MetaCSV 0.0.10

Tools for documentation-aware data reading, writing, and analysis

=======
MetaCSV
=======


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``metacsv`` - Tools for documentation-aware data reading, writing, and analysis

See the full documentation at ReadTheDocs_

.. _ReadTheDocs: http://metacsv.rtfd.org

Overview
=========

**MetaCSV** provides tools to read in CSV data with a yaml-compliant header
directly into a ``pandas`` ``Series``, ``DataFrame``, or ``Panel`` or an
``xarray`` ``DataArray`` or ``Dataset``.

Data specification
----------------------------

Data can be specified using a yaml-formatted header, with the YAML *start-mark*
string (``---``) above and the YAML *end-mark* string (``...``) below the yaml
block. Only one yaml block is allowed. If the doc-separation string is not the
first (non-whitespace) line in the file, all of the file's contents will be
interpreted by the csv reader. The yaml data can have arbitrary complexity.

.. code-block:: python

>>> import metacsv, numpy as np,
>>> import StringIO as io # import io for python 3
>>> doc = io.StringIO('''
---
author: A Person
date: 2000-01-01
variables:
pop:
name: Population
unit: millions
gdp:
name: Product
unit: 2005 $Bn
...
region,year,pop,gdp
USA,2010,309.3,13599.3
USA,2011,311.7,13817.0
CAN,2010,34.0,1240.0
CAN,2011,34.3,1276.7
''')



Using MetaCSV-formatted files in python
--------------------------------------------


Read MetaCSV-formatted data into python using pandas-like syntax:

.. code-block:: python

>>> df = metacsv.read_csv(doc, index_col=[0,1])
>>> df
<metacsv.core.containers.DataFrame (4, 2)>
pop gdp
region year
USA 2010 309.3 13599.3
2011 311.7 13817.0
CAN 2010 34.0 1240.0
2011 34.3 1276.7

Variables
gdp: OrderedDict([('name', 'Product'), ('unit', '2005 $Bn')])
pop: OrderedDict([('name', 'Population'), ('unit', 'millions')])
Attributes
date: 2000-01-01
author: A Person

These properties can be transferred from one data container to another:

.. code-block:: python

>>> s = metacsv.Series(np.random.random(6))
>>> s
<metacsv.core.containers.Series (6,)>
0 0.881924
1 0.556330
2 0.554700
3 0.221284
4 0.970801
5 0.946414
dtype: float64
>>> s.attrs = df.attrs
>>> s
<metacsv.core.containers.Series (6,)>
0 0.881924
1 0.556330
2 0.554700
3 0.221284
4 0.970801
5 0.946414
dtype: float64

Attributes
date: 2000-01-01
author: A Person


All MetaCSV attributes, including the ``attrs`` Attribute object, can be copied,
assigned to new objects, and deleted. Since these attributes are largely
unstable across normal pandas data processing, it is recommended that attributes
be copied before data work is attempted and then reassigned before IO
conversions.


Exporting MetaCSV data to other formats
-----------------------------------------------

CSV
~~~~~~~~~

A MetaCSV ``Series`` or ``DataFrame`` can be written as a yaml-prefixed CSV
using the same ``to_csv`` syntax as it's ``pandas`` counterpart:

.. code-block:: python

>>> df.attrs['new attribute'] = 'changed in python!'
>>> df.to_csv('my_new_data.csv')

The resulting csv will include a yaml-formatted header with the original
metadata updated to include attr['new attribute'].,


pandas
~~~~~~~~~~~~~~~

The coordinates and MetaCSV attributes can be easily stripped from a MetaCSV
Container:

.. code-block:: python

>>> df.to_pandas()
pop gdp
region year
USA 2010 309.3 13599.3
2011 311.7 13817.0
CAN 2010 34.0 1240.0
2011 34.3 1276.7



xarray/netCDF
~~~~~~~~~~~~~~~

`xArray <http://xarray.pydata.org/>`_ provides a pandas-like interface to
operating on indexed ``ndarray`` data. It is modeled on the ``netCDF`` data
storage format used frequently in climate science, but is useful for many
applications with higher-order data.



.. code-block:: python

>>> ds = df.to_xarray()
>>> ds
<xarray.Dataset>
Dimensions: (region: 2, year: 2)
Coordinates:
* region (region) object 'USA' 'CAN'
* year (year) int64 2010 2011
Data variables:
pop (region, year) float64 309.3 311.7 34.0 34.3
gdp (region, year) float64 1.36e+04 1.382e+04 1.24e+03 1.277e+03
Attributes:
date: 2000-01-01
author: A Person
>>> ds.to_netcdf('my_netcdf_data.nc')

Pickling
~~~~~~~~~

Pickling works just like pandas.

