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[pkgsrc/trunk]: pkgsrc py-mol: remove
details: https://anonhg.NetBSD.org/pkgsrc/rev/1abba6095aef
branches: trunk
changeset: 374248:1abba6095aef
user: wiz <wiz%pkgsrc.org@localhost>
date: Thu Feb 17 09:36:02 2022 +0000
description:
py-mol: remove
This package is from 2012, the current version is from 2020.
A replacement candidate is in wip/py-mol but needs more work.
One of the last users of py-numpy16 in pkgsrc.
diffstat:
biology/Makefile | 3 +-
biology/py-mol/DESCR | 4 -
biology/py-mol/Makefile | 50 --
biology/py-mol/PLIST | 967 ------------------------------------------------
biology/py-mol/distinfo | 5 -
doc/CHANGES-2022 | 3 +-
6 files changed, 3 insertions(+), 1029 deletions(-)
diffs (truncated from 1073 to 300 lines):
diff -r 02697c544f3b -r 1abba6095aef biology/Makefile
--- a/biology/Makefile Thu Feb 17 09:16:36 2022 +0000
+++ b/biology/Makefile Thu Feb 17 09:36:02 2022 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.77 2021/08/31 15:56:42 bacon Exp $
+# $NetBSD: Makefile,v 1.78 2022/02/17 09:36:02 wiz Exp $
#
COMMENT= Software for the biological sciences
@@ -63,7 +63,6 @@
SUBDIR+= py-biopython
SUBDIR+= py-cutadapt
SUBDIR+= py-dnaio
-SUBDIR+= py-mol
SUBDIR+= py-pydicom
SUBDIR+= racon
SUBDIR+= rasmol
diff -r 02697c544f3b -r 1abba6095aef biology/py-mol/DESCR
--- a/biology/py-mol/DESCR Thu Feb 17 09:16:36 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,4 +0,0 @@
-PyMOL is a molecular visualization program. It excels at 3D
-visualization of proteins, small molecules, density, surfaces, and
-trajectories. It also includes molecular editing, ray tracing, and
-movies.
diff -r 02697c544f3b -r 1abba6095aef biology/py-mol/Makefile
--- a/biology/py-mol/Makefile Thu Feb 17 09:16:36 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,50 +0,0 @@
-# $NetBSD: Makefile,v 1.39 2022/01/10 18:46:54 wiz Exp $
-
-DISTNAME= pymol-v1.5.0.1
-PKGNAME= ${PYPKGPREFIX}-${DISTNAME:S/pymol-v/mol-/}
-EGG_NAME= pymol-1.5.0.1
-PKGREVISION= 10
-CATEGORIES= biology
-MASTER_SITES= ${MASTER_SITE_SOURCEFORGE:=pymol/}
-EXTRACT_SUFX= .tar.bz2
-
-MAINTAINER= pkgsrc-users%NetBSD.org@localhost
-HOMEPAGE= http://www.pymol.org/
-COMMENT= Molecular Visualization System
-
-PYTHON_VERSIONED_DEPENDENCIES= Pmw
-PYTHON_VERSIONS_ACCEPTED= 27 # not yet ported as of 1.5.0.1
-
-WRKSRC= ${WRKDIR}/pymol
-
-USE_TOOLS+= csh:run
-
-CONFLICTS= pymol-[0-9]*
-
-USE_LANGUAGES= c c++
-
-REPLACE_CSH= test/vdiff
-REPLACE_PYTHON= test/cyg test/run test/show test/win.py modules/pmg_tk/startup/apbs_tools.py
-
-# not used
-CHECK_PORTABILITY_SKIP+= setup/*
-
-INSTALLATION_DIRS= bin
-
-# Gross hack
-PYSETUPBUILDTARGET= install ${_PYSETUPINSTALLARGS}
-
-post-install:
- cd ${WRKSRC} && ${SETENV} ${MAKE_ENV} PYTHONPATH=${DESTDIR}${PREFIX}/${PYSITELIB} ${PYTHONBIN} setup2.py install ${_PYSETUPINSTALLARGS}
