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py-ete3: Python Environment for (phylogenetic) Tree Exploration
Module Name: pkgsrc-wip
Committed By: Jason Bacon <bacon%NetBSD.org@localhost>
Pushed By: outpaddling
Date: Mon Nov 5 12:11:10 2018 -0600
Changeset: 2c48e13a265a714fd672cb72d93cb7cde33a18ea
Modified Files:
Makefile
Added Files:
py-ete3/DESCR
py-ete3/Makefile
py-ete3/PLIST
py-ete3/distinfo
Log Message:
py-ete3: Python Environment for (phylogenetic) Tree Exploration
To see a diff of this commit:
https://wip.pkgsrc.org/cgi-bin/gitweb.cgi?p=pkgsrc-wip.git;a=commitdiff;h=2c48e13a265a714fd672cb72d93cb7cde33a18ea
Please note that diffs are not public domain; they are subject to the
copyright notices on the relevant files.
diffstat:
Makefile | 1 +
py-ete3/DESCR | 4 +
py-ete3/Makefile | 24 ++
py-ete3/PLIST | 738 +++++++++++++++++++++++++++++++++++++++++++++++++++++++
py-ete3/distinfo | 6 +
5 files changed, 773 insertions(+)
diffs:
diff --git a/Makefile b/Makefile
index 14b47646a1..c744f0714a 100644
--- a/Makefile
+++ b/Makefile
@@ -3247,6 +3247,7 @@ SUBDIR+= py-epipy
SUBDIR+= py-equation
SUBDIR+= py-errorhandler
SUBDIR+= py-escher
+SUBDIR+= py-ete3
SUBDIR+= py-etk-docking
SUBDIR+= py-etmtk
SUBDIR+= py-event
diff --git a/py-ete3/DESCR b/py-ete3/DESCR
new file mode 100644
index 0000000000..397c16bfe1
--- /dev/null
+++ b/py-ete3/DESCR
@@ -0,0 +1,4 @@
+The Environment for Tree Exploration (ETE) is a Python programming toolkit that
+assists in the recontruction, manipulation, analysis and visualization of
+phylogenetic trees (although clustering trees or any other tree-like data
+structure are also supported).
diff --git a/py-ete3/Makefile b/py-ete3/Makefile
new file mode 100644
index 0000000000..51b8c85624
--- /dev/null
+++ b/py-ete3/Makefile
@@ -0,0 +1,24 @@
+# $NetBSD$
+#
+###########################################################
+# Generated by fbsd2pkg #
+# Mon Nov 5 11:59:21 CST 2018 #
+###########################################################
+
+DISTNAME= ete3-${PV}
+PKGNAME= ${PYPKGPREFIX}-ete3-${PV}
+CATEGORIES= biology
+MASTER_SITES= ${MASTER_SITE_PYPI:=e/ete3/}
+
+MAINTAINER= bacon%NetBSD.org@localhost
+HOMEPAGE= https://pypi.python.org/pypi/ete3
+COMMENT= Python Environment for (phylogenetic) Tree Exploration
+LICENSE= gnu-gpl-v3
+
+REPLACE_PYTHON= ete3/tools/ete.py ete3/tools/ete_build.py
+
+PV= 3.1.1
+
+.include "../../lang/python/egg.mk"
+.include "../../lang/python/application.mk"
+.include "../../mk/bsd.pkg.mk"
diff --git a/py-ete3/PLIST b/py-ete3/PLIST
new file mode 100644
index 0000000000..406ab6d4e5
--- /dev/null
+++ b/py-ete3/PLIST
@@ -0,0 +1,738 @@
+@comment $NetBSD$
+bin/ete3
+ete3/tools/ete_build.cfg
+${PYSITELIB}/${EGG_INFODIR}/PKG-INFO
+${PYSITELIB}/${EGG_INFODIR}/SOURCES.txt
+${PYSITELIB}/${EGG_INFODIR}/dependency_links.txt
+${PYSITELIB}/${EGG_INFODIR}/entry_points.txt
+${PYSITELIB}/${EGG_INFODIR}/top_level.txt
+${PYSITELIB}/ete3/__init__.py
+${PYSITELIB}/ete3/__init__.pyc
+${PYSITELIB}/ete3/__init__.pyo
+${PYSITELIB}/ete3/_ph.py
+${PYSITELIB}/ete3/_ph.pyc
+${PYSITELIB}/ete3/_ph.pyo
+${PYSITELIB}/ete3/citation.py
+${PYSITELIB}/ete3/citation.pyc
+${PYSITELIB}/ete3/citation.pyo
+${PYSITELIB}/ete3/clustering/__init__.py
+${PYSITELIB}/ete3/clustering/__init__.pyc
+${PYSITELIB}/ete3/clustering/__init__.pyo
+${PYSITELIB}/ete3/clustering/clustertree.py
+${PYSITELIB}/ete3/clustering/clustertree.pyc
+${PYSITELIB}/ete3/clustering/clustertree.pyo
+${PYSITELIB}/ete3/clustering/clustvalidation.py
+${PYSITELIB}/ete3/clustering/clustvalidation.pyc
+${PYSITELIB}/ete3/clustering/clustvalidation.pyo
+${PYSITELIB}/ete3/coretype/__init__.py
+${PYSITELIB}/ete3/coretype/__init__.pyc
+${PYSITELIB}/ete3/coretype/__init__.pyo
+${PYSITELIB}/ete3/coretype/arraytable.py
+${PYSITELIB}/ete3/coretype/arraytable.pyc
+${PYSITELIB}/ete3/coretype/arraytable.pyo
+${PYSITELIB}/ete3/coretype/seqgroup.py
+${PYSITELIB}/ete3/coretype/seqgroup.pyc
+${PYSITELIB}/ete3/coretype/seqgroup.pyo
+${PYSITELIB}/ete3/coretype/tree.py
+${PYSITELIB}/ete3/coretype/tree.pyc
+${PYSITELIB}/ete3/coretype/tree.pyo
+${PYSITELIB}/ete3/evol/__init__.py
+${PYSITELIB}/ete3/evol/__init__.pyc
+${PYSITELIB}/ete3/evol/__init__.pyo
+${PYSITELIB}/ete3/evol/control.py
+${PYSITELIB}/ete3/evol/control.pyc
+${PYSITELIB}/ete3/evol/control.pyo
+${PYSITELIB}/ete3/evol/evoltree.py
+${PYSITELIB}/ete3/evol/evoltree.pyc
+${PYSITELIB}/ete3/evol/evoltree.pyo
+${PYSITELIB}/ete3/evol/model.py
+${PYSITELIB}/ete3/evol/model.pyc
+${PYSITELIB}/ete3/evol/model.pyo
+${PYSITELIB}/ete3/evol/parser/__init__.py
+${PYSITELIB}/ete3/evol/parser/__init__.pyc
+${PYSITELIB}/ete3/evol/parser/__init__.pyo
+${PYSITELIB}/ete3/evol/parser/codemlparser.py
+${PYSITELIB}/ete3/evol/parser/codemlparser.pyc
+${PYSITELIB}/ete3/evol/parser/codemlparser.pyo
+${PYSITELIB}/ete3/evol/parser/slrparser.py
+${PYSITELIB}/ete3/evol/parser/slrparser.pyc
+${PYSITELIB}/ete3/evol/parser/slrparser.pyo
+${PYSITELIB}/ete3/evol/utils.py
+${PYSITELIB}/ete3/evol/utils.pyc
+${PYSITELIB}/ete3/evol/utils.pyo
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/.gitignore
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/EXAMPLE
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/Makefile
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/README
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/src/levenshtein.c
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/tests/README
+${PYSITELIB}/ete3/ncbi_taxonomy/SQLite-Levenshtein/tests/levenshtein-test.sql
+${PYSITELIB}/ete3/ncbi_taxonomy/__init__.py
+${PYSITELIB}/ete3/ncbi_taxonomy/__init__.pyc
+${PYSITELIB}/ete3/ncbi_taxonomy/__init__.pyo
+${PYSITELIB}/ete3/ncbi_taxonomy/ncbiquery.py
+${PYSITELIB}/ete3/ncbi_taxonomy/ncbiquery.pyc
+${PYSITELIB}/ete3/ncbi_taxonomy/ncbiquery.pyo
+${PYSITELIB}/ete3/nexml/__init__.py
+${PYSITELIB}/ete3/nexml/__init__.pyc
+${PYSITELIB}/ete3/nexml/__init__.pyo
+${PYSITELIB}/ete3/nexml/_nexml.py
+${PYSITELIB}/ete3/nexml/_nexml.pyc
+${PYSITELIB}/ete3/nexml/_nexml.pyo
+${PYSITELIB}/ete3/nexml/_nexml_tree.py
+${PYSITELIB}/ete3/nexml/_nexml_tree.pyc
+${PYSITELIB}/ete3/nexml/_nexml_tree.pyo
+${PYSITELIB}/ete3/orthoxml/__init__.py
+${PYSITELIB}/ete3/orthoxml/__init__.pyc
+${PYSITELIB}/ete3/orthoxml/__init__.pyo
+${PYSITELIB}/ete3/orthoxml/_orthoxml.py
+${PYSITELIB}/ete3/orthoxml/_orthoxml.pyc
+${PYSITELIB}/ete3/orthoxml/_orthoxml.pyo