.. code-block:: python

>>> df.to_pickle('my_metacsv_pickle.pkl')
>>> metacsv.read_pickle('my_metacsv_pickle.pkl')
<metacsv.core.containers.DataFrame (4, 2)>
pop gdp
region year
USA 2010 309.3 13599.3
2011 311.7 13817.0
CAN 2010 34.0 1240.0
2011 34.3 1276.7

Variables
gdp: OrderedDict([('name', 'Product'), ('unit', '2005 $Bn')])
pop: OrderedDict([('name', 'Population'), ('unit', 'millions')])
Attributes
date: 2000-01-01
author: A Person



Others
~~~~~~~~~

Currently, MetaCSV only supports conversion to CSV and to netCDF through the
``xarray`` module. However, feel free to suggest additional features and to
contribute your own!



Conversion to other types on the fly
-----------------------------------------------

Special conversion utilities allow you to convert any metacsv, pandas, or xarray
container or a CSV filepath into any other type in this group.

* to_csv

``to_csv`` allows you to write any container or csv file to a metacsv-formatted
csv file. Keyword arguments ``attrs``, ``coords``, and ``variables`` will be
attached to the data before it is written. Any conflicts in these attributes
will be updated with the arguments to this function

.. code-block:: python

>>> import pandas as pd, numpy as np, xarray as xr, metacsv
>>> df = pd.DataFrame(np.random.random((3,4)), columns=list('abcd'))
>>> df
a b c d
0 0.558083 0.665184 0.226173 0.339905
1 0.541712 0.835804 0.326078 0.179103
2 0.332869 0.435573 0.904612 0.823884

>>> metacsv.to_csv(df, 'mycsv.csv', attrs={'author': 'my name', 'date': '2015-12-31'})
>>>
>>> df2 = metacsv.read_csv('mycsv.csv', index_col=[0])
>>> df2
<metacsv.core.containers.DataFrame (3, 4)>
a b c d
0 0.558083 0.665184 0.226173 0.339905
1 0.541712 0.835804 0.326078 0.179103
2 0.332869 0.435573 0.904612 0.823884

Attributes
date: 2015-12-31
author: my name

>>> metacsv.to_csv(df2, 'mycsv.csv', attrs={'author': 'new name'})
>>>
>>> metacsv.read_csv('mycsv.csv', index_col=[0])
<metacsv.core.containers.DataFrame (3, 4)>
a b c d
0 0.558083 0.665184 0.226173 0.339905
1 0.541712 0.835804 0.326078 0.179103
2 0.332869 0.435573 0.904612 0.823884

Attributes
date: 2015-12-31
author: new name

* to_xarray

``to_xarray`` returns any container or csv file as an xarray container. Table
data (CSV files and DataFrames) will create ``xarray.Dataset`` objects, while
Series objects will create ``xarray.DataArray`` objects. Keyword arguments
``attrs``, ``coords``, and ``variables`` will be attached to the data before it
is written. Any conflicts in these attributes will be updated with the arguments
to this function.

* to_dataarray

``to_dataarray`` returns any container or csv file as an ``xarray.DataArray``.
Table data (CSV files and DataFrames) will be stacked, with columns re-arranged
as new ``xarray.Coordinates``. Keyword arguments ``attrs``, ``coords``, and
``variables`` will be attached to the data before it is written. Any conflicts
in these attributes will be updated with the arguments to this function.

* to_dataset

``to_dataarray`` returns any container or csv file as an ``xarray.DataArray``.
Table data (CSV files and DataFrames) will be stacked, with columns re-arranged
as new ``xarray.Coordinates``. Keyword arguments ``attrs``, ``coords``, and
``variables`` will be attached to the data before it is written. Any conflicts
in these attributes will be updated with the arguments to this function.

* to_pandas

``to_pandas`` strips special attributes and returns an ordinary ``Series`` or
``DataFrame`` object.


Special attributes
-----------------------------------------------

The ``coords`` and ``variables`` attributes are keywords and are not simply
passed to the MetaCSV object's ``attrs`` attribute.


Variables
~~~~~~~~~~~~~

