Software Updates 2020

2020-11-19 : Mathics, gprMax, and pybedtools

  • Tools:
    • (new) Mathics – a general-purpose computer algebra system (CAS). It is an open-source alternative to Mathematica.
    • (new) file managers: nnn, ranger, and lfm
    • (upd) various system package updates
  • Python 3 (system-wide):
    • (new) gprMax – electromagnetic simulation software
    • (new) pybedtools – is widely used for genomic interval manipulation or “genome algebra”
    • (upd) various packages updates

2020-11-09 : RDkit, Matplotlib Venn and data8 datascience

  • Python 3 (Anaconda 2020)
    • (new) RDkit 2020.09.1 – Open-Source Cheminformatics Software
    • (new) matplotlib_venn
    • (upd) various package updates
  • Python 3 (system-wide)
    • (new) datascience by data8 – written for use in Berkeley’s DS 8 course and contains useful functionality for investigating and graphically displaying data.
    • (upd) various package updates
  • Linux system
    • (upd) various package updates

2020-11-01: Sage 9.2

../_images/sage9.2-3d-ani.png

2020-10-28: Pandoc 2.11

2020-10-12: RPC info, PyCaret, R 4.0.3, …

  • Utils:
    • (new) rpcinfo – makes an RPC call to an RPC server and reports what it finds
  • R:
    • (upd) R 4.0.3
    • various package updates
  • Python 3 (system-wide):
    • (new) pycaret 2.1.2 – an open source, low-code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment
    • various package updates
  • Julia:
    • (upd) Julia 1.5.2

2020-09-28: aTSA, BERT and pyGIMLi

  • Node.js:
    • (upd) typescript 4.0.2, prettier@2.1.1, webpack@4.44.1, coffeescript@2.5.1, data-cli@0.10.1, ijavascript@5.2.0, …
  • R (system-wide):
    • (new) aTSA – Contains some tools for testing, analyzing time series data and fitting popular time series models such as ARIMA, Moving Average and Holt Winters, etc.
    • (upd) various packages
  • Python 3 (system-wide):
  • Python 3 (Anaconda 2020):
    • (new) pyGIMLi– an open-source multi-method library for modelling and inversion in geophysics
    • (new) BERT – a software package for modelling and inversion of Electrical Resistivity Tomography data
    • (upd) various packages
  • Utilities:

2020-09-12: Regular update

2020-09-01: Julia 1.5.1

  • Julia:
    • updated to 1.5.1
    • various package updates
  • Python (system-wide):
  • R (system-wide)
    • various package updates
  • Software

2020-08-18: Ubuntu 20.04

The default environment for new projects changed: learn more …

2020-08-14/18.04: Regular update of Ubuntu 18.04

Cumulative updates to various software package environments.

2020-07-31: Cumulative Updates

Yet another round of cumulative updates to Linux, Python and R and a new tool grepcidr.

2020-07-16: Minor/Bugfixes

This is a cumulative update with several small changes and bugfixes. For example a dependency problem for PyTorch. A noteworthy new library is Epidemics-on-Networks for Python 3 (system-wide), e.g. EoN example test.

2020-06-20: Updating SnapPy in SageMath

2020-06-06: Prophet and pmdarima

  • Python 3 (system-wide)
    • (new) pmdarima 1.6.1 – ARIMA estimators for Python
    • (new) fbprophet – Prophet is 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.
    • (upd) numba 0.49.1, numpy 1.18.5

2020-05-27: Sage 9.1 and Node.js 12

2020-05-20

2020-05-12: Octave 5.2.0

2020-05-10: QuSpin and RmdFormats

  • Python 3 (Anaconda 2019):
    • (new) QuSpin 0.3.4 – Python package for exact diagonalization and quantum dynamics of arbitrary boson, fermion and spin many-body systems. QuSpin supports the use of various (user-defined) symmetries for one and higher-dimensional lattice systems, (imaginary) time evolution following arbitrary user-specified driving protocols, and constrained Hilbert spaces.
  • Python 3 (system-wide)
    • (fix) the /ext/bin/tensorboard wrapper script works again
    • (upd) dask/distributed 2.16.0
  • R (system-wide)
    • (new) rmdformats – provides several HTML output formats of unique and attractive styles for RMarkdown
    • various package updates …

2020-05-08: Fixing Keras

2020-05-04: Stellargraph

  • Python 3 (system-wide)
  • R (system-wide)
    • (new) genlasso 1.4 – Provides fast algorithms for computing the solution path for generalized lasso problems
    • (new) coronavirus 0.1 – Provides a daily summary of the Coronavirus (COVID-19) cases by state/province
    • many additional packages and updates
  • Jupyter Notebooks:
    • (rem) disabling deprecated and little useful kernels:
      • Julia 1.3: use Julia 1.4
      • Sage’s Python 2: use Sage’s Python mode. also, starting with 9.0 it’s Python 3
      • Sage’s R: use R (system-wide), there is no reason left to use this one

