--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/.hgtags	Wed Feb 04 15:56:20 2009 -0500
@@ -0,0 +1,1 @@
+5f9ffefa9ca8040e18e1a69fdbbe34b8a19099bc sequencelabelling 20090130-rerun

--- a/bin/dbdict-query	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/usr/bin/env python
-from dbdict.tools import standalone_query
-standalone_query()

--- a/bin/dbdict-run	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/usr/bin/env python
-from pylearn.dbdict.newstuff import run_cmdline
-run_cmdline()

--- a/bin/dbdict-run-job	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,3 +0,0 @@
-#!/usr/bin/env python
-from dbdict.tools import standalone_run_job
-standalone_run_job()

--- a/pylearn/algorithms/cost.py	Wed Feb 04 15:56:00 2009 -0500
+++ b/pylearn/algorithms/cost.py	Wed Feb 04 15:56:20 2009 -0500
@@ -10,6 +10,7 @@
 """
 
 import theano.tensor as T
+from theano.tensor.xlogx import xlogx
 
 def quadratic(target, output, axis=1):
     return T.mean(T.sqr(target - output), axis=axis)
@@ -28,5 +29,5 @@
     different shapes then the result will be garbled.
     """
     return -(target * T.log(output) + (1 - target) * T.log(1 - output)) \
-            + (T.xlogx(target) + T.xlogx(1 - target))
+            + (xlogx(target) + xlogx(1 - target))
 #    return cross_entropy(target, output, axis) - cross_entropy(target, target, axis)

--- a/pylearn/algorithms/logistic_regression.py	Wed Feb 04 15:56:00 2009 -0500
+++ b/pylearn/algorithms/logistic_regression.py	Wed Feb 04 15:56:20 2009 -0500
@@ -68,6 +68,10 @@
         self.regularized_cost = self.unregularized_cost + self.l1_cost + self.l2_cost
         self._loss_zero_one = T.mean(T.neq(self.argmax, self.target))
 
+        # Softmax being computed directly.
+	# TODO: Move somewhere else, more clean.
+        self.softmax_unsupervised = nnet.softmax(self.linear_output)
+
         # METHODS
         if 0: #TODO: PENDING THE BETTER IMPLEMENTATION ABOVE
             self.predict = module.Method([self.input], self.argmax)

--- a/pylearn/dbdict/__init__.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1 +0,0 @@
-from api0 import sqlite_file_db, sqlite_memory_db, postgres_db

--- a/pylearn/dbdict/api0.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,585 +0,0 @@
-from sqlalchemy import create_engine, desc
-import sqlalchemy.pool
-from sqlalchemy.orm import sessionmaker
-from sqlalchemy import Table, Column, MetaData, ForeignKey    
-from sqlalchemy import Integer, String, Float, Boolean, DateTime, Text, Binary
-from sqlalchemy.databases import postgres
-from sqlalchemy.orm import mapper, relation, backref, eagerload
-from sqlalchemy.sql import operators, select
-from sql_commands import crazy_sql_command
-
-class Todo(Exception): """Replace this with some working code!"""
-
-class DbHandle (object):
-    """
-    This class also provides filtering shortcuts that hide the names of the
-    DbHandle internal databases.
-
-    Attributes:
-    dict_table
-    pair_table
-    link_table
-
-
-
-    dict_table
-
-        An SqlAlchemy-mapped class corresponding to database table with the
-        following schema:
-
-            Column('id', Integer, primary_key=True)
-            Column('create', DateTime)
-            Column('write', DateTime)
-            Column('read', DateTime)
-
-            #TODO: reconsider create/read/write
-
-    pair_table
-
-        An SqlAlchemy-mapped class corresponding to database table with the
-        following schema:
-
-            Column('id', Integer, primary_key=True)
-            Column('name', String(128))
-            Column('ntype', Boolean)
-            Column('fval', Double)
-            Column('sval', Text))
-            Column('bval', Blob)  
-
-            #TODO: Consider difference between text and binary
-            #TODO: Consider adding a 'type' column
-            #TODO: Consider union?
-            #TODO: Are there stanard ways of doing this kind of thing?
-
-    link_table
-
-        An SqlAlchemy-mapped class corresponding to database table with the
-        following schema:
-
-            Column('dict_id', Integer, ForeignKey('%s.id' % t_trial), primary_key=True),
-            Column('keyval_id', Integer, ForeignKey('%s.id' % t_keyval), primary_key=True))
-
-    """
-
-    e_bad_table = 'incompatible columns in table'
-
-    def __init__(h_self, Session, engine, dict_table, pair_table, link_table):
-        h_self._engine = engine;
-        h_self._dict_table = dict_table
-        h_self._pair_table = pair_table
-        h_self._link_table = link_table
-
-        #TODO: replace this crude algorithm (ticket #17)
-        if ['id', 'create', 'write', 'read', 'status', 'priority','hash'] != [c.name for c in dict_table.c]:
-            raise ValueError(h_self.e_bad_table, dict_table)
-        if ['id', 'name', 'ntype', 'fval', 'sval', 'bval'] != [c.name for c in pair_table.c]:
-            raise ValueError(h_self.e_bad_table, pair_table)
-        if ['dict_id', 'pair_id'] != [c.name for c in link_table.c]:
-            raise ValueError(h_self.e_bad_table, pair_table)
-
-        h_self._session_fn = Session
-
-        class KeyVal (object):
-            """KeyVal interfaces between python types and the database.
-
-            It encapsulates heuristics for type conversion.
-            """
-            def __init__(k_self, name, val):
-                k_self.name = name
-                k_self.val = val
-            def __repr__(k_self):
-                return "<Param(%s,'%s', %s)>" % (k_self.id, k_self.name, repr(k_self.val))
-            def __get_val(k_self):
-                val = None
-                if k_self.fval is not None: val = [int, float][k_self.ntype](k_self.fval)
-                if k_self.bval is not None: val = eval(str(k_self.bval))
-                if k_self.sval is not None: val = k_self.sval
-                return  val
-            def __set_val(k_self, val):
-                if isinstance(val, (str,unicode)):
-                    k_self.fval = None
-                    k_self.bval = None
-                    k_self.sval = val
-                else:
-                    k_self.sval = None
-                    try:
-                        f = float(val)
-                    except (TypeError, ValueError):
-                        f = None
-                    if f is None: #binary data
-                        k_self.bval = repr(val)
-                        assert eval(k_self.bval) == val
-                        k_self.fval = None
-                        k_self.ntype = None
-                    else:
-                        k_self.bval = None
-                        k_self.fval = f
-                        k_self.ntype = isinstance(val,float)
-            val = property(__get_val, __set_val)
-
-        mapper(KeyVal, pair_table)
-        
-        class Dict (object):
-            """
-            Instances are dict-like objects with additional features for
-            communicating with an active database.
-
-            This class will be mapped by SqlAlchemy to the dict_table.
-
-            Attributes:
-            handle - reference to L{DbHandle} (creator)
-
-            """
-            def __init__(d_self, session=None):
-                if session is None:
-                    s = h_self._session_fn()
-                    s.add(d_self) #d_self transient -> pending
-                    s.commit()    #d_self -> persistent
-                    s.close()     #d_self -> detached
-                else:
-                    s = session
-                    s.save(d_self)
-
-            _forbidden_keys = set(['session'])
-
-            #
-            # dictionary interface
-            #
-
-            def __contains__(d_self, key):
-                for a in d_self._attrs:
-                    if a.name == key:
-                        return True
-                return False
-
-            def __eq__(self, other):
-                return dict(self) == dict(other)
-            def __neq__(self, other):
-                return dict(self) != dict(other)
-
-            def __getitem__(d_self, key):
-                for a in d_self._attrs:
-                    if a.name == key:
-                        return a.val
-                raise KeyError(key)
-
-            def __setitem__(d_self, key, val, session=None):
-                if session is None:
-                    s = h_self._session_fn()
-                    s.add(d_self)
-                    d_self._set_in_session(key, val, s)
-                    s.commit()
-                    s.close()
-                else:
-                    s = session
-                    s.add(d_self)
-                    d_self._set_in_session(key, val, s)
-
-            def __delitem__(d_self, key, session=None):
-                if session is None:
-                    s = h_self._session_fn()
-                    commit_close = True
-                else:
-                    s = session
-                    commit_close = False
-                s.add(d_self)
-
-                #find the item to delete in d_self._attrs
-                to_del = None
-                for i,a in enumerate(d_self._attrs):
-                    if a.name == key:
-                        assert to_del is None
-                        to_del = (i,a)
-                if to_del is None:
-                    raise KeyError(key)
-                else:
-                    i, a = to_del
-                    s.delete(a)
-                    del d_self._attrs[i]
-                if commit_close:
-                    s.commit()
-                    s.close()
-
-            def iteritems(d_self):
-                return d_self.items()
-
-            def items(d_self):
-                return [(kv.name, kv.val) for kv in d_self._attrs]
-            
-            def keys(d_self):
-                return [kv.name for kv in d_self._attrs]
-
-            def values(d_self):
-                return [kv.val for kv in d_self._attrs]
-
-            def update(d_self, dct, session=None, **kwargs):
-                """Like dict.update(), set keys from kwargs"""
-                if session is None:
-                    s = h_self._session_fn()
-                    commit_close = True
-                else:
-                    s = session
-                    commit_close = False
-                s.add(d_self)
-                for k, v in dct.items():
-                    d_self._set_in_session(k, v, s)
-                for k, v in kwargs.items():
-                    d_self._set_in_session(k, v, s)
-
-                if commit_close:
-                    s.commit()
-                    s.close()
-
-            def get(d_self, key, default):
-                try:
-                    return d_self[key]
-                except KeyError:
-                    return default
-
-            def __str__(self):
-                return 'Dict'+ str(dict(self))
-
-            #
-            # database stuff
-            #
-
-            def refresh(d_self, session=None): 
-                """Sync key-value pairs from database to self
-
-                @param session: use the given session, and do not commit.
-                
-                """
-                if session is None:
-                    session = h_self._session_fn()
-                    session.add(d_self) #so session knows about us
-                    session.refresh(d_self)
-                    session.commit()
-                    session.close()
-                else:
-                    session.add(d_self) #so session knows about us
-                    session.refresh(self.dbrow)
-
-            def delete(d_self, session=None):
-                """Delete this dictionary from the database
-                
-                @param session: use the given session, and do not commit.
-                """
-                if session is None:
-                    session = h_self._session_fn()
-                    session.add(d_self) #so session knows about us
-                    session.delete(d_self) #mark for deletion
-                    session.commit()
-                    session.close()
-                else:
-                    session.add(d_self) #so session knows about us
-                    session.delete(d_self)
-
-            # helper routine by update() and __setitem__
-            def _set_in_session(d_self, key, val, session):
-                """Modify an existing key or create a key to hold val"""
-                
-                #FIRST SOME MIRRORING HACKS
-                if key == 'dbdict.status':
-                    ival = int(val)
-                    d_self.status = ival
-                if key == 'dbdict.sql.priority':
-                    fval = float(val)
-                    d_self.priority = fval
-                if key == 'dbdict.hash':
-                    ival = int(val)
-                    d_self.hash = ival
-
-                if key in d_self._forbidden_keys:
-                    raise KeyError(key)
-                created = None
-                for i,a in enumerate(d_self._attrs):
-                    if a.name == key:
-                        assert created == None
-                        created = h_self._KeyVal(key, val)
-                        d_self._attrs[i] = created
-                if not created:
-                    created = h_self._KeyVal(key, val)
-                    d_self._attrs.append(created)
-                session.save(created)
-
-        mapper(Dict, dict_table,
-                properties = {
-                    '_attrs': relation(KeyVal, 
-                        secondary=link_table, 
-                        cascade="all, delete-orphan")
-                    })
-
-        class _Query (object):
-            """
-            Attributes:
-            _query - SqlAlchemy.Query object
-            """
-
-            def __init__(q_self, query):
-                q_self._query = query
-
-            def __iter__(q_self):
-                return q_self.all().__iter__()
-
-            def __getitem__(q_self, item):
-                return q_self._query.__getitem__(item)
-
-            def filter_eq(q_self, kw, arg):
-                """Return a Query object that restricts to dictionaries containing
-                the given kwargs"""
-
-                #Note: when we add new types to the key columns, add them here
-                q = q_self._query
-                T = h_self._Dict
-                if isinstance(arg, (str,unicode)):
-                    q = q.filter(T._attrs.any(name=kw, sval=arg))
-                else:
-                    try:
-                        f = float(arg)
-                    except (TypeError, ValueError):
-                        f = None
-                    if f is None:
-                        q = q.filter(T._attrs.any(name=kw, bval=repr(arg)))
-                    else:
-                        q = q.filter(T._attrs.any(name=kw, fval=f))
-
-                return h_self._Query(q)
-
-            def filter_eq_dct(q_self, dct):
-                rval = q_self
-                for key, val in dct.items():
-                    rval = rval.filter_eq(key,val)
-                return rval
-
-            def all(q_self):
-                """Return an iterator over all matching dictionaries.
-
-                See L{SqlAlchemy.Query}
-                """
-                return q_self._query.all()
-
-            def count(q_self):
-                """Return the number of matching dictionaries.
-
-                See L{SqlAlchemy.Query}
-                """
-                return q_self._query.count()
-
-            def first(q_self):
-                """Return some matching dictionary, or None
-                See L{SqlAlchemy.Query}
-                """
-                return q_self._query.first()
-
-            def all_ordered_by(q_self, key, desc=False):
-                """Return query results, sorted.
-
-                @type key: string or tuple of string or list of string
-                @param: keys by which to sort the results.
-
-                @rtype: list of L{DbHandle._Dict} instances
-                @return: query results, sorted by given keys
-                """
-
-                # order_by is not easy to do in SQL based on the data structures we're
-                # using.  Considering we support different data types, it may not be
-                # possible at all.
-                #
-                # It would be easy if 'pivot' or 'crosstab' were provided as part of the
-                # underlying API, but they are not. For example, read this:
-                # http://www.simple-talk.com/sql/t-sql-programming/creating-cross-tab-queries-and-pivot-tables-in-sql/
-
-                # load query results
-                results = list(q_self.all())
-
-                if isinstance(key, (tuple, list)):
-                    val_results = [([d[k] for k in key], d) for d in results]
-                else:
-                    val_results = [(d[key], d) for d in results]
-
-                val_results.sort() #interesting: there is an optional key parameter
-                if desc:
-                    val_results.reverse()
-                return [vr[-1] for vr in val_results]
-
-        h_self._KeyVal = KeyVal
-        h_self._Dict = Dict
-        h_self._Query = _Query
-
-    def __iter__(h_self):
-        s = h_self.session()
-        rval = list(h_self.query(s).__iter__())
-        s.close()
-        return rval.__iter__()
-
-    def insert_kwargs(h_self, session=None, **dct):
-        """
-        @rtype:  DbHandle with reference to self
-        @return: a DbHandle initialized as a copy of dct
-        
-        @type dct: dict-like instance whose keys are strings, and values are
-        either strings, integers, floats
-
-        @param dct: dictionary to insert
-
-        """
-        return h_self.insert(dct, session=session)
-
-    def insert(h_self, dct, session=None):
-        """
-        @rtype:  DbHandle with reference to self
-        @return: a DbHandle initialized as a copy of dct
-        
-        @type dct: dict-like instance whose keys are strings, and values are
-        either strings, integers, floats
-
-        @param dct: dictionary to insert
-
-        """
-        if session is None:
-            s = h_self.session()
-            rval = h_self._Dict(s)
-            if dct: rval.update(dct, session=s)
-            s.commit()
-            s.close()
-        else:
-            rval = h_self._Dict(session)
-            if dct: rval.update(dct, session=session)
-        return rval
-
-    def query(h_self, session):
-        """Construct an SqlAlchemy query, which can be subsequently filtered
-        using the instance methods of DbQuery"""
-        return h_self._Query(session.query(h_self._Dict)\
-                        .options(eagerload('_attrs')))
-
-    def createView(h_self, view):
-
-        s = h_self.session()
-        cols = []
-        
-        for col in view.columns:
-            if col.name is "id":
-                continue;
-            elif isinstance(col.type, (Integer,Float)):
-                cols.append([col.name,'fval']);
-            elif isinstance(col.type,String):
-                cols.append([col.name,'sval']);
-            elif isinstance(col.type,Binary):
-                cols.append([col.name,'bval']);
-            else:
-                assert "Error: wrong column type in view",view.name;
-        
-        # generate raw sql command string
-        viewsql = crazy_sql_command(view.name, cols, \
-                                    h_self._dict_table.name, \
-                                    h_self._pair_table.name, \
-                                    h_self._link_table.name);
-        
-        #print 'Creating sql view with command:\n', viewsql;
-
-        h_self._engine.execute(viewsql);
-        s.commit();
-        s.close()
-
-        class MappedClass(object):
-            pass
-
-        mapper(MappedClass, view)
-
-        return MappedClass
-
-    def session(h_self):
-        return h_self._session_fn()
-
-    def get(h_self, id):
-        s = h_self.session()
-        rval = s.query(h_self._Dict).get(id)
-        if rval:
-            #eagerload hack
-            str(rval)
-            rval.id
-        s.close()
-        return rval
-
-
-        
-
-def db_from_engine(engine, 
-        table_prefix='DbHandle_default_',
-        trial_suffix='trial',
-        keyval_suffix='keyval',
-        link_suffix='link'):
-    """Create a DbHandle instance
-
-    @type engine: sqlalchemy engine (e.g. from create_engine)
-    @param engine: connect to this database for transactions
-
-    @type table_prefix: string
-    @type trial_suffix: string
-    @type keyval_suffix: string
-    @type link_suffix: string
-
-    @rtype: DbHandle instance
-
-    @note: The returned DbHandle will use three tables to implement the
-    many-to-many pattern that it needs: 
-     - I{table_prefix + trial_suffix},
-     - I{table_prefix + keyval_suffix}
-     - I{table_prefix + link_suffix}
-
-    """
-    Session = sessionmaker(autoflush=True, autocommit=False)
-
-    metadata = MetaData()
-
-    t_trial = Table(table_prefix+trial_suffix, metadata,
-            Column('id', Integer, primary_key=True),
-            Column('create', DateTime),
-            Column('write', DateTime),
-            Column('read', DateTime),
-            Column('status', Integer),
-            Column('priority', Float(53)),
-            Column('hash', postgres.PGBigInteger)
-            )
-
-    t_keyval = Table(table_prefix+keyval_suffix, metadata,
-            Column('id', Integer, primary_key=True),
-            Column('name', String(128), nullable=False), #name of attribute
-            Column('ntype', Boolean),
-            Column('fval', Float(53)),
-            Column('sval', Text),
-            Column('bval', Binary))
-
-    t_link = Table(table_prefix+link_suffix, metadata,
-            Column('dict_id', Integer, ForeignKey('%s.id' % t_trial),
-                primary_key=True),
-            Column('pair_id', Integer, ForeignKey('%s.id' % t_keyval),
-                primary_key=True))
-
-    metadata.bind = engine
-    metadata.create_all() # no-op when tables already exist
-    #warning: tables can exist, but have incorrect schema
-    # see bug mentioned in DbHandle constructor
-
-    return DbHandle(Session, engine, t_trial, t_keyval, t_link)
-
-def sqlite_memory_db(echo=False, **kwargs):
-    """Return a DbHandle backed by a memory-based database"""
-    engine = create_engine('sqlite:///:memory:', echo=False)
-    return db_from_engine(engine, **kwargs)
-
-def sqlite_file_db(filename, echo=False, **kwargs):
-    """Return a DbHandle backed by a file-based database"""
-    engine = create_engine('sqlite:///%s' % filename, echo=False)
-    return db_from_engine(engine, **kwargs)
-
-def postgres_db(user, password, host, database, echo=False, poolclass=sqlalchemy.pool.NullPool, **kwargs):
-    """Create an engine to access a postgres_dbhandle
-    """
-    db_str ='postgres://%(user)s:%(password)s@%(host)s/%(database)s' % locals()
-
-    engine = create_engine(db_str, echo=echo, poolclass=poolclass)
-
-    return db_from_engine(engine, **kwargs)
-

