Add two Martin's codes

pages/software.rst

@@ -1,3 +1,4 @@
+
 .. link: 
 .. description: 
 .. tags: 
@@ -13,32 +14,35 @@ of our projects:
 `SEP`_
 ------
 
-SEP is a Python and C library for source detection and photometry,
-adapted from the SourceExtractor code base. It makes the
-SourceExtractor background and detection algorithms available directly
-from Python and (eventually) Julia. `SEP on GitHub`_.
+SEP is a Python and C library for source detection and photometry, adapted from the SourceExtractor code base. It makes the SourceExtractor background and detection algorithms available directly from Python and (eventually) Julia.
 
-====
+Links:
 
-.. image:: /images/sncosmo.png
-   :height: 40px
-   :align: left
+- http://sep.readthedocs.org
+- http://github.com/kbarbary/sep
+
+====
 
 `SNCosmo`_
 ----------
 
-SNCosmo is a Python package for supernova cosmology data analysis and
-simulation. `SNCosmo on GitHub`_.
+SNCosmo is a Python package for supernova cosmology data analysis and simulation.
 
-====
+Links:
+
+- http://sncosmo.github.io
+- http://github.com/sncosmo/sncosmo
 
+====
 
 `Dierckx.jl`_
 -------------
 
-Dierckx.jl is a package for 1-d and 2-d splines in Julia. It's a
-wrapper of the dierckx Fortran library available from NETLIB, the same
-library underlying the spline classes in scipy.interpolate.
+Dierckx.jl is a package for 1-d and 2-d splines in Julia. It's a wrapper of the dierckx Fortran library available from NETLIB, the same library underlying the spline classes in scipy.interpolate.
+
+Links:
+
+- http://github.com/kbarbary/Dierckx.jl
 
 ====
 
@@ -47,20 +51,31 @@ library underlying the spline classes in scipy.interpolate.
 
 cosmoxi2d provides theoretical predictions for the two-dimensional galaxy correlation function.  This code was used to analyze `DR9 <http://adsabs.harvard.edu/abs/2012MNRAS.426.2719R>`_, `DR10, and DR11 <http://adsabs.harvard.edu/abs/2014MNRAS.439.3504S>`_ the SDSS-III BOSS CMASS galaxy sample and derive cosmological constraints on the geometry of the universe and the growth rate of cosmic structure.
 
+Links:
+
+- https://github.com/bareid/cosmoxi2d
+
 ====
 
 `kdcount`_
 ----------
 
 kdcount is a simple python extension for brute force pair-counting of point data sets. Pair-counting is the fundamental of estimating correlation functions from imaging and spectroscopy survey catalogues of quasars, galaxies, and Lyman-alpha forest.
 
+Links:
+
+- https://github.com/rainwoodman/kdcount
+
 ====
 
 `pypm`_
 -------
 
-pypm is a set of python modules for particle mesh calculation with MPI parallel python. It also provides tools
-to measure power spectrum, and construct Friend-of-Friend halso from n-body simulations.
+pypm is a set of python modules for particle mesh calculation with MPI parallel python. It also provides tools to measure power spectrum, and construct Friend-of-Friend halso from n-body simulations.
+
+Links:
+
+- https://github.com/rainwoodman/pypm
 
 ====
 
@@ -69,13 +84,84 @@ to measure power spectrum, and construct Friend-of-Friend halso from n-body simu
 
 pfft-python is a thin python extension layer of the massively parallel faster fourier transformation library, PFFT. Fast Fourier Transform is the core component of Particle-Mesh based gravity solvers, which simulate the formation of large scale structure, galaxies and dark matter halos.
 
-.. _`Dierckx.jl`: http://github.com/kbarbary/Dierckx.jl
-.. _`SEP`: http://sep.readthedocs.org
-.. _`SEP on GitHub`: http://github.com/kbarbary/sep
-.. _`SNCosmo`: http://sncosmo.github.io
-.. _`SNCosmo on GitHub`: http://github.com/sncosmo/sncosmo
-.. _`cosmoxi2d`: https://github.com/bareid/cosmoxi2d
-.. _`kdcount`: https://github.com/rainwoodman/kdcount
-.. _`pypm`: https://github.com/rainwoodman/pypm
-.. _`pfft-python`: https://github.com/rainwoodman/pfft-python
+Links:
+
+- https://github.com/rainwoodman/pfft-python
+
+====
+
+`Copter`_
+---------
+
+a C++ class library written by Jordan Carlson to compute predictions for different cosmological perturbation theory schemes.
+
+Links:
+
+- http://mwhite.berkeley.edu/Copter/
+
+====
+
+`BoxRemap`_
+-----------
+
+a new technique to remap the cubical domain of a cosmological simulation into simple non-cubical shapes.
+
+Links:
+
+- http://mwhite.berkeley.edu/BoxRemap/
+
+====
+
+`ImagingLSS`_
+-------------
+
+Code for doing large-scale structure studies with the imaging data.
+
+Links:
+
+- http://github.com/desihub/imaginglss/
+
+====
+
+`LiteMangle`_
+-------------
+
+Light-weight library for some Mangle routines.
+
+Links:
+
+- http://github.com/martinjameswhite/litemangle
+
+====
+
+`mockFactory`_
+--------------
+
+
+
+Links:
+
+- https://github.com/mockFactory
+
+====
+
+`CLPT_GSRSD`_
+-------------
+
+Convolution Lagrangian Perturbation Theory (CLPT) and Gaussian Streaming Redshift-Space Distortions (GSRSD)
+
+Links:
+
+- https://github.com/wll745881210/CLPT_GSRSD
+
+====
+
+`recon_code`_
+-------------
+
+Code to perform density field reconstruction for baryon acoustic oscillation (BAO) experiments
+
+Links:
+
+- https://github.com/martinjameswhite/recon_code
 