+${PYSITELIB}/ete3/parser/__init__.py
+${PYSITELIB}/ete3/parser/__init__.pyc
+${PYSITELIB}/ete3/parser/__init__.pyo
+${PYSITELIB}/ete3/parser/fasta.py
+${PYSITELIB}/ete3/parser/fasta.pyc
+${PYSITELIB}/ete3/parser/fasta.pyo
+${PYSITELIB}/ete3/parser/newick.py
+${PYSITELIB}/ete3/parser/newick.pyc
+${PYSITELIB}/ete3/parser/newick.pyo
+${PYSITELIB}/ete3/parser/paml.py
+${PYSITELIB}/ete3/parser/paml.pyc
+${PYSITELIB}/ete3/parser/paml.pyo
+${PYSITELIB}/ete3/parser/phylip.py
+${PYSITELIB}/ete3/parser/phylip.pyc
+${PYSITELIB}/ete3/parser/phylip.pyo
+${PYSITELIB}/ete3/parser/text_arraytable.py
+${PYSITELIB}/ete3/parser/text_arraytable.pyc
+${PYSITELIB}/ete3/parser/text_arraytable.pyo
+${PYSITELIB}/ete3/phylo/__init__.py
+${PYSITELIB}/ete3/phylo/__init__.pyc
+${PYSITELIB}/ete3/phylo/__init__.pyo
+${PYSITELIB}/ete3/phylo/evolevents.py
+${PYSITELIB}/ete3/phylo/evolevents.pyc
+${PYSITELIB}/ete3/phylo/evolevents.pyo
+${PYSITELIB}/ete3/phylo/phylotree.py
+${PYSITELIB}/ete3/phylo/phylotree.pyc
+${PYSITELIB}/ete3/phylo/phylotree.pyo
+${PYSITELIB}/ete3/phylo/reconciliation.py
+${PYSITELIB}/ete3/phylo/reconciliation.pyc
+${PYSITELIB}/ete3/phylo/reconciliation.pyo
+${PYSITELIB}/ete3/phylo/spoverlap.py
+${PYSITELIB}/ete3/phylo/spoverlap.pyc
+${PYSITELIB}/ete3/phylo/spoverlap.pyo
+${PYSITELIB}/ete3/phylomedb/__init__.py
+${PYSITELIB}/ete3/phylomedb/__init__.pyc
+${PYSITELIB}/ete3/phylomedb/__init__.pyo
+${PYSITELIB}/ete3/phylomedb/phylomeDB.py
+${PYSITELIB}/ete3/phylomedb/phylomeDB.pyc
+${PYSITELIB}/ete3/phylomedb/phylomeDB.pyo
+${PYSITELIB}/ete3/phylomedb/phylomeDB3.py
+${PYSITELIB}/ete3/phylomedb/phylomeDB3.pyc
+${PYSITELIB}/ete3/phylomedb/phylomeDB3.pyo
+${PYSITELIB}/ete3/phyloxml/__init__.py
+${PYSITELIB}/ete3/phyloxml/__init__.pyc
+${PYSITELIB}/ete3/phyloxml/__init__.pyo
+${PYSITELIB}/ete3/phyloxml/_phyloxml.py
+${PYSITELIB}/ete3/phyloxml/_phyloxml.pyc
+${PYSITELIB}/ete3/phyloxml/_phyloxml.pyo
+${PYSITELIB}/ete3/phyloxml/_phyloxml_tree.py
+${PYSITELIB}/ete3/phyloxml/_phyloxml_tree.pyc
+${PYSITELIB}/ete3/phyloxml/_phyloxml_tree.pyo
+${PYSITELIB}/ete3/test/__init__.py
+${PYSITELIB}/ete3/test/__init__.pyc
+${PYSITELIB}/ete3/test/__init__.pyo
+${PYSITELIB}/ete3/test/datasets.py
+${PYSITELIB}/ete3/test/datasets.pyc
+${PYSITELIB}/ete3/test/datasets.pyo
+${PYSITELIB}/ete3/test/ete_evol_data/CladeModelCD/ECP_EDN_15.fasta
+${PYSITELIB}/ete3/test/ete_evol_data/CladeModelCD/ECP_EDN_15.nw
+${PYSITELIB}/ete3/test/ete_evol_data/L_example/alignment_L_measuring_evol.fasta
+${PYSITELIB}/ete3/test/ete_evol_data/L_example/measuring_L_tree.nw
+${PYSITELIB}/ete3/test/ete_evol_data/S_example/ali.fasta
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+${PYSITELIB}/ete3/test/ete_evol_data/S_example/paml/M1/algn
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+${PYSITELIB}/ete3/test/ete_evol_data/S_example/paml/M1/out
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+${PYSITELIB}/ete3/test/ete_evol_data/S_example/paml/M1/rst1
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+${PYSITELIB}/ete3/treeview/_about.pyc
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+${PYSITELIB}/ete3/treeview/_show_codeml.pyo
