisealigner.c
@@ -202,7 +204,6 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Blast/
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Applications.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/NCBIWWW.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/NCBIXML.py
-lib/python${MODPY_VERSION}/site-packages/Bio/Blast/Record.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/__init__.py
 ${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}/
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}Applications.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -211,10 +212,14 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}NCBIWWW.${MOD
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}NCBIWWW.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}NCBIXML.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}NCBIXML.${MODPY_PYC_MAGIC_TAG}pyc
-lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}Record.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
-lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}Record.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}_parser.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}_parser.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}_writers.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/${MODPY_PYCACHE}_writers.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/_parser.py
+lib/python${MODPY_VERSION}/site-packages/Bio/Blast/_writers.py
 lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/
 lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/__init__.py
 ${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/CAPS/${MODPY_PYCACHE}/
@@ -466,6 +471,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/elink_020122.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/epost.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/esearch.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/esummary-v1.dtd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/esummary_clinvar.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/esummary_gene.dtd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/format.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/htmltable.dtd
@@ -554,6 +560,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/DTDs/xmlspecchars.ent
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/Parser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/IPGReportSet.xsd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/NCBI_BlastOutput2.mod.xsd
+lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/XSDs/NCBI_BlastOutput2.xsd
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/__init__.py
 ${MODPY_COMMENT}lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/${MODPY_PYCACHE}/
 lib/python${MODPY_VERSION}/site-packages/Bio/Entrez/${MODPY_PYCACHE}Parser.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -776,6 +784,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/NeighborSearch.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBExceptions.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBList.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBMLParser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PDBParser.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PICIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/PSEA.py
@@ -823,6 +832,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBIO.${MODPY_P
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBIO.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBList.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBList.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBMLParser.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBMLParser.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBParser.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PDBParser.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}PICIO.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -851,6 +862,10 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Superimposer.${
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}Superimposer.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}__init__.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}alphafold_db.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}alphafold_db.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}binary_cif.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}binary_cif.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}cealign.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}cealign.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}ic_data.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -867,6 +882,10 @@ lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}qcprot.${MODPY_
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}qcprot.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}vectors.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/${MODPY_PYCACHE}vectors.${MODPY_PYC_MAGIC_TAG}pyc
+@so lib/python${MODPY_VERSION}/site-packages/Bio/PDB/_bcif_helper.${MODPY_PYC_MAGIC_TAG}so
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/alphafold_db.py
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/bcifhelpermodule.c
+lib/python${MODPY_VERSION}/site-packages/Bio/PDB/binary_cif.py
 @so lib/python${MODPY_VERSION}/site-packages/Bio/PDB/ccealign.${MODPY_PYC_MAGIC_TAG}so
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/ccealignmodule.c
 lib/python${MODPY_VERSION}/site-packages/Bio/PDB/cealign.py
@@ -1168,6 +1187,7 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AbiIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/AceIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/FastaIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/GckIO.py
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/GfaIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/IgIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/InsdcIO.py
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/Interfaces.py
@@ -1194,6 +1214,8 @@ lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}FastaIO.${MOD
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}FastaIO.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}GckIO.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}GckIO.${MODPY_PYC_MAGIC_TAG}pyc
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}GfaIO.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
+lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}GfaIO.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}IgIO.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}IgIO.${MODPY_PYC_MAGIC_TAG}pyc
 lib/python${MODPY_VERSION}/site-packages/Bio/SeqIO/${MODPY_PYCACHE}InsdcIO.${MODPY_PYC_MAGIC_TAG}${MODPY_PYOEXTENSION}
@@ -1444,8 +1466,7 @@ lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}.dist-inf
 lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}.dist-info/WHEEL
 lib/python${MODPY_VERSION}/site-packages/biopython-${MODPY_EGG_VERSION}.dist-info/top_level.txt
 share/doc/py-biopython/
-share/doc/py-biopython/Tutorial.pdf
-share/doc/py-biopython/biopdb_faq.pdf
+share/doc/py-biopython/Biopython_doc.pdf
 share/examples/py-biopython/
 share/examples/py-biopython/ACT_example.py
 share/examples/py-biopython/PF05371_seed.sth