25,955 Works

PyWavelets/pywt: PyWavelets 1.1.1

Gregory R. Lee, Ralf Gommers, Kai Wohlfahrt, Filip Wasilewski, Aaron O'Leary, Holger Nahrstaedt, David Menéndez Hurtado, Alexandre Sauvé, Thomas Arildsen, Helder Oliveira, Daniel M. Pelt, Ankit Agrawal, SylvainLan, Michel Pelletier, Matthew Brett, Frank Yu, Saket Choudhary, Daniele Tricoli, Luke M Craig, Lokesh Ravindranathan, Jonathan Dan, Jakirkham, Jacopo Antonello, Dawid Laszuk, Daniel Goertzen … & Asnt
This release is functionally identical to 1.1.0. This release modifiedsetup.pyto mark the package as Python 3.5+ only sopip`` will not try to install 1.1.1 on older Python versions. To prevent pip from trying to install 1.1.0 on older Python, the source tarball for 1.1.0 was removed from PyPI.

nutriverse/zscorer: zscorer v0.3.1

Ernest Guevarra
Fourth release of zscorer. In this release: fixed an issue with wrong URLs in README documentation. fixed an issue when calculating BMI-for-age where measurements are 0 resulting in error rather than providing an NA value. Now, when values for measurements are 0, the zscore produced is NA. updated MUAC for age to allow for calculation for children up to 19 years old based on article by Jay Berkeley and colleagues. updated Shiny app and added...

timetag/ETA: ETA 0.6.4

Zuzeng Lin & Lucas Schweickert
fixing the problem that incremental_cut function uses the wrong item in the cut definition for ByteSize (#89) supports scientific notation for Tools in Instrument Designer (#95) solving an issue that gets the frontend stuck (#94) wait_till_presnese is renamed to wait_for_data (#93) updated correlation recipe to support HydraHarp T2 and T3 formats as well as quTAG format implemented improved realtime script into Realtime.eta, Lifetime.eta add cut_modifier_syncrate for override the syncrate from the timetag header NOTE: wait_till_presnese...

JuliaOpt/SDPA.jl: v0.2.1

Benoît Legat, Juan Pablo Vielma & Eric Hanson
A changelog is being generated, please check back in a few minutes.


Suhas Somnath, Emily Costa, CompPhysChris & Ramav87
Bug fixes associated with dtype_utils.stack_real_to_target_dtype Bug fixes associated with latest numpy and h5py versions breaking USIDataset Improvements to MPI portions of the Process class Parts of plot_utils now work with dask.array inputs

kundajelab/deeplift: Added ability to provide a random state for dinucleotide shuffling

Av Shrikumar, Ji-Sung Kim, Annashcherbina, Pgreenside, AnjaSei, Amr , Kirill Timofeev & Johnny Israeli
(so that the random state doesn't have to be controlled by setting the numpy random seed externally, which doesn't always play will with jupyter notebooks)

geoschem/geos-chem: GEOS-Chem 12.6.0

The International GEOS-Chem User Community
GEOS-Chem 12.6.0
Released 18 Oct 2019 Contains the following updates: Combined heterogeneous chemistry updates, includes N2O5, NO3, NO2 reactive uptake updates Subgrid cloud NOy chemistry HNO3 cold-temperature deposition Quick fix for aerosol pH calculation when dry Remove isoprene in VBS (leaving aqueous) Updated aerosol hygroscopicity and optics Add EDGAR BCPI and BCPO emissions for remaining sectors to DICE-Africa Simple parameterization for CO2 dependence of stomatal resistance (off by default) Aerosol nitrate photolysis option (off by...

korpling/ANNIS beta.3

Thomas Krause, Weißenfels Benjamin, R. Tom, IrinaGlushanok, Martin Klotz, SHUO ZHANG, Luke Gessler, Amir Zeldes, Fab-Bar, Stephan Druskat, Adrianeboyd, Egon W. Stemle, Thomas N, Lari Lampen & Florian Petran
ANNIS is an open source, versatile web browser-based search and visualization architecture for complex multilevel linguistic corpora with diverse types of annotation.

scikit-hep/awkward-array: 0.12.14

Jim Pivarski, Charles Escott, Michael Hedges, Nicholas Smith, Mason Proffitt, Charlie Escott, Jonas Rembser, Jaydeep Nandi, Bfis, Doug Davis, Henry Schreiner, Pratyush Das, Peter Fackeldey, Nollde & Benkrikler
Fixes #205 with PR #206. Also the first version that drops awkward-numba from the tests and deployment. See Awkward 1.0.