--- a/pylearn/dbdict/crap.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,256 +0,0 @@
-
-from __future__ import absolute_import
-
-import os, sys, socket, datetime, copy, tempfile, shutil
-from .dconfig import Config, load
-from .api0 import sqlite_memory_db
-from .api0 import postgres_serial
-
-
-class Job(object):
-    @classmethod
-    def is_a_default_option(cls, key, val):
-        if callable(val):
-            return False
-        if key.startswith('_'):
-            return False
-        if key in ('job_module', 'job_symbol'):
-            return False
-        return True
-
-    @classmethod
-    def options(cls):
-        opts = [attr for attr in dir(cls) 
-            if cls.is_a_default_option(attr, getattr(cls, attr))]
-        opts.sort()
-        return opts
-
-
-    def __init__(self, config):
-        for key, val in config.items():
-            if self.is_a_default_option(key, val):
-                if hasattr(self, key):
-                    setattr(self, key, val)
-                else:
-                    raise AttributeError("Job has no such option:", key)
-
-    @classmethod
-    def print_defaults(cls):
-        for attr in cls.options():
-            print attr, '=', getattr(cls, attr)
-
-    def print_config(self, outfile=sys.stdout):
-        for attr in self.options():
-            print >> outfile, attr, '=', getattr(self, attr)
-
-    def save_config(self, outfile=sys.stdout):
-        """Like print_config, but with parsable format rather than human-readable format"""
-        kwargs = dict([(attr,getattr(self, attr)) for attr  in self.options()])
-        Config(**kwargs).save_file(outfile)
-
-def run_job(fn=None, cwd=None,
-
-        config_path = 'job_config.py',
-        result_path = 'job_result.py',
-        stdout_path = 'stdout',
-        stderr_path = 'stderr',
-        work_dir = 'workdir'
-        ):
-    cwd = os.getcwd() if cwd is None else cwd
-
-def _pop_cwd():
-    try:
-        cwd = sys.argv.pop(0)
-        if not cwd.startswith('/'):
-            cwd = os.path.join(os.getcwd(), cwd)
-    except IndexError:
-        cwd = os.getcwd()
-    return cwd
-
-
-class RunJob(object):
-    """
-    """
-
-    path_perf = 'job_perf.py'
-    path_results = 'job_results.py'
-    path_config = 'job_config.py'
-    path_fullconfig = 'job_fullconfig.py'
-    path_stdout = 'stdout'
-    path_stderr = 'stderr'
-    path_workdir = 'workdir'
-    
-    def __init__(self, exename):
-        pass
-
-    def _load_config(self, cwd = None):
-        cwd = _pop_cwd() if cwd is None else cwd
-        config = load(os.path.join(cwd, self.path_config))
-        return config
-    
-    def _load_job_class(self, config=None):
-        config = self._load_config() if config is None else config
-        job_module_name = config.job_module
-        job_symbol = config.job_symbol
-        #level=0 -> absolute imports
-        #fromlist=[None] -> evaluate the rightmost element of the module name, when it has
-        #                   dots (e.g., "A.Z" will return module Z)
-        job_module = __import__(job_module_name, fromlist=[None], level=0)
-        try:
-            job_class = getattr(job_module, job_symbol)
-        except:
-            print >> sys.stderr, "failed to load job class:", job_module_name, job_symbol
-            raise
-        return job_class
-
-    def print_config(self):
-        config = self._load_config()
-        job_class = self._load_job_class(config)
-        job = job_class(config)
-        job.print_config()
-
-    def run(self):
-        cwd = _pop_cwd()
-        config = self._load_config(cwd)
-        job_class = self._load_job_class(config)
-        job = job_class(config)
-
-        job.save_config(open(os.path.join(cwd, self.path_fullconfig),'w'))
-
-        perf = Config()
-        perf.host_name = socket.gethostname()
-        perf.start_time = str(datetime.datetime.now())
-        perf.save(os.path.join(cwd, self.path_perf))
-
-        stdout_orig = sys.stdout
-        stderr_orig = sys.stderr
-
-        try:
-            sys.stdout = open(os.path.join(cwd, self.path_stdout), 'w')
-            sys.stderr = open(os.path.join(cwd, self.path_stderr), 'w')
-
-            #
-            # mess around with the working directory
-            #
-
-            wd = os.path.join(cwd, self.path_workdir)
-            try:
-                os.mkdir(wd)
-            except OSError, e:
-                print >> sys.stderr, "trouble making wordking directory:"
-                print >> sys.stderr, e
-                print >> sys.stderr, "ignoring error and proceeding anyway"
-            try:
-                os.chdir(wd)
-            except:
-                pass
-
-            print >> sys.stderr, "cwd:", os.getcwd()
-
-            #
-            # run the job...
-            #
-
-            #TODO load the results file before running the job, to resume job
-            results = Config()
-
-            job_rval = job.run(results)
-
-            #TODO: use the return value to decide whether the job should be resumed or not,
-            #      False  means run is done
-            #      True   means the job has yielded, but should be continued
-            results.save(os.path.join(cwd, self.path_results))
-
-        finally:
-            #put back stderr and stdout
-            sys.stdout = stdout_orig
-            sys.stderr = stderr_orig
-            perf.end_time = str(datetime.datetime.now())
-            perf.save(os.path.join(cwd, self.path_perf))
-
-    def defaults(self):
-        job_class = self._load_job_class()
-        job_class.print_defaults()
-
-def standalone_run_job():
-    exe = RunJob(sys.argv.pop(0))
-    try:
-        cmd = sys.argv.pop(0)
-        fn = getattr(exe, cmd)
-    except IndexError:
-        fn = getattr(exe, 'run')
-    except AttributeError:
-        print >> sys.stderr, "command not supported", cmd
-
-    fn()
-
-def build_db(cwd, db=None):
-    """WRITEME"""
-    db = sqlite_memory_db() if db is None else db
-    for e in os.listdir(cwd):
-        e = os.path.join(cwd, e)
-        try:
-            e_config = open(os.path.join(e, 'job_config.py'))
-        except:
-            e_config = None
-
-        try: 
-            e_sentinel = open(os.path.join(e, '__jobdir__'))
-        except:
-            e_sentinel = None
-
-        if not (e_config or e_sentinel):
-            continue #this is not a job dir
-
-        if e_config:
-            e_config.close()
-            config = load(os.path.join(e, 'job_config.py'))
-            kwargs = copy.copy(config.__dict__)
-            try:
-                results = load(os.path.join(e, 'job_results.py'))
-                kwargs.update(results.__dict__)
-            except:
-                pass
-            try:
-                perf = load(os.path.join(e, 'job_perf.py'))
-                kwargs.update(perf.__dict__)
-            except:
-                pass
-
-            #TODO: this is a backward-compatibility hack for AISTATS*09
-            if 'perf_jobdir' not in kwargs:
-                kwargs['perf_jobdir'] = e
-            if 'perf_workdir' not in kwargs:
-                kwargs['perf_workdir'] = os.path.join(e, 'workdir')
-
-            entry = db.insert(kwargs)
-
-        if e_sentinel:
-            print >> sys.stderr, "NOT-IMPLEMENTED: RECURSION INTO SUBDIRECTORY", e
-    return db
-
-
-class RunQuery(object):
-
-    def __init__(self, exename):
-        pass
-
-    def run(self):
-        cwd = _pop_cwd()
-        db = build_db(cwd)
-        for entry in db.query().all():
-            print entry.items()
-
-
-def standalone_query():
-    exe = RunQuery(sys.argv.pop(0))
-    try:
-        cmd = sys.argv.pop(0)
-        fn = getattr(exe, cmd)
-    except IndexError:
-        fn = getattr(exe, 'run')
-    except AttributeError:
-        print >> sys.stderr, "command not supported", cmd
-
-    fn()
-

--- a/pylearn/dbdict/dbdict_run.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,78 +0,0 @@
-import sys, signal
-from .tools import DictProxyState, load_state_fn, run_state
-
-# N.B.
-# don't put exotic imports here
-# see what I did with def sql() below... since we shouldn't try to import that stuff unless we
-# need it.
-
-_experiment_usage = """Usage:
-    dbdict-experiment <cmd>
-
-Commands:
-
-    help    Print help. (You're looking at it.)
-
-    cmdline Obtain experiment configuration by evaluating the commandline
-    sql     Obtain experiment configuration by querying an sql database
-
-Help on individual commands might be available by typing 'dbdict-experiment <cmd> help'
-
-"""
-    #dbdict  Obtain experiment configuration by loading a dbdict file
-
-def _dispatch_cmd(self, stack=sys.argv):
-    try:
-        cmd = stack.pop(0)
-    except IndexError:
-        cmd = 'help'
-    try:
-        fn = getattr(self, cmd)
-    except AttributeError:
-        print >> sys.stderr, "command not supported", cmd
-        fn = self.help
-    fn()
-
-class RunCmdline(object):
-    def __init__(self):
-        try:
-            dct = eval('dict(' + sys.argv.pop(0) + ')')
-        except Exception, e:
-            print >> sys.stderr, "Exception:", e
-            self.help()
-            return
-
-        channel_rval = [None]
-
-        def on_sigterm(signo, frame):
-            channel_rval[0] = 'stop'
-
-        #install a SIGTERM handler that asks the run_state function to return
-        signal.signal(signal.SIGTERM, on_sigterm)
-        signal.signal(signal.SIGINT, on_sigterm)
-
-        def channel(*args, **kwargs):
-            return channel_rval[0]
-
-        run_state(dct, channel)
-        print dct
-
-    def help(self):
-        print >> sys.stderr, "Usage: dbdict-experiment cmdline <config>"
-
-
-class RunExperiment(object):
-    """This class handles the behaviour of the dbdict-run script."""
-    def __init__(self):
-        exe = sys.argv.pop(0)
-        #print 'ARGV', sys.argv
-        _dispatch_cmd(self)
-
-    def sql(self):
-        from .dbdict_run_sql import run_sql
-        return run_sql()
-
-    cmdline = RunCmdline
-
-    def help(self):
-        print _experiment_usage # string not inlined so as not to fool VIM's folding mechanism

