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        "author": "The Priesemann Group",
        "author_email": "paul.spitzner@ds.mpg.de",
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            "License :: OSI Approved :: BSD License",
            "Operating System :: OS Independent",
            "Programming Language :: Python",
            "Programming Language :: Python :: 3.6",
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        "description": "# Mr. Estimator\n\n[![Latest Version](https://img.shields.io/pypi/v/mrestimator.svg)](https://pypi.python.org/pypi/mrestimator/)\n[![Documentation](https://readthedocs.org/projects/mrestimator/badge/?version=latest&style=flat)](https://mrestimator.readthedocs.io/en/latest/)\n[![License](https://img.shields.io/pypi/l/mrestimator.svg)](https://opensource.org/licenses/BSD-3-Clause)\n[![Supported Python Versions](https://img.shields.io/pypi/pyversions/mrestimator.svg)](https://pypi.python.org/pypi/mrestimator/)\n\nWelcome to the Toolbox for the Multistep Regression Estimator (\"Mister Estimator\").\n\nIf you find bugs, encounter unexpected behaviour or want to comment, please let us know via mail or open an issue on github. Any input is greatly appreciated.\n\n- [Documentation](https://mrestimator.readthedocs.io/en/latest/)\n- [Getting Started](https://mrestimator.readthedocs.io/en/latest/doc/gettingstarted.html)\n- [Python Package index](https://pypi.org/project/mrestimator)\n- [Github](https://github.com/Priesemann-Group/mrestimator)\n- [arXiv (a nicely-formated PDF)](https://arxiv.org/abs/2007.03367)\n- Details on the multistep regression estimator: [J. Wilting and V. Priesemann, Nat. Commun. 9, 2325 (2018)](https://doi.org/10.1038/s41467-018-04725-4)\n\nIf you use our toolbox for a scientific publication please cite it as\n`Spitzner FP, Dehning J, Wilting J, Hagemann A, P. Neto J, Zierenberg J, et al. (2021) MR. Estimator, a toolbox to determine intrinsic timescales from subsampled spiking activity. PLoS ONE 16(4): e0249447. https://doi.org/10.1371/journal.pone.0249447`\n\n## Dependencies\n- Python (>=3.5)\n- numpy (>=1.11.0)\n- scipy (>=1.0.0)\n- matplotlib (>=1.5.3)\n\n## Optional Dependencies\n- numba (>=0.44), for parallelization\n- tqdm, for progress bars\n\nWe recommend (and develop with) the latest stable versions of the dependencies, at the time of writing that is\nPython 3.7.0, numpy 1.15.1, scipy 1.1.0 and matplotlib 2.2.3.\n\n\n## What's new\n\n### 18.10.2021 [v0.1.8](https://pypi.org/project/mrestimator/0.1.8)\n* is a quick bugfix. We had to disable numba parallelization for the time being.\n\n### 07.05.2021 Now published in [PLOS ONE](https://doi.org/10.1371/journal.pone.0249447).\n\n### 08.07.2020 Our paper draft is now on arXiv\n* [arXiv:2007.03367](https://arxiv.org/abs/2007.03367): \"MR. Estimator, a toolbox to determine intrinsic timescales from subsampled spiking activity\".\n* Additional scripts and downloadable data to recreate the figure on triallength are available on [gin](https://gin.g-node.org/pspitzner/mrestimator_triallength/src/master).\n\n\n\n## Installation\nAssuming a working Python3 environment, usually you can install via pip (also installs the optional dependencies):\n\n```\npip3 install 'mrestimator[full]'\n```\n\nTo install (or update an existing installation) with optional dependencies:\n\n```\npip3 install -U 'mrestimator[full]'\n```\n\nIf you run into problems during installation, they are most likely due to numpy and scipy.\nYou may check the [official scipy.org documentation](https://scipy.org/install.html) or try using anaconda as outlined below.\n\n### Install Using Anaconda\n\nWe sincerely recommend using conda, more so if you are unsure about the dependencies on your system or lack administrator priviliges. It is easy to install, allows you to manage different versions of Python and if something breaks, you can role back and reinstall easily - all without leaving your user directory.\n\nHead over to [anaconda.com](https://www.anaconda.com/download/), and download the installer for Python 3.7.\n\nAfter following the installation instructions (default settings are fine for most users),\nstart a new python session by typing ```python``` in a new terminal window.\nYou will see something similar to the following:\n\n```\nPython 3.7.0 (default, Jun 28 2018, 07:39:16)\n[Clang 4.0.1 (tags/RELEASE_401/final)] :: Anaconda, Inc. on darwin\nType \"help\", \"copyright\", \"credits\" or \"license\" for more information.\n>>>\n```\n\nEnd the session (```exit()``` or Ctrl-D) and type ```conda list```, which will output a list of the packages that came bundled with anaconda.\nAll dependencies for Mr. Estimator are included.\n\nOptionally, you can create a new environment (e.g. named 'myenv') for the toolbox ```conda create --name myenv```\nand activate it with ``source activate myenv`` (``activate myenv`` on windows).\nFor more details on managing environments with conda, see [here](https://conda.io/docs/user-guide/tasks/manage-environments.html).\n\nNow install using pip: ```pip install 'mrestimator[full]'``` and afterwards you should be able to import the module into any python3 session\n\n```\npython\n>>> import mrestimator as mre\nINFO     Loaded mrestimator v0.1.6, writing to /tmp/mre_paul/\n```\n\n### Manual Installation\n\nClone the repository via ssh or https\n\n```\ngit clone git@github.com:Priesemann-Group/mrestimator.git\ngit clone https://github.com/Priesemann-Group/mrestimator.git\n```\n\nAnd optionally,\n\n```\nexport PYTHONPATH=\"${PYTHONPATH}:$(pwd)/mrestimator\"\n```\n\nThis line adds the downloaded directory to your `PYTHONPATH` environment\nvariable, so that it will be found automatically when importing. If you want to add the path\nautomatically when you login, you can add it to your `~/.bashrc` or `~/.profile`:\n\n```\necho 'export PYTHONPATH=\"${PYTHONPATH}:'$(pwd)'/mrestimator\"' >> ~/.bashrc\n```\n\n### Pre-release versions\n\nYou can upgrade to pre-release versions using pip\n\n```\npip install -U --pre 'mrestimator[full]'\n```\n\nTo revert to the stable version, run\n\n```\npip install mrestimator==0.1.6\n```\n\nor\n\n```\npip install --force-reinstall mrestimator\n```\n\nfor a complete (longer) reinstall of all dependencies.\n\n### Parallelization and running on clusters\n\nPer default, the toolbox and its dependencies use all threads available on the host machine.\nWhile this is great if running locally, it is undesired for distributed computing as the workload manager expects jobs of serial queues to only use one thread.\nTo disable multi-threading, you can set the following environment variables (e.g. at the beginning of a job file)\n\n```\nexport OPENBLAS_NUM_THREADS=1\nexport MKL_NUM_THREADS=1\nexport NUMEXPR_NUM_THREADS=1\nexport OMP_NUM_THREADS=1\nexport NUMBA_NUM_THREADS=1\n```",
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