scikit-hep/uproot: 3.10.7

Jim Pivarski, Pratyush Das, Dmitri Smirnov, Chris Burr, Matthew Feickert, Noah Biederbeck, Nicholas Smith, Jonas Rembser, Henry Schreiner, Hans Dembinski, Benkrikler, R. Marcel, Daniel Marley, Ruggero Turra, Michele Peresano & Chao Gu
PR #380, which fixes #367.

nf-core/rnaseq: nf-core/rnaseq version 1.4.2

Phil Ewels, Rickard Hammarén, Alexander Peltzer, Denis Moreno, Maxime Garcia, Rfenouil, Marchoeppner, Senthilkumar Panneerselvam, F. Sven, Jun-Wan, Johannes Alneberg, Aanil, Sofia Haglund, Paolo Di Tommaso, Anders Jemt, KochTobi, Lavanya Veeravalli, Colin Davenport, Rad Suchecki, Max Natthawut Adulyanukosol, Francesco , Denis OMeally & Chuan Wang
Version 1.4.2 Minor version release for keeping Git History in sync No changes with respect to 1.4.1 on pipeline level

casadi/casadi: 3.5.1

Joel Andersson, Jgillis, Casadibot, Greg Horn, Nielsvd, Robin Verschueren, Toivoh, Jack Vreeken, Scott Kovach, James Goppert, Timmercy, Christopher Dembia, Andrew Wagner, Andres Codas, Vitalij , Mikhail Katliar, Gabriel Hackebeil, Kozatt, Markus Friedrich, Doducle, Boris Belousov, Paul-Scott, Nicholas Bianco, Justin Carpentier & Jorn Baayen
Install Grab a binary from the table (for MATLAB, use the newest compatible version below): <table> <tr><th></th><th>Windows</th><th>Linux</th><th>Mac</th></tr> <tr> <th>Matlab</th> <td><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-matlabR2016a-v3.5.1.zip">R2016a</a> or later,<br /><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-matlabR2014b-v3.5.1.zip">R2014b</a>,<br /> <a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-matlabR2014a-v3.5.1.zip">R2014a</a>,<br /> <a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-matlabR2013a-v3.5.1.zip">R2013a</a> or R2013b</td> <td><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-linux-matlabR2014b-v3.5.1.tar.gz">R2014b</a> or later,<br /><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-linux-matlabR2014a-v3.5.1.tar.gz">R2014a</a></td> <td><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-osx-matlabR2015a-v3.5.1.tar.gz">R2015a</a> or later,<br /><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-osx-matlabR2014b-v3.5.1.tar.gz">R2014b</a>,<br /><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-osx-matlabR2014a-v3.5.1.tar.gz">R2014a</a></td> </tr> <tr> <th>Octave</th> <td> 4.4.1 (<a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-4.4.1-w32-v3.5.1.zip">32bit</a> / <a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-4.4.1-w64-v3.5.1.zip">64bit</a>), <br /> 4.4.0 (<a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-4.4.0-w32-v3.5.1.zip">32bit</a> / <a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-4.4.0-w64-v3.5.1.zip">64bit</a>), <br /> 5.1.0 (<a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-5.1.0-w32-v3.5.1.zip">32bit</a> / <a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-windows-octave-5.1.0-w64-v3.5.1.zip">64bit</a>)</td> <td><a href="https://github.com/casadi/casadi/releases/download/3.5.1/casadi-linux-octave-4.4.1-v3.5.1.tar.gz">4.4.1</a>,...

ga4gh/tool-registry-service-schemas: 2.0.0

Denis Yuen, Gary Luu, Brian O'Connor, Susheel Varma, Chris Llanwarne, Yasset Perez-Riverol, Paolo Di Tommaso, Olivier Sallou, Michael R. Crusoe, Jeff Gentry, Geraldine Van Der Auwera & David Mohs
Pending plenary

pycroscopy/pycroscopy: 0.60.4

Suhas Somnath, CompPhysChris, Ramav87, Numan Laanait, Str-Eat, Carlo , Raj Giridharagopal, Anugrah-Saxena, Ondrejdyck, Enrique A. Lopez-Guerra, Liambcollins, Magnus Nord, Kongjy & Joshua C Agar
A small primarily bugfix-related update to pycroscopy. Most changes are under the hood. Briefly, this new release has: Translator updates: Changes to trKPFM translator to add additional dimensions, several bugfixes A variety of small bug fixes Added method 'is_valid_file' to most routine translators Fixes and updates to examples in the documentation Edits to PiFM Translator and addition of a bandpass filter class to processing/fft

ubccr/xdmod: Open XDMoD 8.5.0 Release Candidate 2

Joe White, Steve Gallo, Greg Dean, Ben Plessinger, Jeffrey T. Palmer, Ryanrath, Rudra Chakraborty, Tom Yearke, Jeremy Pearce, Jeanette Sperhac, Mkzia, Treydock, Trevor Petrus, Simon Flood, Mjuwit, Ericblau, The XDMoD Team, Samathy Barratt, Kilian Cavalotti & Agervase
An open framework for collecting and analyzing HPC metrics.

samapriya/porder: porder: Simple CLI for Planet ordersV2 API

Samapriya Roy
Ordersv2 is the next iteration of Planet's API is the next iteration of Planet's API in getting Analysis Ready Data (ARD) delivered to you. Orders v2 allows you to improved functionality in this domain, including the capability to submit a number of images in a batch order, and perform operations such as the top of atmospheric reflectance, compression, coregistration and also enhanced notifications such as email and webhooks. Based on your access you can use...

