Some structure for package installation

.gitattributes

@@ -0,0 +1 @@
+formula/COMMIT_INFO.txt export-subst

.gitignore

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+build/
+doc/_build/
+*.pyc
+dist/

COPYING

@@ -0,0 +1,30 @@
+Copyright (c) 2005-2011, nipy developers
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are
+met:
+
+    * Redistributions of source code must retain the above copyright
+       notice, this list of conditions and the following disclaimer.
+
+    * Redistributions in binary form must reproduce the above
+       copyright notice, this list of conditions and the following
+       disclaimer in the documentation and/or other materials provided
+       with the distribution.
+
+    * Neither the name of the nipy developers nor the names of any
+       contributors may be used to endorse or promote products derived
+       from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+"AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
+A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
+OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
+SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
+LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
+DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
+THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

MANIFEST.in

@@ -0,0 +1,7 @@
+include AUTHOR COPYING Makefile* MANIFEST.in setup* README.*
+include Changelog TODO
+recursive-include doc *
+# put this stuff back into setup.py (package_data) once I'm enlightened
+# enough to accomplish this herculean task
+recursive-include formula/data *
+include formula/COMMIT_INFO.txt

Makefile

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+PYTHON = python
+COVERAGE_REPORT=coverage
+
+clean:
+	$(MAKE) -C doc clean
+	-rm -rf build
+	-rm *-stamp
+
+distclean: clean
+	-rm MANIFEST
+	-rm $(COVERAGE_REPORT)
+	@find . -name '*.py[co]' \
+		 -o -name '*.a' \
+		 -o -name '*,cover' \
+		 -o -name '.coverage' \
+		 -o -iname '*~' \
+		 -o -iname '*.kcache' \
+		 -o -iname '*.pstats' \
+		 -o -iname '*.prof' \
+		 -o -iname '#*#' | xargs -L10 rm -f
+
+# Print out info for possible install methods
+check-version-info:
+	$(PYTHON) -c 'from nisext.testers import info_from_here; info_from_here("formula")'
+
+# Run tests from installed code
+installed-tests:
+	$(PYTHON) -c 'from nisext.testers import tests_installed; tests_installed("formula")'
+
+# Run tests from installed code
+sdist-tests:
+	$(PYTHON) -c 'from nisext.testers import sdist_tests; sdist_tests("formula")'
+
+bdist-egg-tests:
+	$(PYTHON) -c 'from nisext.testers import bdist_egg_tests; bdist_egg_tests("formula")'
+
+source-release: distclean
+	python -m compileall .
+	make distclean
+	python setup.py sdist --formats=gztar,zip

README.txt

@@ -0,0 +1,46 @@
+=======
+Formula
+=======
+
+This package contains an implementation of symbolic statistical models in
+Python.
+
+The implementation is of a full algebra of factors and numerical variables in
+statistical models.
+
+It has some similarities to model formulae in R, but differs in that the rules
+for the creation of design matrices are more completely defined by the model
+algebra.
+
+An earlier version of this package is in nipy_.
+
+Mailing Lists
+=============
+
+Please see the developer's list here::
+
+    http://mail.scipy.org/mailman/listinfo/nipy-devel
+
+Code
+====
+
+You can find our sources and single-click downloads:
+
+* `Main repository`_ on Github.
+* Documentation_ for all releases and current development tree.
+* Download as a tar/zip file the `current trunk`_.
+* Downloads of all `available releases`_.
+
+.. _nipy: http://nipy.org
+.. _main repository: http://github.com/jonathan-taylor/formula
+.. _documentation: http://github.com/jonathan-taylor/formula
+.. _current trunk: http://github.com/jonathan-taylor/formula/archives/master
+.. _available releases: http://github.com/jonathan-taylor/formula/downloads
+
+License
+=======
+
+formula is licensed under the terms of the BSD license.  Please the COPYING file
+in the formula distribution.
+
+.. vim:syntax=rst

formula/COMMIT_INFO.txt

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+# This is an ini file that may contain information about the code state
+[commit hash]
+# The line below may contain a valid hash if it has been substituted during 'git archive'
+archive_subst_hash=$Format:%h$
+# This line may be modified by the install process
+install_hash=

