From 6c81dd7154ef49e8ac77842900efd2c64a87caf2 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Tue, 11 Nov 2008 11:02:15 -0500 Subject: [PATCH] Added ez_setup.py installation wrapper and cleaned up License info. --- LICENSE | 674 ++++++++++++++++++++++++++++++++++++++++++ MANIFEST.in | 1 + README | 8 + calibcant/__init__.py | 24 ++ calibcant/common.py | 23 ++ ez_setup.py | 275 +++++++++++++++++ setup.py | 61 ++++ 7 files changed, 1066 insertions(+) create mode 100644 LICENSE create mode 100644 MANIFEST.in create mode 100644 ez_setup.py create mode 100644 setup.py diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..94a9ed0 --- /dev/null +++ b/LICENSE @@ -0,0 +1,674 @@ + GNU GENERAL PUBLIC LICENSE + Version 3, 29 June 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU General Public License is a free, copyleft license for +software and other kinds of works. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..1aba38f --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1 @@ +include LICENSE diff --git a/README b/README index bf5945b..036e38f 100644 --- a/README +++ b/README @@ -1,3 +1,10 @@ +Scripts and python modules to calibrate AFM cantilevers via the +"Thermal tune" method: + 1/2 k_B T = 1/2 K x^2 +The analysis uses the expected power spectral density (PSD) of a +damped simple harmonic oscillator to filter out noise from the +measured PSD. + == Dependencies == linfit (depends in turn on scipy.stats.linregress) @@ -17,6 +24,7 @@ Then fit slope with $ cat stderr not cutting + ** vibs ** Create a two-column ascii data file for fitting bumps with (for example) diff --git a/calibcant/__init__.py b/calibcant/__init__.py index e69de29..05f8fad 100644 --- a/calibcant/__init__.py +++ b/calibcant/__init__.py @@ -0,0 +1,24 @@ +# calibcant - tools for thermally calibrating AFM cantilevers +# +# Copyright (C) 2007,2008, William Trevor King +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License as +# published by the Free Software Foundation; either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA +# 02111-1307, USA. +# +# The author may be contacted at on the Internet, or +# write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St., +# Philadelphia PA 19104, USA. + +from common import VERSION diff --git a/calibcant/common.py b/calibcant/common.py index a93adfd..24e5f1d 100644 --- a/calibcant/common.py +++ b/calibcant/common.py @@ -1,3 +1,26 @@ +# calibcant - tools for thermally calibrating AFM cantilevers +# +# Copyright (C) 2007,2008, William Trevor King +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU General Public License as +# published by the Free Software Foundation; either version 3 of the +# License, or (at your option) any later version. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. +# See the GNU General Public License for more details. +# +# You should have received a copy of the GNU General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA +# 02111-1307, USA. +# +# The author may be contacted at on the Internet, or +# write to Trevor King, Drexel University, Physics Dept., 3141 Chestnut St., +# Philadelphia PA 19104, USA. + import config VERSION="0.2" diff --git a/ez_setup.py b/ez_setup.py new file mode 100644 index 0000000..14cd450 --- /dev/null +++ b/ez_setup.py @@ -0,0 +1,275 @@ +#!python +"""Bootstrap setuptools installation + +If you want to use setuptools in your package's setup.py, just include this +file in the same directory with it, and add this to the top of your setup.py:: + + from ez_setup import use_setuptools + use_setuptools() + +If you want to require a specific version of setuptools, set a download +mirror, or use an alternate download directory, you can do so by supplying +the appropriate options to ``use_setuptools()``. + +This file can also be run as a script to install or upgrade setuptools. +""" +import sys +DEFAULT_VERSION = "0.6c9" +DEFAULT_URL = "http://pypi.python.org/packages/%s/s/setuptools/" % sys.version[:3] + +md5_data = { + 'setuptools-0.6b1-py2.3.egg': '8822caf901250d848b996b7f25c6e6ca', + 'setuptools-0.6b1-py2.4.egg': 'b79a8a403e4502fbb85ee3f1941735cb', + 'setuptools-0.6b2-py2.3.egg': '5657759d8a6d8fc44070a9d07272d99b', + 'setuptools-0.6b2-py2.4.egg': '4996a8d169d2be661fa32a6e52e4f82a', + 'setuptools-0.6b3-py2.3.egg': 'bb31c0fc7399a63579975cad9f5a0618', + 'setuptools-0.6b3-py2.4.egg': '38a8c6b3d6ecd22247f179f7da669fac', + 'setuptools-0.6b4-py2.3.egg': '62045a24ed4e1ebc77fe039aa4e6f7e5', + 'setuptools-0.6b4-py2.4.egg': '4cb2a185d228dacffb2d17f103b3b1c4', + 'setuptools-0.6c1-py2.3.egg': 'b3f2b5539d65cb7f74ad79127f1a908c', + 'setuptools-0.6c1-py2.4.egg': 'b45adeda0667d2d2ffe14009364f2a4b', + 'setuptools-0.6c2-py2.3.egg': 'f0064bf6aa2b7d0f3ba0b43f20817c27', + 