Variables are attributes which apply to speicific columns or data variables. In
MetaCSV containers, variables are displayed as a separate set of attributes. On
conversion to ``xarray``, these attributes are assigned to variable-specific
``attrs``:

.. code-block:: python

>>> ds = df.to_xarray()
>>> ds
<xarray.Dataset>
Dimensions: (index: 4)
Coordinates:
* index (index) int64 0 1 2 3
Data variables:
region (index) object 'USA' 'USA' 'CAN' 'CAN'
year (index) int64 2010 2011 2010 2011
pop (index) float64 309.3 311.7 34.0 34.3
gdp (index) float64 1.36e+04 1.382e+04 1.24e+03 1.277e+03
Attributes:
date: 2000-01-01
author: A Person

>>> ds.pop
<xarray.DataArray 'pop' (index: 4)>
array([ 309.3, 311.7, 34. , 34.3])
Coordinates:
* index (index) int64 0 1 2 3
Attributes:
name: Population
unit: millions

Note that at present, variables are not persistent across slicing operations.

**parse_vars**

Variables have a special argument to ``read_csv``: ``parse_vars`` allows parsing of one-line variable definitions in the format ``var: description [unit]``:

.. code-block:: python

>>> doc = io.StringIO('''
---
author: A Person
date: 2000-01-01
variables:
pop: Population [millions]
gdp: Product [2005 $Bn]
...
region,year,pop,gdp
USA,2010,309.3,13599.3
USA,2011,311.7,13817.0
CAN,2010,34.0,1240.0
CAN,2011,34.3,1276.7
''')

>>> metacsv.read_csv(doc, index_col=0, parse_vars=True)
<metacsv.core.containers.DataFrame (4, 3)>
year pop gdp
region
USA 2010 309.3 13599.3
USA 2011 311.7 13817.0
CAN 2010 34.0 1240.0
CAN 2011 34.3 1276.7

Variables
gdp: {u'description': 'Product', u'unit': '2005 $Bn'}
pop: {u'description': 'Population', u'unit': 'millions'}
Attributes
date: 2000-01-01
author: A Person

