SciPy is an open source scientific computing library for the Python programming language. SciPy 1.0 was released in late 2017, about 16 years after the original version 0.1 release. SciPy has become a de facto standard for leveraging scientific algorithms in the Python programming language, with more than 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories, and millions of downloads per year. This includes usage of SciPy in almost half of all machine learning projects on GitHub, and usage by high profile projects including LIGO gravitational wave analysis and creation of the first-ever image of a black hole (M87). The library includes functionality spanning clustering, Fourier transforms, integration, interpolation, file I/O, linear algebra, image processing, orthogonal distance regression, minimization algorithms, signal processing, sparse matrix handling, computational geometry, and statistics. In this work, we provide an overview of the capabilities and development practices of the SciPy library and highlight some recent technical developments.

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SciPy 1.0--Fundamental Algorithms for Scientific Computing in Python

Array programming provides a powerful, compact and expressive syntax for accessing, manipulating and operating on data in vectors, matrices and higher-dimensional arrays. NumPy is the primary array programming library for the Python language. It has an essential role in research analysis pipelines in fields as diverse as physics, chemistry, astronomy, geoscience, biology, psychology, materials science, engineering, finance and economics. For example, in astronomy, NumPy was an important part of the software stack used in the discovery of gravitational waves1 and in the first imaging of a black hole2. Here we review how a few fundamental array concepts lead to a simple and powerful programming paradigm for organizing, exploring and analysing scientific data. NumPy is the foundation upon which the scientific Python ecosystem is constructed. It is so pervasive that several projects, targeting audiences with specialized needs, have developed their own NumPy-like interfaces and array objects. Owing to its central position in the ecosystem, NumPy increasingly acts as an interoperability layer between such array computation libraries and, together with its application programming interface (API), provides a flexible framework to support the next decade of scientific and industrial analysis. NumPy is the primary array programming library for Python; here its fundamental concepts are reviewed and its evolution into a flexible interoperability layer between increasingly specialized computational libraries is discussed.

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Array programming with NumPy

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.

/pdf/scipy-1-0-fundamental-algorithms-for-scientific-computing-in-45othhotbu.pdf

SciPy 1.0: fundamental algorithms for scientific computing in Python.

The status of experimental tests of general relativity and of theoretical frameworks for analyzing them is reviewed and updated. Einstein’s equivalence principle (EEP) is well supported by experiments such as the Eotvos experiment, tests of local Lorentz invariance and clock experiments. Ongoing tests of EEP and of the inverse square law are searching for new interactions arising from unification or quantum gravity. Tests of general relativity at the post-Newtonian level have reached high precision, including the light deflection, the Shapiro time delay, the perihelion advance of Mercury, the Nordtvedt effect in lunar motion, and frame-dragging. Gravitational wave damping has been detected in an amount that agrees with general relativity to better than half a percent using the Hulse-Taylor binary pulsar, and a growing family of other binary pulsar systems is yielding new tests, especially of strong-field effects. Current and future tests of relativity will center on strong gravity and gravitational waves.

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The Confrontation Between General Relativity and Experiment

Many physically motivated extensions to general relativity (GR) predict significant deviations at energies present in massive neutron stars. We report the measurement of a 2.01 $\pm $ 0.04 solar mass (M$_\odot $) pulsar in a 2.46-h orbit around a 0.172 $\pm $ 0.003 M$_\odot $ white dwarf. The high pulsar mass and the compact orbit make this system a sensitive laboratory of a previously untested strong-field gravity regime. Thus far, the observed orbital decay agrees with GR, supporting its validity even for the extreme conditions present in the system. The resulting constraints on deviations support the use of GR-based templates for ground-based gravitational wave detection experiments. Additionally, the system strengthens recent constraints on the properties of dense matter and provides novel insight to binary stellar astrophysics and pulsar recycling.

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A massive pulsar in a compact relativistic binary

We present a phase-coherent timing solution for RX J0420.0-5022, the coolest (kT {approx_equal} 45 eV) and fastest-spinning (P = 3.45 s) of the seven so-called isolated neutron stars (INSs). Using 14 observations with the XMM-Newton spacecraft in 2010 and 2011, we were able to measure a spin-down rate {nu}-dot = (-2.3 {+-} 0.2) x 10{sup 15} Hz s{sup -1} (P-dot =(2.8{+-}0.3)x10{sup -14} s s{sup -1}), from which we infer a dipolar magnetic field of 1.0 x 10{sup 13} G. With reasonable confidence we were able to extend the timing solution back to archival XMM-Newton from 2002 and 2003, giving the same solution but with considerably more precision. This gives RX J0420.0-5022 the lowest dipole magnetic field of the INSs. Our spectroscopy does not confirm the broad absorption feature at 0.3 keV hinted at in earlier observations, although difficulties in background subtraction near that energy make conclusions difficult. With this, all six of the INSs that have confirmed periodicities now have constrained spin-downs from coherent solutions. The evidence that the INSs are qualitatively different from rotation-powered pulsars now appears robust, with the likely conclusion that their characteristic ages are systematically older than their true ages, because their fields have decayed. Themore » field decay probably also causes them to be systematically hotter than pulsars of the same (true) age.« less

A coherent timing solution for the nearby, thermally emitting isolated neutron star rx j0420.0-5022

We report on the identification of the optical counterpart of the binary millisecond pulsar PSR J1911-5958A, located in the outskirts of the globular cluster NGC 6752. At the position of the pulsar we find an object with $V=22.08$, $B-V=0.38$, $U-B=-0.49$. The object is blue with respect to the cluster main sequence by 0.8 mag in $B-V$. We argue that the object is the white dwarf companion of the pulsar. Comparison with white dwarf cooling models shows that this magnitude and colors are consistent with a low-mass white dwarf at the distance of NGC 6752. If associated with NGC 6752, the white dwarf is relatively young, $\la$$2\,$Gyr, which sets constraints on the formation of the binary and its ejection from the core of the globular cluster.

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Optical identification of the companion to PSR J1911-5958A, the pulsar binary in the outskirts of NGC 6752

Infrared Spectroscopy of Low-Mass X-ray Binaries

RX J0720.4-3125 is the third brightest neutron star in the soft X-ray sky and has been a source of mystery since its discovery, as its long 8-s period separates it from the population of typical radio pulsars. Three models were proposed for this source: a neutron star accreting from the interstellar medium, an off-beam radio pulsar, or an old, cooling magnetar. Using data from Chandra, ROSAT, and BeppoSAX we are able to place an upper limit to the period derivative, $|\dot{P}| < 3.6\times10^{-13}{s s}^{-1}$ (3-$\sigma$). While our upper limit on $\dot P$ allows for the accretion model, this model is increasingly untenable for another similar but better studied neutron star, RX J1856.5-3754, and we therefore consider the accretion model unlikely for RX J0720.4-3125. We constrain the initial magnetic field of RX J0720.4-3125 to be $\lsim 10^{14}$ G based on cooling models, suggesting that it is not and never was a magnetar, but is instead middle-aged neutron star. We propose that it is either a long-period high-magnetic field pulsar with $\dot P\sim 10^{-13}{s s}^{-1}$ similar to PSR J1814-1744, or a neutron star born with an initial period of $\approx 8.3$ s and $\dot P\sim 10^{-15}{s s}^{-1}$. The proximity of RX J0720.4-3125 is strongly suggestive of a large population of such objects; if so, radio pulsar surveys must have missed many of these sources.

X-ray Timing of the Enigmatic Neutron Star RX J0720.4-3125

We present optical and near-infrared observations with Keck of the binary millisecond pulsar PSR J0751+1807. We detect a faint, red object -with R = 25.08 ± 0.07, B - R = 2.5 ± 0.3, and R - I = 0.90 ± 0.10 - at the celestial position of the pulsar and argue that it is the white dwarf companion of the pulsar. The colours are the reddest among all known white dwarfs, and indicate a very low temperature, T eff ≈ 4000 K. This implies that the white dwarf cannot have the relatively thick hydrogen envelope that is expected on evolutionary grounds. Our observations pose two puzzles. First, while the atmosphere was expected to be pure hydrogen, the colours are inconsistent with this composition. Second given the low temperature, irradiation by the pulsar should be important, but we see no evidence for it. We discuss possible solutions to these puzzles.

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M. H. van Kerkwijk

Papers

A coherent timing solution for the nearby, thermally emitting isolated neutron star rx j0420.0-5022

Optical identification of the companion to PSR J1911-5958A, the pulsar binary in the outskirts of NGC 6752

Infrared Spectroscopy of Low-Mass X-ray Binaries

X-ray Timing of the Enigmatic Neutron Star RX J0720.4-3125

The ultra-cool white dwarf companion of PSR J0751+1807