'setuptools-0.6c2-py2.4.egg': '616192eec35f47e8ea16cd6a122b7277', + 'setuptools-0.6c3-py2.3.egg': 'f181fa125dfe85a259c9cd6f1d7b78fa', + 'setuptools-0.6c3-py2.4.egg': 'e0ed74682c998bfb73bf803a50e7b71e', + 'setuptools-0.6c3-py2.5.egg': 'abef16fdd61955514841c7c6bd98965e', + 'setuptools-0.6c4-py2.3.egg': 'b0b9131acab32022bfac7f44c5d7971f', + 'setuptools-0.6c4-py2.4.egg': '2a1f9656d4fbf3c97bf946c0a124e6e2', + 'setuptools-0.6c4-py2.5.egg': '8f5a052e32cdb9c72bcf4b5526f28afc', + 'setuptools-0.6c5-py2.3.egg': 'ee9fd80965da04f2f3e6b3576e9d8167', + 'setuptools-0.6c5-py2.4.egg': 'afe2adf1c01701ee841761f5bcd8aa64', + 'setuptools-0.6c5-py2.5.egg': 'a8d3f61494ccaa8714dfed37bccd3d5d', + 'setuptools-0.6c6-py2.3.egg': '35686b78116a668847237b69d549ec20', + 'setuptools-0.6c6-py2.4.egg': '3c56af57be3225019260a644430065ab', + 'setuptools-0.6c6-py2.5.egg': 'b2f8a7520709a5b34f80946de5f02f53', + 'setuptools-0.6c7-py2.3.egg': '209fdf9adc3a615e5115b725658e13e2', + 'setuptools-0.6c7-py2.4.egg': '5a8f954807d46a0fb67cf1f26c55a82e', + 'setuptools-0.6c7-py2.5.egg': '45d2ad28f9750e7434111fde831e8372', + 'setuptools-0.6c8-py2.3.egg': '50759d29b349db8cfd807ba8303f1902', + 'setuptools-0.6c8-py2.4.egg': 'cba38d74f7d483c06e9daa6070cce6de', + 'setuptools-0.6c8-py2.5.egg': '1721747ee329dc150590a58b3e1ac95b', + 'setuptools-0.6c9-py2.3.egg': 'a83c4020414807b496e4cfbe08507c03', + 'setuptools-0.6c9-py2.4.egg': '260a2be2e5388d66bdaee06abec6342a', + 'setuptools-0.6c9-py2.5.egg': 'fe67c3e5a17b12c0e7c541b7ea43a8e6', +} + +import sys, os +try: from hashlib import md5 +except ImportError: from md5 import md5 + +def _validate_md5(egg_name, data): + if egg_name in md5_data: + digest = md5(data).hexdigest() + if digest != md5_data[egg_name]: + print >>sys.stderr, ( + "md5 validation of %s failed! (Possible download problem?)" + % egg_name + ) + sys.exit(2) + return data + +def use_setuptools( + version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, + download_delay=15 +): + """Automatically find/download setuptools and make it available on sys.path + + `version` should be a valid setuptools version number that is available + as an egg for download under the `download_base` URL (which should end with + a '/'). `to_dir` is the directory where setuptools will be downloaded, if + it is not already available. If `download_delay` is specified, it should + be the number of seconds that will be paused before initiating a download, + should one be required. If an older version of setuptools is installed, + this routine will print a message to ``sys.stderr`` and raise SystemExit in + an attempt to abort the calling script. + """ + was_imported = 'pkg_resources' in sys.modules or 'setuptools' in sys.modules + def do_download(): + egg = download_setuptools(version, download_base, to_dir, download_delay) + sys.path.insert(0, egg) + import setuptools; setuptools.bootstrap_install_from = egg + try: + import pkg_resources + except ImportError: + return do_download() + try: + pkg_resources.require("setuptools>="+version); return + except pkg_resources.VersionConflict, e: + if was_imported: + print >>sys.stderr, ( + "The required version of setuptools (>=%s) is not available, and\n" + "can't be installed while this script is running. Please install\n" + " a more recent version first, using 'easy_install -U setuptools'." + "\n\n(Currently using %r)" + ) % (version, e.args[0]) + sys.exit(2) + else: + del pkg_resources, sys.modules['pkg_resources'] # reload ok + return do_download() + except pkg_resources.DistributionNotFound: + return do_download() + +def download_setuptools( + version=DEFAULT_VERSION, download_base=DEFAULT_URL, to_dir=os.curdir, + delay = 15 +): + """Download setuptools from a specified location and return its filename + + `version` should be a valid setuptools version number that is available + as an egg for download under the `download_base` URL (which should end + with a '/'). `to_dir` is the directory where the egg will be downloaded. + `delay` is the number of seconds to pause before an actual download attempt. + """ + import urllib2, shutil + egg_name = "setuptools-%s-py%s.egg" % (version,sys.version[:3]) + url = download_base + egg_name + saveto = os.path.join(to_dir, egg_name) + src = dst = None + if not os.path.exists(saveto): # Avoid repeated downloads + try: + from distutils import log + if delay: + log.warn(""" +--------------------------------------------------------------------------- +This script requires setuptools version %s to run (even to display +help). I will attempt to download it for you (from +%s), but +you may need to enable firewall access for this script first. +I will start the download in %d seconds. + +(Note: if this machine does not have