- ${INSTALL_SCRIPT} ${WRKSRC}/pymol ${DESTDIR}${PREFIX}/bin/pymol${PYVERSSUFFIX}
-
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../graphics/freetype2/buildlink3.mk"
-.include "../../graphics/glew/buildlink3.mk"
-.include "../../graphics/freeglut/buildlink3.mk"
-.include "../../graphics/png/buildlink3.mk"
-.include "../../lang/python/application.mk"
-.include "../../lang/python/versioned_dependencies.mk"
-.include "../../lang/python/egg.mk"
-.include "../../math/py-numpy/buildlink3.mk"
-.include "../../mk/bsd.pkg.mk"
diff -r 02697c544f3b -r 1abba6095aef biology/py-mol/PLIST
--- a/biology/py-mol/PLIST Thu Feb 17 09:16:36 2022 +0000
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,967 +0,0 @@
-@comment $NetBSD: PLIST,v 1.7 2022/01/10 18:46:54 wiz Exp $
-bin/pymol${PYVERSSUFFIX}
-${PYSITELIB}/chempy/__init__.py
-${PYSITELIB}/chempy/__init__.pyc
-${PYSITELIB}/chempy/__init__.pyo
-${PYSITELIB}/chempy/arc.py
-${PYSITELIB}/chempy/arc.pyc
-${PYSITELIB}/chempy/arc.pyo
-${PYSITELIB}/chempy/bmin/__init__.py
-${PYSITELIB}/chempy/bmin/__init__.pyc
-${PYSITELIB}/chempy/bmin/__init__.pyo
-${PYSITELIB}/chempy/bmin/commands.py
-${PYSITELIB}/chempy/bmin/commands.pyc
-${PYSITELIB}/chempy/bmin/commands.pyo
-${PYSITELIB}/chempy/bmin/realtime.py
-${PYSITELIB}/chempy/bmin/realtime.pyc
-${PYSITELIB}/chempy/bmin/realtime.pyo
-${PYSITELIB}/chempy/bmin/state.py
-${PYSITELIB}/chempy/bmin/state.pyc
-${PYSITELIB}/chempy/bmin/state.pyo
-${PYSITELIB}/chempy/bmin/util.py
-${PYSITELIB}/chempy/bmin/util.pyc
-${PYSITELIB}/chempy/bmin/util.pyo
-${PYSITELIB}/chempy/bond_amber.py
-${PYSITELIB}/chempy/bond_amber.pyc
-${PYSITELIB}/chempy/bond_amber.pyo
-${PYSITELIB}/chempy/bond_mmff.py
-${PYSITELIB}/chempy/bond_mmff.pyc
-${PYSITELIB}/chempy/bond_mmff.pyo
-${PYSITELIB}/chempy/bonds.py
-${PYSITELIB}/chempy/bonds.pyc
-${PYSITELIB}/chempy/bonds.pyo
-${PYSITELIB}/chempy/brick.py
-${PYSITELIB}/chempy/brick.pyc
-${PYSITELIB}/chempy/brick.pyo
-${PYSITELIB}/chempy/cc1.py
-${PYSITELIB}/chempy/cc1.pyc
-${PYSITELIB}/chempy/cc1.pyo
-${PYSITELIB}/chempy/cex.py
-${PYSITELIB}/chempy/cex.pyc
-${PYSITELIB}/chempy/cex.pyo
-${PYSITELIB}/chempy/champ/__init__.py
-${PYSITELIB}/chempy/champ/__init__.pyc
-${PYSITELIB}/chempy/champ/__init__.pyo
-${PYSITELIB}/chempy/champ/_champ.so
-${PYSITELIB}/chempy/champ/amber99.py
-${PYSITELIB}/chempy/champ/amber99.pyc
-${PYSITELIB}/chempy/champ/amber99.pyo
-${PYSITELIB}/chempy/champ/assign.py
-${PYSITELIB}/chempy/champ/assign.pyc
-${PYSITELIB}/chempy/champ/assign.pyo
-${PYSITELIB}/chempy/champ/formal_charges.py
-${PYSITELIB}/chempy/champ/formal_charges.pyc
-${PYSITELIB}/chempy/champ/formal_charges.pyo
-${PYSITELIB}/chempy/charge.py
-${PYSITELIB}/chempy/charge.pyc
-${PYSITELIB}/chempy/charge.pyo
-${PYSITELIB}/chempy/cif.py
-${PYSITELIB}/chempy/cif.pyc
-${PYSITELIB}/chempy/cif.pyo
-${PYSITELIB}/chempy/cpv.py
-${PYSITELIB}/chempy/cpv.pyc
