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      SciPy 1.0: fundamental algorithms for scientific computing in Python

      review-article
      1 , 2 , , 2 , 3 , 4 , 5 , 6 , 7 , 8 , , 9 , , 10 , 11 , 12 , 13 , 14 , 15 , 14 , 16 , 17 , 14 , 18 , 19 , 20 , 5 , 5 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 6 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , SciPy 1.0 Contributors
      Nature Methods
      Nature Publishing Group US
      Computational biology and bioinformatics, Biophysical chemistry, Technology

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          Abstract

          SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.

          Abstract

          This Perspective describes the development and capabilities of SciPy 1.0, an open source scientific computing library for the Python programming language.

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          Most cited references46

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          Finding scientific topics.

          A first step in identifying the content of a document is determining which topics that document addresses. We describe a generative model for documents, introduced by Blei, Ng, and Jordan [Blei, D. M., Ng, A. Y. & Jordan, M. I. (2003) J. Machine Learn. Res. 3, 993-1022], in which each document is generated by choosing a distribution over topics and then choosing each word in the document from a topic selected according to this distribution. We then present a Markov chain Monte Carlo algorithm for inference in this model. We use this algorithm to analyze abstracts from PNAS by using Bayesian model selection to establish the number of topics. We show that the extracted topics capture meaningful structure in the data, consistent with the class designations provided by the authors of the articles, and outline further applications of this analysis, including identifying "hot topics" by examining temporal dynamics and tagging abstracts to illustrate semantic content.
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            Is Open Access

            Probabilistic programming in Python using PyMC3

            Probabilistic programming allows for automatic Bayesian inference on user-defined probabilistic models. Recent advances in Markov chain Monte Carlo (MCMC) sampling allow inference on increasingly complex models. This class of MCMC, known as Hamiltonian Monte Carlo, requires gradient information which is often not readily available. PyMC3 is a new open source probabilistic programming framework written in Python that uses Theano to compute gradients via automatic differentiation as well as compile probabilistic programs on-the-fly to C for increased speed. Contrary to other probabilistic programming languages, PyMC3 allows model specification directly in Python code. The lack of a domain specific language allows for great flexibility and direct interaction with the model. This paper is a tutorial-style introduction to this software package.
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              Monotone Piecewise Cubic Interpolation

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                Author and article information