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+${PYSITELIB}/ete3/treeview/about.ui
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+${PYSITELIB}/ete3/treeview/drawer.py
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+${PYSITELIB}/ete3/treeview/ete_icon.png
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+${PYSITELIB}/ete3/treeview/ete_resources_rc.pyc
+${PYSITELIB}/ete3/treeview/ete_resources_rc.pyo
+${PYSITELIB}/ete3/treeview/export_pdf.png
+${PYSITELIB}/ete3/treeview/faces.py
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+${PYSITELIB}/ete3/treeview/faces.pyo
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+${PYSITELIB}/ete3/treeview/filesave.png
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+${PYSITELIB}/ete3/treeview/fit_tree.png
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+${PYSITELIB}/ete3/treeview/image_properties.ui
+${PYSITELIB}/ete3/treeview/layouts.py
+${PYSITELIB}/ete3/treeview/layouts.pyc
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+${PYSITELIB}/ete3/treeview/node_gui_actions.pyo
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+${PYSITELIB}/ete3/treeview/qt.pyo
+${PYSITELIB}/ete3/treeview/qt4_circular_render.py
+${PYSITELIB}/ete3/treeview/qt4_circular_render.pyc
+${PYSITELIB}/ete3/treeview/qt4_circular_render.pyo
+${PYSITELIB}/ete3/treeview/qt4_compile_resources.sh
+${PYSITELIB}/ete3/treeview/qt4_face_render.py
+${PYSITELIB}/ete3/treeview/qt4_face_render.pyc
+${PYSITELIB}/ete3/treeview/qt4_face_render.pyo
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+${PYSITELIB}/ete3/treeview/qt4_rect_render.pyc
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+${PYSITELIB}/ete3/treeview/qt4_render.py
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+${PYSITELIB}/ete3/treeview/search_dialog.ui
+${PYSITELIB}/ete3/treeview/show_dist.png
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+${PYSITELIB}/ete3/treeview/templates.py
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+${PYSITELIB}/ete3/treeview/x_expand.png
+${PYSITELIB}/ete3/treeview/x_reduce.png
+${PYSITELIB}/ete3/treeview/y_expand.png
+${PYSITELIB}/ete3/treeview/y_reduce.png
+${PYSITELIB}/ete3/treeview/zoom_in.png
+${PYSITELIB}/ete3/treeview/zoom_out.png
+${PYSITELIB}/ete3/utils.py
+${PYSITELIB}/ete3/utils.pyc
+${PYSITELIB}/ete3/utils.pyo
+${PYSITELIB}/ete3/version.py
+${PYSITELIB}/ete3/version.pyc
+${PYSITELIB}/ete3/version.pyo
+${PYSITELIB}/ete3/webplugin/__init__.py
+${PYSITELIB}/ete3/webplugin/__init__.pyc
+${PYSITELIB}/ete3/webplugin/__init__.pyo
+${PYSITELIB}/ete3/webplugin/webapp.py
+${PYSITELIB}/ete3/webplugin/webapp.pyc
+${PYSITELIB}/ete3/webplugin/webapp.pyo
diff --git a/py-ete3/distinfo b/py-ete3/distinfo
new file mode 100644
index 0000000000..2aaea5d9ed
--- /dev/null
+++ b/py-ete3/distinfo
@@ -0,0 +1,6 @@
+$NetBSD$
+
+SHA1 (ete3-3.1.1.tar.gz) = 33cc4d23872008c0e7b3daf459548e995437953a
+RMD160 (ete3-3.1.1.tar.gz) = 4e00e75a20c8c4f7d7bf738f8ca091fcd569a8e0
+SHA512 (ete3-3.1.1.tar.gz) = 9463431d2b7387f39be5c7111ac792967c689ce9d22cbd9e4fdfd1db4b4c7b14edaccbaab92d4d9b025d563b4ecd97cfc20b0e0a3ac328461c04e05100c4e152
+Size (ete3-3.1.1.tar.gz) = 10504887 bytes
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