--- a/pylearn/dbdict/dbdict_run_sql.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,446 +0,0 @@
-"""Code related to using the api0 dictionary table to run experiments.
-
-This module has been tested with postgres.
-
-"""
-
-import sys, os, socket, tempfile, shutil, copy, time
-import numpy # for the random wait time in book_unstarted_trial
-
-import sqlalchemy
-from sqlalchemy import create_engine, desc
-from sqlalchemy.orm import eagerload
-import psycopg2, psycopg2.extensions 
-
-from .api0 import db_from_engine, postgres_db
-from .tools import run_state, DictProxyState, COMPLETE, INCOMPLETE, SYMBOL, MODULE # tools
-from .dconfig import save_items
-
-# _TEST CONCURRENCY
-# To ensure that concurrency is handled properly by the consumer (book_dct)
-# set this flag to True and (manually) run the following test.
-#
-# Launch two processes side by side, starting one of them a few seconds after the other.
-# There is an extra sleep(10) that will delay each process's job dequeue.
-#
-# You should see that the process that started first gets the job,
-# and the process that started second tries to get the same job, 
-# fails, and then gets another one instead.
-_TEST_CONCURRENCY = False
-
-_help = """Usage:
-dbdict-run sql postgres://<user>:<pass>@<host>/<db>/<api0-table> <experiment-root>
-
-    user        - postgres username
-    pass        - password
-    hostname    - the network address of the host on which a postgres server is 
-                  running (on port ??)
-    database    - a database served by the postgres server on <hostname>
-    api0-table  - the name (actually, table_prefix) associated with tables, 
-                  created by dbdict.api0.
-
-    experiment-root - a local or network path.  Network paths begin with ssh://
-                  E.g. /tmp/blah
-                       ssh://mammouth:blah
-                       ssh://foo@linux.org:/tmp/blah
-
-Experiment-root is used to store the file results of experiments.  If a job with a given <id>
-creates file 'a.txt', and directory 'b' with file 'foo.py', then these will be rsync'ed to the
-experiment-root when job <id> has finished running.  They will be found here:
-
-    <experiment-root>/<db>/<api0-table>/<id>/workdir/a.txt
-    <experiment-root>/<db>/<api0-table>/<id>/workdir/b/foo.py
-
-Files 'stdout', 'stderr', and 'state.py' will be created.
-
-    <experiment-root>/<db>/<api0-table>/<id>/stdout   - opened for append
-    <experiment-root>/<db>/<api0-table>/<id>/stderr   - opened for append
-    <experiment-root>/<db>/<api0-table>/<id>/state.py - overwritten with database version
-
-If a job is restarted or resumed, then those files are rsync'ed back to the current working
-directory, and stdout and stderr are re-opened for appending.  When a resumed job stops for
-the second (or more) time, the cwd is rsync'ed back to the experiment-root.  In this way, the
-experiment-root accumulates the results of experiments that run.
-
-"""
-
-STATUS = 'dbdict_sql_status'
-PRIORITY = 'dbdict_sql_priority'
-HOST = 'dbdict_sql_hostname'
-HOST_WORKDIR = 'dbdict_sql_host_workdir'
-PUSH_ERROR = 'dbdict_sql_push_error'
-
-START = 0
-"""dbdict_status == START means a experiment is ready to run"""
-
-RUNNING = 1
-"""dbdict_status == RUNNING means a experiment is running on dbdict_hostname"""
-
-DONE = 2
-"""dbdict_status == DONE means a experiment has completed (not necessarily successfully)"""
-
-RESTART_PRIORITY = 2.0
-"""Stopped experiments are marked with this priority"""
-
-
-def postgres_serial(user, password, host, database, **kwargs):
-    """Return a DbHandle instance that communicates with a postgres database at transaction
-    isolation_level 'SERIALIZABLE'.
-
-    :param user: a username in the database
-    :param password: the password for the username
-    :param host: the network address of the host on which the postgres server is running
-    :param database: a database served by the postgres server
-    
-    """
-    this = postgres_serial
-
-    if not hasattr(this,'engine'):
-        def connect():
-            c = psycopg2.connect(user=user, password=password, database=database, host=host)
-            c.set_isolation_level(psycopg2.extensions.ISOLATION_LEVEL_SERIALIZABLE)
-            return c
-        pool_size = 0
-        this.engine = create_engine('postgres://'
-                ,creator=connect
-                ,pool_size=0 # should force the app release connections
-                )
-
-    db = db_from_engine(this.engine, **kwargs)
-    db._is_serialized_session_db = True
-    return db
-
-
-def add_experiments_to_db(exp_cls, jobs, db, verbose=0, add_dups=False, type_check=None):
-    """Add experiments paramatrized by exp_cls and jobs[i] to database db.
-
-    Default behaviour is to ignore jobs which are already in the database.
-
-    If type_check is a class (instead of None) then it will be used as a type declaration for
-    all the elements in each job dictionary.  For each key,value pair in the dictionary, there
-    must exist an attribute,value pair in the class meeting the following criteria:
-    the attribute and the key are equal, and the types of the values are equal.
-
-    :param exp_cls: The Experiment class to run these experiments.
-    :param jobs: The parameters of experiments to run.
-    :type jobs: an iterable object over dictionaries
-    :param verbose: print which jobs are added and which are skipped
-    :param add_dups: False will ignore a job if it matches (on all items()) with a db entry.
-    :type add_dups: Bool
-
-    :returns: list of (Bool,job[i]) in which the flags mean the corresponding job actually was
-    inserted.
-
-    """
-    rval = []
-    for job in jobs:
-        job = copy.copy(job)
-        do_insert = add_dups or (None is db.query(**job).first())
-
-        if do_insert:
-            if type_check:
-                for k,v in job.items():
-                    if type(v) != getattr(type_check, k):
-                        raise TypeError('Experiment contains value with wrong type',
-                                ((k,v), getattr(type_check, k)))
-
-            job[STATUS] = START
-            job[SYMBOL] = exp_cls.__name__
-            job[MODULE] = exp_cls.__module__
-            job[PRIORITY] = 1.0
-            if verbose:
-                print 'ADDING  ', job
-            db.insert(job)
-            rval.append((True, job))
-        else:
-            if verbose:
-                print 'SKIPPING', job
-            rval.append((False, job))
-
-
-def book_dct_postgres_serial(db, retry_max_sleep=10.0, verbose=0):
-    """Find a trial in the lisa_db with status START.
-
-    A trial will be returned with dbdict_status=RUNNING.
-
-    Returns None if no such trial exists in DB.
-
-    This function uses a serial access to the lisadb to guarantee that no other
-    process will retrieve the same dct.  It is designed to facilitate writing
-    a "consumer" for a Producer-Consumer pattern based on the database.
-
-    """
-    print >> sys.stderr, """#TODO: use the priority field, not the status."""
-    print >> sys.stderr, """#TODO: ignore entries with key PUSH_ERROR."""
-
-    s = db._session
-
-    # NB. we need the query and attribute update to be in the same transaction
-    assert s.autocommit == False 
-
-    dcts_seen = set([])
-    keep_trying = True
-
-    dct = None
-    while (dct is None) and keep_trying:
-        #build a query
-        q = s.query(db._Dict)
-        q = q.options(eagerload('_attrs')) #hard-coded in api0
-        q = q.filter(db._Dict._attrs.any(name=STATUS, fval=START))
-
-        #try to reserve a dct
-        try:
-            #first() may raise psycopg2.ProgrammingError
-            dct = q.first()
-
-            if dct is not None:
-                assert (dct not in dcts_seen)
-                if verbose: print 'book_unstarted_dct retrieved, ', dct
-                dct._set_in_session(STATUS, RUNNING, s)
-                if 1:
-                    if _TEST_CONCURRENCY:
-                        print >> sys.stderr, 'SLEEPING BEFORE BOOKING'
-                        time.sleep(10)
-
-                    #commit() may raise psycopg2.ProgrammingError
-                    s.commit()
-                else:
-                    print >> sys.stderr, 'DEBUG MODE: NOT RESERVING JOB!', dct
-                #if we get this far, the job is ours!
-            else:
-                # no jobs are left
-                keep_trying = False
-        except (psycopg2.OperationalError,
-                sqlalchemy.exceptions.ProgrammingError), e:
-            #either the first() or the commit() raised
-            s.rollback() # docs say to do this (or close) after commit raises exception
-            if verbose: print 'caught exception', e
-            if dct:
-                # first() succeeded, commit() failed
-                dcts_seen.add(dct)
-                dct = None
-            wait = numpy.random.rand(1)*retry_max_sleep
-            if verbose: print 'another process stole our dct. Waiting %f secs' % wait
-            time.sleep(wait)
-    return dct
-
-def book_dct(db):
-    print >> sys.stderr, """#TODO: use the priority field, not the status."""
-    print >> sys.stderr, """#TODO: ignore entries with key self.push_error."""
-
-    return db.query(dbdict_status=START).first()
-
-def parse_dbstring(dbstring):
-    postgres = 'postgres://'
-    assert dbstring.startswith(postgres)
-    dbstring = dbstring[len(postgres):]
-
-    #username_and_password
-    colon_pos = dbstring.find('@')
-    username_and_password = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    colon_pos = username_and_password.find(':')
-    if -1 == colon_pos:
-        username = username_and_password
-        password = None
-    else:
-        username = username_and_password[:colon_pos]
-        password = username_and_password[colon_pos+1:]
-    
-    #hostname
-    colon_pos = dbstring.find('/')
-    hostname = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    #dbname
-    colon_pos = dbstring.find('/')
-    dbname = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    #tablename
-    tablename = dbstring
-
-    if password is None:
-        password = open(os.getenv('HOME')+'/.dbdict_%s'%dbname).readline()[:-1]
-    if False:
-        print 'USERNAME', username
-        print 'PASS', password
-        print 'HOST', hostname
-        print 'DB', dbname
-        print 'TABLE', tablename
-
-    return username, password, hostname, dbname, tablename
-
-class ExperimentLocation(object):
-    def __init__(self, root, dbname, tablename, id):
-        ssh_prefix='ssh://'
-        if root.startswith(ssh_prefix):
-            root = root[len(ssh_prefix):]
-            #at_pos = root.find('@')
-            colon_pos = root.find(':')
-            self.host, self.path = root[:colon_pos], root[colon_pos+1:]
-        else:
-            self.host, self.path = '', root
-        self.dbname = dbname
-        self.tablename = tablename
-        self.id = id
-
-    def rsync(self, direction):
-        """The directory at which experiment-related files are stored.
-
-        :returns: "<host>:<path>", of the sort used by ssh and rsync.
-        """
-        if self.host:
-            path = os.path.join(
-                    ':'.join([self.host, self.path]), 
-                    self.dbname, 
-                    self.tablename, 
-                    self.id)
-        else:
-            path = os.path.join(self.path, 
-                    self.dbname, self.tablename, self.id)
-
-        if direction == 'push':
-            rsync_cmd = 'rsync -a * "%s/"' % path
-        elif direction == 'pull':
-            rsync_cmd = 'rsync -a "%s/" .' % path
-        else:
-            raise Exception('invalid direction', direction)
-
-        rsync_rval = os.system(rsync_cmd)
-        if rsync_rval != 0:
-            raise Exception('rsync failure', (rsync_rval, rsync_cmd))
-
-    def pull(self):
-        return self.rsync('pull')
-
-    def push(self):
-        return self.rsync('push')
-
-    def touch(self):
-        path = os.path.join(self.path, self.dbname, self.tablename, self.id)
-        if self.host:
-            host = self.host
-            touch_cmd = ('ssh %(host)s  "mkdir -p \'%(path)s\' && cd \'%(path)s\' '
-            '&& touch stdout stderr && mkdir workdir"' % locals())
-        else:
-            touch_cmd = ("mkdir -p '%(path)s' && cd '%(path)s' "
-            '&& touch stdout stderr && mkdir workdir' % locals())
-        print "ECHO", touch_cmd
-        touch_rval = os.system(touch_cmd)
-        if 0 != touch_rval:
-            raise Exception('touch failure', (touch_rval, touch_cmd))
-
-    def delete(self):
-        #something like ssh %s 'rm -Rf %s' should work, but it's pretty scary...
-        raise NotImplementedError()
-
-def run_sql():
-    try:
-        username, password, hostname, dbname, tablename = parse_dbstring(sys.argv.pop(0))
-    except Exception, e:
-        print >> sys.stderr, e
-        print >> sys.stderr, _help
-        raise
-
-    #set experiment_root
-    try:
-        exproot = sys.argv.pop(0)
-    except:
-        exproot = os.getcwd()
-
-    if not exproot.startswith('/'):
-        exproot = os.path.join(os.getcwd(), exproot)
-
-    #TODO: THIS IS A GOOD IDEA RIGHT?
-    #   It makes module-lookup work based on cwd-relative paths
-    #   But possibly has really annoying side effects?  Is there a cleaner
-    #   way to change the import path just for loading the experiment class?
-    sys.path.insert(0, os.getcwd())
-
-    #TODO: refactor this so that we can use any kind of database (not just postgres)
-
-    #a serialized session is necessary for jobs not be double-booked by listeners running
-    #in parallel on the cluster.
-    db = postgres_serial(user=username, 
-            password=password, 
-            host=hostname,
-            database=dbname,
-            table_prefix=tablename)
-
-    while True:
-        dct = book_dct_postgres_serial(db, verbose=1)
-        if dct is None:
-            break
-
-        try:
-            #
-            # chdir to a temp folder
-            # 
-            workdir = tempfile.mkdtemp()
-            print >> sys.stderr, "INFO RUNNING ID %i IN %s" % (dct.id, workdir)
-            os.chdir(workdir)
-    
-            # not sure where else to put this...
-            dct[HOST] = socket.gethostname()
-            dct[HOST_WORKDIR] = workdir
-
-            exploc = ExperimentLocation(exproot, dbname, tablename, str(dct.id))
-
-            #
-            # pull cwd contents
-            #
-            exploc.touch()
-            exploc.pull()
-
-            #
-            # run the experiment
-            # 
-            old_stdout, old_stderr = sys.stdout, sys.stderr
-            sys.stdout, sys.stderr = open('stdout', 'a+'), open('stderr', 'a+')
-            assert RUNNING == dct[STATUS] #set by get_dct
-            os.chdir(os.path.join(workdir, 'workdir'))
-            try:
-                run_rval = run_state(DictProxyState(dct))
-            except Exception, e:
-                run_rval = COMPLETE
-                print >> sys.stderr, 'Exception:', e
-                print >> old_stderr, '#TODO: print a bigger traceback to stderr'
-            sys.stdout, sys.stderr = old_stdout, old_stderr
-
-            #
-            # push the results back to the experiment_root
-            #
-            try:
-                os.chdir(workdir)
-                #pickle the state #TODO: write it human-readable
-                #cPickle.dump(dict((k,v) for k,v in dct.items()), open('state.pickle','w'))
-                save_items(dct.items(), open('state.py', 'w'))
-                exploc.push()
-            except Exception, e:
-                dct[PUSH_ERROR] = str(e)
-                raise
-
-            # Cleanup the tempdir
-            # TODO: put this in a 'finally' block?
-            #
-            shutil.rmtree(workdir, ignore_errors=True)
-
-        except:
-            dct[STATUS] = DONE
-            dct[PRIORITY] = None
-            raise
-
-        if run_rval is INCOMPLETE:
-            #mark the job as needing restarting
-            dct[STATUS] = START
-            dct[PRIORITY] = RESTART_PRIORITY
-        else:
-            #mark the job as being done
-            dct[STATUS] = DONE
-            dct[PRIORITY] = None
-
-        break  # don't actually loop
-
-