Lepton: An Automaton for Literate Executable Papers

Sébastien Li-Thiao-Té
Lepton is a tool for reproducible research. This release improves the documentation better instructions for obtaining the software better instructions for compiling a complete fibonacci example

compomics/cellmissy: v1.4.1 New manual, extra example data

Gwendolien Sergeant, Niels Hulstaert, Ndmeulem, Paola Masuzzo & Alejandra Gonzalez-Beltran
We have updated the manual! It now contains area, single-cell and dose-response analysis. We mention the example dose-response data AND have added example single-cell data for generic import. Should you want to see anything else in the manual or more in depth, feel free to open an issue. Also some bugfixes.

STEN 1.0: Statistical Toolbox for Electrical Neuroimaging

Jean-François Knebel & Michael Philipp Notter
What is STEN? STEN is an open source software toolbox based on Python and R that can be used to compute statistics on several measures of electro- and magnetoencephalographic (EEG and MEG) signals. STEN enables the sample-point and sensor-wise analysis of EEG and MEG data, but also at the level of Global Field Power (GFP) and distributed neural source estimations (e.g. LAURA or LORETTA) by means of parametric and non-parametric (bootstrapping) repeated measure ANOVAs, ANCOVAs...

STEN 1.0: Statistical Toolbox for Electrical Neuroimaging

Jean-François Knebel & Michael Philipp Notter
What is STEN? STEN is an open source software toolbox based on Python and R that can be used to compute statistics on several measures of electro- and magnetoencephalographic (EEG and MEG) signals. STEN enables the sample-point and sensor-wise analysis of EEG and MEG data, but also at the level of Global Field Power (GFP) and distributed neural source estimations (e.g. LAURA or LORETTA) by means of parametric and non-parametric (bootstrapping) repeated measure ANOVAs, ANCOVAs...

HypothesisWorks/hypothesis: Hypothesis for Python - version 4.41.2

David R. MacIver, Zac Hatfield-Dodds, Pyup.Io Bot, Alex Chan, Stuart Cook, David Chudzicki, Ryan Soklaski, Jwg4, Alex Willmer, Tyler , Kyle Reeve, Mulkieran, Christopher Armstrong, Grigorios Giannakopoulos, Tyler Gibbons, Jeremy Thurgood, Paul Stiverson, Emmanuel Leblond, SuperStormer, Alexander Shorin, Peter C Kroon, Tom Prince, Mathieu PATUREL, Dwest-Netflix, Tom McDermott … & Thomas Kluyver
This patch changes some internal hashes to SHA384, to better support users subject to FIPS-140. There is no user-visible API change. Thanks to Paul Kehrer for this contribution! The canonical version of these notes (with links) is on readthedocs.

Infection Dating Tool

Eduard Grebe, Shelley N Facente, Andrew Powrie, Jarryd Gerber, Keith Grootboom, Gareth Priede & Alex Welte
This tool enables systematic interpretation of diagnostic test histories into formal plausible infection intervals, using data on "diagnostic delays" (i.e. window periods) of tests, and particular (dated) positive and negative test results. It outputs a detectable infection interval: Earliest Plausible Date of Detectable Infection (EP-DDI), Latest Plausible DDI (LP-DDI) and the midpoint of the interval as an infection time 'point estimate' or Estimated Date of Detectable Infection (EDDI). Detectable infection (for HIV) is by default...

MITgcm/MITgcm: checkpoint67m

Jean-Michel Campin, Patrick Heimbach, Martin Losch, Gael Forget, Edhill3, Alistair Adcroft, Amolod, Dimitris Menemenlis, Dfer22, Chris Hill, Oliver Jahn, Jeff Scott, Stephdut, Matt Mazloff, Baylorfk, Antnguyen13, Ed Doddridge, Ian Fenty, Michael Bates, Torge Martin, Ryan Abernathey, Samarkhatiwala, Timothy Smith, Jonathan Lauderdale, Hongandyan … & Andrew T. T. McRae
Entire previous MITgcm manual has been converted into (rst) docs including all the tutorial example docs.

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