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.

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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 report on Keck optical BVRI images and spectroscopy of the companion of the binary millisecond pulsar PSR J0218+4232. A faint bluish (V = 24.2, B - V = 0.25) counterpart is observed at the pulsar location. Spectra of this counterpart reveal Balmer lines which confirm that the companion is a helium-core white dwarf. We find that the white dwarf has a temperature of T_(eff) = 8060 ± 150 K. Unfortunately, the spectra are of insufficient quality to put a strong constraint on the surface gravity, although the best fit is for low log g and hence low mass (~0.2 M_⊙), as expected. We compare predicted white dwarf cooling ages with the characteristic age of the pulsar and find similar values for white dwarf masses of 0.19 to 0.3 M_⊙. These masses would imply a distance of 2.5 to 4 kpc to the system. The spectroscopic observations also enable us to estimate the mass ratio between the white dwarf and the pulsar. We find q = 7.5 ± 2.4, which is consistent with the current knowledge of white dwarf companions to millisecond pulsars.

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Temperature and cooling age of the white dwarf companion of PSR J0218+4232

We present a high-resolution echelle spectrum taken with the Very Large Telescope and analyse archival Hubble Space Telescope photometry of the recently identified companion of the eclipsing millisecond radio pulsar PSR J1740-5340 in the globular cluster NGC 6397. From the spectrum, we show that the companion is metal poor, as expected for a member of NGC 6397. Using synthetic photometry, and assuming a true distance modulus of 12.13 ′ 0.15 mag and a colour excess of E B - V = 0.179, we derive a radius of 1.60 ′ 0.17 R O . and an effective temperature of 5410 ′ 50 K, implying a luminosity of 2.0 ′ 0.4 L O . (1σ errors). These properties make it similar to the so-called "sub-subgiants" in the old open cluster M67 and "red stragglers" in 47 Tuc, which have luminosities comparable to those of turn-off stars, but cooler temperatures and larger radii. The light curve of the companion is well described by ellipsoidal variations, and despite the incomplete (∼60%) phase coverage, we are able to derive good constraints on a number of the system parameters. In particular, for the inclination we find a 2-σ lower limit of i > 48° (i > 46° at 3σ). Assuming a pulsar mass of 1.2 < M M S P < 2.4 M O ., this implies a companion mass in the range 0.14 < M c o m p < 0.38 M O .. Combined with the photometric constraint, we find a best fit for i ≃ 50° and M c o m p ≃ 0.3 M O .. We infer a Roche lobe filling factor by radius of ∼97%. Surprisingly, we find no evidence whatsoever for irradiation of the companion, despite the high inferred rotational energy loss of the pulsar (E ≃ 1.4 × 10 3 5 ergs - 1 ). We discuss possible reasons, but find most lacking. We hypothesise that the system is a triple, and that the acceleration due to a third body in a wide orbit around the binary led to an overestimate of the intrinsic spin-down rate and hence the spin-down luminosity. This can be tested by further timing observations. We also discuss two other puzzles, viz., the system's location far outside the cluster core and the companion's large radius and luminosity. We suggest that the system was formed in a binary-binary encounter in the core, due to which the system acquired a substantial velocity, and the companion - which must have been a somewhat evolved turn-off star - lost much of its envelope. We suggest other "red stragglers" and "sub-subgiants" might have formed by similarly drastic encounters.

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The eclipsing millisecond pulsar PSR J1740-5340 and its red straggler companion

We present Hubble Space Telescope/STIS, Keck J- and Ks-band, and VLA 332 and 1400 MHz images of the region around the soft γ-ray Repeater SGR 1900+14. No nonstellar sources were detected at the position of SGR 1900+14, giving 3 σ limits of S332 MHz < 6 mJy, S1.4 GHz < 1.5 mJy, m50CCD 29.0 mag, J 22.8 mag, Ks 20.8 mag (point sources), and S332 MHz < 6.1 mJy arcmin-2, S1.4 GHz < 6.2 mJy arcmin-2 (extended emission). Given the very high extinction, the STIS and J-band nondetections are not constraining, but the Ks-band limit rules out basic accretion disk models for SGR 1900+14 and is almost comparable in depth to the Ks-band detection for the anomalous X-ray pulsar 4U 0142+61. Finally, we report the detection in this field of three new candidate supernova remnants, SNRs G043.5+00.6, G042.0-00.1, and G041.5+00.4.

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Deep Radio, Optical, and Infrared Observations of SGR 1900+14

We present K band photometry of the region including the radio error box of the soft X-ray tran- sient 4U 1630 47 during its 1998 outburst. We detect a variable source at K =1 6:1 mag located inside the radio error circle which we identify as the counterpart to the X-ray source. We discuss the properties of the source, and conclude that it is most likely a black-hole X-ray binary similar to 4U 1543 47, GRO J1655 40 or SAX J1819.3 2525, containing a relatively early-type secondary.

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The IR counterpart of the black-hole candidate 4U 1630-47

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M. H. van Kerkwijk

Papers

Temperature and cooling age of the white dwarf companion of PSR J0218+4232

The eclipsing millisecond pulsar PSR J1740-5340 and its red straggler companion

Deep Radio, Optical, and Infrared Observations of SGR 1900+14

The IR counterpart of the black-hole candidate 4U 1630-47

Infrared spectroscopy of low-mass X-ray binaries