--- a/pylearn/dbdict/dconfig.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,145 +0,0 @@
-import sys
-#
-#
-# Utility
-#
-#
-
-class Config (object):
-    """A class to store experiment configurations.
-
-    Configuration variables are stored in class instance __dict__.  This class
-    ensures that keys are alphanumeric strings, and that values can be rebuilt
-    from their representations.
-
-    It can be serialized to/from a python file.
-    
-    """
-    def __init__(self, __dict__=None, **kwargs):
-        if __dict__:
-            Config.__checkkeys__(*__dict__.keys())
-            self.__dict__.update(__dict__)
-        if kwargs:
-            Config.__checkkeys__(*kwargs.keys())
-            self.__dict__.update(kwargs)
-
-    def __setattr__(self, attr, value):
-        Config.__checkkeys__(attr)
-        self.__dict__[attr] = value
-
-    def __hash__(self):
-        """Compute a hash string from a dict, based on items().
-
-        @type dct: dict of hashable keys and values.
-        @param dct: compute the hash of this dict
-
-        @rtype: string
-
-        """
-        items = list(self.items())
-        items.sort()
-        return hash(repr(items))
-
-    def keys(self):
-        return self.__dict__.keys()
-
-    def items(self):
-        return self.__dict__.items()
-
-    def update(self, dct):
-        Config.__checkkeys__(*dct.keys())
-        self.__dict__.update(dct)
-
-    def save_file(self, f=sys.stdout):
-        items = self.items()
-        items.sort()
-        save_dictlike(items, f)
-
-    def save(self, filename):
-        """Write a python file as a way of serializing a dictionary
-
-        @type filename: string
-        @param filename: filename to open (overwrite) to save dictionary contents
-
-        @return None
-
-        """
-        f = open(filename, 'w')
-        self.save_file(f)
-        f.close()
-
-    def update_fromfile(self, filename):
-        """Read the local variables from a python file
-
-        @type filename: string, filename suitable for __import__()
-        @param filename: a file whose module variables will be returned as a
-        dictionary
-
-        @rtype: dict
-        @return: the local variables of the imported filename
-
-        @note:
-        This implementation silently ignores all module symbols that don't meet
-        the standards enforced by L{Config.__checkkeys__}. This is meant to
-        ignore module special variables.
-
-        """
-        #m = __import__(filename) #major security problem, or feature?
-        f = open(filename)
-        for line in f:
-            if line.startswith('#'):
-                continue
-            line = line[:-1] #trim the '\n'
-            tokens = line.split(' ')
-            try:
-                key = tokens[0]
-                assert '=' == tokens[1]
-            except:
-                raise Exception('trouble parsing line:', line)
-            repr_val = ' '.join(tokens[2:])
-            val = eval(repr_val)
-            setattr(self, key, val)
-
-    @staticmethod
-    def __checkkeys__(*args):
-        conf = Config()
-        for k in args:
-            #must be string
-            if type(k) != str:
-                raise KeyError(k)
-            #mustn't be part of Config class interface
-            if hasattr(conf, k):
-                raise KeyError(k)
-            #all alphanumeric
-            for c in k:
-                if c not in ('abcdefghijklmnopqrstuvwxyz'
-                        'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-                        '_0123456789'):
-                    raise KeyError(k)
-            #no symbols that look like reserved symbols
-            if k[:2]=='__' and k[-2:]=='__' and len(k)>4:
-                raise KeyError(k)
-
-def load(*filenames):
-    rval = Config()
-    for filename in filenames:
-        rval.update_fromfile(filename)
-    return rval
-
-def save_items(items, f):
-    """Write a python file as a way of serializing a dictionary
-
-    @type f: writable file-like object
-    @param f: the attributes of this object will be written here
-
-    @return None
-
-    """
-    print >> f, "#File generated by dbdict.dconfig.save_items"
-    for key, val in items:
-        Config.__checkkeys__(key) 
-        # should never raise... illegal keys are not
-        # supposed to ever get into the dictionary
-        repr_val = repr(val)
-        assert val == eval(repr_val)
-        print >> f, key, '=', repr_val

--- a/pylearn/dbdict/design.txt	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,316 +0,0 @@
-
-TODO
-====
-
-- Class interface for jobs (SHAPING UP)
-
-- How exactly will state work (STILL A MYSTERY sql vs. file vs. script)
-    - How to insert jobs
-    - How to retrieve jobs
-
-- How will the driver work (rsync / file conventions)
-
-
-
-Components
-==========
-
-DbDict
-------
-
-A DbDict is a restricted dictionary.
-
-It's keys are restricted to simple types, simple enough to be stored into a
-database.  Strings, integers, floating-points.
-
-
-Experiment
-----------
-
-An Experiment is a python class with methods like start(), run(), stop().  A
-user should make an Experiment class whose run() method does some computations
-like training a neural network and measuring test errors, training an SVM,
-doing some feature extraction, etc.
-
-An Experiment's arguments are stored in a DbDict.
-
-The results of an experiment can be stored in two places: in a DbDict (for
-easy SQL searching later on) and in files.
-
-
-ExperimentLauncher
-------------------
-
-Experiments are not standalone executables, they need to be run by some
-additional code.  There are several ways to launch an experiment:
-
-- running on your local machine vs. cluster vs. condor vs. mammouth
-
-- loading the arguments from the commandline vs. file vs. SQL query 
-
-- running alone, or running in parallel with other experiments.
-
-The ExperimentLauncher is an executable python program that can run
-experiments in these different ways.
-
-
-
-Workflow (How to run experiments)
-=================================
-
-First, you'll need a Python program to compute what you want.  Think about how
-long it will take and whether you will want to be able to resume after being
-stopped.
-
-If you want to run a simple or short experiment that is not restartable,
-simply extend dbdict.Experiment like this:
-
-.. code-block:: python
-
-    class MyExperiment(dbdict.Experiment):
-
-        def __init__(self, dct):
-            self.dct = dct
-
-        def run(self):
-            
-            # compute something
-            result = self.dct.a * self.dct.b
-
-            # store it 
-            self.dct.result = result
-
-            # write some other results to a file
-            f = open('some_file', 'w')
-            print >> f, "hello from the job?"
-
-            # return False or None to indicate the job is done
-
-If you want to run a more elaborate experiment, then extend dbdict.Experiment
-like this:
-
-.. code-block:: python
-
-    class MyRestartableExperiment(dbdict.Experiment):
-
-        def __init__(self, state):
-            """Called once per lifetime of the class instance.  Can be used to
-            create new jobs and save them to the database.   This function will not
-            be called when a Job is retrieved from the database.
-
-            Parent creates keys: dbdict_id, dbdict_module, dbdict_symbol, dbdict_state.
-
-            dbdict_state = NEW  (possibilities: NEW, RUNNING, DONE)
-
-            """
-
-        def start(self):
-            """Called once per lifetime of the compute job.
-
-            This is a good place to initialize internal variables.
-
-            After this function returns, either stop() or run() will be called.
-            
-            dbdict_state -> RUNNING
-
-            """
-
-        def resume(self):
-            """Called to resume computations on a previously stop()'ed job.  The
-            os.getcwd() is just like it was after some previous stop() command.
-
-            This is a good place to load internal variables from os.getcwd().
-
-            dbdict_state -> RUNNING
-            
-            """
-
-        def run(self, channel):
-            """Called after start() or resume().
-            
-            channel() may return different things at different times.  
-                None   - run should continue.
-                'stop' - the job should save state as soon as possible because
-                         the process may soon be terminated
-
-            When this function returns, dbdict_state -> DONE.
-            """
-
-
-Having written your Experiment subclass, you can now test it directly, or
-using the ExperimentLauncher.
-
-.. code-block:: python
-
-    if __name__ == '__main__':
-        
-        class Config(object):
-            a = 3
-            b = 50
-        
-        experiment = MyExperiment(Config())
-        experiment.run()
-
-.. code-block:: bash
-
-    dbdict-run my_file.MyExperiment 'dict(a=3, b=50)'
-
-
-To run a batch of experiments on a cluster using 3 concurrent processes using
-the SQL-based job list, you have to insert the jobs into a database table, and
-then launch 10 instances of dbdict-run.
-
-.. code-block:: python
-    
-    from dbdict.tools import insert, view_table
-
-    def add_jobs():
-        experiment_module = 'my_repo.some_file' #match you module name
-        experiment_symbol = 'MyExperiment'      #match your class name
-        experiment_name = 'showing some stuff'
-        for a in 3, 4, 5:
-            for b in 0.0, 0.1, 3.0:
-                insert(locals(), ignore_duplicates=False)
-    add_jobs()
-
-    dbdict_run_table('my_launcher_view', experiment_name='showing_some_stuff')
-
-
-
-.. code-block:: bash
-
-    dbidispatch --condor dbdict-run sql <dbstring> my_launcher_view
-
-
-
-Component Documentation
-=======================
-
-DbDict
-------
-
-
-Experiment
-----------
-
-class Experiment(object):
-
-    new_stdout == 'job_stdout'
-    new_stderr == 'job_stderr'
-
-    def remap_stdout(self):
-        """
-        Called before start and resume.  
-
-        Parent-class behaviour is to replace sys.stdout with open(self.new_stdout, 'w+').
-
-        """
-
-    def remap_stderr(self):
-        """
-        Called before start and resume.
-        
-        """
-
-    def tempdir(self):
-        """
-        Return the recommended filesystem location for temporary files.
-
-        The idea is that this will be a fast, local disk partition, suitable
-        for temporary storage.
-        
-        Files here will not generally be available at the time of resume().
-
-        The return value of this function may be controlled by one or more
-        environment variables.  
-        
-        Will return $DBDICT_EXPERIMENT_TEMPDIR if present.
-        Failing that, will return $TMP/username-dbdict/hash(self)
-        Failing that, will return /tmp/username-dbdict/hash(self)
-
-        .. note::
-            Maybe we should use Python stdlib's tempdir mechanism. 
-
-        """
-
-
-Environment Variables
-=====================
-
-
-TMP - sometimes used by Experiment.tempdir()
-
-DBDICT_EXPERIMENT_TEMPDIR - used by Experiment.tempdir()
-
-
-JOB DRIVER
-----------
-
-When a job is started, save:
-
-- workdir
-
-- dir
-
-- network (e.g. mammouth vs. diro... where are jobdir and workdir?
-  Alternatively, automatically rsync finished jobs' workdir and jobdir to diro.)
-
-
-dbdict-run-job
---------------
-
-prepare job dir
-~~~~~~~~~~~~~~~~
-
-On iro, cd to fringant2/.../job_id/
-
-when restarting on mammouth, cd to somewhere and rsync -r fringant2/.../job_id job_id
-
-after stopping on mammouth rsync -r job_id fringant2/.../job_id
-
-.. note: 
-    What to do on error in rsync?  Where to report problems?
-
-.. note: 
-    What to do with stderr, stdout?  
-
-job queue table
-~~~~~~~~~~~~~~~
-New table: id job_id priority
-
-This is the table that dbdict-run-job will pop jobs from.
-
-
-How to run experiments using DbDict
------------------------------------
-
-- Inherit from tools.Job.  This is where you put the logic that takes some
-  parameters, and computes some results associated with those parameters.
-
-- Write a loop that creates a bunch of Jobs, and then tests to see if they are
-  already in the db before inserting them.
-
-- Insert the new job ids and priority into the qu
-- Save result files, and files needed for job resume to os.getcwd().
-
-- Save non-result files to a TEMP directory, obtained by e.g. self.gettmpdir()
-  from inside a Job instance.
-
-- Load datasets through pylearn.  Pylearn has internal configuration that allows
-  it to find files both on mammouth and DIRO networks.  You just call
-  MNIST.head() or shapeset1.train_valid_test() and bingo.
-
-- Manage experiments in a postgres database.  Which ones have been queued, which
-  ones are running, which are finished, simple results, etc.
-
-- To analyze results, select from PG and create a dedicated table in sqlite.
-  Make columns for all the dictionary keys from all the selected entries.
-
-
-
-When running classification experiments
----------------------------------------
-
-Have convention of saving (train, valid, test) X (NLL, RATE).
-Should the convention be enforced?  How?
-

--- a/pylearn/dbdict/experiment.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,122 +0,0 @@
-"""Helper code for implementing dbdict-compatible jobs"""
-import inspect, sys, copy
-
-#State values should be instances of these types:
-INT = type(0)
-FLT = type(0.0)
-STR = type('')
-
-COMPLETE = None    #jobs can return this by returning nothing as well
-INCOMPLETE = True  #jobs can return this and be restarted
-
-def subdict(dct, prefix):
-    """Return the dictionary formed by keys in `dct` that start with the string `prefix`.
-
-    In the returned dictionary, the `prefix` is removed from the keynames.
-    Updates to the sub-dict are reflected in the original dictionary.
-
-    Example:
-        a = {'aa':0, 'ab':1, 'bb':2}
-        s = subdict(a, 'a') # returns dict-like object with keyvals {'a':0, 'b':1}
-        s['a'] = 5
-        s['c'] = 9
-        # a == {'aa':5, 'ab':1, 'ac':9, 'bb':2}
-
-    """
-    class SubDict(object):
-        def __copy__(s):
-            rval = {}
-            rval.update(s)
-            return rval
-        def __eq__(s, other):
-            if len(s) != len(other): 
-                return False
-            for k in other:
-                if other[k] != s[k]:
-                    return False
-            return True
-        def __len__(s):
-            return len(s.items())
-        def __str__(s):
-            d = {}
-            d.update(s)
-            return str(d)
-        def keys(s):
-            return [k[len(prefix):] for k in dct if k.startswith(prefix)]
-        def values(s):
-            return [dct[k] for k in dct if k.startswith(prefix)]
-        def items(s):
-            return [(k[len(prefix):],dct[k]) for k in dct if k.startswith(prefix)]
-        def update(s, other):
-            for k,v in other.items():
-                self[k] = v
-        def __getitem__(s, a):
-            return dct[prefix+a]
-        def __setitem__(s, a, v):
-            dct[prefix+a] = v
-
-    return SubDict()
-
-def subdict_copy(dct, prefix):
-    return copy.copy(subdict(dct, prefix))
-
-def call_with_kwargs_from_dict(fn, dct, logfile='stderr'):
-    """Call function `fn` with kwargs taken from dct.
-
-    When fn has a '**' parameter, this function is equivalent to fn(**dct).
-
-    When fn has no '**' parameter, this function removes keys from dct which are not parameter
-    names of `fn`.  The keys which are ignored in this way are logged to the `logfile`.  If
-    logfile is the string 'stdout' or 'stderr', then errors are logged to sys.stdout or
-    sys.stderr respectively.
-
-    The reason this function exists is to make it easier to provide default arguments and 
-
-    :param fn: function to call
-    :param dct: dictionary from which to take arguments of fn
-    :param logfile: log ignored keys to this file
-    :type logfile: file-like object or string 'stdout' or string 'stderr'
-
-    :returns: fn(**<something>)
-
-    """
-    argspec = inspect.getargspec(fn)
-    argnames = argspec[0]
-    if argspec[2] == None: #if there is no room for a **args type-thing in fn...
-        kwargs = {}
-        for k,v in dct.items():
-            if k in argnames:
-                kwargs[k] = v
-            else:
-                if not logfile:
-                    pass
-                elif logfile == 'stderr':
-                    print >> sys.stderr, "WARNING: DictProxyState.call_substate ignoring key-value pair:", k, v
-                elif logfile == 'stdout':
-                    print >> sys.stdout, "WARNING: DictProxyState.call_substate ignoring key-value pair:", k, v
-                else:
-                    print >> logfile, "WARNING: DictProxyState.call_substate ignoring key-value pair:", k, v
-        return fn(**kwargs)
-    else:
-        #there is a **args type thing in fn. Here we pass everything.
-        return fn(**dct)
-
-#MAKE YOUR OWN DBDICT-COMPATIBLE EXPERIMENTS IN THIS MODEL
-def sample_experiment(state, channel):
-
-    #read from the state to obtain parameters, configuration, etc.
-    print >> sys.stdout, state.items()
-
-    import time
-    for i in xrange(100):
-        time.sleep(1)
-        # use the channel to know if the job should stop ASAP
-        if channel() == 'stop':
-            break
-
-    # modify state to record results
-    state['answer'] = 42
-
-    #return either INCOMPLETE or COMPLETE to indicate that the job should be re-run or not.
-    return COMPLETE
-

