Software Updates 2022

2022-11-25: Various updates

  • R (system-wide):

    • (new) msImpute – Imputation of label-free mass spectrometry peptides

    • (new) ComplexUpset – Create Complex UpSet Plots Using ‘ggplot2’ Components

  • Python 3 (system-wide):

    • various updates

  • Executables:

    • various updates

2022-10-29: Sage 9.7

  • Sage:

    • (upd) the system-wide default is now version 9.7. Run sage_select in a Linux Terminal to learn how to switch back to an earlier version.

  • Executables:

    • Various updates to software packages, python libs, R, etc.

2022-10-17: Fixing Julia/Pluto

  • Julia:

    • (fix) tweaking globally installed packages, updating Pluto notebook server, to fix it.

2022-10-13: More packages …

  • Python 3 (system-wide):

    • (new) mapclassify – open-source python library for Choropleth map classification

    • (new) lsqfit – least-squares fitting of noisy data by multi-dimensional, nonlinear functions of arbitrarily many parameters, each with a (Bayesian) prior

    • (new) gvar – representing, manipulating, and simulating Gaussian random variables numerically

  • Julia:

    • (upd) updating packages, and there is still 1.7 around

  • System:

    • as usual, various Linux, R and Python package updates

2022-10-03: Sage 9.7 and Julia 1.8

  • Sage:

    • (new) Sagemath 9.7 now available, although not the default yet.

  • Julia:

    • (new) Julia 1.8 Jupyter Kernel and julia-1.8 command-line available now.

  • System:

    • as usual, various Linux, R and Python package updates

2022-09-14: Fixing ipywidgets

Note

As a quick reminder, in Project Settings → Project Control → Software Environment, you can select “20.04 // Previous” to select the most recent “stable” software environment. It lags one or more versions behind what is available as “Default”.

  • Python3 (system-wide):

2022-09-13: Fixing HoloViews

  • Python3 (system-wide):

    • (upd) holoviews 1.15.0 to fix a compatibility issue

2022-09-12: Various updates

  • R (system-wide):

    • (new) gprofiler2: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via ‘g:Profiler’

  • System:

    • as usual, various Linux, R and Python package updates

2022-08-17: Python packages

  • Python: small updates to a few packages to fix incompatibilities

    • black 22.6 – we also added it to the list of tools to check up on

    • papermill 2.4.0 – a tool for parameterizing and executing Jupyter Notebooks

    • pyarrow 9.0.0 – a development platform for in-memory analytics

2022-08-15: Updates

  • System:

    • as usual, various Linux, R and Python package updates

2022-07-19: VSCode reverted

2022-07-18: Node 14

  • Executables:
  • System:

    • as usual, various Linux, R and Python package updates

2022-06-24: More Updates …

  • System:

    • as usual, various Linux, R and Python package updates

2022-05-30: Octave 7.1.0 and Sage 9.6

  • System wide:
    • (upd) SageMath 9.6 available via Jupyter Kernel, sage-9.6 on the command line and by default in Sage Worksheets.

      • (upd) Python 3.10: the “Python 3 (Sage)” kernel runs version 3.10, which is inside of the default Sage’s Python environment. (Python 3.10 example)

    • (upd) Octave 7.1.0 available by default.

    • (upd) Rust 1.61.0

  • System:

    • as usual, various Linux, R and Python package updates

2022-05-07: R 4.2

  • R (system-wide):

    • (upd) R 4.2 + many packages

    • Not yet ready for 4.2? In Settings → Control → Software Environment, you can select Ubuntu 20.04/2022-04-19.

  • Python3 (system-wide):

    • (new) prophet – a procedure for forecasting time series data based on an additive model where non-linear trends are fit with yearly, weekly, and daily seasonality, plus holiday effects

    • (new) pyspice – Simulate Electronic Circuit using Python and the Ngspice / Xyce Simulators

    • (new) timml – an analytic element model for steady multi-layer flow

  • System:

    • as usual, various Linux, R and Python package updates

2022-04-19: Various updates …

  • Python3 (system-wide) & System:

    • as usual, various Linux, R and Python package updates

  • Python 3 (system-wide):

    • (fix) resolved an xlrd <-> pandas incompatibility for reading older Excel xls files.

2022-03-24: New Anaconda Environment

  • (new) Anaconda 2021:

    • Despite we already have the year 2022, the installer is versioned as 2021.11, hence that name.

    • Most of the packages that were installed in Anaconda 2020 are also installed here.

    • The Python version is 3.9.

    • Anaconda 2020 will stay around, but updates or additional packages will go into the 2021 edition.

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

    • as usual, various Linux, R and Python package updates

2022-03-19: Bioconductor Maintenance

  • R:
  • System:

    • various Linux, R and Python package updates

2022-03-08: Regular update

  • System:

    • various Linux, R and Python package updates

2022-02-27: Removing PyPy Notebooks

  • Jupyter:

    • removing pypy kernel, since it is broken. pypy3 still available on the command-line.

  • Sage:

    • admcycles: updated to be compatible with 9.5

  • Executables:

    • (new) valgrind

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

2022-02-12: Sage 9.5

  • Sage:
  • Python:

    • (new) numpyro 0.8.0 – Probabilistic programming with NumPy powered by JAX for autograd and JIT compilation

    • (upd) various routine pkg updates

  • Julia:

    • (upd) Version 1.7.2

  • Executables:

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

2021-12-13: Julia 1.7 & various updates

  • Julia:

    • (new) Version 1.7 now available

  • Python 3:

    • (upd) routine upgrades

  • Executables:

    • (new) GNU C Compiler version 10: gcc-10, g++-10, …

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