CVS commit: pkgsrc/biology/py-dna-features-viewer

["Jason Bacon" <bacon%netbsd.org@localhost>]

Module Name:    pkgsrc
Committed By:   bacon
Date:           Sun Nov  5 17:54:43 UTC 2023

Added Files:
        pkgsrc/biology/py-dna-features-viewer: DESCR Makefile PLIST distinfo

Log Message:
biology/py-dna-features-viewer: Visualize DNA features

DNA Features Viewer is a Python library to visualize DNA features,
e.g.  from GenBank or Gff files.  DNA Features Viewer can plot
sequence maps linearly or circularly, with or without nucleotide
sequence and amino-acid sequences. The plotter automatically produces
clear plots even for sequences with many overlapping features and
long labels. The library plays well with Matplotlib and Biopython,
and the figures can be saved in different formats (PNG, JPEG, SVG,
PDF), e.g. for report generation or LIMS interfaces.


To generate a diff of this commit:
cvs rdiff -u -r0 -r1.1 pkgsrc/biology/py-dna-features-viewer/DESCR \
    pkgsrc/biology/py-dna-features-viewer/Makefile \
    pkgsrc/biology/py-dna-features-viewer/PLIST \
    pkgsrc/biology/py-dna-features-viewer/distinfo

Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.

Added files:

Index: pkgsrc/biology/py-dna-features-viewer/DESCR
diff -u /dev/null pkgsrc/biology/py-dna-features-viewer/DESCR:1.1
--- /dev/null   Sun Nov  5 17:54:43 2023
+++ pkgsrc/biology/py-dna-features-viewer/DESCR Sun Nov  5 17:54:43 2023
@@ -0,0 +1,8 @@
+DNA Features Viewer is a Python library to visualize DNA features,
+e.g.  from GenBank or Gff files.  DNA Features Viewer can plot
+sequence maps linearly or circularly, with or without nucleotide
+sequence and amino-acid sequences. The plotter automatically produces
+clear plots even for sequences with many overlapping features and
+long labels. The library plays well with Matplotlib and Biopython,
+and the figures can be saved in different formats (PNG, JPEG, SVG,
+PDF), e.g. for report generation or LIMS interfaces.
Index: pkgsrc/biology/py-dna-features-viewer/Makefile
diff -u /dev/null pkgsrc/biology/py-dna-features-viewer/Makefile:1.1
--- /dev/null   Sun Nov  5 17:54:43 2023
+++ pkgsrc/biology/py-dna-features-viewer/Makefile      Sun Nov  5 17:54:43 2023
@@ -0,0 +1,19 @@
+# $NetBSD: Makefile,v 1.1 2023/11/05 17:54:43 bacon Exp $
+
+DISTNAME=      dna_features_viewer-3.1.3
+PKGNAME=       ${PYPKGPREFIX}-dna-features-viewer-3.1.3
+CATEGORIES=    biology
+MASTER_SITES=  ${MASTER_SITE_PYPI:=d/dna-features-viewer/}
+
+MAINTAINER=    bacon%NetBSD.org@localhost
+HOMEPAGE=      https://pypi.python.org/project/dna-features-viewer/
+COMMENT=       Python library to visualize DNA features, e.g. GenBank or Gff files
+LICENSE=       mit
+
+DEPENDS=       ${PYPKGPREFIX}-matplotlib>=3:../../graphics/py-matplotlib \
+               ${PYPKGPREFIX}-biopython>0:../../biology/py-biopython \
+               ${PYPKGPREFIX}-bcbio-gff>0:../../biology/py-bcbio-gff \
+               ${PYPKGPREFIX}-packaging>0:../../devel/py-packaging
+
+.include "../../lang/python/egg.mk"
+.include "../../mk/bsd.pkg.mk"
Index: pkgsrc/biology/py-dna-features-viewer/PLIST
diff -u /dev/null pkgsrc/biology/py-dna-features-viewer/PLIST:1.1
--- /dev/null   Sun Nov  5 17:54:43 2023
+++ pkgsrc/biology/py-dna-features-viewer/PLIST Sun Nov  5 17:54:43 2023
@@ -0,0 +1,60 @@
+@comment $NetBSD: PLIST,v 1.1 2023/11/05 17:54:43 bacon Exp $
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/requires.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.py
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.pyc
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslator.pyo
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.py
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.pyc
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BiopythonTranslatorBase.pyo
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.py
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.pyc
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/BlackBoxlessLabelTranslator.pyo
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/__init__.py
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/__init__.pyc
+${PYSITELIB}/dna_features_viewer/BiopythonTranslator/__init__.pyo
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/ArrowWedge.py
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/ArrowWedge.pyc
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/ArrowWedge.pyo
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.py
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.pyc
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/CircularGraphicRecord.pyo
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/__init__.py
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/__init__.pyc
+${PYSITELIB}/dna_features_viewer/CircularGraphicRecord/__init__.pyo
+${PYSITELIB}/dna_features_viewer/GraphicFeature.py
+${PYSITELIB}/dna_features_viewer/GraphicFeature.pyc
+${PYSITELIB}/dna_features_viewer/GraphicFeature.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/BokehPlottableMixin.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/BokehPlottableMixin.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/BokehPlottableMixin.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/GraphicRecord.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/GraphicRecord.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/GraphicRecord.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MatplotlibPlottableMixin.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/MultilinePlottableMixin.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/SequenceAndTranslationMixin.pyo
+${PYSITELIB}/dna_features_viewer/GraphicRecord/__init__.py
+${PYSITELIB}/dna_features_viewer/GraphicRecord/__init__.pyc
+${PYSITELIB}/dna_features_viewer/GraphicRecord/__init__.pyo
+${PYSITELIB}/dna_features_viewer/__init__.py
+${PYSITELIB}/dna_features_viewer/__init__.pyc
+${PYSITELIB}/dna_features_viewer/__init__.pyo
+${PYSITELIB}/dna_features_viewer/biotools.py
+${PYSITELIB}/dna_features_viewer/biotools.pyc
+${PYSITELIB}/dna_features_viewer/biotools.pyo
+${PYSITELIB}/dna_features_viewer/compute_features_levels.py
+${PYSITELIB}/dna_features_viewer/compute_features_levels.pyc
+${PYSITELIB}/dna_features_viewer/compute_features_levels.pyo
+${PYSITELIB}/dna_features_viewer/version.py
+${PYSITELIB}/dna_features_viewer/version.pyc
+${PYSITELIB}/dna_features_viewer/version.pyo
Index: pkgsrc/biology/py-dna-features-viewer/distinfo
diff -u /dev/null pkgsrc/biology/py-dna-features-viewer/distinfo:1.1
--- /dev/null   Sun Nov  5 17:54:43 2023
+++ pkgsrc/biology/py-dna-features-viewer/distinfo      Sun Nov  5 17:54:43 2023
@@ -0,0 +1,5 @@
+$NetBSD: distinfo,v 1.1 2023/11/05 17:54:43 bacon Exp $
+
+BLAKE2s (dna_features_viewer-3.1.3.tar.gz) = 96afa139d207b7d3c4f43f3f9d5f22926fbd2655b686f84ea43d120f5b697ac5
+SHA512 (dna_features_viewer-3.1.3.tar.gz) = eb73fb9f362c5b53e16e2ce96876ffd5c59da991e39dccf870c2c2ee89f8ea8199ef5c45a423c79ae3c1e66806cac7d2b24f681ee36cbaa8fdea3d66859df368
+Size (dna_features_viewer-3.1.3.tar.gz) = 40331 bytes