--- a/pylearn/dbdict/newstuff.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,1013 +0,0 @@
-
-from __future__ import with_statement
-
-from collections import defaultdict
-import re, sys, inspect, os, signal, tempfile, shutil, socket
-import traceback
-
-import sql
-
-
-################################################################################
-### misc
-################################################################################
-
-class DD(dict):
-    def __getattr__(self, attr):
-        return self[attr]
-    def __setattr__(self, attr, value):
-        self[attr] = value
-    def __str__(self):
-        return 'DD%s' % dict(self)
-    def __repr__(self):
-        return str(self)
-
-################################################################################
-### resolve
-################################################################################
-
-def resolve(name, try_import=True):
-    """
-    Resolve a string of the form X.Y...Z to a python object by repeatedly using getattr, and
-    __import__ to introspect objects (in this case X, then Y, etc. until finally Z is loaded).
-
-    """
-    symbols = name.split('.')
-    builder = __import__(symbols[0])
-    try:
-        for sym in symbols[1:]:
-            try:
-                builder = getattr(builder, sym)
-            except AttributeError, e:
-                if try_import:
-                    __import__(builder.__name__, fromlist=[sym])
-                    builder = getattr(builder, sym)
-                else:
-                    raise e
-    except (AttributeError, ImportError), e:
-        raise type(e)('Failed to resolve compound symbol %s' % name, e)
-    return builder
-
-################################################################################
-### dictionary
-################################################################################
-
-def convert(obj):
-    try:
-        return eval(obj, {}, {})
-    except (NameError, SyntaxError):
-        return obj
-
-def flatten(obj):
-    """nested dictionary -> flat dictionary with '.' notation """
-    d = {}
-    def helper(d, prefix, obj):
-        if isinstance(obj, (str, int, float, list, tuple)):
-            d[prefix] = obj #convert(obj)
-        else:
-            if isinstance(obj, dict):
-                subd = obj
-            else:
-                subd = obj.state()
-                subd['__builder__'] = '%s.%s' % (obj.__module__, obj.__class__.__name__)
-            for k, v in subd.iteritems():
-                pfx = '.'.join([prefix, k]) if prefix else k
-                helper(d, pfx, v)
-    helper(d, '', obj)
-    return d
-
-def expand(d):
-    """inverse of flatten()"""
-    #def dd():
-        #return DD(dd)
-    struct = DD()
-    for k, v in d.iteritems():
-        if k == '':
-            raise NotImplementedError()
-        else:
-            keys = k.split('.')
-        current = struct
-        for k2 in keys[:-1]:
-            current = current.setdefault(k2, DD())
-        current[keys[-1]] = v #convert(v)
-    return struct
-
-def realize(d):
-    if not isinstance(d, dict):
-        return d
-    d = dict((k, realize(v)) for k, v in d.iteritems())
-    if '__builder__' in d:
-        builder = resolve(d.pop('__builder__'))
-        return builder(**d)
-    return d
-
-def make(d):
-    return realize(expand(d))
-
-################################################################################
-### errors
-################################################################################
-
-class UsageError(Exception):
-    pass
-
-################################################################################
-### parsing and formatting
-################################################################################
-
-def parse(*strings):
-    d = {}
-    for string in strings:
-        s1 = re.split(' *= *', string, 1)
-        s2 = re.split(' *:: *', string, 1)
-        if len(s1) == 1 and len(s2) == 1:
-            raise UsageError('Expected a keyword argument in place of "%s"' % s1[0])
-        elif len(s1) == 2:
-            k, v = s1
-            v = convert(v)
-        elif len(s2) == 2:
-            k, v = s2
-            k += '.__builder__'
-        d[k] = v
-    return d
-
-def format_d(d, sep = '\n', space = True):
-    d = flatten(d)
-    pattern = "%s = %r" if space else "%s=%r"
-    return sep.join(pattern % (k, v) for k, v in d.iteritems())
-
-def format_help(topic):
-    if topic is None:
-        return 'No help.'
-    elif isinstance(topic, str):
-        help = topic
-    elif hasattr(topic, 'help'):
-        help = topic.help()
-    else:
-        help = topic.__doc__
-    if not help:
-        return 'No help.'
-
-    ss = map(str.rstrip, help.split('\n'))
-    try:
-        baseline = min([len(line) - len(line.lstrip()) for line in ss if line])
-    except:
-        return 'No help.'
-    s = '\n'.join([line[baseline:] for line in ss])
-    s = re.sub(string = s, pattern = '\n{2,}', repl = '\n\n')
-    s = re.sub(string = s, pattern = '(^\n*)|(\n*$)', repl = '')
-
-    return s
-
-################################################################################
-### single channels
-################################################################################
-
-# try:
-#     import greenlet
-# except:
-#     try:
-#         from py import greenlet
-#     except:
-#         print >>sys.stderr, 'the greenlet module is unavailable'
-#         greenlet = None
-
-
-class Channel(object):
-
-    COMPLETE = property(lambda s:None,
-            doc=("Experiments should return this value to "
-                "indicate that they are done (if not done, return `Incomplete`"))
-    INCOMPLETE = property(lambda s:True,
-            doc=("Experiments should return this value to indicate that "
-            "they are not done (if done return `COMPLETE`)"))
-    
-    START = property(lambda s: 0,
-            doc="dbdict.status == START means a experiment is ready to run")
-    RUNNING = property(lambda s: 1,
-            doc="dbdict.status == RUNNING means a experiment is running on dbdict_hostname")
-    DONE = property(lambda s: 2,
-            doc="dbdict.status == DONE means a experiment has completed (not necessarily successfully)")
-
-    # Methods to be used by the experiment to communicate with the channel
-
-    def save(self):
-        """
-        Save the experiment's state to the various media supported by
-        the Channel.
-        """
-        raise NotImplementedError()
-
-    def switch(self, message = None):
-        """
-        Called from the experiment to give the control back to the channel.
-        The following return values are meaningful:
-          * 'stop' -> the experiment must stop as soon as possible. It may save what
-            it needs to save. This occurs when SIGTERM or SIGINT are sent (or in
-            user-defined circumstances).
-        switch() may give the control to the user. In this case, the user may
-        resume the experiment by calling switch() again. If an argument is given
-        by the user, it will be relayed to the experiment.
-        """
-        pass
-
-    def __call__(self, message = None):
-        return self.switch(message)
-
-    def save_and_switch(self):
-        self.save()
-        self.switch()
-
-    # Methods to run the experiment
-
-    def setup(self):
-        pass
-
-    def __enter__(self):
-        pass
-
-    def __exit__(self):
-        pass
-
-    def run(self):
-        pass
-
-
-
-class JobError(Exception):
-    RUNNING = 0
-    DONE = 1
-    NOJOB = 2
-
-
-class SingleChannel(Channel):
-
-    def __init__(self, experiment, state):
-        self.experiment = experiment
-        self.state = state
-        self.feedback = None
-
-        #TODO: make this a property and disallow changing it during a with block
-        self.catch_sigterm = True
-        self.catch_sigint = True
-
-    def switch(self, message = None):
-        feedback = self.feedback
-        self.feedback = None
-        return feedback
-
-    def run(self, force = False):
-        self.setup()
-
-        status = self.state.dbdict.get('status', self.START)
-        if status is self.DONE and not force:
-            # If you want to disregard this, use the --force flag (not yet implemented)
-            raise JobError(JobError.RUNNING,
-                           'The job has already completed.')
-        elif status is self.RUNNING and not force:
-            raise JobError(JobError.DONE,
-                           'The job is already running.')
-        self.state.dbdict.status = self.RUNNING
-
-        v = self.COMPLETE
-        with self: #calls __enter__ and then __exit__
-            try:
-                v = self.experiment(self.state, self)
-            finally:
-                self.state.dbdict.status = self.DONE if v is self.COMPLETE else self.START
-
-        return v
-
-    def on_sigterm(self, signo, frame):
-        # SIGTERM handler. It is the experiment function's responsibility to
-        # call switch() often enough to get this feedback.
-        self.feedback = 'stop'
-
-    def __enter__(self):
-        # install a SIGTERM handler that asks the experiment function to return
-        # the next time it will call switch()
-        if self.catch_sigterm:
-            self.prev_sigterm = signal.getsignal(signal.SIGTERM)
-            signal.signal(signal.SIGTERM, self.on_sigterm)
-        if self.catch_sigint:
-            self.prev_sigint = signal.getsignal(signal.SIGINT)
-            signal.signal(signal.SIGINT, self.on_sigterm)
-        return self
-
-    def __exit__(self, type, value, tb_traceback, save = True):
-        if type:
-            try:
-                raise type, value, tb_traceback
-            except:
-                traceback.print_exc()
-        if self.catch_sigterm:
-            signal.signal(signal.SIGTERM, self.prev_sigterm)
-            self.prev_sigterm = None
-        if self.catch_sigint:
-            signal.signal(signal.SIGINT, self.prev_sigint)
-            self.prev_sigint = None
-        if save:
-            self.save()
-        return True
-
-
-class StandardChannel(SingleChannel):
-
-    def __init__(self, path, experiment, state, redirect_stdout = False, redirect_stderr = False):
-        super(StandardChannel, self).__init__(experiment, state)
-        self.path = os.path.realpath(path)
-        self.redirect_stdout = redirect_stdout
-        self.redirect_stderr = redirect_stderr
-
-    def save(self):
-        with open(os.path.join(self.path, 'current.conf'), 'w') as current:
-            current.write(format_d(self.state))
-            current.write('\n')
-
-    def __enter__(self):
-        self.old_cwd = os.getcwd()
-        os.chdir(self.path)
-        if self.redirect_stdout:
-            self.old_stdout = sys.stdout
-            sys.stdout = open('stdout', 'a')
-        if self.redirect_stderr:
-            self.old_stderr = sys.stderr
-            sys.stderr = open('stderr', 'a')
-        return super(StandardChannel, self).__enter__()
-
-    def __exit__(self, type, value, traceback):
-        rval = super(StandardChannel, self).__exit__(type, value, traceback, save = False)
-        if self.redirect_stdout:
-            sys.stdout.close()
-            sys.stdout = self.old_stdout
-        if self.redirect_stderr:
-            sys.stderr.close()
-            sys.stderr = self.old_stderr
-        os.chdir(self.old_cwd)
-        self.save()
-        return rval
-
-    def setup(self):
-        if not os.path.isdir(self.path):
-            os.makedirs(self.path)
-        with self:
-            origf = os.path.join(self.path, 'orig.conf')
-            if not os.path.isfile(origf):
-                with open(origf, 'w') as orig:
-                    orig.write(format_d(self.state))
-                    orig.write('\n')
-            currentf = os.path.join(self.path, 'current.conf')
-            if os.path.isfile(currentf):
-                with open(currentf, 'r') as current:
-                    self.state = expand(parse(*map(str.strip, current.readlines())))
-
-
-class RSyncException(Exception):
-    pass
-
-class RSyncChannel(StandardChannel):
-
-    def __init__(self, path, remote_path, experiment, state, redirect_stdout = False, redirect_stderr = False):
-        super(RSyncChannel, self).__init__(path, experiment, state, redirect_stdout, redirect_stderr)
-
-        ssh_prefix='ssh://'
-        if remote_path.startswith(ssh_prefix):
-            remote_path = remote_path[len(ssh_prefix):]
-            colon_pos = remote_path.find(':')
-            self.host = remote_path[:colon_pos]
-            self.remote_path = remote_path[colon_pos+1:]
-        else:
-            self.host = ''
-            self.remote_path = os.path.realpath(remote_path)
-
-    def rsync(self, direction):
-        """The directory at which experiment-related files are stored.
-        """
-
-        path = self.path
-
-        remote_path = self.remote_path
-        if self.host:
-            remote_path = ':'.join([self.host, remote_path])
-
-        # TODO: use something more portable than os.system
-        if direction == 'push':
-            rsync_cmd = 'rsync -ac "%s/" "%s/"' % (path, remote_path)
-        elif direction == 'pull':
-            rsync_cmd = 'rsync -ac "%s/" "%s/"' % (remote_path, path)
-        else:
-            raise RSyncException('invalid direction', direction)
-
-        rsync_rval = os.system(rsync_cmd)
-        if rsync_rval != 0:
-            raise RSyncException('rsync failure', (rsync_rval, rsync_cmd))
-
-    def touch(self):
-        if self.host:
-            host = self.host
-            touch_cmd = ('ssh %(host)s  "mkdir -p \'%(path)s\'"' % dict(host = self.host,
-                                                                        path = self.remote_path))
-        else:
-            touch_cmd = ("mkdir -p '%(path)s'" % dict(path = self.remote_path))
-        # print "ECHO", touch_cmd
-        touch_rval = os.system(touch_cmd)
-        if 0 != touch_rval:
-            raise Exception('touch failure', (touch_rval, touch_cmd))
-
-    def pull(self):
-        return self.rsync('pull')
-
-    def push(self):
-        return self.rsync('push')
-
-    def save(self):
-        super(RSyncChannel, self).save()
-        self.push()
-
-    def setup(self):
-        self.touch()
-        self.pull()
-        super(RSyncChannel, self).setup()
-
-
-class DBRSyncChannel(RSyncChannel):
-
-    RESTART_PRIORITY = 2.0
-
-    def __init__(self, username, password, hostname, dbname, tablename, path, remote_root, redirect_stdout = False, redirect_stderr = False):
-        self.username, self.password, self.hostname, self.dbname, self.tablename \
-            = username, password, hostname, dbname, tablename
-
-        self.db = sql.postgres_serial(
-            user = self.username, 
-            password = self.password, 
-            host = self.hostname,
-            database = self.dbname,
-            table_prefix = self.tablename)
-
-        self.dbstate = sql.book_dct_postgres_serial(self.db)
-        if self.dbstate is None:
-            raise JobError(JobError.NOJOB,
-                           'No job was found to run.')
-
-        try:
-            state = expand(self.dbstate)
-            experiment = resolve(state.dbdict.experiment)
-            remote_path = os.path.join(remote_root, self.dbname, self.tablename, str(self.dbstate.id))
-            super(DBRSyncChannel, self).__init__(path, remote_path, experiment, state, redirect_stdout, redirect_stderr)
-        except:
-            self.dbstate['dbdict.status'] = self.DONE
-            raise
-
-    def save(self):
-        super(DBRSyncChannel, self).save()
-        self.dbstate.update(flatten(self.state))
-    
-    def setup(self):
-        # Extract a single experiment from the table that is not already running.
-        # set self.experiment and self.state
-        super(DBRSyncChannel, self).setup()
-        self.state.dbdict.sql.host_name = socket.gethostname()
-        self.state.dbdict.sql.host_workdir = self.path
-        self.dbstate.update(flatten(self.state))
-
-    def run(self):
-        # We pass the force flag as True because the status flag is
-        # already set to RUNNING by book_dct in __init__
-        v = super(DBRSyncChannel, self).run(force = True)
-        if v is self.INCOMPLETE and self.state.dbdict.sql.priority != self.RESTART_PRIORITY:
-            self.state.dbdict.sql.priority = self.RESTART_PRIORITY
-            self.save()
-        return v
-
-
-
-################################################################################
-### running
-################################################################################
-
-import optparse
-OptionParser = optparse.OptionParser
-# class OptionParser(optparse.OptionParser):
-#     def error(self, message):
-#         pass
-
-def parse_and_run(command, arguments):
-    parser, runner = runner_registry.get(command, (None, None))
-    if not runner:
-        raise UsageError('Unknown runner: "%s"' % command)
-    if parser:
-        options, arguments = parser.parse_args(arguments)
-    else:
-        options = optparse.Values()
-    run(runner, [options] + arguments)
-
-def run(runner, arguments):
-    argspec = inspect.getargspec(runner)
-    minargs = len(argspec[0])-(len(argspec[3]) if argspec[3] else 0)
-    maxargs = len(argspec[0])
-    if minargs > len(arguments) or maxargs < len(arguments) and not argspec[1]:
-        s = format_help(runner)
-        raise UsageError(s)
-    runner(*arguments)
-
-runner_registry = dict()
-
-
-parser_cmdline = OptionParser(usage = '%prog cmdline [options] <experiment> <parameters>')
-parser_cmdline.add_option('-f', '--force', action = 'store_true', dest = 'force', default = False,
-                          help = 'force running the experiment even if it is already running or completed')
-parser_cmdline.add_option('--redirect-stdout', action = 'store_true', dest = 'redirect_stdout', default = False,
-                          help = 'redirect stdout to the workdir/stdout file')
-parser_cmdline.add_option('--redirect-stderr', action = 'store_true', dest = 'redirect_stderr', default = False,
-                          help = 'redirect stderr to the workdir/stdout file')
-parser_cmdline.add_option('-r', '--redirect', action = 'store_true', dest = 'redirect', default = False,
-                          help = 'redirect stdout and stderr to the workdir/stdout and workdir/stderr files')
-parser_cmdline.add_option('-w', '--workdir', action = 'store', dest = 'workdir', default = None,
-                          help = 'the working directory in which to run the experiment')
-parser_cmdline.add_option('-n', '--dry-run', action = 'store_true', dest = 'dry_run', default = False,
-                          help = 'use this option to run the whole experiment in a temporary working directory (cleaned after use)')
-parser_cmdline.add_option('-2', '--sigint', action = 'store_true', dest = 'allow_sigint', default = False,
-        help = 'allow sigint (CTRL-C) to interrupt a process')
-
-def runner_cmdline(options, experiment, *strings):
-    """
-    Start an experiment with parameters given on the command line.
-
-    Usage: cmdline [options] <experiment> <parameters>
-
-    Run an experiment with parameters provided on the command
-    line. See the help topics for experiment and parameters for
-    syntax information.
-
-    Example use:
-        dbdict-run cmdline mymodule.my_experiment \\
-            stopper::pylearn.stopper.nsteps \\ # use pylearn.stopper.nsteps
-            stopper.n=10000 \\ # the argument "n" of nsteps is 10000
-            lr=0.03
-    """
-    state = expand(parse(*strings))
-    state.setdefault('dbdict', DD()).experiment = experiment
-    experiment = resolve(experiment)
-    if options.workdir and options.dry_run:
-        raise UsageError('Please use only one of: --workdir, --dry-run.')
-    if options.workdir:
-        workdir = options.workdir
-    elif options.dry_run:
-        workdir = tempfile.mkdtemp()
-    else:
-        workdir = format_d(state, sep=',', space = False)
-    channel = StandardChannel(workdir,
-                              experiment, state,
-                              redirect_stdout = options.redirect or options.redirect_stdout,
-                              redirect_stderr = options.redirect or options.redirect_stderr)
-    channel.catch_sigint = not options.allow_sigint
-    channel.run(force = options.force)
-    if options.dry_run:
-        shutil.rmtree(workdir, ignore_errors=True)
-        
-runner_registry['cmdline'] = (parser_cmdline, runner_cmdline)
-
-
-
-
-parser_filemerge = OptionParser(usage = '%prog filemerge [options] <experiment> <file> <file2> ...')
-parser_filemerge.add_option('-f', '--force', action = 'store_true', dest = 'force', default = False,
-                          help = 'force running the experiment even if it is already running or completed')
-parser_filemerge.add_option('--redirect-stdout', action = 'store_true', dest = 'redirect_stdout', default = False,
-                          help = 'redirect stdout to the workdir/stdout file')
-parser_filemerge.add_option('--redirect-stderr', action = 'store_true', dest = 'redirect_stderr', default = False,
-                          help = 'redirect stderr to the workdir/stdout file')
-parser_filemerge.add_option('-r', '--redirect', action = 'store_true', dest = 'redirect', default = False,
-                          help = 'redirect stdout and stderr to the workdir/stdout and workdir/stderr files')
-parser_filemerge.add_option('-w', '--workdir', action = 'store', dest = 'workdir', default = None,
-                          help = 'the working directory in which to run the experiment')
-parser_filemerge.add_option('-n', '--dry-run', action = 'store_true', dest = 'dry_run', default = False,
-                          help = 'use this option to run the whole experiment in a temporary working directory (cleaned after use)')
-
-def runner_filemerge(options, experiment, mainfile, *other_files):
-    """
-    Start an experiment with parameters given in files.
-
-    Usage: filemerge [options] <experiment> <file> <file2> ...
-
-    Run an experiment with parameters provided in plain text files.
-    A single experiment will be run with the union of all the
-    parameters listed in the files.
-
-    Example:
-    <in file blah1.txt>
-    text.first = "hello"
-    text.second = "world"
-
-    <in file blah2.txt>
-    number = 12
-    numbers.a = 55
-    numbers.b = 56
-
-    Given these files, the following command using filemerge:
-    $ dbdict-run filemerge mymodule.my_experiment blah1.txt blah2.txt
-
-    is equivalent to this one using cmdline:
-    $ dbdict-run cmdline mymodule.my_experiment \\
-        text.first=hello text.second=world \\
-        number=12 numbers.a=55 numbers.b=56
-    """
-    with open(mainfile) as f:
-        _state = parse(*map(str.strip, f.readlines()))
-    for file in other_files:
-        if '=' in file:
-            _state.update(parse(file))
-        else:
-            with open(file) as f:
-                _state.update(parse(*map(str.strip, f.readlines())))
-    state = expand(_state)
-    state.setdefault('dbdict', DD()).experiment = experiment
-    experiment = resolve(experiment)
-    if options.workdir and options.dry_run:
-        raise UsageError('Please use only one of: --workdir, --dry-run.')
-    if options.workdir:
-        workdir = options.workdir
-    elif options.dry_run:
-        workdir = tempfile.mkdtemp()
-    else:
-        workdir = format_d(state, sep=',', space = False)
-    channel = StandardChannel(workdir,
-                              experiment, state,
-                              redirect_stdout = options.redirect or options.redirect_stdout,
-                              redirect_stderr = options.redirect or options.redirect_stderr)
-    channel.run(force = options.force)
-    if options.dry_run:
-        shutil.rmtree(workdir, ignore_errors=True)
-        
-runner_registry['filemerge'] = (parser_filemerge, runner_filemerge)
-
-
-
-
-parser_sqlschedule = OptionParser(usage = '%prog sqlschedule [options] <tablepath> <experiment> <parameters>')
-parser_sqlschedule.add_option('-f', '--force', action = 'store_true', dest = 'force', default = False,
-                              help = 'force adding the experiment to the database even if it is already there')
-
-def runner_sqlschedule(options, dbdescr, experiment, *strings):
-    """
-    Schedule a job to run using the sql command.
-
-    Usage: sqlschedule <tablepath> <experiment> <parameters>
-
-    See the experiment and parameters topics for more information about
-    these parameters.
-
-    Assuming that a postgres database is running on `host`, contains a
-    database called `dbname` and that `user` has the permissions to
-    create, read and modify tables on that database, tablepath should
-    be of the following form:
-        postgres://user:pass@host/dbname/tablename
-
-    If no table is named `tablename`, one will be created
-    automatically. The state corresponding to the experiment and
-    parameters specified in the command will be saved in the database,
-    but no experiment will be run.
-
-    To run an experiment scheduled using sqlschedule, see the sql
-    command.
-
-    Example use:
-        dbdict-run sqlschedule postgres://user:pass@host/dbname/tablename \\
-            mymodule.my_experiment \\
-            stopper::pylearn.stopper.nsteps \\ # use pylearn.stopper.nsteps
-            stopper.n=10000 \\ # the argument "n" of nsteps is 10000
-            lr=0.03
-    """
-
-    try:
-        username, password, hostname, dbname, tablename \
-            = sql.parse_dbstring(dbdescr)
-    except:
-        raise UsageError('Wrong syntax for dbdescr')
-
-    db = sql.postgres_serial(
-        user = username, 
-        password = password, 
-        host = hostname,
-        database = dbname,
-        table_prefix = tablename)
-
-    state = parse(*strings)
-    resolve(experiment) # we try to load the function associated to the experiment
-    state['dbdict.experiment'] = experiment
-    sql.add_experiments_to_db([state], db, verbose = 1, add_dups = options.force)
-
-runner_registry['sqlschedule'] = (parser_sqlschedule, runner_sqlschedule)
-
-
-
-parser_sqlschedule_filemerge = OptionParser(usage = '%prog sqlschedule_filemerge [options] <tablepath> <experiment> <parameters|files>')
-parser_sqlschedule_filemerge.add_option('-f', '--force', action = 'store_true', dest = 'force', default = False,
-                                        help = 'force adding the experiment to the database even if it is already there')
-
-def runner_sqlschedule_filemerge(options, dbdescr, experiment, mainfile, *other_files):
-    """
-    Schedule a job to run using the sql command using parameter files.
-
-    This command is to sqlschedule what the filemerge command is to
-    cmdline.
-    """
-
-    try:
-        username, password, hostname, dbname, tablename \
-            = sql.parse_dbstring(dbdescr)
-    except:
-        raise UsageError('Wrong syntax for dbdescr')
-
-    db = sql.postgres_serial(
-        user = username, 
-        password = password, 
-        host = hostname,
-        database = dbname,
-        table_prefix = tablename)
-
-    with open(mainfile) as f:
-        _state = parse(*map(str.strip, f.readlines()))
-    for file in other_files:
-        if '=' in file:
-            _state.update(parse(file))
-        else:
-            with open(file) as f:
-                _state.update(parse(*map(str.strip, f.readlines())))
-    state = _state
-
-    resolve(experiment) # we try to load the function associated to the experiment
-    state['dbdict.experiment'] = experiment
-    sql.add_experiments_to_db([state], db, verbose = 1, add_dups = options.force)
-
-runner_registry['sqlschedule_filemerge'] = (parser_sqlschedule_filemerge, runner_sqlschedule_filemerge)
-
-
-
-
-parser_sql = OptionParser(usage = '%prog sql [options] <tablepath> <exproot>')
-parser_sql.add_option('-n', dest = 'n', type = 'int', default = 1,
-                      help = 'Run N experiments sequentially (default 1) '
-                      '(if N is <= 0, runs as many experiments as possible).')
-
-def runner_sql(options, dbdescr, exproot):
-    """
-    Run jobs from a sql table.
-
-    Usage: sql <tablepath> <exproot>
-
-    The jobs should be scheduled first with the sqlschedule command.
-
-    Assuming that a postgres database is running on `host`, contains a
-    database called `dbname` and that `user` has the permissions to
-    create, read and modify tables on that database, tablepath should
-    be of the following form:
-        postgres://user:pass@host/dbname/tablename
-
-    exproot can be a local path or a remote path. Examples of exproots:
-        /some/local/path
-        ssh://some_host:/some/remote/path # relative to the filesystem root
-        ssh://some_host:other/remote/path # relative to the HOME on some_host
-
-    The exproot will contain a subdirectory hierarchy corresponding to
-    the dbname, tablename and job id which is a unique integer.
-
-    The sql runner will pick any job in the table which is not running
-    and is not done and will terminate when that job ends. You may call
-    the same command multiple times, sequentially or in parallel, to
-    run as many unfinished jobs as have been scheduled in that table
-    with sqlschedule.
-
-    Example use:
-        dbdict-run sql \\
-            postgres://user:pass@host/dbname/tablename \\
-            ssh://central_host:myexperiments
-    """
-    try:
-        username, password, hostname, dbname, tablename \
-            = sql.parse_dbstring(dbdescr)
-    except:
-        raise UsageError('Wrong syntax for dbdescr')
-
-    n = options.n if options.n else -1
-    nrun = 0
-    try:
-        while n != 0:
-            workdir = tempfile.mkdtemp()
-            #print 'wdir', workdir
-            channel = DBRSyncChannel(username, password, hostname, dbname, tablename,
-                                     workdir,
-                                     exproot,
-                                     redirect_stdout = True,
-                                     redirect_stderr = True)
-            channel.run()
-            shutil.rmtree(workdir, ignore_errors=True)
-            n -= 1
-            nrun += 1
-    except JobError, e:
-        if e.args[0] == JobError.NOJOB:
-            print 'No more jobs to run (run %i jobs)' % nrun
-
-runner_registry['sql'] = (parser_sql, runner_sql)
-
-    
-
-
-
-def runner_help(options, topic = None):
-    """
-    Get help for a topic.
-
-    Usage: help <topic>
-    """
-    def bold(x):
-        return '\033[1m%s\033[0m' % x
-    if topic is None:
-        print bold('Topics: (use help <topic> for more info)')
-        print 'example        Example of defining and running an experiment.'
-        print 'experiment     How to define an experiment.'
-        print 'parameters     How to list the parameters for an experiment.'
-        print
-        print bold('Available commands: (use help <command> for more info)')
-        for name, (parser, command) in sorted(runner_registry.iteritems()):
-            print name.ljust(20), format_help(command).split('\n')[0]
-        return
-    elif topic == 'experiment':
-        helptext = """
-
-        dbdict-run serves to run experiments. To define an experiment, you
-        only have to define a function respecting the following protocol in
-        a python file or module:
-
-        def my_experiment(state, channel):
-           # experiment code goes here
-
-        The return value of my_experiment may be channel.COMPLETE or
-        channel.INCOMPLETE. If the latter is returned, the experiment may
-        be resumed at a later point. Note that the return value `None`
-        is interpreted as channel.COMPLETE.
-
-        If a command defined by dbdict-run has an <experiment> parameter,
-        that parameter must be a string such that it could be used in a
-        python import statement to import the my_experiment function. For
-        example if you defined my_experiment in my_module.py, you can pass
-        'my_module.my_experiment' as the experiment parameter.
-
-        When entering my_experiment, the current working directory will be
-        set for you to a directory specially created for the experiment.
-        The location and name of that directory vary depending on which
-        dbdict-run command you run. You may create logs, save files, pictures,
-        results, etc. in it.
-
-        state is an object containing the parameters given to the experiment.
-        For example, if you run the followinc command:
-
-        dbdict-run cmdline my_module.my_experiment a.x=6
-
-        `state.a.x` will contain the integer 6, and so will `state['a']['x']`.
-        If the state is changed, it will be saved when the experiment ends
-        or when channel.save() is called. The next time the experiment is run
-        with the same working directory, the modified state will be provided.
-
-        It is not recommended to store large amounts of data in the state.  It
-        should be limited to scalar or string parameters. Results such as
-        weight matrices should be stored in files in the working directory.
-
-        channel is an object with the following important methods:
-
-         - channel.switch() (or channel()) will give the control back to the
-            user, if it is appropriate to do so. If a call to channel.switch()
-            returns the string 'stop', it typically means that the signal
-            SIGTERM (or SIGINT) was received. Therefore, the experiment may be
-            killed soon, so it should save and return True or
-            channel.INCOMPLETE so it can be resumed later. This should be
-            checked periodically or data loss may be incurred.
-
-         - channel.save() will save the current state. It is automatically
-            called when the function returns, but it is a good idea to do it
-            periodically.
-
-         - channel.save_and_switch() is an useful shortcut to do both operations
-            described above.
-        """
-
-    elif topic == 'parameters':
-        helptext = """
-        If a command takes <parameters> arguments, the arguments should each
-        take one of the following forms:
-
-        key=value
-
-          Set a parameter with name `key` to `value`. The value will be casted
-          to an appropriate type automatically and it will be accessible to
-          the experiment using `state.key`.
-
-          If `key` is a dotted name, the value will be set in nested
-          dictionaries corresponding to each part.
-
-          Examples:
-            a=1           state.a <- 1
-            b=2.3         state.b <- 2.3
-            c.d="hello"   state.c.d <- "hello"
-
-        key::builder
-
-          This is equivalent to key.__builder__=builder.
-
-          The builder should be a symbol that can be used with import or
-          __import__ and it should be callable.
-
-          If a key has a builder defined, the experiment code may easily make
-          an object out of it using the `make` function. `obj = make(state.key)`.
-          This will call the builder on the substate corresponding to state.key,
-          as will be made clear in the example:
-
-          Example:
-            regexp::re.compile
-            regexp.pattern='a.*c'
-
-          from pylearn.dbdict.newstuff import make
-          def experiment(state, channel):
-              regexp = make(state.regexp) # regexp is now re.compile(pattern = 'a.*c')
-              print regexp.sub('blahblah', 'hello abbbbc there')
-
-          If the above experiment was called with the state produced by the
-          parameters in the example, it would print 'hello blahblah there'.
-        """
-
-    elif topic == 'example':
-        helptext = """
-        Example of an experiment that trains some model for 100000 iterations:
-
-        # defined in: my_experiments.py
-        def experiment(state, channel):
-            try:
-                model = cPickle.load(open('model', 'r'))
-            except:
-                model = my_model(state.some_param, state.other_param)
-                state.n = 0
-            dataset = my_dataset(skipto = state.n)
-            for i in xrange(100000 - state.n):
-                model.update(dataset.next())
-                if i and i % 1000 == 0:
-                    if channel.save_and_switch() == 'stop':
-                        state.n += i + 1
-                        rval = channel.INCOMPLETE
-                        break
-            else:
-                state.result = model.cost(some_test_set)
-                rval = channel.COMPLETE
-            cPickle.dump(model, open('model', 'w'))
-            return rval
-
-        And then you could run it this way:
-        
-        dbdict-run cmdline my_experiments.experiment \\
-                           some_param=1 \\
-                           other_param=0.4
-
-        Or this way:
-
-        dbdict-run sqlschedule postgres://user:pass@host/dbname/tablename \\
-                           my_experiments.experiment \\
-                           some_param=1 \\
-                           other_param=0.4
-
-        dbdict-run sql postgres://user:pass@host/dbname/tablename exproot
-
-        You need to make sure that the module `my_experiments` is accessible
-        from python. You can check with the command
-
-        $ python -m my_experiments
-        """
-    else:
-        helptext = runner_registry.get(topic, None)[1]
-    print format_help(helptext)
-
-runner_registry['help'] = (None, runner_help)
-
-################################################################################
-### main
-################################################################################
-
-def run_cmdline():
-    try:
-        if len(sys.argv) <= 1:
-            raise UsageError('Usage: %s <run_type> [<arguments>*]' % sys.argv[0])
-        cmd = None
-        args = []
-        for arg in sys.argv[1:]:
-            if cmd is not None or arg.startswith('-'):
-                args.append(arg)
-            else:
-                cmd = arg
-        parse_and_run(cmd, args)
-    except UsageError, e:
-        print 'Usage error:'
-        print e
-
-if __name__ == '__main__':
-    run_cmdline()
-
-