                Contributors
                scipy.articles@gmail.com
                scipy.articles@gmail.com
                scipy.articles@gmail.com
                Journal
                Nat Methods
                Nat. Methods
                Nature Methods
                Nature Publishing Group US (New York )
                1548-7091
                1548-7105
                3 February 2020
                3 February 2020
                2020
                : 17
                : 3
                : 261-272
                Affiliations
                [1 ]ISNI 0000 0001 1013 7965, GRID grid.9681.6, University of Jyväskylä, ; Jyväskylä, Finland
                [2 ]Quansight LLC, Austin, TX USA
                [3 ]ISNI 0000 0004 0459 167X, GRID grid.66875.3a, Ultrasound Imaging, Mayo Clinic, ; Rochester, MN USA
                [4 ]ISNI 0000 0004 1936 9115, GRID grid.253294.b, Electrical Engineering, , Brigham Young University, ; Provo, UT USA
                [5 ]GRID grid.504464.7, Enthought, Inc., ; Austin, TX USA
                [6 ]Anaconda Inc., Austin, TX USA
                [7 ]ISNI 000000012222461X, GRID grid.253547.2, BioResource and Agricultural Engineering Department, , California Polytechnic State University, ; San Luis Obispo, CA USA
                [8 ]ISNI 0000 0000 9632 6718, GRID grid.19006.3e, Department of Mathematics, , University of California Los Angeles, ; Los Angeles, CA USA
                [9 ]ISNI 0000 0004 0428 3079, GRID grid.148313.c, Los Alamos National Laboratory, ; Los Alamos, NM USA
                [10 ]Independent researcher, Tokyo, Japan
                [11 ]ISNI 0000 0004 0578 2005, GRID grid.410682.9, National Research University Higher School of Economics, ; Moscow, Russia
                [12 ]Independent researcher, Saue, Estonia
                [13 ]ISNI 0000000110107715, GRID grid.6988.f, Department of Mechanics and Applied Mathematics, , Institute of Cybernetics at Tallinn Technical University, ; Tallinn, Estonia
                [14 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, Berkeley Institute for Data Science, , University of California Berkeley, ; Berkeley, CA USA
                [15 ]Independent researcher, New York, NY USA
                [16 ]ISNI 0000 0004 1936 7486, GRID grid.6572.6, School of Psychology, , University of Birmingham, ; Edgbaston, Birmingham UK
                [17 ]Independent researcher, San Francisco, CA USA
                [18 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, Division of Biostatistics, , University of California Berkeley, ; Berkeley, CA USA
                [19 ]WayRay LLC, Skolkovo Innovation Center, Moscow, Russia
                [20 ]ISNI 0000 0004 0432 8812, GRID grid.1089.0, Australian Nuclear Science and Technology Organisation, ; Lucas Heights, NSW Australia
                [21 ]ISNI 0000000122986657, GRID grid.34477.33, Institute for Learning and Brain Sciences, , University of Washington, ; Seattle, WA USA
                [22 ]ISNI 0000 0001 2184 9220, GRID grid.266683.f, College of Information and Computing Sciences, , University of Massachusetts Amherst, ; Amherst, MA USA
                [23 ]Independent researcher, Amsterdam, the Netherlands
                [24 ]ISNI 0000 0001 2181 7878, GRID grid.47840.3f, Berkeley Center for Cosmological Physics, , University of California Berkeley, ; Berkeley, CA USA
                [25 ]ISNI 0000 0004 0491 2576, GRID grid.423270.0, Bruker Biospin Corp., ; Billerica, MA USA
                [26 ]ISNI 0000000122986657, GRID grid.34477.33, University of Washington, ; Seattle, WA USA
                [27 ]Independent researcher, Toulouse, France
                [28 ]Independent researcher, Montreal, Quebec Canada
                [29 ]ISNI 0000 0001 0176 7631, GRID grid.22557.37, New Technologies Research Centre, , University of West Bohemia, ; Plzeň, Czech Republic
                [30 ]ISNI 0000 0004 1936 9115, GRID grid.253294.b, Department of Mathematics, , Brigham Young University, ; Provo, UT USA
                [31 ]ISNI 0000 0004 1936 9924, GRID grid.89336.37, Oden Institute for Computational Engineering and Sciences, , The University of Texas at Austin, ; Austin, TX USA
                [32 ]Independent researcher, Belmont, Massachusetts USA
                [33 ]Space Dynamics Laboratory, North Logan, UT USA
                [34 ]Independent researcher, Logan, Utah USA
                [35 ]Anton Pannekoek Institute, Amsterdam, The Netherlands
                [36 ]ISNI 0000 0001 2181 4888, GRID grid.8430.f, Graduate Program in Electrical Engineering, , Universidade Federal de Minas Gerais, ; Belo Horizonte, Brazil
                [37 ]GRID grid.432839.7, Google LLC, ; Montreal, Quebec Canada
                [38 ]GRID grid.420451.6, Google LLC, ; Cambridge, MA USA
                [40 ]ISNI 0000 0004 0502 9283, GRID grid.22401.35, International Centre for Theoretical Sciences, , Tata Institute of Fundamental Research, ; Bengaluru, India
                [41 ]ISNI 0000 0001 1015 3164, GRID grid.418391.6, Department of Physics, , Birla Institute of Technology and Science, ; Pilani, India
