[pkgsrc/trunk]: pkgsrc/biology/py-mol Reimport biology/pymol as py-mol, and c...

To: pkgsrc-changes-hg%NetBSD.org@localhost
Subject: [pkgsrc/trunk]: pkgsrc/biology/py-mol Reimport biology/pymol as py-mol, and c...
From: wiz <wiz%pkgsrc.org@localhost>
Date: Thu, 14 Oct 2021 05:11:20 +0000
details:   https://anonhg.NetBSD.org/pkgsrc/rev/811d401a7bd3
branches:  trunk
changeset: 532126:811d401a7bd3
user:      wiz <wiz%pkgsrc.org@localhost>
date:      Sun Aug 12 03:19:18 2007 +0000

description:
Reimport biology/pymol as py-mol, and change its PKGNAME to follow the
python-in-pkgsrc standards.

Add conflict with old pkgname.

Keep PKGREVISION even though the package has a new name to confuse the
users less.

diffstat:

 biology/py-mol/DESCR    |    4 +
 biology/py-mol/Makefile |   47 ++
 biology/py-mol/PLIST    |  778 ++++++++++++++++++++++++++++++++++++++++++++++++
 biology/py-mol/distinfo |    5 +
 4 files changed, 834 insertions(+), 0 deletions(-)

diffs (truncated from 850 to 300 lines):

diff -r 1966e43946b7 -r 811d401a7bd3 biology/py-mol/DESCR
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-mol/DESCR      Sun Aug 12 03:19:18 2007 +0000
@@ -0,0 +1,4 @@
+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 1966e43946b7 -r 811d401a7bd3 biology/py-mol/Makefile
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-mol/Makefile   Sun Aug 12 03:19:18 2007 +0000
@@ -0,0 +1,47 @@
+# $NetBSD: Makefile,v 1.1.1.1 2007/08/12 03:19:18 wiz Exp $
+
+DISTNAME=      pymol-0_98-src
+PKGNAME=       ${PYPKGPREFIX}-mol-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}/pymol-0.98
+PYDISTUTILSPKG=        yes
+PYBINMODULE=   yes
+PYSETUP=       setup.py
+
+CONFLICTS=     pymol-[0-9]*
+
+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 1966e43946b7 -r 811d401a7bd3 biology/py-mol/PLIST
--- /dev/null   Thu Jan 01 00:00:00 1970 +0000
+++ b/biology/py-mol/PLIST      Sun Aug 12 03:19:18 2007 +0000
@@ -0,0 +1,778 @@
+@comment $NetBSD: PLIST,v 1.1.1.1 2007/08/12 03:19:19 wiz 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
+${PYSITELIB}/pymol/controlling.pyo
+${PYSITELIB}/pymol/creating.py
+${PYSITELIB}/pymol/creating.pyc
+${PYSITELIB}/pymol/creating.pyo
+${PYSITELIB}/pymol/editing.py
+${PYSITELIB}/pymol/editing.pyc
+${PYSITELIB}/pymol/editing.pyo
+${PYSITELIB}/pymol/editor.py
+${PYSITELIB}/pymol/editor.pyc
+${PYSITELIB}/pymol/editor.pyo
+${PYSITELIB}/pymol/experimenting.py
+${PYSITELIB}/pymol/experimenting.pyc
+${PYSITELIB}/pymol/experimenting.pyo
+${PYSITELIB}/pymol/exporting.py
+${PYSITELIB}/pymol/exporting.pyc
+${PYSITELIB}/pymol/exporting.pyo
+${PYSITELIB}/pymol/externing.py
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