Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/idsia/sacred

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.
https://github.com/idsia/sacred

infrastructure machine-learning mongodb python reproducibility reproducible-research reproducible-science

Last synced: 11 days ago
JSON representation

Sacred is a tool to help you configure, organize, log and reproduce experiments developed at IDSIA.

Awesome Lists containing this project

README 

        
Sacred

======



    | *Every experiment is sacred*

    | *Every experiment is great*

    | *If an experiment is wasted*

    | *God gets quite irate*



|pypi| |py_versions| |license| |rtfd| |doi|



|build| |coverage| |code_quality| |black|



Sacred is a tool to help you configure, organize, log and reproduce experiments.

It is designed to do all the tedious overhead work that you need to do around

your actual experiment in order to:



- keep track of all the parameters of your experiment

- easily run your experiment for different settings

- save configurations for individual runs in a database

- reproduce your results



Sacred achieves this through the following main mechanisms:



-  **Config Scopes** A very convenient way of the local variables in a function

   to define the parameters your experiment uses.

-  **Config Injection**: You can access all parameters of your configuration

   from every function. They are automatically injected by name.

-  **Command-line interface**: You get a powerful command-line interface for each

   experiment that you can use to change parameters and run different variants.

-  **Observers**: Sacred provides Observers that log all kinds of information

   about your experiment, its dependencies, the configuration you used,

   the machine it is run on, and of course the result. These can be saved

   to a MongoDB, for easy access later.

-  **Automatic seeding** helps controlling the randomness in your experiments,

   such that the results remain reproducible.



Example

-------

+------------------------------------------------+--------------------------------------------+

| **Script to train an SVM on the iris dataset** | **The same script as a Sacred experiment** |

+------------------------------------------------+--------------------------------------------+

| .. code:: python                               | .. code:: python                           |

|                                                |                                            |

|  from numpy.random import permutation          |   from numpy.random import permutation     |

|  from sklearn import svm, datasets             |   from sklearn import svm, datasets        |

|                                                |   from sacred import Experiment            |

|                                                |   ex = Experiment('iris_rbf_svm')          |

|                                                |                                            |

|                                                |   @ex.config                               |

|                                                |   def cfg():                               |

|  C = 1.0                                       |     C = 1.0                                |

|  gamma = 0.7                                   |     gamma = 0.7                            |

|                                                |                                            |

|                                                |   @ex.automain                             |

|                                                |   def run(C, gamma):                       |

|  iris = datasets.load_iris()                   |     iris = datasets.load_iris()            |

|  perm = permutation(iris.target.size)          |     per = permutation(iris.target.size)    |

|  iris.data = iris.data[perm]                   |     iris.data = iris.data[per]             |

|  iris.target = iris.target[perm]               |     iris.target = iris.target[per]         |

|  clf = svm.SVC(C=C, kernel='rbf',              |     clf = svm.SVC(C=C, kernel='rbf',       |

|          gamma=gamma)                          |             gamma=gamma)                   |

|  clf.fit(iris.data[:90],                       |     clf.fit(iris.data[:90],                |

|          iris.target[:90])                     |             iris.target[:90])              |

|  print(clf.score(iris.data[90:],               |     return clf.score(iris.data[90:],       |

|                  iris.target[90:]))            |                      iris.target[90:])     |

+------------------------------------------------+--------------------------------------------+



Documentation

-------------

The documentation is hosted at `ReadTheDocs `_. You can also `Ask Sacred Guru `_, it is a Sacred-focused AI to answer your questions.



Installing

----------

You can directly install it from the Python Package Index with pip:



    pip install sacred



Or if you want to do it manually you can checkout the current version from git

and install it yourself:



   | git clone https://github.com/IDSIA/sacred.git

   | cd sacred

   | python setup.py install



You might want to also install the ``numpy`` and the ``pymongo`` packages. They are

optional dependencies but they offer some cool features:



    pip install numpy pymongo



Tests

-----

The tests for sacred use the `pytest `_ package.

You can execute them by running ``pytest`` in the sacred directory like this:



    pytest



There is also a config file for `tox `_ so you

can automatically run the tests for various python versions like this:



    tox



Update pytest version

+++++++++++++++++++++



If you update or change the pytest version, the following files need to be changed:



- ``dev-requirements.txt``

- ``tox.ini``

- ``test/test_utils.py``

- ``setup.py``



Contributing

------------

If you find a bug, have a feature request or want to discuss something general you are welcome to open an

`issue `_. If you have a specific question related

to the usage of sacred, please ask a question on StackOverflow under the

`python-sacred tag `_. We value documentation

a lot. If you find something that should be included in the documentation please

document it or let us know whats missing. If you are using Sacred in one of your projects and want to share

your code with others, put your repo in the `Projects using Sacred _ list.

Pull requests are highly welcome!



Frontends

---------

At this point there are three frontends to the database entries created by sacred (that I'm aware of).

They are developed externally as separate projects.



`Omniboard `_

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: docs/images/omniboard-table.png

.. image:: docs/images/omniboard-metric-graphs.png



Omniboard is a web dashboard that helps in visualizing the experiments and metrics / logs collected by sacred.

Omniboard is written with React, Node.js, Express and Bootstrap.



`Incense `_

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: docs/images/incense-artifact.png

.. image:: docs/images/incense-metric.png



Incense is a Python library to retrieve runs stored in a MongoDB and interactively display metrics and artifacts

in Jupyter notebooks.



`Sacredboard `_

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: docs/images/sacredboard.png



Sacredboard is a web-based dashboard interface to the sacred runs stored in a

MongoDB.



`Neptune `_

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: docs/images/neptune-compare.png

.. image:: docs/images/neptune-collaboration.png



Neptune is a metadata store for MLOps, built for teams that run a lot of experiments.

It gives you a single place to log, store, display, organize, compare, and query all your model-building metadata via API available for both Python and R programming languages:



.. image:: docs/images/neptune-query-api.png



In order to log your sacred experiments to Neptune, all you need to do is add an observer:



.. code-block:: python



    from neptune.new.integrations.sacred import NeptuneObserver

    ex.observers.append(NeptuneObserver(api_token='',

                                        project=''))



For more info, check the `Neptune + Sacred integration guide `_.



`SacredBrowser `_

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

.. image:: docs/images/sacred_browser.png



SacredBrowser is a PyQt4 application to browse the MongoDB entries created by

sacred experiments.

Features include custom queries, sorting of the results,

access to the stored source-code, and many more.

No installation is required and it can connect to a local

database or over the network.



`Prophet `_

+++++++++++++++++++++++++++++++++++++++++++++++

Prophet is an early prototype of a webinterface to the MongoDB entries created by

sacred experiments, that is discontinued.

It requires you to run `RestHeart `_ to access the database.



Related Projects

----------------



`Sumatra `_

++++++++++++++++++++++++++++++++++++++++++++++

   | Sumatra is a tool for managing and tracking projects based on numerical

   | simulation and/or analysis, with the aim of supporting reproducible research.

   | It can be thought of as an automated electronic lab notebook for

   | computational projects.



Sumatra takes a different approach by providing commandline tools to initialize

a project and then run arbitrary code (not just python).

It tracks information about all runs in a SQL database and even provides a nice browser tool.

It integrates less tightly with the code to be run, which makes it easily

applicable to non-python experiments.

But that also means it requires more setup for each experiment and

configuration needs to be done using files.

Use this project if you need to run non-python experiments, or are ok with the additional setup/configuration overhead.



`Future Gadget Laboratory `_

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

   | FGLab is a machine learning dashboard, designed to make prototyping

   | experiments easier. Experiment details and results are sent to a database,

   | which allows analytics to be performed after their completion. The server

   | is FGLab, and the clients are FGMachines.



Similar to Sumatra, FGLab is an external tool that can keep track of runs from

any program. Projects are configured via a JSON schema and the program needs to

accept these configurations via command-line options.

FGLab also takes the role of a basic scheduler by distributing runs over several

machines.



License

-------

This project is released under the terms of the `MIT license `_.



Citing Sacred

-------------

`K. Greff, A. Klein, M. Chovanec, F. Hutter, and J. Schmidhuber, ‘The Sacred Infrastructure for Computational Research’,

in Proceedings of the 15th Python in Science Conference (SciPy 2017), Austin, Texas, 2017, pp. 49–56

`_.



.. |pypi| image:: https://img.shields.io/pypi/v/sacred.svg

    :target: https://pypi.python.org/pypi/sacred

    :alt: Current PyPi Version



.. |py_versions| image:: https://img.shields.io/pypi/pyversions/sacred.svg

    :target: https://pypi.python.org/pypi/sacred

    :alt: Supported Python Versions



.. |license| image:: https://img.shields.io/badge/license-MIT-blue.png

    :target: http://choosealicense.com/licenses/mit/

    :alt: MIT licensed



.. |rtfd| image:: https://readthedocs.org/projects/sacred/badge/?version=latest&style=flat

    :target: https://sacred.readthedocs.io/en/stable/

    :alt: ReadTheDocs



.. |doi| image:: https://zenodo.org/badge/doi/10.5281/zenodo.16386.svg

    :target: http://dx.doi.org/10.5281/zenodo.16386

    :alt: DOI for this release



.. |build| image:: https://github.com/IDSIA/sacred/actions/workflows/test.yml/badge.svg

    :target: https://github.com/IDSIA/sacred/actions/workflows/test.yml/badge.svg

    :alt: Github Actions PyTest



.. |coverage| image:: https://coveralls.io/repos/IDSIA/sacred/badge.svg

    :target: https://coveralls.io/r/IDSIA/sacred

    :alt: Coverage Report



.. |code_quality| image:: https://scrutinizer-ci.com/g/IDSIA/sacred/badges/quality-score.png?b=master

    :target: https://scrutinizer-ci.com/g/IDSIA/sacred/

    :alt: Code Scrutinizer Quality



.. |black| image:: https://img.shields.io/badge/code%20style-black-000000.svg

    :target: https://github.com/ambv/black

    :alt: Code style: black