--- a/pylearn/dbdict/sample_create_jobs.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,135 +0,0 @@
-import sys, subprocess
-
-from .dconfig import Config
-from .tools import Job # tools.py
-
-#
-# Models
-#
-
-class OldSampleJob(Job):
-    """ Sample Job object.  Cut and paste this for your own experiments.  """
-
-    # default parameters for the job
-    # config file parameters must be from this list.
-    a = 0
-    b = 0
-    c = 'a'
-    d = 0.0
-
-    def run(self, results, dry_run=False):
-        # attributes that you set in 'results' will be saved to job_results.py, next to
-        # job_config.py when this function returns.
-        results.f = self.a * self.b
-
-        # The current working directory (cwd) is writable and readable
-        # it will also be left alone after the job terminates
-        f = open('some_file', 'w')
-        print >> f, "hello from the job?"
-
-        return True #restart this job
-
-
-
-class SampleJobState():
-
-    # default parameters for the job
-    # config file parameters must be from this list.
-    a = 0
-    b = 0
-    c = 'a'
-    d = 0.0
-
-
-sample_job_table = Table('my_table_for_testing', metadata,
-        Column('a', Integer),
-        Column('b', Float(53)))
-
-metadata.create_all()
-
-mapper(SampleJobState, sample_job_table)
-
-s = SampleJobState()
-s.a = 5
-s.b = 8.2
-
-if Session().query(SampleJobState).filter_by(a=5, b=8.2).any():
-    break;
-else:
-    Session().save(s).commit()
-
-
-class SampleJob(Job):
-    """ Sample Job object.  Cut and paste this for your own experiments.  """
-
-    def __init__(self, state):
-        pass
-
-    def start(self):
-        pass
-
-    def resume(self):
-        pass
-
-    def run(self, switch = lambda : 'continue'):
-        # attributes that you set in 'results' will be saved to job_results.py, next to
-        # job_config.py when this function returns.
-        params.f = params.a * params.b
-
-        
-        # The current working directory (cwd) is writable and readable
-        # it will also be left alone after the job terminates
-        f = open('some_file', 'w')
-        print >> f, "hello from the job?"
-        while True:
-            time.sleep(5)
-            if switch() == 'stop':
-                break
-
-        return True #continue running if possible...
-
-    def stop(self): 
-        pass
-
-
-    def run(self, state, dry_run=False):
-
-def some_jobs(a = 0,
-        b = 2):
-    job_module = 'dbdict.sample_create_jobs'
-    job_symbol = 'SampleJob'
-    for c in ('a', 'b', 'c'):
-        for d in [0.0, 9.9]:
-            yield locals()
-
-def create(generator):
-    """Create a set of job directories"""
-    jobs = []
-    dispatch = sys.stdout #open('jobs','w')
-
-    for config in generator:
-        #print '   config', config
-        configdir = 'job_%016x'% abs(hash(config))
-        jobs.append(configdir)
-        create_dirs = True
-        dry_run = 0
-        if not dry_run:
-            if create_dirs and subprocess.call(('mkdir', configdir)):
-                print >> sys.stderr, 'Error creating directory: ', configdir
-            else:
-                #no problem creating the directory
-                config.save(configdir + '/job_config.py')
-                print >> dispatch, "dbdict-run-job run", configdir
-        else:
-            #print configdir
-            pass
-    dispatch.close()
-
-if __name__ == '__main__':
-    create(some_jobs())
-
-    j = SampleJob(SampleJobState())
-    j.start()
-    j.run()
-
-

