-CalibCant was written by:
+calibcant was written by:
W. Trevor King <wking@drexel.edu>
include COPYING
-include ez_setup.py
+++ /dev/null
-.PHONY : all check dist clean
-
-all : dummy_py
-
-dummy_py : setup.py calibcant/*.py
- python setup.py install --home=~
- echo "dummy for Makefile dependencies" > $@
-
-check : all
- echo "No checks currently implemented"
-
-dist :
- python setup.py sdist
- scp dist/calibcant*tar.gz einstein:public_html/code/python/
-
-clean :
- python setup.py clean
- rm -rf build dist calibcant.egg-info
- rm -f dummy_py *.pyc
-Scripts and python modules to calibrate AFM cantilevers via the
-"Thermal tune" method:
+calibcant: tools for thermally calibrating AFM cantilevers
+
+Calculates the spring constant `k` of a cantilever using the
+equipartition theorem:
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)
-
-*** Command line interface ***
-
-** bumps **
-
-Create a two-column ascii data file for fitting bumps with (for example)
- $ int16s_to_ascii_array ~/rsrch/data/z_piezo_calib/20080116/20080116090005_bump_surface_Z_piezo_output \
- ~/rsrch/data/z_piezo_calib/20080116/20080116090005_bump_surface_Deflection_input > d
-
-Then fit slope with
- $ python calibcant_bump_analyze.py -c d > stdout 2> stderr
- $ cat stdout
- 0.00958650972452
- $ cat stderr
- not cutting
-
-
-** vibs **
-
-Create a two-column ascii data file for fitting bumps with (for example)
- $ cd ~/src/comedi_simult_AIO
- $ cmd -c0 -n1 -F200000 -N2097152 > vib.raw # 2097152 = 2^21 points ~= 10 seconds of data
- $ unitary_avg_fft_from_raw.py vib.raw
-Creates vib.raw.psd, with frequency in Hz in the first column, and amplitude in Volts^2/Hz in the second column.
-Then get the variance with
- $ cd ~/src/calibrate_cantilever
- $ python psd_filter_analyze.py -s9 -tmedian -g ~/src/comedi_simult_AIO/vib.raw 2> check.gp
- <Lorentzian-fit-variance>
-You can check the validity of the fit with
- $ gnuplot check.gp -
-And adjust the min and max of the fitted frequency range as neccessary
- $ python psd_filter_analyze.py -s9 -tmedian -m1000 -M8500 -g ~/src/comedi_simult_AIO/vib.raw 2> check.gp
- <new Lorentzian-fit-variance>
-Until the fit looks reasonable.
-
-
-** calibrating **
-
-Once you've assembled a few slopes, vibs, and Ts, put it all together to calculate k with
- $ python calibcant_analyze.py -vC 0.02,0.03,0.025 22.5,22.1 6e-9,5.5e-9 > stdout 2> stderr
- $ cat stdout
- 456.069575483
- $ cat stderr
- Variable (units) : mean +/- std. dev. (relative error)
- Cantilever k (pN/nm) : 456.07 +/- 146.671 (0.321599)
- photoSensitivity**2 (V/nm)**2 : 0.000641667 +/- 0.000204464 (0.318645)
- T (K) : 295.45 +/- 0.2 (0.000676933)
- 1/Vphoto**2 (1/V)**2 : 1.74242e+08 +/- 7.57576e+06 (0.0434783)
+
+Packages
+========
+
+Gentoo
+------
+
+I've packaged calibcant for Gentoo. You need layman_ and my `wtk
+overlay`_. Install with::
+
+ # emerge -av app-portage/layman
+ # layman --add wtk
+ # emerge -av sci-physics/calibcant
+
+.. _layman: http://layman.sourceforge.net/
+.. _wtk overlay: http://www.physics.drexel.edu/~wking/unfolding-disasters/posts/Gentoo_overlay/
+
+
+Dependencies
+============
+
+calibcant requires the following Python modules:
+
+* linfit (depends in turn on scipy.stats.linregress)
+* TODO
+
+* Numpy_
+* Scipy_
+* PyYAML_ (for saving and loading playlists)
+* Matplotlib_ (for generating plots)
+* wxPython_ (for the GUI)
+
+.. _Python: http://www.python.org/
+.. _Numpy: http://numpy.scipy.org/
+.. _Scipy: http://www.scipy.org/
+.. _PyYAML: http://pyyaml.org/
+.. _Matplotlib: http://matplotlib.sourceforge.net/
+.. _wxPython: http://www.wxpython.org/
+
+
+Getting the source
+==================
+
+calibcant is available as a Git_ repository::
+
+ $ git clone http://www.physics.drexel.edu/~wking/code/git/calibcant.git
+
+There are also periodic bundled releases. For example, get version
+0.5 as a gzipped tarball with::
+
+ $ wget http://www.physics.drexel.edu/~wking/code/python/calibcant-0.5.tar.gz
+ $ tar -xzvf calibcant-0.5.tar.gz
+
+.. _Git: http://git-scm.com/
+
+
+Installation
+============
+
+After downloading, change to the source directory and run::
+
+ $ python setup.py install
+
+to install calibcant. Run::
+
+ $ python setup.py install --help
+
+to see a list of installation options you may want to configure.