network access, please obtain the file + + %s + +and place it in this directory before rerunning this script.) +---------------------------------------------------------------------------""", + version, download_base, delay, url + ); from time import sleep; sleep(delay) + log.warn("Downloading %s", url) + src = urllib2.urlopen(url) + # Read/write all in one block, so we don't create a corrupt file + # if the download is interrupted. + data = _validate_md5(egg_name, src.read()) + dst = open(saveto,"wb"); dst.write(data) + finally: + if src: src.close() + if dst: dst.close() + return os.path.realpath(saveto) + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +def main(argv, version=DEFAULT_VERSION): + """Install or upgrade setuptools and EasyInstall""" + try: + import setuptools + except ImportError: + egg = None + try: + egg = download_setuptools(version, delay=0) + sys.path.insert(0,egg) + from setuptools.command.easy_install import main + return main(list(argv)+[egg]) # we're done here + finally: + if egg and os.path.exists(egg): + os.unlink(egg) + else: + if setuptools.__version__ == '0.0.1': + print >>sys.stderr, ( + "You have an obsolete version of setuptools installed. Please\n" + "remove it from your system entirely before rerunning this script." + ) + sys.exit(2) + + req = "setuptools>="+version + import pkg_resources + try: + pkg_resources.require(req) + except pkg_resources.VersionConflict: + try: + from setuptools.command.easy_install import main + except ImportError: + from easy_install import main + main(list(argv)+[download_setuptools(delay=0)]) + sys.exit(0) # try to force an exit + else: + if argv: + from setuptools.command.easy_install import main + main(argv) + else: + print "Setuptools version",version,"or greater has been installed." + print '(Run "ez_setup.py -U setuptools" to reinstall or upgrade.)' + +def update_md5(filenames): + """Update our built-in md5 registry""" + + import re + + for name in filenames: + base = os.path.basename(name) + f = open(name,'rb') + md5_data[base] = md5(f.read()).hexdigest() + f.close() + + data = [" %r: %r,\n" % it for it in md5_data.items()] + data.sort() + repl = "".join(data) + + import inspect + srcfile = inspect.getsourcefile(sys.modules[__name__]) + f = open(srcfile, 'rb'); src = f.read(); f.close() + + match = re.search("\nmd5_data = {\n([^}]+)}", src) + if not match: + print >>sys.stderr, "Internal error!" + sys.exit(2) + + src = src[:match.start(1)] + repl + src[match.end(1):] + f = open(srcfile,'w') + f.write(src) + f.close() + + +if __name__=='__main__': + if len(sys.argv)>2 and sys.argv[1]=='--md5update': + update_md5(sys.argv[2:]) + else: + main(sys.argv[1:]) + + + + + + diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..43318f7 --- /dev/null +++ b/setup.py @@ -0,0 +1,61 @@ +"""CalibCant: tools for thermally calibrating AFM cantilevers + +Requires + * TODO + +Git repository: +http://www.physics.drexel.edu/~wking/code/git/calibcant.git +""" + +classifiers = """\ +Development Status :: 2 - Pre-Alpha +Intended Audience :: Developers +Intended Audience :: Science/Research +Operating System :: POSIX +Operating System :: Unix +License :: OSI Approved :: GNU General Public License (GPL) +Programming Language :: Python +Topic :: Scientific/Engineering +Topic :: Software Development :: Libraries :: Python Modules +""" + +# http://peak.telecommunity.com/DevCenter/setuptools#using-setuptools-without-bundling-it +import ez_setup +ez_setup.use_setuptools() + +from setuptools import setup, find_packages + +# patch distutils if it can't cope with the "classifiers" or +# "download_url" keywords +from sys import version +if version < '2.2.3': + from distutils.dist import DistributionMetadata + DistributionMetadata.classifiers = None + DistributionMetadata.download_url = None + +import calibcant +VERSION = calibcant.VERSION + +doclines = __doc__.split("\n") + +setup(name="calibcant", + version=VERSION, + maintainer="W. Trevor King", + maintainer_email="wking@drexel.edu", + url = "http://www.physics.drexel.edu/~wking/code/python/", + download_url = "http://www.physics.drexel.edu/~wking/code/python/calibcant-%s.tar.gz" % VERSION, + license = "GNU General Public License (GPL)", + platforms = ["all"], + description = doclines[0], + long_description = "\n".join(doclines[2:]), + classifiers = filter(None, classifiers.split("\n")), + py_modules = ['ez_setup'], + packages = find_packages(), + ) + +# use packages to include subdirectory packages +# use py_modules to include single-module packages +# use ext_modules to include extension modules +# see +# http://www.python.org/doc/2.5.2/dist/listing-modules.html +# http://www.python.org/doc/2.5.2/dist/describing-extensions.html -- 2.26.2