--- a/pylearn/dbdict/scratch.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,451 +0,0 @@
-import threading, time, commands, os, sys, math, random, datetime
-
-import psycopg2, psycopg2.extensions
-from sqlalchemy import create_engine, desc
-from sqlalchemy.orm import sessionmaker
-from sqlalchemy import Table, Column, MetaData, ForeignKey    
-from sqlalchemy import Integer, String, Float, DateTime
-from sqlalchemy.orm import mapper, relation, backref, eagerload
-from sqlalchemy.sql import operators, select
-
-
-##########
-#
-# Connection stuff
-#
-#
-
-if 0:
-    _db_host = 'jais.iro.umontreal.ca'
-
-    def _pwd():
-        if not hasattr(_pwd,'rval'):
-            pw_cmd = 'ssh bergstrj@grieg.iro.umontreal.ca cat .lisa_db'
-            rval = commands.getoutput(pw_cmd)
-        return rval
-
-    def engine():
-        """Create an engine to access lisa_db on gershwin
-
-        This function caches the return value between calls.
-        """
-        if not hasattr(engine,'rval'):
-            pw = _pwd()
-            db_str ='postgres://bergstrj:%s@%s/lisa_db' % (pw,_db_host) 
-            echo = False #spews pseudo-sql to stdout
-            engine.rval = create_engine(db_str
-                    ,pool_size=1 # should force the app release extra connections
-                    # releasing connections should let us schedule more jobs, since each one operates 
-                    # autonomously most of the time, just checking the db rarely.
-                    # TODO: optimize this for large numbers of jobs
-                    ,echo=echo
-                    )
-        return engine.rval
-
-    def engine_serializable():
-        """Create an engine to access lisa_db on gershwin, which uses serializable
-        transaction mode.
-
-        This function caches the return value between calls.
-        """
-
-        this = engine_serializable
-
-        if not hasattr(this,'rval'):
-            pw = _pwd()
-            def connect():
-                c = psycopg2.connect(user='bergstrj',
-                        password=pw,
-                        database='lisa_db',
-                        host='gershwin.iro.umontreal.ca')
-                c.set_isolation_level(psycopg2.extensions.ISOLATION_LEVEL_SERIALIZABLE)
-                return c
-            pool_size=0
-            this.rval = create_engine('postgres://'
-                    ,creator=connect
-                    ,pool_size=0 # should force the app release connections
-                    )
-        return this.rval
-
-
-    Session = sessionmaker(bind=engine(), autoflush=True, transactional=True)
-    SessionSerial = sessionmaker(bind=engine_serializable(),
-            autoflush=True, transactional=True)
-
-else:
-    from sqlalchemy import create_engine
-    from sqlalchemy.orm import sessionmaker
-    engine = create_engine('sqlite:///:memory:', echo=False)
-    Session = sessionmaker(bind=engine, autoflush=True, transactional=True)
-    SessionSerial = Session
-
-
-################
-#
-# Database setup
-#
-table_prefix='bergstrj_scratch_test_'
-metadata = MetaData()
-
-def table_with_id(name, *args):
-    return Table(name, metadata,
-        Column('id', Integer, primary_key=True),
-        *args)
-
-t_trial = table_with_id(table_prefix+'trial',
-        Column('desc', String(256)), #comment: why running this trial?
-        Column('priority', Float(53)), #aka Double
-        Column('start', DateTime),
-        Column('finish', DateTime),
-        Column('host', String(256)))
-
-t_keyval = table_with_id(table_prefix+'keyval',
-        Column('name', String(32), nullable=False), #name of attribute
-        Column('fval', Float(53)), #aka Double
-        Column('ival', Integer),
-        Column('sval', String(256))) #TODO: store text (strings of unbounded length)
-
-t_trial_keyval = table_with_id(table_prefix+'trial_keyval',
-        Column('trial_id', Integer, ForeignKey('%s.id' % t_trial)),
-        Column('keyval_id', Integer, ForeignKey('%s.id' % t_keyval)))
-
-class _KeyVal(object):
-    @staticmethod
-    def cache(name, val, session, create=True):
-        #TODO: consider using a local cache to remove the need to query db
-        #      this takes advantage of common usage, which is to only add KeyVal
-        #      pairs.
-        #check if it is in the DB
-        q = session.query(_KeyVal)
-        if isinstance(val, float):
-            q = q.filter_by(name=name, fval=val)
-        elif isinstance(val, int):
-            q = q.filter_by(name=name, ival=val)
-        elif isinstance(val, str):
-            q = q.filter_by(name=name, sval=val)
-        else:
-            raise TypeError(val)
-        rval = q.first()
-        if rval is None and create:
-            rval = _KeyVal(name, val)
-        session.save_or_update(rval)
-        return rval
-
-    def __init__(self, name, val):
-        self.name = name
-        self.val = val
-    def __get_val(self):
-        val = None
-        if self.fval is not None: val = self.fval
-        if self.ival is not None: val = self.ival
-        if self.sval is not None: val = self.sval
-        return  val
-    def __set_val(self, val):
-        if isinstance(val, float):
-            self.fval = val
-            self.ival = None
-            self.sval = None
-        elif isinstance(val, int):
-            self.fval = None
-            self.ival = val
-            self.sval = None
-        elif isinstance(val, str):
-            self.fval = None
-            self.ival = None
-            self.sval = val
-        else:
-            raise TypeError(val)
-    val = property(__get_val, __set_val)
-    def __repr__(self):
-        return "<Param(%s,'%s', %s)>" % (self.id, self.name, repr(self.val))
-mapper(_KeyVal, t_keyval)
-
-
-###################
-#
-# Job interface
-#
-
-class Trial(object):
-    _native_cols = 'desc', 'priority', 'start', 'finish', 'host'
-
-    #TODO: remove these forbidden keynames, and let all keynames work properly
-    _forbidden_keynames = set(['filter', 'desc', 
-            'priority', 'start', 'finish', 'host',
-            'create', 'max_sleep', 'max_retry', 'session', 'c',
-            'abort', 'complete'])
-
-    #TODO: unittest cases to verify that having these kinds of keys is OK
-
-    class ReserveError(Exception): """reserve failed"""
-
-    @staticmethod
-    def filter(session=None, **kwargs):
-        """Construct a query for Trials.
-
-        @param kwargs: each (kw,arg) pair in kwargs, will restrict the list of
-        Trials to those such that the 'kw' attr has been associated with the job,
-        and it has value 'arg'
-
-        @return SqlAlchemy query object
-
-        @note: will raise TypeError if any arg in kwargs has a type other than
-        float, int or string.
-
-        """
-        if session is None: 
-            session = Session()
-        q = session.query(Trial)
-        for col in Trial._native_cols:
-            if col in kwargs:
-                q = q.filter_by(**{col:kwargs[col]})
-                del kwargs[col]
-        for kw, arg in kwargs.items():
-            if isinstance(arg, float):
-                q = q.filter(Trial._attrs.any(name=kw, fval=arg))
-            elif isinstance(arg, int):
-                q = q.filter(Trial._attrs.any(name=kw, ival=arg))
-            elif isinstance(arg, str):
-                q = q.filter(Trial._attrs.any(name=kw, sval=arg))
-            else:
-                raise TypeError(arg)
-        return q
-
-    @staticmethod
-    def reserve_unique(query_fn, max_retry=10, max_sleep=5.0):
-        """Reserve an un-reserved job.
-        
-        @param query_fn: build the query for the trial to reserve (see
-        L{reserve_unique_kw} for example usage).
-
-        @param max_retry: try this many times to reserve a job before raising an exception
-
-        @param max_sleep: L{time.sleep} up to this many seconds between retry attempts
-
-        @return a trial which was reserved (uniquely) by this function call.  If
-        no matching jobs remain, return None.
-        
-        """
-        s = SessionSerial()
-        retry = max_retry
-        trial = None
-
-        while (trial is None) and retry:
-
-            q = query_fn(s.query(Trial))
-            q = q.options(eagerload('_attrs')) #TODO is this a good idea?
-
-            trial = q.first()
-            if trial is None:
-                return None # no jobs match the query
-            else:
-                try:
-                    trial.reserve(session=s)
-                except Trial.ReserveError, e:
-                    s.rollback()
-                    waittime = random.random() * max_sleep
-                    if debug: print 'another process stole our trial. Waiting %f secs' % wait
-                    time.sleep(waittime)
-                    retry -= 1
-        if trial: 
-            s.expunge(trial)
-        s.close()
-        return trial
-
-    @staticmethod
-    def reserve_unique_kw(max_retry=10, max_sleep=5.0, **kwargs):
-        """Call reserve_unique with a query function that matches jobs with
-        attributes (and values) given by kwargs.  Results are sorted by
-        priority.
-
-        """
-        assert 'start' not in kwargs
-        assert 'query_fn' not in kwargs
-        def query_fn(q):
-            q = q.filter_by(start=None,
-                    **kwargs).order_by(desc(Trial.c.priority))
-            return q
-
-
-        return Trial.reserve_unique(query_fn, max_retry, max_sleep)
-
-    def __init__(self, desc=None, priority=None, start=None, finish=None, host=None, **kwargs):
-        self.desc = desc
-        self.priority = priority
-        self.start = start
-        self.finish = finish
-        self.host = host
-        self.attrs.update(kwargs)
-    def __repr__(self):
-        return "<Trial(%s, '%s', %s, '%s', %s, %s)>" \
-                %(str(self.id), self.desc, self.priority, self.host,
-                        self.start, self.finish)
-
-    def _get_attrs(self):
-        #This bit of code makes it so that you can type something like:
-        #
-        # trial.attrs.score = 50
-        # 
-        # It will use the self._attrs list of _KeyVal instances as a backend,
-        # because these pseudo-attributes (here 'score') are not stored in any
-        # object's __dict__.
-        class AttrCatcher(object):
-            #TODO: make these methods faster with better data structures
-            def __getattr__(attr_self, attr):
-                attrlist = self._attrs
-                for i,a in enumerate(attrlist):
-                    if a.name == attr:
-                        return a.val
-                raise AttributeError(attr)
-            def __setattr__(attr_self, attr, val):
-                n = 0
-                s = Session()
-                assert attr not in Trial._forbidden_keynames
-                for i,a in enumerate(self._attrs):
-                    if a.name == attr:
-                        attrlist[i] = _KeyVal.cache(attr,val, s)
-                        n += 1
-                assert n <= 1
-                if n == 0:
-                    self._attrs.append(_KeyVal.cache(attr,val, s))
-                s.commit()
-            def __iter__(_self):
-                def gen():
-                    return self._attrs.__iter__()
-                return gen()
-            def update(attr_self, dct):
-                for k,v in dct.items():
-                    setattr(attr_self, k, v)
-                            
-        #we can't add attributes to self, so just do this...
-        return AttrCatcher() #seriously, allocate a new one each time
-    attrs = property(_get_attrs, doc = ("Provide attribute-like access to the"
-        " key-value pairs associated with this trial"))
-    def reserve(self, session): #session should have serialized isolation mode
-        """Reserve the job for the current process, to the exclusion of all
-        other processes.  In other words, lock it."""
-
-        serial_self = session.query(Trial).get(self.id)
-        if serial_self.start is not None:
-            raise Trial.ReserveError(self.host)
-        serial_self.start = datetime.datetime.now()
-        serial_self.host = 'asdf' #TODO: get hostname
-        try:
-            session.commit()
-        except Exception, e:
-            # different db backends raise different exceptions when a
-            # commit fails, so here we just treat all problems the same 
-            #s.rollback() # doc says rollback or close after commit exception
-            session.close()
-            raise Trial.ReserveError(self.host)
-
-        #Session().refresh(self) #load changes to serial_self into self
-
-    def abort(self):
-        """Reset job to be available for reservation.
-
-        @return None
-
-        @note: Raises exception if job is finished
-        
-        """
-        if self.finish is not None:
-            raise Exception('wtf?')
-        self.start = None
-        self.host = None
-        s = Session()
-        s.save_or_update(self)
-        s.commit()
-
-    def complete(self, **kwargs):
-        """Mark job self as finished and update attrs with kwargs."""
-        self.attrs.update(kwargs)
-        self.finish = datetime.datetime.now()
-        s = Session()
-        s.save_or_update(self)
-        s.commit()
-
-mapper(Trial, t_trial,
-        properties = {
-            '_attrs': relation(_KeyVal, 
-                secondary=t_trial_keyval, 
-                cascade="delete-orphan")
-            })
-
-metadata.create_all(engine) # does nothing when tables already exist
-
-
-
-
-############
-#
-# Test Stuff
-#
-#
-
-if __name__ == '__main__':
-    s = Session()
-
-    def add_some_jobs():
-        dvalid, dtest = 'dvalid', 'dtest file'
-        desc = 'debugging'
-
-        def blah():
-            for lr in [0.001, 0.01]:
-                for scale in [0.0001 * math.sqrt(10.0)**i for i in range(4)]:
-                    for rng_seed in [4, 5, 6]:
-                        for priority in [None, 1, 2]:
-                            yield dict(locals())
-
-        for kwargs in blah():
-            t = Trial(desc=desc, dvalid=dvalid, dtest=dtest, **kwargs)
-            s.save(t)
-
-    def work(jobtype):
-        try:
-            jid = reserve(jobtype)
-        except StopIteration:
-            return
-
-        def blah(*args):
-            print 'blah: ', args
-        dct = get_next()
-
-    add_some_jobs()
-
-    if 0:
-        for t in s.query(Trial):
-            print 'saved:', t, [a.name for a in list(t.attrs)]
-
-    def yield_unique_jobs():
-        while True:
-            rval = Trial.reserve_unique_kw()
-            if rval is None:
-                break
-            else:
-                yield rval
-
-    if 0:
-        for job in yield_unique_jobs():
-            print 'yielded job', job
-            job.complete(score=random.random())
-
-    if 0:
-        for t in s.query(Trial):
-            print 'final:', t, [a.name for a in list(t.attrs)]
-
-    q = s.query(Trial)
-    #q = q.order_by(Trial.attrs)
-    q = q.filter(Trial._attrs.any(name='rng_seed', ival=5))
-    #q = q.filter(Trial._attrs.all(name='lr').order_by(_KeyVal.c.fval))
-
-    print dir(q)
-
-
-    print q
-    for t in q.all():
-        print 'final:', t, [a.name for a in list(t.attrs)]
-        t.homebrew = 6
-
-
-

