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.

The khmer package is a freely available software library for working efficiently with fixed length DNA words, or k-mers. khmer provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruijn graph partitioning, and digital normalization. khmer is implemented in C++ and Python, and is freely available under the BSD license at  https://github.com/dib-lab/khmer/.

Eight forages (alfalfa, birdsfoot trefoil, red clover, bromegrass, orchardgrass, perennial ryegrass, quackgrass, and timothy) at three maturities were evaluated for ruminal DM, CP, and NDF degradation kinetics. Duplicate dacron bags were incubated for 0, 3, 6, 10, 13, 25, 48, and 72 h in two late lactation Holstein cows fitted with ruminal cannulas over eight experimental periods. Species and maturity effects were observed for soluble, slow, and undegraded fractions; degradation rate; and ruminally degradable DM, CP, and NDF. Significant species by maturity interactions also were evident for fractions and ruminal degradabilities of DM, CP, and NDF. Legumes exhibited more extensive ruminal DM degradation than did grasses. No clear trends were evident in rate of ruminal CP degradation between legumes and grasses. Mature grasses were lowest in ruminally degradable CP. Legumes exhibited a higher undegraded fraction and faster degradation rate of slowly degraded NDF fractions, resulting in similar ruminally degraded NDF for legumes and grasses. Extensive differences in ruminal degradation kinetics existed between perennial legume and grass species and maturities. Species by maturity interactions were diverse, making categorization of degradation characteristics of legumes and grasses difficult.

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Six multiparous, ruminally cannulated Holstein cows (46 DIM, 584 kg of BW) and 6 primiparous Holstein cows (35 DIM, 506 kg of BW) were used in two 6 x 6 Latin squares with 21-d periods to examine the effects of level of non-fiber carbohydrate, source of fibrous carbohydrate, and Aspergillus oryzae fermentation extract on intake, digestion, and milk production. Treatments were 42 and 36% non-fiber carbohydrate; shelled corn and soybean meal were replaced partially by beet pulp and dried brewers grains or soy hulls and dried brewers grains in 36% non-fiber carbohydrate diets. These three diets then were supplemented with 0 or 3 g/d of A. oryzae. Milk production and composition and DMI were not significantly affected by level or source of carbohydrate, although intake of NDF was significantly higher for 36% non-fiber carbohydrate diets. Total tract apparent digestibilities of ADF and NDF were higher for 36% non-fiber carbohydrate diets. Supplementation with A. oryzae did not significantly affect DMI, milk production, or total tract apparent digestibilities; however, milk fat content was decreased. Partial replacement of corn with fibrous carbohydrate sources, beet pulp and soy hulls, did not adversely affect intake or milk production in early lactation cows fed alfalfa silage-based diets.