From: W. Trevor King Date: Fri, 28 Jan 2011 19:27:43 +0000 (-0500) Subject: Cleaned up README and package with pure distutils (vs. setuputils). X-Git-Tag: 0.6~1 X-Git-Url: http://git.tremily.us/?a=commitdiff_plain;h=880506f0341764c5b7f979fcc51bb0798cd97474;p=calibcant.git Cleaned up README and package with pure distutils (vs. setuputils). Also: * Don't make calibcant modules executible. Scripts should be handled explicitly through distutils. * Ran ./update_copyright.py --- diff --git a/AUTHORS b/AUTHORS index 001c6ee..bcdc62f 100644 --- a/AUTHORS +++ b/AUTHORS @@ -1,2 +1,2 @@ -CalibCant was written by: +calibcant was written by: W. Trevor King diff --git a/MANIFEST.in b/MANIFEST.in index 9353b6b..eb762f3 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -1,2 +1 @@ include COPYING -include ez_setup.py diff --git a/Makefile b/Makefile deleted file mode 100644 index 8514b79..0000000 --- a/Makefile +++ /dev/null @@ -1,19 +0,0 @@ -.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 diff --git a/README b/README index 036e38f..49a243b 100644 --- a/README +++ b/README @@ -1,58 +1,84 @@ -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 - -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 - -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 diff --git a/calibcant/T_analyze.py b/calibcant/T_analyze.py old mode 100755 new mode 100644 index 32751fc..219a603 --- a/calibcant/T_analyze.py +++ b/calibcant/T_analyze.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/calibcant/__init__.py b/calibcant/__init__.py index c890f4f..b5ccc23 100644 --- a/calibcant/__init__.py +++ b/calibcant/__init__.py @@ -1,21 +1,21 @@ # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . __version__ = '0.5' diff --git a/calibcant/analyze.py b/calibcant/analyze.py old mode 100755 new mode 100644 index b8e4c71..073d7b4 --- a/calibcant/analyze.py +++ b/calibcant/analyze.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/calibcant/bump.py b/calibcant/bump.py index 08c4c36..7d36864 100644 --- a/calibcant/bump.py +++ b/calibcant/bump.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/calibcant/bump_analyze.py b/calibcant/bump_analyze.py old mode 100755 new mode 100644 index 88a9648..71f75e8 --- a/calibcant/bump_analyze.py +++ b/calibcant/bump_analyze.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/calibcant/calibrate.py b/calibcant/calibrate.py old mode 100755 new mode 100644 index c2fb1b8..54279a5 --- a/calibcant/calibrate.py +++ b/calibcant/calibrate.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/calibcant/common.py b/calibcant/common.py index d303344..4594f5c 100644 --- a/calibcant/common.py +++ b/calibcant/common.py @@ -1,21 +1,21 @@ # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . from . import config diff --git a/calibcant/config.py b/calibcant/config.py index aa2f0a2..7715cd2 100644 --- a/calibcant/config.py +++ b/calibcant/config.py @@ -1,21 +1,21 @@ # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """Define some variables to configure the package for a particular lab diff --git a/calibcant/filter.py b/calibcant/filter.py index 67b5117..e8696c5 100644 --- a/calibcant/filter.py +++ b/calibcant/filter.py @@ -1,5 +1,3 @@ -#!/usr/bin/python - """ windowed_filter(array, winfunc, s) with winfuncs : diff --git a/calibcant/psd_filter_analyze.py b/calibcant/psd_filter_analyze.py old mode 100755 new mode 100644 index 29c9641..8523081 --- a/calibcant/psd_filter_analyze.py +++ b/calibcant/psd_filter_analyze.py @@ -1,5 +1,3 @@ -#!/usr/bin/python - if __name__ == "__main__" : import sys diff --git a/calibcant/vib_analyze.py b/calibcant/vib_analyze.py old mode 100755 new mode 100644 index 2d5e601..7805801 --- a/calibcant/vib_analyze.py +++ b/calibcant/vib_analyze.py @@ -1,23 +1,21 @@ -#!/usr/bin/python -# # calibcant - tools for thermally calibrating AFM cantilevers # -# Copyright (C) 2008-2010 W. Trevor King +# Copyright (C) 2008-2011 W. Trevor King # -# 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 # . """ diff --git a/ez_setup.py b/ez_setup.py deleted file mode 100644 index 14cd450..0000000 --- a/ez_setup.py +++ /dev/null @@ -1,275 +0,0 @@ -#!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 index abfbe09..a1d9f3e 100644 --- a/setup.py +++ b/setup.py @@ -1,11 +1,4 @@ -"""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 @@ -19,46 +12,37 @@ 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 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 diff --git a/update_copyright.py b/update_copyright.py index d1caaa6..ce067d0 100755 --- a/update_copyright.py +++ b/update_copyright.py @@ -1,21 +1,21 @@ -#!/usr/bin/python +#!/usr/bin/env python # -# Copyright (C) 2010 W. Trevor King +# Copyright (C) 2010-2011 W. Trevor King # -# 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 # . """Automatically update copyright boilerplate. @@ -37,7 +37,7 @@ import time PROJECT_INFO = { - 'project': 'CalibCant', + 'project': 'calibcant', 'vcs': 'Git', }