formula/__init__.py

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+# Init for formula
+import os
+
+from .info import __version__, long_description as __doc__
+
+from .pkg_info import get_pkg_info as _get_pkg_info
+get_info = lambda : _get_pkg_info(os.path.dirname(__file__))

formula/info.py

@@ -1,15 +1,16 @@
-""" This file contains defines parameters for nipy that we use to fill
-settings in setup.py, the nipy top-level docstring, and for building the
-docs.  In setup.py in particular, we exec this file, so it cannot import nipy
+""" This file contains defines parameters for formula that we use to fill
+settings in setup.py, the formula top-level docstring, and for building the
+docs.  In setup.py in particular, we exec this file, so it cannot import formula
 """
 
-# nipy version information.  An empty _version_extra corresponds to a
+# formula version information.  An empty _version_extra corresponds to a
 # full release.  '.dev' as a _version_extra string means this is a development
 # version
 _version_major = 0
-_version_minor = 0
-_version_micro = 1
+_version_minor = 1
+_version_micro = 0
 _version_extra = '.dev'
+# _version_extra = ''
 
 # Format expected by setup.py and doc/source/conf.py: string of form "X.Y.Z"
 __version__ = "%s.%s.%s%s" % (_version_major,
@@ -25,45 +26,80 @@
                "Programming Language :: Python",
                "Topic :: Scientific/Engineering"]
 
-description  = 'A package to build design matrices for regression models'
+description  = 'Symbolic statistical formulae'
 
 # Note: this long_description is actually a copy/paste from the top-level
 # README.txt, so that it shows up nicely on PyPI.  So please remember to edit
 # it only in one place and sync it correctly.
-long_description = \
-"""
+long_description = """
 =======
 Formula
 =======
 
-Formula is a python project for building
-design matrices for regression models.
+This package contains an implementation of symbolic statistical models in
+Python.
+
+The implementation is of a full algebra of factors and numerical variables in
+statistical models.
+
+It has some similarities to model formulae in R, but differs in that the rules
+for the creation of design matrices are more completely defined by the model
+algebra.
+
+An earlier version of this package is in nipy_.
+
+Mailing Lists
+=============
+
+Please see the developer's list here::
+
+    http://mail.scipy.org/mailman/listinfo/nipy-devel
+
+Code
+====
+
+You can find our sources and single-click downloads:
 
+* `Main repository`_ on Github.
+* Documentation_ for all releases and current development tree.
+* Download as a tar/zip file the `current trunk`_.
+* Downloads of all `available releases`_.
+
+.. _nipy: http://nipy.org
+.. _main repository: http://github.com/jonathan-taylor/formula
+.. _documentation: http://github.com/jonathan-taylor/formula
+.. _current trunk: http://github.com/jonathan-taylor/formula/archives/master
+.. _available releases: http://github.com/jonathan-taylor/formula/downloads
+
+License
+=======
+
+formula is licensed under the terms of the BSD license.  Please the COPYING file
+in the formula distribution.
 """
 
+# versions for dependencies
+NUMPY_MIN_VERSION='1.2'
+SYMPY_MIN_VERSION='0.7.0'
+
+# Main setup parameters
 NAME                = 'formula'
-MAINTAINER          = "formula developers"
-MAINTAINER_EMAIL    = ""
+MAINTAINER          = "Jonathan Taylor"
+MAINTAINER_EMAIL    = "[email protected]"
 DESCRIPTION         = description
 LONG_DESCRIPTION    = long_description
-URL                 = ""
-DOWNLOAD_URL        = ""
+URL                 = "http://github.com/jonathan-taylor/formula"
+DOWNLOAD_URL        = "http://github.com/jonathan-taylor/formula/downloads"
 LICENSE             = "BSD license"
 CLASSIFIERS         = CLASSIFIERS
-AUTHOR              = "formula developers"
-AUTHOR_EMAIL        = ""
+AUTHOR              = "Jonathan Taylor"
+AUTHOR_EMAIL        = "[email protected]"
 PLATFORMS           = "OS Independent"
 MAJOR               = _version_major
 MINOR               = _version_minor
 MICRO               = _version_micro
 ISRELEASE           = _version_extra == ''
 VERSION             = __version__
-REQUIRES            = ["numpy", "sympy"]
-STATUS              = 'alpha'
-
-# versions
-NUMPY_MIN_VERSION='1.3'
-SYMPY_MIN_VERSION = '0.6.7'
-
-
-
+PROVIDES            = ["formula"]
+REQUIRES            = ["numpy (>=%s)" % NUMPY_MIN_VERSION,
+                       "sympy (>=%s)" % SYMPY_MIN_VERSION]