+
+
+Usage
+=====
+
+You can... While there are a number of command-line scripts
+TODO
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
__version__ = '0.5'
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
from . import config
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""Define some variables to configure the package for a particular lab
-#!/usr/bin/python
-
"""
windowed_filter(array, winfunc, s)
with winfuncs :
-#!/usr/bin/python
-
if __name__ == "__main__" :
import sys
-#!/usr/bin/python
-#
# calibcant - tools for thermally calibrating AFM cantilevers
#
-# Copyright (C) 2008-2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2008-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""
+++ /dev/null
-#!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:])
-
-
-
-
-
-
-"""CalibCant: tools for thermally calibrating AFM cantilevers
-
-Requires
- * TODO
-
-Git repository:
-http://www.physics.drexel.edu/~wking/code/git/calibcant.git
-"""
+"calibcant: tools for thermally calibrating AFM cantilevers"
classifiers = """\
Development Status :: 2 - Pre-Alpha
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 distutils.core import setup
+from os import walk
+import os.path
-from setuptools import setup, find_packages
+from calibcant import __version__
-# 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__
+def find_packages(root='calibcant'):
+ packages = []
+ prefix = '.'+os.path.sep
+ for dirpath,dirnames,filenames in walk(root):
+ if '__init__.py' in filenames:
+ if dirpath.startswith(prefix):
+ dirpath = dirpath[len(prefix):]
+ packages.append(dirpath.replace(os.path.sep, '.'))
+ return packages
-doclines = __doc__.split("\n")
+packages = find_packages()
-setup(name="calibcant",
+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")),
- packages = find_packages(),
- dependency_links = [
- "http://www.physics.drexel.edu/~wking/code/python/"
- ],
- install_requires = ['piezo >= 0.3'],
+ 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 = __doc__,
+ long_description = open('README', 'r').read(),
+ classifiers = filter(None, classifiers.split('\n')),
+ packages = packages,
+ provides = ['calibcant (%s)' % __version__],
+ requires = ['piezo (>= 0.3)'],
)
-
-# 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
-#!/usr/bin/python
+#!/usr/bin/env python
#
-# Copyright (C) 2010 W. Trevor King <wking@drexel.edu>
+# Copyright (C) 2010-2011 W. Trevor King <wking@drexel.edu>
#
-# This file is part of CalibCant.
+# This file is part of calibcant.
#
-# CalibCant is free software: you can redistribute it and/or
+# calibcant is free software: you can redistribute it and/or
# modify it under the terms of the GNU Lesser General Public
# License as published by the Free Software Foundation, either
# version 3 of the License, or (at your option) any later version.
#
-# CalibCant is distributed in the hope that it will be useful,
+# calibcant 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 Lesser General Public License for more details.
#
# You should have received a copy of the GNU Lesser General Public
-# License along with CalibCant. If not, see
+# License along with calibcant. If not, see
# <http://www.gnu.org/licenses/>.
"""Automatically update copyright boilerplate.
PROJECT_INFO = {
- 'project': 'CalibCant',
+ 'project': 'calibcant',
'vcs': 'Git',
}
projects / calibcant.git / commitdiff