software_to_json.py

@@ -0,0 +1,131 @@
+"""
+    This simple script converts the current software.rst page to a json file.
+"""
+import json
+import urllib2
+import os
+TOKEN = os.environ["GITHUB_OAUTH2_TOKEN"]
+
+def buildjson():
+    with file('pages/software.rst', 'r') as ff:
+        lines = ff.readlines()
+
+    def parse(lines):
+        STARTED = 1
+        state = 0
+        for line in lines:
+            line = line.strip()
+            if len(line) == 0:
+                continue
+            if state < STARTED:
+                if line == '====':
+                    state = STARTED
+                    entry = {}
+                    L = []
+                continue
+            else:
+                if line.startswith('---'):
+                    entry['ProjectName'] = L[-1][1:-2]
+                    L = []
+                    continue
+                elif line.startswith('.. _'):
+                    if 'Links' not in entry:
+                        entry['Links'] = []
+                    entry['Links'].append(line[line.index(':')+1:].strip())
+                    continue 
+                elif line == 'Links:':
+                    continue
+                elif line.startswith('- http'):
+                    if 'Links' not in entry:
+                        entry['Links'] = []
+                    entry['Links'].append(line[2:].strip())
+                    continue 
+                elif line == '====':
+                    entry['Description'] = ' '.join(L)
+                    yield entry
+                    entry = {}
+                    L = []
+                else:
+                    L.append(line)
+        entry['Description'] = ' '.join(L)
+        yield entry
+
+    entries = [entry for entry in parse(lines) ]
+    with file('software.json', 'w') as ff:
+        json.dump(entries, ff, sort_keys=True,
+                      indent=4, separators=(',', ': '))
+
+def fixjson():
+    with file('software.json', 'r') as ff:
+        entries = json.load(ff)
+    class NotGithubURL(Exception): pass
+    def parse_github_url(url):
+        """ returns the :owner and :repo field """
+        if 'github.com' in url:
+            url = url.strip('/')
+            slashes = url.split('/')
+            if slashes[-2].endswith('github.com'):
+                # this is a org
+                return slashes[-1],
+            else:
+                return slashes[-2], slashes[-1]
+        else:
+            raise NotGithubURL("Not a Github URL");
+    for entry in entries:
+        if len(entry['Description'].strip()) == 0:
+            for url in entry['Links']:
+                try:
+                    result = parse_github_url(url)
+                    if len(result) == 2:
+                        req = urllib2.Request("https://api.github.com/repos/%s/%s" % result)
+                    elif len(result) == 1:
+                        req = urllib2.Request("https://api.github.com/orgs/%s" % result)
+                    else:
+                        raise RuntimeError
+
+                    req.add_header('Authorization', 'token %s' % TOKEN)
+                    ff = urllib2.urlopen(req)
+                    data = json.load(ff)
+                    if data['description']:
+                        entry['Description'] = data['description']
+                    else:
+                        pass
+                except NotGithubURL:
+                    continue
+    with file('software.json', 'w') as ff:
+        json.dump(entries, ff, sort_keys=True,
+                      indent=4, separators=(',', ': '))
+
+def buildrst():
+    header="""
+.. link: 
+.. description: 
+.. tags: 
+.. date: 2014/02/08 12:19:51
+.. title: Software
+.. slug: software
+
+BCCP develops open-source software for use in cosmology. Here are some
+of our projects:
+
+"""
+    with file('software.json', 'r') as ff:
+        entries = json.load(ff)
+    with file('software.rst', 'w') as ff:
+        ff.write(header)
+        for entry in entries:
+            ff.write('====\n\n')
+            ff.write('`%s`_\n' % entry['ProjectName'])
+            ff.write('-' * (len(entry['ProjectName']) + 3))
+            ff.write('\n\n')
+            ff.write('%s\n\n' % entry['Description'])
+            if len(entry['Links']) > 0:
+                ff.write('Links:\n\n')
+                for link in entry['Links']:
+                    ff.write('- %s\n' % link)
+            ff.write('\n')
+
+# these really should be subcommands!
+buildjson()
+fixjson()
+buildrst()