2020-04-25: R 3.6.3 and Julia 1.4.1

  • R (system-wide)
    • (upd) Upgrading R to 3.6.3 -- "Holding the Windsock" and many R packages
    • (rem) Removing r-cran-bvs, r-cran-haplo.ccs, and r-cran-haplo.stats, because they were holding back updating R
  • Julia
  • Python 3 (system-wide)
    • (new) ruptures 1.0.3 – a Python library for off-line change point detection
    • (upd) pwlf 2.0.0, pyDOE 0.3.8, numba 0.49.0, numpy 1.18.3
  • Python 3 (Anaconda 2019):

2020-04-16 COBOL (GnuCOBOL)

  • Software:
    • (new) COBOL via GnuCOBOL – an acronym for “common business-oriented language”). Created in the 1960’s, it is a compiled English-like computer programming language designed for business use. It is imperative, procedural and, since 2002, object-oriented. – cobol example file
    • (upd) Rust
      • rustc +stable: 1.42.0
      • rustc +beta: 1.43.0-beta.5
      • rustc +nightly: 1.44.0-nightly
    • (new) Intel MKL intel-mkl-64bit-2020.1-102 – The Fastest and Most-Used Math Library for Intel®-Based Systems
      • use via export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64
  • Python 3 (system-wide):
  • SageMath:
    • (upd) development version 9.1.rc0

2020-04-08: healpy 1.13

  • Python 3 and Anaconda 2019:
    • (new) healpy 1.13.0`` – a Python package to handle pixelated data on the sphere
  • System.
    • (upd) bazel 3.0.0
    • (upd) various system package updates, including R packages

2020-03-30: Julia 1.4

2020-03-20:

  • Python 3 Anaconda 2019
  • Python 3 system-wide
  • Software
    • (new) libnetcdff6 (4.4.4+ds-3) and libnetcdff-dev (4.4.4+ds-3)
  • R (system-wide)
    • (new) markovchain 0.8.4
    • (upd) various packages …

2020-02-29: Async I/O in Jupyter Notebooks

  • Python 3

    • (upd) various Jupyter libs: jupyter-client 6.0.0, jupyter-console 6.1.0, jupyterhub 1.1.0, jupyterlab 1.2.6, ipykernel 5.1.4, ipython 7.12.0, …

      This means you work seamlessly with Python 3’s async/await coroutines in the system-wide Python3 kernel:

      import asyncio

async def main():
    print('hello')
    await asyncio.sleep(1)
    print('world')

await main()

    • (new) folium 0.10.1 – maps of the world. try import folium; folium.Map(location=[45.523, -122.675], width=750, height=500)

    • (upd) requests 2.23.0, cython 0.29.15, numba 0.48.0, numpy 1.17.5, curio 1.0, nest-asyncio 1.2.3, biopython 1.76

    • (upd) PyTest related: pytest-5.3.5, pytest-doctestplus-0.5.0, pytest-forked-1.1.3, pytest-html-2.0.1, pytest-mock-2.0.0, pytest-pylint-0.15.0, hypothesis-5.5.4, pytest-astropy-0.8.0

  • Software
  • LEAN
    • (upd) mathlib 2020-02-27 nightly build (LEAN 3.6.0 and mathlib aren’t compatible yet, hence no update of LEAN itself)
  • R
    • (new) mltools 0.3.5 – A collection of machine learning helper functions, particularly assisting in the Exploratory Data Analysis phase.

2020-02-21: LEAN 3.5.1 and JavaScript Kernel

2020-02-16: Pandas 1.0 and Octave 5.2.0

2020-02-03: AstroPy 4.0

2020-01-29 Rust 1.40

  • Software:
    • (upd) a round of updating Rust:
      • stable: 1.40.0
      • beta: 1.41.0-beta.2
      • nightly: 1.42.0-nightly
  • Python 3 and Anaconda 2019:
    • (new) pgmpy 0.1.9 – a python library for working with Probabilistic Graphical Models
  • Python 3:
    • (new) okpy 1.14.19 – OK autogrades programming assignments, facilitates submission, composition feedback, and analytics for your class. It’s installed for the Linux Terminal and run ok --help for more info.
    • (new) pyreadstat 0.2.9 – read and write sas (sas7bdat, sas7bcat, xport), spps (sav, zsav, por) and stata (dta) data files into/from pandas dataframes
    • (new) bitarray 1.2.1 – efficient arrays of booleans
    • (new) ifsFractals 1.17.4 – fast IFS fractal generation (ifs fractals example)
    • (upd) PyTorch 1.3.1, joblib 0.14.1, drive-cli 2.1.0, seaborn 0.10.0, numba 0.47.0

2020-01-19: SentimentAnalysis R package

2020-01-05: SageMath 9.0 based on Python 3

  • SageMath:
  • Julia:
    • new year cleanup: only supporting 1.0 LTS and newer versions – currently 1.3.1 – which is the default Julia on CoCalc now.
    • (upd) re-installing all packages will lead to various updates
    • (new) ApproxFun and SpecialMatrices in 1.3.1
  • Software:
    • (upd) bazel 2.0.0, pypy 7.3.0, xpra 3.0.4
    • and various Linux package updates, including R packages
  • Python 3:
  • Python 2:
    • Python 2 is still available, but w/o maintenance.
    • If you require specific setups for old libraries and python 2, we can setup a custom software environment.
  • R: