added more Python modules

15 files changed, 212 insertions, 2 deletions

diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py
index 615c2a7fe4..992dd8ec70 100644
--- a/var/spack/packages/hdf5/package.py
+++ b/var/spack/packages/hdf5/package.py
@@ -18,12 +18,14 @@ class Hdf5(Package):
 
     # TODO: currently hard-coded to use OpenMPI
     def install(self, spec, prefix):
+
         configure(
             "--prefix=%s" % prefix,
             "--with-zlib=%s" % spec['zlib'].prefix,
             "--enable-parallel",
-            "CC=%s" % spec['openmpi'].prefix.bin + "/mpicc",
-            "CXX=%s" % spec['openmpi'].prefix.bin + "/mpic++")
+            "--enable-shared",
+            "CC=%s" % spec['mpich'].prefix.bin + "/mpicc",
+            "CXX=%s" % spec['mpich'].prefix.bin + "/mpic++")
 
         make()
         make("install")
diff --git a/var/spack/packages/py-basemap/package.py b/var/spack/packages/py-basemap/package.py
new file mode 100644
index 0000000000..8955bf8827
--- /dev/null
+++ b/var/spack/packages/py-basemap/package.py
@@ -0,0 +1,24 @@
+from spack import *
+import os
+
+class PyBasemap(Package):
+    """The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python."""
+    homepage = "http://matplotlib.org/basemap/"
+    url      = "https://downloads.sourceforge.net/project/matplotlib/matplotlib-toolkits/basemap-1.0.7/basemap-1.0.7.tar.gz"
+
+    version('1.0.7', '48c0557ced9e2c6e440b28b3caff2de8')
+
+    geos_version = {'1.0.7' : '3.3.3'}
+
+    extends('python')
+    depends_on('py-numpy')
+    depends_on('py-matplotlib')
+    depends_on('py-pil')
+
+    def install(self, spec, prefix):
+        with working_dir('geos-%s' % self.geos_version[str(self.version)]):
+            configure("--prefix=" + prefix)
+            make()
+            make("install")
+        os.environ['GEOS_DIR'] = prefix
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-biopython/package.py b/var/spack/packages/py-biopython/package.py
new file mode 100644
index 0000000000..2ed04c389e
--- /dev/null
+++ b/var/spack/packages/py-biopython/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyBiopython(Package):
+    """It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics."""
+    homepage = "http://biopython.org/wiki/Main_Page"
+    url      = "http://biopython.org/DIST/biopython-1.65.tar.gz"
+
+    version('1.65', '143e7861ade85c0a8b5e2bbdd1da1f67')
+
+    extends('python')
+    depends_on('py-mx')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-gnuplot/package.py b/var/spack/packages/py-gnuplot/package.py
new file mode 100644
index 0000000000..0a2c073a49
--- /dev/null
+++ b/var/spack/packages/py-gnuplot/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyGnuplot(Package):
+    """Gnuplot.py is a Python package that allows you to create graphs from within Python using the gnuplot plotting program."""
+    homepage = "http://gnuplot-py.sourceforge.net/"
+    url      = "http://downloads.sourceforge.net/project/gnuplot-py/Gnuplot-py/1.8/gnuplot-py-1.8.tar.gz"
+
+    version('1.8', 'abd6f571e7aec68ae7db90a5217cd5b1')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-h5py/package.py b/var/spack/packages/py-h5py/package.py
new file mode 100644
index 0000000000..f72b3ac06e
--- /dev/null
+++ b/var/spack/packages/py-h5py/package.py
@@ -0,0 +1,18 @@
+from spack import *
+import re
+
+class PyH5py(Package):
+    """The h5py package provides both a high- and low-level interface to the HDF5 library from Python."""
+    homepage = "https://pypi.python.org/pypi/h5py"
+    url      = "https://pypi.python.org/packages/source/h/h5py/h5py-2.4.0.tar.gz"
+
+    version('2.4.0', '80c9a94ae31f84885cc2ebe1323d6758')
+
+    extends('python', ignore=lambda f: re.match(r'cy*', f))
+    depends_on('hdf5')
+    depends_on('py-numpy')
+    depends_on('py-cython')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'configure', '--hdf5=%s' % spec['hdf5'].prefix)
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-matplotlib/package.py b/var/spack/packages/py-matplotlib/package.py
index 836273c923..270a1ebfe4 100644
--- a/var/spack/packages/py-matplotlib/package.py
+++ b/var/spack/packages/py-matplotlib/package.py
@@ -1,4 +1,5 @@
 from spack import *
+import os
 
 class PyMatplotlib(Package):
     """Python plotting package."""
@@ -18,3 +19,19 @@ class PyMatplotlib(Package):
 
     def install(self, spec, prefix):
         python('setup.py', 'install', '--prefix=%s' % prefix)
+        if str(self.version) == '1.4.2':
+            # hack to fix configuration file
+            config_file = None
+            for p,d,f in os.walk(prefix.lib):
+                for file in f:
+                    if file.find('matplotlibrc') != -1:
+                        config_file = join_path(p, 'matplotlibrc')
+                        print config_file
+            if config_file == None:
+                raise InstallError('could not find config file')
+            filter_file(r'backend      : pyside',
+                        'backend      : Qt4Agg',
+                        config_file)
+            filter_file(r'#backend.qt4 : PyQt4',
+                        'backend.qt4 : PySide',
+                        config_file)
diff --git a/var/spack/packages/py-mpi4py/package.py b/var/spack/packages/py-mpi4py/package.py
new file mode 100644
index 0000000000..fdea340dc2
--- /dev/null
+++ b/var/spack/packages/py-mpi4py/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyMpi4py(Package):
+    """This package provides Python bindings for the Message Passing Interface (MPI) standard. It is implemented on top of the MPI-1/MPI-2 specification and exposes an API which grounds on the standard MPI-2 C++ bindings."""
+    homepage = "https://pypi.python.org/pypi/mpi4py"
+    url      = "https://pypi.python.org/packages/source/m/mpi4py/mpi4py-1.3.1.tar.gz"
+
+    version('1.3.1', 'dbe9d22bdc8ed965c23a7ceb6f32fc3c')
+    extends('python')
+    depends_on('mpi')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-mx/package.py b/var/spack/packages/py-mx/package.py
new file mode 100644
index 0000000000..717ee0562b
--- /dev/null
+++ b/var/spack/packages/py-mx/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyMx(Package):
+    """The eGenix.com mx Base Distribution for Python is a collection of professional quality software tools which enhance Python's usability in many important areas such as fast text searching, date/time processing and high speed data types."""
+    homepage = "http://www.egenix.com/products/python/mxBase/"
+    url      = "https://downloads.egenix.com/python/egenix-mx-base-3.2.8.tar.gz"
+
+    version('3.2.8', '9d9d3a25f9dc051a15e97f452413423b')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pil/package.py b/var/spack/packages/py-pil/package.py
new file mode 100644
index 0000000000..743b761981
--- /dev/null
+++ b/var/spack/packages/py-pil/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyPil(Package):
+    """The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities."""
+
+    homepage = "http://www.pythonware.com/products/pil/"
+    url      = "http://effbot.org/media/downloads/Imaging-1.1.7.tar.gz"
+
+    version('1.1.7', 'fc14a54e1ce02a0225be8854bfba478e')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pmw/package.py b/var/spack/packages/py-pmw/package.py
new file mode 100644
index 0000000000..56131811e9
--- /dev/null
+++ b/var/spack/packages/py-pmw/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyPmw(Package):
+    """Pmw is a toolkit for building high-level compound widgets, or megawidgets, constructed using other widgets as component parts."""
+    homepage = "https://pypi.python.org/pypi/Pmw"
+    url      = "https://pypi.python.org/packages/source/P/Pmw/Pmw-2.0.0.tar.gz"
+
+    version('2.0.0', 'c7c3f26c4f5abaa99807edefee578fc0')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-pylint/package.py b/var/spack/packages/py-pylint/package.py
new file mode 100644
index 0000000000..ebde861f94
--- /dev/null
+++ b/var/spack/packages/py-pylint/package.py
@@ -0,0 +1,16 @@
+from spack import *
+import re
+
+class PyPylint(Package):
+    """array processing for numbers, strings, records, and objects."""
+    homepage = "https://pypi.python.org/pypi/pylint"
+    url      = "https://pypi.python.org/packages/source/p/pylint/pylint-1.4.1.tar.gz"
+
+    version('1.4.1', 'df7c679bdcce5019389038847e4de622')
+
+#    extends('python')
+    extends('python', ignore=lambda f:re.match(r"site.py*", f))
+    depends_on('py-nose')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-rpy2/package.py b/var/spack/packages/py-rpy2/package.py
new file mode 100644
index 0000000000..3817059911
--- /dev/null
+++ b/var/spack/packages/py-rpy2/package.py
@@ -0,0 +1,14 @@
+from spack import *
+
+class PyRpy2(Package):
+    """rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions."""
+    homepage = "https://pypi.python.org/pypi/rpy2"
+    url      = "https://pypi.python.org/packages/source/r/rpy2/rpy2-2.5.4.tar.gz"
+
+    version('2.5.4', '115a20ac30883f096da2bdfcab55196d')
+
+    extends('python')
+    depends_on('py-setuptools')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scientificpython/package.py b/var/spack/packages/py-scientificpython/package.py
new file mode 100644
index 0000000000..73600e6cb9
--- /dev/null
+++ b/var/spack/packages/py-scientificpython/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyScientificpython(Package):
+    """ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization."""
+    homepage = "https://sourcesup.renater.fr/projects/scientific-py/"
+    url      = "https://sourcesup.renater.fr/frs/download.php/4411/ScientificPython-2.8.1.tar.gz"
+
+    version('2.8.1', '73ee0df19c7b58cdf2954261f0763c77')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-scikit-learn/package.py b/var/spack/packages/py-scikit-learn/package.py
new file mode 100644
index 0000000000..c59c05a619
--- /dev/null
+++ b/var/spack/packages/py-scikit-learn/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PyScikitLearn(Package):
+    """"""
+    homepage = "https://pypi.python.org/pypi/scikit-learn"
+    url      = "https://pypi.python.org/packages/source/s/scikit-learn/scikit-learn-0.15.2.tar.gz"
+
+    version('0.15.2', 'd9822ad0238e17b382a3c756ea94fe0d')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)
diff --git a/var/spack/packages/py-sympy/package.py b/var/spack/packages/py-sympy/package.py
new file mode 100644
index 0000000000..c17e35b95f
--- /dev/null
+++ b/var/spack/packages/py-sympy/package.py
@@ -0,0 +1,13 @@
+from spack import *
+
+class PySympy(Package):
+    """SymPy is a Python library for symbolic mathematics."""
+    homepage = "https://pypi.python.org/pypi/sympy"
+    url      = "https://pypi.python.org/packages/source/s/sympy/sympy-0.7.6.tar.gz"
+
+    version('0.7.6', '3d04753974306d8a13830008e17babca')
+
+    extends('python')
+
+    def install(self, spec, prefix):
+        python('setup.py', 'install', '--prefix=%s' % prefix)