-${PYSITELIB}/chempy/cpv.pyo
-${PYSITELIB}/chempy/dictdb.py
-${PYSITELIB}/chempy/dictdb.pyc
-${PYSITELIB}/chempy/dictdb.pyo
-${PYSITELIB}/chempy/fast/__init__.py
-${PYSITELIB}/chempy/fast/__init__.pyc
-${PYSITELIB}/chempy/fast/__init__.pyo
-${PYSITELIB}/chempy/fragments/__init__.py
-${PYSITELIB}/chempy/fragments/__init__.pyc
-${PYSITELIB}/chempy/fragments/__init__.pyo
-${PYSITELIB}/chempy/gamess1.py
-${PYSITELIB}/chempy/gamess1.pyc
-${PYSITELIB}/chempy/gamess1.pyo
-${PYSITELIB}/chempy/gms.py
-${PYSITELIB}/chempy/gms.pyc
-${PYSITELIB}/chempy/gms.pyo
-${PYSITELIB}/chempy/hetatm.py
-${PYSITELIB}/chempy/hetatm.pyc
-${PYSITELIB}/chempy/hetatm.pyo
-${PYSITELIB}/chempy/io.py
-${PYSITELIB}/chempy/io.pyc
-${PYSITELIB}/chempy/io.pyo
-${PYSITELIB}/chempy/lst.py
-${PYSITELIB}/chempy/lst.pyc
-${PYSITELIB}/chempy/lst.pyo
-${PYSITELIB}/chempy/mae.py
-${PYSITELIB}/chempy/mae.pyc
-${PYSITELIB}/chempy/mae.pyo
-${PYSITELIB}/chempy/map.py
-${PYSITELIB}/chempy/map.pyc
-${PYSITELIB}/chempy/map.pyo
-${PYSITELIB}/chempy/mass.py
-${PYSITELIB}/chempy/mass.pyc
-${PYSITELIB}/chempy/mass.pyo
-${PYSITELIB}/chempy/mmd.py
-${PYSITELIB}/chempy/mmd.pyc
-${PYSITELIB}/chempy/mmd.pyo
-${PYSITELIB}/chempy/models.py
-${PYSITELIB}/chempy/models.pyc
-${PYSITELIB}/chempy/models.pyo
-${PYSITELIB}/chempy/mol.py
-${PYSITELIB}/chempy/mol.pyc
-${PYSITELIB}/chempy/mol.pyo
-${PYSITELIB}/chempy/mol2.py
-${PYSITELIB}/chempy/mol2.pyc
-${PYSITELIB}/chempy/mol2.pyo
-${PYSITELIB}/chempy/neighbor.py
-${PYSITELIB}/chempy/neighbor.pyc
-${PYSITELIB}/chempy/neighbor.pyo
-${PYSITELIB}/chempy/pdb.py
-${PYSITELIB}/chempy/pdb.pyc
-${PYSITELIB}/chempy/pdb.pyo
-${PYSITELIB}/chempy/pkl.py
-${PYSITELIB}/chempy/pkl.pyc
-${PYSITELIB}/chempy/pkl.pyo
-${PYSITELIB}/chempy/place.py
-${PYSITELIB}/chempy/place.pyc
-${PYSITELIB}/chempy/place.pyo
-${PYSITELIB}/chempy/protein.py
-${PYSITELIB}/chempy/protein.pyc
-${PYSITELIB}/chempy/protein.pyo
-${PYSITELIB}/chempy/protein_amber.py
-${PYSITELIB}/chempy/protein_amber.pyc
-${PYSITELIB}/chempy/protein_amber.pyo
-${PYSITELIB}/chempy/protein_amber99.py
-${PYSITELIB}/chempy/protein_amber99.pyc
-${PYSITELIB}/chempy/protein_amber99.pyo
-${PYSITELIB}/chempy/protein_mmff.py
-${PYSITELIB}/chempy/protein_mmff.pyc
-${PYSITELIB}/chempy/protein_mmff.pyo
-${PYSITELIB}/chempy/protein_residues.py
-${PYSITELIB}/chempy/protein_residues.pyc
-${PYSITELIB}/chempy/protein_residues.pyo
-${PYSITELIB}/chempy/sdf.py
-${PYSITELIB}/chempy/sdf.pyc
-${PYSITELIB}/chempy/sdf.pyo
-${PYSITELIB}/chempy/solvate.py
-${PYSITELIB}/chempy/solvate.pyc
-${PYSITELIB}/chempy/solvate.pyo
-${PYSITELIB}/chempy/tinker/__init__.py
-${PYSITELIB}/chempy/tinker/__init__.pyc
-${PYSITELIB}/chempy/tinker/__init__.pyo
-${PYSITELIB}/chempy/tinker/amber.py
-${PYSITELIB}/chempy/tinker/amber.pyc
-${PYSITELIB}/chempy/tinker/amber.pyo
-${PYSITELIB}/chempy/tinker/keyword.py
-${PYSITELIB}/chempy/tinker/keyword.pyc
-${PYSITELIB}/chempy/tinker/keyword.pyo
-${PYSITELIB}/chempy/tinker/realtime.py
-${PYSITELIB}/chempy/tinker/realtime.pyc
-${PYSITELIB}/chempy/tinker/realtime.pyo
-${PYSITELIB}/chempy/tinker/state.py
-${PYSITELIB}/chempy/tinker/state.pyc
-${PYSITELIB}/chempy/tinker/state.pyo
-${PYSITELIB}/chempy/water_amber.py
-${PYSITELIB}/chempy/water_amber.pyc
-${PYSITELIB}/chempy/water_amber.pyo
-${PYSITELIB}/chempy/water_residues.py
-${PYSITELIB}/chempy/water_residues.pyc
-${PYSITELIB}/chempy/water_residues.pyo
-${PYSITELIB}/chempy/xyz.py
-${PYSITELIB}/chempy/xyz.pyc
-${PYSITELIB}/chempy/xyz.pyo
-${PYSITELIB}/pmg_tk/ColorEditor.py
-${PYSITELIB}/pmg_tk/ColorEditor.pyc
-${PYSITELIB}/pmg_tk/ColorEditor.pyo
-${PYSITELIB}/pmg_tk/Demo.py
-${PYSITELIB}/pmg_tk/Demo.pyc
-${PYSITELIB}/pmg_tk/Demo.pyo
-${PYSITELIB}/pmg_tk/PMGApp.py
-${PYSITELIB}/pmg_tk/PMGApp.pyc
-${PYSITELIB}/pmg_tk/PMGApp.pyo
-${PYSITELIB}/pmg_tk/PyMOLMapLoad.py
-${PYSITELIB}/pmg_tk/PyMOLMapLoad.pyc
-${PYSITELIB}/pmg_tk/PyMOLMapLoad.pyo
-${PYSITELIB}/pmg_tk/SetEditor.py
-${PYSITELIB}/pmg_tk/SetEditor.pyc
-${PYSITELIB}/pmg_tk/SetEditor.pyo
-${PYSITELIB}/pmg_tk/Setting.py
-${PYSITELIB}/pmg_tk/Setting.pyc
-${PYSITELIB}/pmg_tk/Setting.pyo
-${PYSITELIB}/pmg_tk/__init__.py
-${PYSITELIB}/pmg_tk/__init__.pyc
-${PYSITELIB}/pmg_tk/__init__.pyo
-${PYSITELIB}/pmg_tk/skins/__init__.py
-${PYSITELIB}/pmg_tk/skins/__init__.pyc
-${PYSITELIB}/pmg_tk/skins/__init__.pyo
-${PYSITELIB}/pmg_tk/skins/normal/ColorMap.py
-${PYSITELIB}/pmg_tk/skins/normal/ColorMap.pyc
-${PYSITELIB}/pmg_tk/skins/normal/ColorMap.pyo
-${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.py
-${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.pyc
-${PYSITELIB}/pmg_tk/skins/normal/ColorRampModel.pyo
-${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.py
-${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.pyc
-${PYSITELIB}/pmg_tk/skins/normal/ModalWindow.pyo
-${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.py
-${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.pyc
-${PYSITELIB}/pmg_tk/skins/normal/SimpleColorChooser.pyo
-${PYSITELIB}/pmg_tk/skins/normal/__init__.py
-${PYSITELIB}/pmg_tk/skins/normal/__init__.pyc
-${PYSITELIB}/pmg_tk/skins/normal/__init__.pyo
-${PYSITELIB}/pmg_tk/skins/normal/builder.py
-${PYSITELIB}/pmg_tk/skins/normal/builder.pyc
-${PYSITELIB}/pmg_tk/skins/normal/builder.pyo
-${PYSITELIB}/pmg_tk/skins/normal/hist.py
-${PYSITELIB}/pmg_tk/skins/normal/hist.pyc
-${PYSITELIB}/pmg_tk/skins/normal/hist.pyo
-${PYSITELIB}/pmg_tk/skins/normal/volume.py
-${PYSITELIB}/pmg_tk/skins/normal/volume.pyc
-${PYSITELIB}/pmg_tk/skins/normal/volume.pyo
-${PYSITELIB}/pmg_tk/startup/__init__.py
-${PYSITELIB}/pmg_tk/startup/__init__.pyc
-${PYSITELIB}/pmg_tk/startup/__init__.pyo
-${PYSITELIB}/pmg_tk/startup/apbs_tools.py
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