                [42 ]Independent researcher, Milan, Italy
                [43 ]ISNI 0000 0001 2297 4381, GRID grid.7704.4, Institute of Environmental Physics, , University of Bremen, ; Bremen, Germany
                [44 ]ISNI 0000 0004 1936 9991, GRID grid.35403.31, Department of Computer Science, , University of Illinois at Urbana-Champaign, ; Urbana, IL USA
                [45 ]Laboratoire Photonique, Numérique et Nanosciences UMR 5298, Université de Bordeaux, Institut d’Optique Graduate School, CNRS, Talence, France
                [46 ]ISNI 0000000122986657, GRID grid.34477.33, The University of Washington eScience Institute, , The University of Washington, ; Seattle, WA USA
                [47 ]ISNI 0000 0001 2322 0493, GRID grid.431393.f, Federal Reserve Board of Governors, ; Washington, DC, USA
                [48 ]Datadog Inc., New York, NY USA
                [49 ]GRID grid.451798.6, HQ, Orexplore, ; Stockholm, Sweden
                [50 ]ISNI 0000 0004 1936 9684, GRID grid.27860.3b, Statistics Department, , University of California - Davis, ; Davis, CA USA
                [51 ]ISNI 0000 0001 0941 6502, GRID grid.189967.8, Emory University, ; Atlanta, GA USA
                [52 ]GRID grid.504129.b, Applied BioMath, ; Concord, MA USA
                [53 ]ISNI 0000 0004 1936 8948, GRID grid.4991.5, Department of Computer Science, , University of Oxford, ; Oxford, UK
                [54 ]ISNI 0000 0000 9780 0901, GRID grid.11469.3b, NeuroInformatics Laboratory, , Bruno Kessler Foundation, ; Trento, Italy
                [55 ]Independent researcher, Chicago, IL USA
                [56 ]ISNI 0000000121885934, GRID grid.5335.0, Department of Engineering, , University of Cambridge, ; Cambridge, UK
                [57 ]ISNI 0000 0001 2176 4817, GRID grid.5399.6, Aix Marseille Univ, CNRS, Centrale Marseille, LMA, ; Marseille, France
                [58 ]ISNI 0000 0001 2190 4373, GRID grid.7700.0, Interdisciplinary Center for Scientific Computing (IWR), , Heidelberg University, ; Heidelberg, Germany
                [59 ]ISNI 0000 0004 0632 0988, GRID grid.423531.2, ABB Corporate Research, ABB AG, ; Ladenburg, Germany
                [60 ]ISNI 0000 0001 1090 0254, GRID grid.6738.a, Institut für Mathematische Optimierung, , Technische Universität Carolo-Wilhelmina zu Braunschweig, ; Braunschweig, Germany
                [61 ]ISNI 0000 0001 2172 9288, GRID grid.5949.1, Independent researcher, ; Cologne, Germany
                [62 ]ISNI 0000 0001 2231 4551, GRID grid.184769.5, Lawrence Berkeley National Laboratory, ; Berkeley, CA USA
                [63 ]ISNI 0000 0001 2108 9006, GRID grid.7307.3, Institut für Physik, , Universität Augsburg, ; Augsburg, Germany
                [64 ]ISNI 0000 0004 1936 9924, GRID grid.89336.37, Applied Research Laboratories, , The University of Texas at Austin, ; Austin, TX USA
                [65 ]ISNI 0000 0001 2179 9593, GRID grid.24827.3b, Department of Radiology, School of Medicine, , University of Cincinnati, ; Cincinnati, OH USA
                [66 ]ISNI 0000 0000 9025 8099, GRID grid.239573.9, Department of Radiology, , Cincinnati Children’s Hospital Medical Center, ; Cincinnati, OH USA
                [67 ]Ascent Robotics Inc., Tokyo, Japan
                [68 ]GRID grid.462182.b, ENSTA Bretagne, ; Brest, France
                [69 ]ISNI 0000 0004 1936 973X, GRID grid.5252.0, Faculty of Physics, , Ludwig-Maximilians-Universität, ; München, Germany
                [70 ]GRID grid.440930.a, Excellence Cluster Universe, ; München, Germany
                [71 ]Independent researcher, Malden, Massachusetts USA
                [72 ]Data Sciences, Chan Zuckerberg Biohub, San Francisco, CA USA
                [73 ]ISNI 0000 0001 0721 6013, GRID grid.8954.0, Faculty of Mechanical Engineering, , University of Ljubljana, ; Ljubljana, Slovenia
                [74 ]ISNI 0000 0004 1936 834X, GRID grid.1013.3, Sydney Informatics Hub, , The University of Sydney, ; Camperdown, NSW Australia
                [75 ]ISNI 0000 0001 2157 0406, GRID grid.7870.8, Instituto de Astrofísica, , Pontificia Universidad Católica de Chile, ; Santiago, Chile
                [76 ]ISNI 0000 0001 1019 2104, GRID grid.450265.0, Max Planck Institute for Extraterrestrial Physics, ; Garching, Germany
                [77 ]ISNI 0000 0004 1936 9713, GRID grid.5719.a, University of Stuttgart, Machine Learning and Robotics Lab, ; Stuttgart, Germany
                [78 ]ISNI 0000 0001 0169 5930, GRID grid.411182.f, Department of Electrical Engineering, , Universidade Federal de Campina Grande, ; Campina Grande, Brazil
                [79 ]ISNI 0000 0001 2153 9986, GRID grid.9764.c, Department of Computer Science, , Kiel University, ; Kiel, Germany
                [80 ]ISNI 0000 0001 2159 2859, GRID grid.170430.1, Planetary Sciences Group and Florida Space Institute and Department of Physics, , University of Central Florida, ; Orlando, FL USA
                [81 ]Independent researcher, Madrid, Spain
                [82 ]ISNI 0000 0004 1936 7857, GRID grid.1002.3, Monash Micro Imaging, , Monash University, ; Clayton, VIC Australia