formula/pkg_info.py

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+import os
+import sys
+import subprocess
+from ConfigParser import ConfigParser
+
+COMMIT_INFO_FNAME = 'COMMIT_INFO.txt'
+
+def pkg_commit_hash(pkg_path):
+    ''' Get short form of commit hash given directory `pkg_path`
+
+    There should be a file called 'COMMIT_INFO.txt' in `pkg_path`.  This is a
+    file in INI file format, with at least one section: ``commit hash``, and two
+    variables ``archive_subst_hash`` and ``install_hash``.  The first has a
+    substitution pattern in it which may have been filled by the execution of
+    ``git archive`` if this is an archive generated that way.  The second is
+    filled in by the installation, if the installation is from a git archive.
+
+    We get the commit hash from (in order of preference):
+
+    * A substituted value in ``archive_subst_hash``
+    * A written commit hash value in ``install_hash`
+    * git's output, if we are in a git repository
+
+    If all these fail, we return a not-found placeholder tuple
+
+    Parameters
+    ----------
+    pkg_path : str
+       directory containing package
+
+    Returns
+    -------
+    hash_from : str
+       Where we got the hash from - description
+    hash_str : str
+       short form of hash
+    '''
+    # Try and get commit from written commit text file
+    pth = os.path.join(pkg_path, COMMIT_INFO_FNAME)
+    if not os.path.isfile(pth):
+        raise IOError('Missing commit info file %s' % pth)
+    cfg_parser = ConfigParser()
+    cfg_parser.read(pth)
+    archive_subst = cfg_parser.get('commit hash', 'archive_subst_hash')
+    if not archive_subst.startswith('$Format'): # it has been substituted
+        return 'archive substitution', archive_subst
+    install_subst = cfg_parser.get('commit hash', 'install_hash')
+    if install_subst != '':
+        return 'installation', install_subst
+    # maybe we are in a repository
+    proc = subprocess.Popen('git rev-parse --short HEAD',
+                            stdout=subprocess.PIPE,
+                            stderr=subprocess.PIPE,
+                            cwd=pkg_path, shell=True)
+    repo_commit, _ = proc.communicate()
+    if repo_commit:
+        return 'repository', repo_commit.strip()
+    return '(none found)', '<not found>'
+
+
+def get_pkg_info(pkg_path):
+    ''' Return dict describing the context of this package
+
+    Parameters
+    ----------
+    pkg_path : str
+       path containing __init__.py for package
+
+    Returns
+    -------
+    context : dict
+       with named parameters of interest
+    '''
+    src, hsh = pkg_commit_hash(pkg_path)
+    import numpy
+    return dict(
+        pkg_path=pkg_path,
+        commit_source=src,
+        commit_hash=hsh,
+        sys_version=sys.version,
+        sys_executable=sys.executable,
+        sys_platform=sys.platform,
+        np_version=numpy.__version__)

formula/tests/__init__.py

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+# Make tests a package

nisext/__init__.py

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+# init for sext package
+""" Setuptools extensions that can be shared across projects
+
+Typical use for these routines is as a git subtree merge
+
+For example::
+
+    # Add a remote pointing to repository
+    git remote add nisext git://github.com/nipy/nisext.git
+    git fetch nisext
+    # Label nisext history as merged
+    git merge -s ours --no-commit nisext/master
+    # Read nisext contents as nisext subdirectory
+    git read-tree --prefix=nisext/ -u nisext/master
+    git commit -m "Merge nisext project as subtree"
+
+Then you would typically add a makefile target like::
+
+    # Update nisext subtree from remote
+    update-nisext:
+            git fetch nisext
+            git merge --squash -s subtree --no-commit nisext/master
+
+and commit when you have changes you want. This allows you to keep the nisext
+tree updated from the upstream repository, but the tree will be there and ready
+for someone without this machinery or remote.
+"""
+