Coordinates
~~~~~~~~~~~~~

The conceptual foundation of coordinates is taken from ``xarray``, where data is
treated as an ndarray rather than a table. If you plan to only work with the
pandas-like features of ``metacsv``, you do not really need coordinates.

That said, specifying the ``coords`` attribute in a csv results in automatic
index handling:

.. code-block:: python

>>> doc = io.StringIO('''
---
author: A Person
date: 2000-01-01
variables:
pop:
name: Population
unit: millions
gdp:
name: Product
unit: 2005 $Bn
coords:
- region
- year
...
region,year,pop,gdp
USA,2010,309.3,13599.3
USA,2011,311.7,13817.0
CAN,2010,34.0,1240.0
CAN,2011,34.3,1276.7
''')

>>> df = metacsv.read_csv(doc)
>>> df
<metacsv.core.containers.DataFrame (4, 2)>
pop gdp
region year
USA 2010 309.3 13599.3
2011 311.7 13817.0
CAN 2010 34.0 1240.0
2011 34.3 1276.7

Coordinates
* region (region) object CAN, USA
* year (year) int64 2010, 2011
Variables
gdp: OrderedDict([('name', 'Product'), ('unit', '2005 $Bn')])
pop: OrderedDict([('name', 'Population'), ('unit', 'millions')])
Attributes
date: 2000-01-01
author: A Person


Coordinates become especially useful, however, when moving to ``xarray`` objects
or ``netCDF`` files. The ``DataFrame`` above will have no trouble, as ``region``
and ``year`` are orthoganal:

.. code-block:: python

>>> df.to_xarray()
<xarray.Dataset>
Dimensions: (region: 2, year: 2)
Coordinates:
* region (region) object 'USA' 'CAN'
* year (year) int64 2010 2011
Data variables:
pop (region, year) float64 309.3 311.7 34.0 34.3
gdp (region, year) float64 1.36e+04 1.382e+04 1.24e+03 1.277e+03
Attributes:
date: 2000-01-01
author: A Person

This becomes more complicated when columns in the index are not independent and
cannot be thought of as orthogonal. In this case, you can specify ``coords`` as
a dict-like attribute either in the CSV header or as an argument to the
conversion method:

.. code-block:: python

doc = io.StringIO('''
---
coords:
region:
regname: 'region'
continent: 'region'
year:
...
region,regname,continent,year,pop,gdp
USA,United States,North America,2010,309.3,13599.3
USA,United States,North America,2011,311.7,13817.0
CAN,Canada,North America,2010,34.0,1240.0
CAN,Canada,North America,2011,34.3,1276.7
''')

>>> metacsv.to_xarray(doc)
<xarray.Dataset>
Dimensions: (region: 2, year: 2)
Coordinates:
* region (region) object 'USA' 'CAN'
* year (year) int64 2010 2011
regname (region) object 'United States' 'Canada'
continent (region) object 'North America' 'North America'
Data variables:
pop (region, year) float64 309.3 311.7 34.0 34.3
gdp (region, year) float64 1.36e+04 1.382e+04 1.24e+03 1.277e+03

Note that the resulting ``Dataset`` is not indexed by the cartesian product of
all four coordinates, but only by the base coordinates, indicated by the ``*``.
Without first setting the ``coords`` attribute this way, the resulting data
would have ``NaN`` values corresponding to ``(USA, Canada)`` and
``(CAN, United States)``.


TODO
============

* Allow automatic coersion of ``xarray.Dataset`` and ``xarray.DataArray``
objects to MetaCSV containers.

* Extend metacsv functionality to ``Panel`` objects

* Make ``coords`` and ``attrs`` persistent across slicing operations
(try ``df['pop'].to_xarray()`` from above example and watch it
fail...)

* Improve hooks between ``pandas`` and ``metacsv``:

- update ``coord`` names on ``df.index.names`` assignment
- update ``coords`` on stack/unstack
- update ``coords`` on

* Improve parser to automatically strip trailing commas and other excel relics

* Enable ``read_csv(engine='C')``... this currently does not work.

* Handle attributes indexed by coord/variable names --> assign to
coord/variable-specific ``attrs``

* Let's start an issue tracker and get rid of this section!

* Should we rethink "special attribute," naming e.g. coords? Maybe these should
have some special prefix like ``_coords`` when included in yaml headers to
avoid confusion with other generic attributes...

* Allow attribute assertions (e.g. ``version='>1.6.0'``) in ``read_csv`` call

* Improve test coverage

* Improve documentation & build readthedocs page



Feature Requests
==================
* Create syntax for ``multi-csv`` --> ``Panel`` or combining using filename
regex
* Eventually? allow for on-disk manipulation of many/large files with
dask/xarray
* Eventually? add xml, SQL, other structured syntax language conversions




============== ==========================================================
Python support Python 2.7, >= 3.3
Source https://github.com/delgadom/metacsv
Docs http://metacsv.rtfd.org
Changelog http://metacsv.readthedocs.org/en/latest/history.html
API http://metacsv.readthedocs.org/en/latest/api.html
Issues https://github.com/delgadom/metacsv/issues
Travis http://travis-ci.org/delgadom/metacsv
Test coverage https://coveralls.io/r/delgadom/metacsv
pypi https://pypi.python.org/pypi/metacsv
Ohloh https://www.ohloh.net/p/metacsv
License `BSD`_.
git repo .. code-block:: bash

$ git clone https://github.com/delgadom/metacsv.git
install dev .. code-block:: bash

$ git clone https://github.com/delgadom/metacsv.git metacsv
$ cd ./metacsv
$ virtualenv .env
$ source .env/bin/activate
$ pip install -e .
tests .. code-block:: bash

$ python setup.py test
============== ==========================================================

.. _BSD: http://opensource.org/licenses/BSD-3-Clause
.. _Documentation: http://metacsv.readthedocs.org/en/latest/
.. _API: http://metacsv.readthedocs.org/en/latest/api.html


=========
Changelog
=========

Here you can find the recent changes to MetaCSV..

.. changelog::
:version: dev
:released: Ongoing

.. change::
:tags: docs

Updated CHANGES.

.. changelog::
:version: 0.0.1
:released: 2016-05-04

.. change::
:tags: project

First release on PyPi.

.. todo:: vim: set filetype=rst: