sacred

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

IDSIA
4255
383
Python

Sacred

| *Every experiment is sacred*
| *Every experiment is great*
| *If an experiment is wasted*
| *God gets quite irate*

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

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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 <http://sacred.readthedocs.org/>. You can also Ask Sacred Guru <https://gurubase.io/g/sacred>, 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 <http://pytest.org/latest/>_ package.
You can execute them by running pytest in the sacred directory like this:

pytest

There is also a config file for tox <https://tox.readthedocs.io/en/latest/>_ 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 <https://github.com/IDSIA/sacred/issues>. If you have a specific question related
to the usage of sacred, please ask a question on StackOverflow under the
python-sacred tag <https://stackoverflow.com/questions/tagged/python-sacred>. 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 <docs/projects_using_sacred.rst>_ 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 <https://github.com/vivekratnavel/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 <https://github.com/JarnoRFB/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 <https://github.com/chovanecm/sacredboard>_
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++
… image:: docs/images/sacredboard.png

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

Neptune <https://neptune.ai/>_
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++
… 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='<YOUR_API_TOKEN>',
                                    project='<YOUR_WORKSPACE/YOUR_PROJECT>'))

For more info, check the Neptune + Sacred integration guide <https://docs.neptune.ai/integrations-and-supported-tools/experiment-tracking/sacred>_.

SacredBrowser <https://github.com/michaelwand/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 <https://github.com/Qwlouse/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 <http://restheart.org>_ to access the database.

Related Projects

Sumatra <https://pythonhosted.org/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 <https://github.com/Kaixhin/FGLab>_
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
| 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 <http://opensource.org/licenses/MIT>_.

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 <http://conference.scipy.org/proceedings/scipy2017/klaus_greff.html>_.

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:alt: MIT licensed

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:alt: ReadTheDocs

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:alt: DOI for this release

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:alt: Coverage Report

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:alt: Code Scrutinizer Quality

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