Software Updates 2021

2021-12-13: Routine updates…

  • Python:

    • (upd) various packages

  • Executables:

    • (upd) routine Linux package updates, including R packages

    • (upd) Jupyter Lab 3.2.5

  • Known issues:

    • Selenium in Python, you can use the “Preivous” software environment instead

2021-11-01: taichi, tikzplotlib, Scikit Optimize

  • Python 3 (system-wide):
  • Executables:

    • (upd) Jupyter Lab 3.2.1

    • (upd) routine Linux package updates, including R packages

2021-10-10: Routine updates

  • (upd) routine updates for system packages, Python and R

2021-09-27: Mathics 4, Scikit-Learn 1.0, Julia 1.6.3

  • Executables:
  • Python (system-wide):

  • various package and system lib updates

2021-09-07: PyPy (Python 3)

  • Python 3:

    • (new) for the audacious: PyPy jupyter kernel.

  • Misc:

    • (upd) as usual, updated Python and Linux/R packages.

2021-09-02: Sage 9.4, NASM, …

  • Executables:

    • (new): SageMath 9.4 – Release Tour Sage 9.4, accessible via the “SageMath 9.4” Jupyter kernel, sage-9.4 on the command-line, or run sage_select 9.4 and restart the Sage Worksheet server. In the future, this will become the default Sage version.

    • (new): NASM 2.15.05 – Netwide Assembler (NASM), an asssembler for the x86 CPU architecture portable to nearly every modern platform

  • Misc:

    • (upd) various updates to the “system-wide” and “Anaconda 2020” Python environments

    • (upd) some Julia packages

    • (upd) Linux packages

2021-08-13: R 4.1.1

  • Executables:

    • (upd) R 4.1.1

    • (new) zig 0.8.0 – a general-purpose programming language and toolchain for maintaining robust, optimal, and reusable software

  • Python 3 (system-wide):

2021-08-02: Octave 6.3.0

2021-08-03: VSCode

  • Python 3 (system-wide)
  • Executables:

    • (new) VSCode Server – available in “+New” or “Settings”

    • (upd) Jupyter Lab 3.1.1

2021-07-26 Julia 1.6.2

  • Julia:

    • (upd) version 1.6.2

    • (upd) all globally installed packages

  • Executables

    • (upd) Jupyter Lab 3.0.16

    • (upd) pandoc 2.14.1

    • (new) Paraview – as a test. Open an x11 desktop, then cd /ext/paraview/current/bin/ and ./paraview.

2021-07-13: flipper in Sage

  • Sage 9.3:

    • (new) flipper – a program for computing the action of mapping classes on laminations on punctured surfaces using ideal triangulation coordinates

2021-07-12: MODIS and PreTeXt

  • Executables:
  • R (system-wide):

    • (new) MODIS – automatizing the creation of time series of raster images derived from MODIS Land Products data

  • various system package updates

2021-07-05: Package updates

Various updates for Python, R and other languages and also Linux system packages.

2021-06-07: Octave 6.2.0 & Bugfixes

  • Executables:
  • R (system-wide):

    • updating Cairo to fix a ggplot2 problem

    • various package updates

  • Python 3 (system-wide):

    • various updates

2021-05-17: HAXE

  • Executables:

    • (new) HAXE 4.2.1 – an open source high-level strictly-typed programming language with a fast optimizing cross-compiler

    • (new) SageMath 9.3: available as sage-9.3 on the command-line and via Jupyter Notebooks. For Sage Worksheets, run sage_select 9.3 first.

2021-04-26: Julia 1.6.1

2021-04-03: R 4.0.5 (“Shake and Throw”)

  • R:

    • (upd) R to 4.0.5

    • (upd) rebuilding/updating all R packages

  • Python 3 (system-wide):

    • (new) Pyro 1.6.0 – Deep universal probabilistic programming with Python and PyTorch

    • (upd) various pkgs

2021-03-21: Julia 1.6

  • Julia:

    • Version 1.6 & rebuilding all pre-installed libraries

  • Python 3 (Anaconda 2020):

    • (new) lmfit – provides a high-level interface to non-linear optimization and curve fitting problems for Python

    • (new) periodictable-py – provides an extensible periodic table of the elements pre-populated with data important to neutron and X-ray scattering experiments

  • Python 3 (system-wide):

    • (new) sktime – specialized time series algorithms and scikit-learn compatible tools to build, tune and validate time series models for multiple learning problems

    • (upd) various libs

2021-03-08: Bioconductor

  • R (system-wide):

    • (upd) refresh of all bioconductor packages, incl. oligo

    • (new) biomaRt – provides an interface to a growing collection of databases

2021-03-05: ASE, Papermill, etc.

  • Software

    • (new) papermill – Papermill is a tool for parameterizing and executing Jupyter Notebooks.

    • (upd) system packages, some python packages, R, etc.

  • Python 3 (Anaconda 2020)

    • (new) ase – The Atomic Simulation Environment (ASE) is a set of tools and Python modules for setting up, manipulating, running, visualizing and analyzing atomistic simulations.*

2021-02-17: Rust 1.5

  • Software

    • (upd) Rust 1.5

    • (upd) various system packages

2021-01-28: Julia 1.5.3, MACS2, …

  • Julia:

    • (upd) to version 1.5.3 and updating all packages we provide per default

  • Software

    • (new) macs2 – Model-based Analysis of ChIP-Seq

    • various system package updates

2021-01-07: More Python libs!

  • Python 3 (system-wide):

    • (new) agate: a Python data analysis library that is optimized for humans instead of machines. It is an alternative to numpy and pandas that solves real-world problems with readable code.

    • (new) scrapy: An open source and collaborative framework for extracting the data you need from websites. In a fast, simple, yet extensible way.

    • (new) squarify: Pure Python implementation of the squarify treemap layout algorithm

    • (new) SHERPA: A Python Hyperparameter Optimization Library

  • various other package and software updates