l/biopython: Upgraded to biopython-1.78.

l/biopython/biopython-1.77-snapgene-utf8.diff

@@ -1,41 +0,0 @@
-commit 86ff00b49004091a95933167824088f7682ee698
-Author: Damien Goutte-Gattat <dgouttegattat@incenp.org>
-Date:   Fri Jul 31 00:18:32 2020 +0100
-
-    SnapGene: Parse XML data as UTF8-encoded strings (#3180).
-    
-    All XML chunks within SnapGene packets should be parsed as UTF-8,
-    as per the XML specification in the absence of an explicit encoding
-    attribute.
-
-diff --git a/Bio/SeqIO/SnapGeneIO.py b/Bio/SeqIO/SnapGeneIO.py
-index 9c8598b50..9464e682f 100644
---- a/Bio/SeqIO/SnapGeneIO.py
-+++ b/Bio/SeqIO/SnapGeneIO.py
-@@ -75,7 +75,7 @@ def _parse_notes_packet(length, data, record):
-     This type of packet contains some metadata about the sequence. They
-     are stored as a XML string with a 'Notes' root node.
-     """
--    xml = parseString(data.decode("ASCII"))
-+    xml = parseString(data.decode("UTF-8"))
-     type = _get_child_value(xml, "Type")
-     if type == "Synthetic":
-         record.annotations["data_file_division"] = "SYN"
-@@ -116,7 +116,7 @@ def _parse_features_packet(length, data, record):
-     which are in a dedicated Primers packet). The data is a XML string
-     starting with a 'Features' root node.
-     """
--    xml = parseString(data.decode("ASCII"))
-+    xml = parseString(data.decode("UTF-8"))
-     for feature in xml.getElementsByTagName("Feature"):
-         quals = {}
- 
-@@ -170,7 +170,7 @@ def _parse_primers_packet(length, data, record):
-     stores primer binding features. The data is a XML string starting
-     with a 'Primers' root node.
-     """
--    xml = parseString(data.decode("ASCII"))
-+    xml = parseString(data.decode("UTF-8"))
-     for primer in xml.getElementsByTagName("Primer"):
-         quals = {}
- 

l/biopython/biopython-1.77-snapgene-wrapping-features.diff

@@ -1,70 +0,0 @@
-commit 119845697972a7ea3d6c2574dd5e2bdbe53b905e
-Author: Damien Goutte-Gattat <dgouttegattat@incenp.org>
-Date:   Fri Jul 31 00:23:29 2020 +0100
-
-    SnapGene: Support features wrapping the origin.
-    
-    A SnapGene file containing a circular sequence may contain feature
-    range specifications that wrap the beginning/end of the sequence,
-    e.g. "3925-2" for a feature starting at position 3925 near the end
-    of the sequence and ending at position 2. This case must be
-    recognized and represented as a CompoundLocation in the SeqRecord
-    object.
-
-diff --git a/Bio/SeqIO/SnapGeneIO.py b/Bio/SeqIO/SnapGeneIO.py
-index 9464e682f..ad1bd3258 100644
---- a/Bio/SeqIO/SnapGeneIO.py
-+++ b/Bio/SeqIO/SnapGeneIO.py
-@@ -109,6 +109,18 @@ def _parse_cookie_packet(length, data, record):
-         raise ValueError("The file is not a valid SnapGene file")
- 
- 
-+def _parse_location(rangespec, strand, record):
-+    start, end = [int(x) for x in rangespec.split("-")]
-+    # Account for SnapGene's 1-based coordinates
-+    start = start - 1
-+    if start > end:
-+        # Range wrapping the end of the sequence
-+        location = FeatureLocation(start, len(record), strand=strand) + FeatureLocation(0, end, strand=strand)
-+    else:
-+        location = FeatureLocation(start, end, strand=strand)
-+    return location
-+
-+
- def _parse_features_packet(length, data, record):
-     """Parse a sequence features packet.
- 
-@@ -135,13 +147,10 @@ def _parse_features_packet(length, data, record):
-         location = None
-         for segment in feature.getElementsByTagName("Segment"):
-             rng = _get_attribute_value(segment, "range")
--            start, end = [int(x) for x in rng.split("-")]
--            # Account for SnapGene's 1-based coordinates
--            start = start - 1
-             if not location:
--                location = FeatureLocation(start, end, strand=strand)
-+                location = _parse_location(rng, strand, record)
-             else:
--                location = location + FeatureLocation(start, end, strand=strand)
-+                location = location + _parse_location(rng, strand, record)
-         if not location:
-             raise ValueError("Missing feature location")
- 
-@@ -182,8 +191,6 @@ def _parse_primers_packet(length, data, record):
-             rng = _get_attribute_value(
-                 site, "location", error="Missing binding site location"
-             )
--            start, end = [int(x) for x in rng.split("-")]
--
-             strand = int(_get_attribute_value(site, "boundStrand", default="0"))
-             if strand == 1:
-                 strand = -1
-@@ -191,7 +198,7 @@ def _parse_primers_packet(length, data, record):
-                 strand = +1
- 
-             feature = SeqFeature(
--                FeatureLocation(start, end, strand=strand),
-+                _parse_location(rng, strand, record),
-                 type="primer_bind",
-                 qualifiers=quals,
-             )

l/biopython/biopython-1.77.tar.gz.sha256

@@ -1 +0,0 @@
-fb1936e9ca9e7af8de1050e84375f23328e04b801063edf0ad73733494d8ec42  biopython-1.77.tar.gz

l/biopython/biopython-1.78.tar.gz.sha256

@@ -0,0 +1 @@
+1ee0a0b6c2376680fea6642d5080baa419fd73df104a62d58a8baf7a8bbe4564  biopython-1.78.tar.gz

l/biopython/biopython.SlackBuild

@@ -30,12 +30,12 @@
 
 # Source package infos
 NAMESRC=${NAMESRC:-biopython}
-VERSION=${VERSION:-1.77}
+VERSION=${VERSION:-1.78}
 ARCHIVE=${ARCHIVE:-$NAMESRC-$VERSION.tar.gz}
 
 # Build infos
 NAMEPKG=${NAMEPKG:-biopython}
-BUILD=${BUILD:-2GGD}
+BUILD=${BUILD:-1GGD}
 ARCH=${ARCH:-$(uname -m | sed 's/^i.86$/i486/;s/^arm.*/arm/')}
 EXT=${EXT:-txz}
 
@@ -82,8 +82,6 @@ cd $TMP
 echo "Building $ARCHIVE..."
 tar xf $CWD/$ARCHIVE
 cd $NAME
-patch -p 1 < $CWD/biopython-1.77-snapgene-utf8.diff
-patch -p 1 < $CWD/biopython-1.77-snapgene-wrapping-features.diff
 CFLAGS=$CPUOPT \
 CXXFLAGS=$CPUOPT \
 python3 setup.py build