                [83 ]ISNI 0000000096214564, GRID grid.266190.a, Department of Molecular, Cellular, and Developmental Biology, , University of Colorado, Boulder, ; Boulder, CO USA
                [84 ]ISNI 0000 0001 2171 9311, GRID grid.21107.35, Department of Physics and Astronomy, , Johns Hopkins University, ; Baltimore, MD USA
                [85 ]Independent researcher, Munich, Germany
                [86 ]ISNI 0000 0004 1936 7822, GRID grid.170205.1, Center for Advanced Radiation Sources, , The University of Chicago, ; Chicago, IL USA
                [87 ]ISNI 0000 0001 2190 1447, GRID grid.10392.39, University of Tübingen, ; Tübingen, Germany
                [88 ]Independent researcher, Rugby, UK
                [89 ]ISNI 0000 0004 0451 3647, GRID grid.499363.2, Two Sigma Investments, ; New York, NY USA
                [90 ]ISNI 0000000123222966, GRID grid.6936.a, Department of Mechanical Engineering, , Technical University of Munich, ; Garching, Germany
                [91 ]Independent researcher, Berkeley, CA USA
                [92 ]Independent researcher, London, UK
                [93 ]ISNI 0000 0001 2172 9288, GRID grid.5949.1, Independent researcher, ; Berlin, Germany
                [94 ]ISNI 0000 0004 1217 7655, GRID grid.419318.6, Intel Corp., ; Austin, TX USA
                [95 ]Independent Researcher, Horten, Norway
                [96 ]Independent researcher, Daly City, CA USA
                [97 ]ISNI 0000 0004 0640 9990, GRID grid.417724.3, D. E. Shaw Research, ; New York, NY USA
                [98 ]ISNI 0000 0001 2286 1424, GRID grid.10420.37, Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, , University of Vienna, ; Vienna, Austria
                [99 ]Independent researcher, Melbourne, Australia
                [100 ]ISNI 0000000121662407, GRID grid.5379.8, School of Physics and Astronomy, , University of Manchester, ; Manchester, UK
                [101 ]ISNI 0000 0001 2167 3675, GRID grid.14003.36, Electrical and Computer Engineering, , University of Wisconsin–Madison, ; Madison, WI USA
                [102 ]ISNI 0000 0004 1757 2822, GRID grid.4708.b, Dipartimento di Informatica, , Università degli Studi di Milano, ; Milan, Italy
                [103 ]ISNI 0000 0000 9280 468X, GRID grid.249801.6, Inter-University Centre for Astronomy and Astrophysics, Ganeshkhind, ; Pune, India
                [104 ]GRID grid.440880.0, Kavli Institute for the Physics and Mathematics of the Universe, ; Kashiwa-shi, Japan
                [105 ]Waymo LLC, Mountain View, CA USA
                [106 ]ISNI 0000 0001 0671 5144, GRID grid.260975.f, Faculty of Engineering, , Niigata University, Nishi-ku, ; Niigata, Japan
                [107 ]ISNI 0000 0001 0694 4940, GRID grid.438526.e, Virginia Polytechnic Institute and State University, ; Blacksburg, VA USA
                [108 ]Aperio Software, Headingley Enterprise and Arts Centre, Leeds, UK
                [109 ]ISNI 0000 0001 2172 9288, GRID grid.5949.1, Independent researcher, ; Duisburg, Germany
                [110 ]GRID grid.66859.34, Broad Institute, ; Cambridge, MA USA
                [111 ]Independent researcher, Gainesville, FL USA
                [112 ]ISNI 0000 0001 2248 7639, GRID grid.7468.d, Department of Psychology, , Humboldt University of Berlin, ; Berlin, Germany
                [113 ]Epiq Solutions, Schaumburg, IL USA
                [114 ]GRID grid.469860.5, Max Planck Institute for Software Systems, ; Kaiserslautern, Germany
                [115 ]ISNI 0000 0001 2179 2404, GRID grid.254880.3, Department of Psychology and Brain Sciences, , Dartmouth College, ; Hanover, NH USA
                [116 ]ISNI 0000 0001 2107 4242, GRID grid.266100.3, Jacobs School of Engineering, , University of California San Diego, ; La Jolla, CA USA
                Author information
                http://orcid.org/0000-0002-0300-3333
                http://orcid.org/0000-0003-4806-3601
                http://orcid.org/0000-0003-2364-6157
                http://orcid.org/0000-0001-9276-1891
                http://orcid.org/0000-0002-5263-5070
                http://orcid.org/0000-0002-4548-3558
                http://orcid.org/0000-0002-5540-4825
                http://orcid.org/0000-0003-3632-8529
                http://orcid.org/0000-0002-2382-8308
                Article
                686
                10.1038/s41592-019-0686-2
                7056644
                32015543
                3f63db69-b23f-4932-8161-0e595fdb9dca
                © The Author(s) 2020

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 28 July 2019
                : 9 October 2019
                : 14 November 2019
                Categories
                Perspective
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                © The Author(s), under exclusive licence to Springer Nature America, Inc. 2020

                Life sciences
                computational biology and bioinformatics,biophysical chemistry,technology
                Life sciences
                computational biology and bioinformatics, biophysical chemistry, technology

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