[pkgsrc/trunk]: pkgsrc/biology Finish move of pymol to py-mol.

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology Finish move of pymol to py-mol.
From: wiz <wiz%pkgsrc.org@localhost>
Date: Thu, 14 Oct 2021 05:11:21 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/029ffaa168ff
branches:  trunk
changeset: 532127:029ffaa168ff
user:      wiz <wiz%pkgsrc.org@localhost>
date:      Sun Aug 12 03:21:06 2007 +0000

description:
Finish move of pymol to py-mol.

diffstat:

 biology/Makefile       |    4 +-
 biology/pymol/DESCR    |    4 -
 biology/pymol/Makefile |   45 --
 biology/pymol/PLIST    |  778 -------------------------------------------------
 biology/pymol/distinfo |    5 -
 5 files changed, 2 insertions(+), 834 deletions(-)

diffs (truncated from 866 to 300 lines):

diff -r 811d401a7bd3 -r 029ffaa168ff biology/Makefile
--- a/biology/Makefile  Sun Aug 12 03:19:18 2007 +0000
+++ b/biology/Makefile  Sun Aug 12 03:21:06 2007 +0000
@@ -1,4 +1,4 @@
-# $NetBSD: Makefile,v 1.26 2005/11/05 01:49:34 minskim Exp $
+# $NetBSD: Makefile,v 1.27 2007/08/12 03:21:06 wiz Exp $
 #
 
 COMMENT=       Software for the biological sciences
@@ -22,7 +22,7 @@
 SUBDIR+=       phylip
 SUBDIR+=       profit
 SUBDIR+=       puzzle
-SUBDIR+=       pymol
+SUBDIR+=       py-mol
 SUBDIR+=       rasmol
 SUBDIR+=       sewer
 SUBDIR+=       stride
diff -r 811d401a7bd3 -r 029ffaa168ff biology/pymol/DESCR
--- a/biology/pymol/DESCR       Sun Aug 12 03:19:18 2007 +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 811d401a7bd3 -r 029ffaa168ff biology/pymol/Makefile
--- a/biology/pymol/Makefile    Sun Aug 12 03:19:18 2007 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,45 +0,0 @@
-# $NetBSD: Makefile,v 1.8 2007/08/11 18:13:13 joerg Exp $
-
-DISTNAME=      pymol-0_98-src
-PKGNAME=       pymol-0.98
-PKGREVISION=   4
-CATEGORIES=    biology
-MASTER_SITES=  ${MASTER_SITE_SOURCEFORGE:=pymol/}
-EXTRACT_SUFX=  .tgz
-
-MAINTAINER=    pkgsrc-users%NetBSD.org@localhost
-HOMEPAGE=      http://pymol.sourceforge.net/
-COMMENT=       Molecular Visualization System
-
-PYTHON_VERSIONS_ACCEPTED=      24 23
-
-WRKSRC=                ${WRKDIR}/${PKGNAME_NOREV}
-PYDISTUTILSPKG=        yes
-PYBINMODULE=   yes
-PYSETUP=       setup.py
-
-REPLACE_PYTHON=        test/cyg test/run test/show test/win.py
-
-post-install:
-       cd ${WRKSRC} && env ${MAKE_ENV} ${PYTHONBIN} setup2.py
-       ${INSTALL_SCRIPT} ${WRKSRC}/pymol.com ${PREFIX}/bin/pymol
-
-.include "../../devel/zlib/buildlink3.mk"
-.include "../../graphics/glu/buildlink3.mk"
-.include "../../graphics/glut/buildlink3.mk"
-.include "../../graphics/png/buildlink3.mk"
-.include "../../math/py-Numeric/buildlink3.mk"
-.include "../../lang/tcl/buildlink3.mk"
-.include "../../x11/tk/buildlink3.mk"
-.include "../../x11/py-Tk/buildlink3.mk"
-.include "../../x11/py-Pmw/buildlink3.mk"
-
-# Note that the website claims this package needs "freeglut", which
-# would mean:
-#  .include "../../graphics/freeglut/buildlink3.mk"
-# However, the package seems to link with "glut" and not with "freeglut",
-# and no other pkgsrc packages seem to use freeglut.
-
-.include "../../lang/python/application.mk"
-.include "../../lang/python/extension.mk"
-.include "../../mk/bsd.pkg.mk"
diff -r 811d401a7bd3 -r 029ffaa168ff biology/pymol/PLIST
--- a/biology/pymol/PLIST       Sun Aug 12 03:19:18 2007 +0000
+++ /dev/null   Thu Jan 01 00:00:00 1970 +0000
@@ -1,778 +0,0 @@
-@comment $NetBSD: PLIST,v 1.2 2005/10/24 20:39:55 rillig Exp $
-bin/pymol
-${PYSITELIB}/chempy/__init__.py
-${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/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
-${PYSITELIB}/chempy/neighbor.py
-${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
-${PYSITELIB}/pmg_tk/SetEditor.py
-${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
-${PYSITELIB}/pmg_tk/skins/normal/__init__.py
-${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
-${PYSITELIB}/pmg_tk/startup/__init__.py
-${PYSITELIB}/pmg_tk/startup/__init__.pyc
-${PYSITELIB}/pmg_tk/startup/__init__.pyo
-${PYSITELIB}/pmg_tk/startup/apbs_tools.py
-${PYSITELIB}/pmg_tk/startup/apbs_tools.pyc
-${PYSITELIB}/pmg_tk/startup/apbs_tools.pyo
-${PYSITELIB}/pmg_tk/startup/remote_pdb_load.py
-${PYSITELIB}/pmg_tk/startup/remote_pdb_load.pyc
-${PYSITELIB}/pmg_tk/startup/remote_pdb_load.pyo
-${PYSITELIB}/pmg_wx/__init__.py
-${PYSITELIB}/pmg_wx/__init__.pyc
-${PYSITELIB}/pmg_wx/__init__.pyo
-${PYSITELIB}/pymol/ExtensionClass.so
-${PYSITELIB}/pymol/__init__.py
-${PYSITELIB}/pymol/__init__.pyc
-${PYSITELIB}/pymol/__init__.pyo
-${PYSITELIB}/pymol/_cmd.so
-${PYSITELIB}/pymol/callback.py
-${PYSITELIB}/pymol/callback.pyc
-${PYSITELIB}/pymol/callback.pyo
-${PYSITELIB}/pymol/cgo.py
-${PYSITELIB}/pymol/cgo.pyc
-${PYSITELIB}/pymol/cgo.pyo
-${PYSITELIB}/pymol/cmd.py
-${PYSITELIB}/pymol/cmd.pyc
-${PYSITELIB}/pymol/cmd.pyo
-${PYSITELIB}/pymol/commanding.py
-${PYSITELIB}/pymol/commanding.pyc
-${PYSITELIB}/pymol/commanding.pyo
-${PYSITELIB}/pymol/contrib.py
-${PYSITELIB}/pymol/contrib.pyc
-${PYSITELIB}/pymol/contrib.pyo
-${PYSITELIB}/pymol/controlling.py
-${PYSITELIB}/pymol/controlling.pyc
-${PYSITELIB}/pymol/controlling.pyo
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