--- a/pylearn/dbdict/sql.py	Wed Feb 04 15:56:00 2009 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,311 +0,0 @@
-
-import sys, os, copy, time
-
-import numpy.random
-
-import sqlalchemy
-import sqlalchemy.pool
-from sqlalchemy import create_engine, desc
-from sqlalchemy.orm import eagerload
-import psycopg2, psycopg2.extensions 
-
-from api0 import db_from_engine, postgres_db, DbHandle
-
-
-EXPERIMENT = 'dbdict.experiment'
-#using the dictionary to store these is too slow
-STATUS = 'dbdict.status'
-HASH = 'dbdict.hash'
-PRIORITY = 'dbdict.sql.priority'
-
-HOST = 'dbdict.sql.hostname'
-HOST_WORKDIR = 'dbdict.sql.host_workdir'
-PUSH_ERROR = 'dbdict.sql.push_error'
-
-START = 0
-RUNNING = 1
-DONE = 2
-FUCKED_UP = 666
-
-_TEST_CONCURRENCY = False
-
-def postgres_serial(user, password, host, database, poolclass=sqlalchemy.pool.NullPool, **kwargs):
-    """Return a DbHandle instance that communicates with a postgres database at transaction
-    isolation_level 'SERIALIZABLE'.
-
-    :param user: a username in the database
-    :param password: the password for the username
-    :param host: the network address of the host on which the postgres server is running
-    :param database: a database served by the postgres server
-    
-    """
-    this = postgres_serial
-
-    if not hasattr(this,'engine'):
-        def connect():
-            c = psycopg2.connect(user=user, password=password, database=database, host=host)
-            c.set_isolation_level(psycopg2.extensions.ISOLATION_LEVEL_SERIALIZABLE)
-            return c
-        this.engine = create_engine('postgres://'
-                ,creator=connect
-                ,poolclass=poolclass
-                )
-
-    db = db_from_engine(this.engine, **kwargs)
-    db._is_serialized_session_db = True
-    return db
-
-def book_dct_postgres_serial(db, retry_max_sleep=10.0, verbose=0):
-    """Find a trial in the lisa_db with status START.
-
-    A trial will be returned with status=RUNNING.
-
-    Returns None if no such trial exists in DB.
-
-    This function uses a serial access to the lisadb to guarantee that no other
-    process will retrieve the same dct.  It is designed to facilitate writing
-    a "consumer" for a Producer-Consumer pattern based on the database.
-
-    """
-    print >> sys.stderr, """#TODO: use the priority field, not the status."""
-    print >> sys.stderr, """#TODO: ignore entries with key PUSH_ERROR."""
-
-    s = db.session() #open a new session
-
-    # NB. we need the query and attribute update to be in the same transaction
-    assert s.autocommit == False 
-
-    dcts_seen = set([])
-    keep_trying = True
-
-    dct = None
-    while (dct is None) and keep_trying:
-        #build a query
-        q = s.query(db._Dict)
-
-        #N.B.
-        # use dedicated column to retrieve jobs, not the dictionary keyval pair
-        # This should be much faster.
-        q = q.filter(db._Dict.status==START)
-        q = q.order_by(db._Dict.priority.desc())
-
-        # this doesn't seem to work, hene the string hack below
-        q = q.options(eagerload('_attrs')) #hard-coded in api0
-
-        #try to reserve a dct
-        try:
-            #first() may raise psycopg2.ProgrammingError
-            dct = q.first()
-
-            if dct is not None:
-                assert (dct not in dcts_seen)
-                if verbose: print 'book_unstarted_dct retrieved, ', dct
-                dct._set_in_session(STATUS, RUNNING, s)
-                if 1:
-                    if _TEST_CONCURRENCY:
-                        print >> sys.stderr, 'SLEEPING BEFORE BOOKING'
-                        time.sleep(10)
-
-                    #commit() may raise psycopg2.ProgrammingError
-                    s.commit()
-                else:
-                    print >> sys.stderr, 'DEBUG MODE: NOT RESERVING JOB!', dct
-                #if we get this far, the job is ours!
-            else:
-                # no jobs are left
-                keep_trying = False
-        except (psycopg2.OperationalError,
-                sqlalchemy.exceptions.ProgrammingError,
-                sqlalchemy.exc.DBAPIError), e:
-            #either the first() or the commit() raised
-            s.rollback() # docs say to do this (or close) after commit raises exception
-            if verbose: print 'caught exception', e
-            if dct:
-                # first() succeeded, commit() failed
-                dcts_seen.add(dct)
-                dct = None
-            wait = numpy.random.rand(1)*retry_max_sleep
-            if verbose: print 'another process stole our dct. Waiting %f secs' % wait
-            time.sleep(wait)
-
-    if dct:
-        str(dct) # for loading of attrs in UGLY WAY!!!
-    s.close()
-    return dct
-
-def book_dct_non_postgres(db):
-    print >> sys.stderr, """#TODO: use the priority field, not the status."""
-    print >> sys.stderr, """#TODO: ignore entries with key self.push_error."""
-
-    raise NotImplementedError()
-
-
-###########
-# Connect
-###########
-
-def parse_dbstring(dbstring):
-    postgres = 'postgres://'
-    if not dbstring.startswith(postgres):
-        raise ValueError('For now, dbdict dbstrings must start with postgres://', dbstring)
-    dbstring = dbstring[len(postgres):]
-
-    #username_and_password
-    colon_pos = dbstring.find('@')
-    username_and_password = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    colon_pos = username_and_password.find(':')
-    if -1 == colon_pos:
-        username = username_and_password
-        password = None
-    else:
-        username = username_and_password[:colon_pos]
-        password = username_and_password[colon_pos+1:]
-    
-    #hostname
-    colon_pos = dbstring.find('/')
-    hostname = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    #dbname
-    colon_pos = dbstring.find('/')
-    dbname = dbstring[:colon_pos]
-    dbstring = dbstring[colon_pos+1:]
-
-    #tablename
-    tablename = dbstring
-
-    if password is None:
-        password = get_password(hostname, dbname)
-
-    if False:
-        print 'USERNAME', username
-        print 'PASS', password
-        print 'HOST', hostname
-        print 'DB', dbname
-        print 'TABLE', tablename
-
-    return username, password, hostname, dbname, tablename
-
-def get_password(hostname, dbname):
-    """Return the current user's password for a given database
-
-    :TODO: Replace this mechanism with a section in the pylearn configuration file
-    """
-    password_path = os.getenv('HOME')+'/.dbdict_%s'%dbname
-    try:
-        password = open(password_path).readline()[:-1] #cut the trailing newline
-    except:
-        raise ValueError( 'Failed to read password for db "%s" from %s' % (dbname, password_path))
-    return password
-
-def db(dbstring):
-    username, password, hostname, dbname, tablename = parse_dbstring(dbstring)
-    try:
-        return postgres_db(username, password, hostname, dbname, table_prefix=tablename)
-    except:
-        print 'Error connecting with password', password
-        raise
-
-
-###########
-# Queue
-###########
-
-def insert_dict(jobdict, db, force_dup=False, session=None, priority=1.0):
-    """Insert a new `job` dictionary into database `db`.
-
-    :param force_dup: forces insertion even if an identical dictionary is already in the db
-
-    """
-    # compute hash for the job, will be used to avoid duplicates
-    job = copy.copy(jobdict)
-    jobhash = hash(`job`)
-
-    if session is None:
-        s = db.session()
-    else:
-        s = session
-
-    do_insert = force_dup or (None is s.query(db._Dict).filter(db._Dict.hash==jobhash).filter(db._Dict.status!=FUCKED_UP).first())
-
-    rval = None
-    if do_insert:
-        if STATUS not in job:
-            job[STATUS] = START
-        if HASH not in job:
-            job[HASH] = jobhash
-        if PRIORITY not in job:
-            job[PRIORITY] = priority
-        rval = db.insert(job, session=s)
-        s.commit()
-
-    if session is None:
-        s.close()
-    return rval
-
-
-def insert_job(experiment_fn, state, db, force_dup=False, session=None, priority=1.0):
-    state = copy.copy(state)
-    experiment_name = experiment_fn.__module__ + '.' + experiment_fn.__name__
-    if EXPERIMENT in state:
-        if state[EXPERIMENT] != experiment_name:
-            raise Exception('Inconsistency: state element %s does not match experiment %s' %(EXPERIMENT, experiment_name))
-    else:
-        state[EXPERIMENT] = experiment_name
-    return insert_dict(state, db, force_dup=force_dup, session=session, priority=priority)
-
-
-# TODO: FIXME: WARNING
-# Should use insert_dict instead of db.insert.  Need one entry point for adding jobs to 
-# database, so that hashing can be done consistently
-def add_experiments_to_db(jobs, db, verbose=0, add_dups=False, type_check=None, session=None):
-    """Add experiments paramatrized by jobs[i] to database db.
-
-    Default behaviour is to ignore jobs which are already in the database.
-
-    If type_check is a class (instead of None) then it will be used as a type declaration for
-    all the elements in each job dictionary.  For each key,value pair in the dictionary, there
-    must exist an attribute,value pair in the class meeting the following criteria:
-    the attribute and the key are equal, and the types of the values are equal.
-
-    :param jobs: The parameters of experiments to run.
-    :type jobs: an iterable object over dictionaries
-    :param verbose: print which jobs are added and which are skipped
-    :param add_dups: False will ignore a job if it matches (on all items()) with a db entry.
-    :type add_dups: Bool
-
-    :returns: list of (Bool,job[i]) in which the flags mean the corresponding job actually was
-    inserted.
-
-    """
-    rval = []
-    for job in jobs:
-        job = copy.copy(job)
-        if session is None:
-            s = db.session()
-            do_insert = force_dup or (None is db.query(s).filter_eq_dct(job).first())
-            s.close()
-        else:
-            do_insert = force_dup or (None is db.query(session).filter_eq_dct(job).first())
-
-        if do_insert:
-            if type_check:
-                for k,v in job.items():
-                    if type(v) != getattr(type_check, k):
-                        raise TypeError('Experiment contains value with wrong type',
-                                ((k,v), getattr(type_check, k)))
-
-            job[STATUS] = START
-            job[PRIORITY] = 1.0
-            if verbose:
-                print 'ADDING  ', job
-            db.insert(job)
-            rval.append((True, job))
-        else:
-            if verbose:
-                print 'SKIPPING', job
-            rval.append((False, job))
-
-