Software Updates 2019

2019-08-10

  • Julia:
    • (new) Package Gen in Julia 1.1

      “A general-purpose probabilistic programming system with programmable inference.”

  • Sagemath:
  • Python
    • (upd) pip-19.2.1, dask-2.2.0, distributed-2.2.0, numba-0.45.1
  • Software:
    • (new) GRASS GIS: grass 7.4.0, grass-gui, etc. + grass-session in Python 2
    • (upd) npm@6.10.3

2019-07-28

  • SageMath
    • (del) removing packages meataxe and p_group_cohomology to avoid a bug.
  • Python 3:
    • (new) Anaconda 2019 – a fresh setup from scratch! It provides Python 3.7 and replaces the Anaconda 5 environment.
    • (rem) Removal of Anaconda3 – it was deprecated and notebooks will tell you to switch the kernel to Anaconda 2019.
    • (dep) Deprecation of Anaconda 5 starts now.
    • (upd) numba 0.44.1 and llvmlite-0.29.0
    • (upd) plotly 4.0.0Plotly 4.0 release notes
  • Software:
    • (upd) Linux package update, including some R packages
    • (upd) yapf 0.28, git-lfs 2.8.0 and xpra 2.5.3

2019-07-15

  • CoCalc Platform
    • (new) Jupyter NBGrading: initial support for creating test cells via the NBGrader toolbar and running validation tests in the notebook.
    • (new) Dedicated VMs: get your own node in CoCalc’s cluster – pricing info.
    • (chg) Jupyter Kernels: renaming “Python 2/3 (Ubuntu Linux)” to “Python 2/3 (system-wide)”. There is no change except for the naming.
    • Library update, adding NBGrader examples
  • R Statistical Software:
    • (upd) Version 3.6.1 and 4000+ packages

      Note

      Compiled packages in projects need to be reinstalled!

  • Python 3:
  • SageMath:
    • (upd) Sage Development version 8.9.beta2
  • Software:
    • (upd) npm 6.10.0 and a couple of global npm packages, e.g. typescript 3.5.3
    • (upd) general Linux package update, including bazel 0.28 and Rust 1.34

2019-07-08

  • SageMath:
    • (new) Version 8.8 becomes the default
    • (upd) Development Version 8.9.beta1
  • Python 3:
    • pip-upgrader: helps managing custom package setups in virtual environments
  • Updating all Custom Software Environments.

2019-06-30

  • (new) SageMath 8.8: general available on CoCalc with various enhancements. When the testing phase passes, it’ll be the default (in about a week). (Sage 8.8 Notebook)

  • Python 3:

  • Linux package update, including imagemagick-6 6.9.7.4.

2019-06-24

  • SageMath:
    • (upd) Development Version 8.8.rc0
  • Python 3:
    • (new) jieba 0.39: “结巴”中文分词:做最好的 Python 中文分词组件
  • Julia 1.1:
    • (new) Distributions
    • (upd) all other global Julia packages, if applicable

2019-06-17

  • SageMath:
    • (upd) Development Version 8.8.rc0
  • Python 3:
    • (upd) dill-0.2.9
  • Software:
    • (upd) Python 3.6.8
    • (upd) xpra 2.5.2
    • (upd) Google Chrome 75
    • (upd) bazel 0.26.1
  • Library:
    • (new) “Public Finance 2018/2019 UCSC”
    • updating entries

2019-06-08

2019-06-02

2019-05-26

  • CoCalc
  • Julia:
  • Python 3:
    • (upd) SciPy 1.3.0
    • (upd) statsmodels updated to recent development version, because of a SciPy incompatibility.
    • (upd) cvxpy 1.0.23
    • (upd) scikit-learn 0.21.2
    • (upd) matplotlib 2.2.4
    • (upd) Dask 1.2.2, dask-ml 0.13.0, and distributed 1.28.1
    • (upd) OpenCV 4.1.0.25 (incl opencv-contrib-python)
    • (upd) pip 19.1.1 (also for python 2)
    • (upd) pytest-4.5.0, pytest-arraydiff-0.3, pytest-astropy-0.5.0, pytest-cov-2.7.1, pytest-doctestplus-0.3.0, pytest-forked-1.0.2, pytest-html-1.20.0, pytest-ipynb-1.1.1, pytest-metadata-1.8.0, pytest-mock-1.10.4, pytest-openfiles-0.3.2, pytest-remotedata-0.3.1, pytest-repeat-0.8.0, pytest-selenium-1.16.0, pytest-timeout-1.3.3, and pytest-xdist-1.28.0
    • (new) pytest-watch-4.2.0 and pytest-testmon-0.9.16
    • (new) nest-asyncio-1.0.0, osbot-aws-0.6.51, osbot-browser-0.3.1, osbot-jupyter-0.4.2, pyee-6.0.0, pyppeteer 0.0.25, and syncer 1.3.0
    • (upd/new) geopandas related: contextily 0.99.0, pysal 2.0.0 (major version update!), esda-2.0.0, libpysal-4.0.1 mercantile-1.0.4 and palettable-3.1.1
    • (new) scikit-rf 0.14.9package for RF/Microwave engineering (also for Anaconda 5). Scikit RF example
  • SageMath:
    • (upd) development version 8.8.beta6
  • Linux Software Updates:
    • rustc 1.32 / cargo 0.33
    • bazel 0.25.3

2019-05-18

  • Sage:
    • updating development version to 8.8.beta5
  • Python 3:
  • Software
    • (new) more BibTeX related packages: search-ccsb, search-citeseer, bibtool, kbibtex, bibclean, bibcursed, bibtex2html, and bibtexconv

2019-05-11

  • CoCalc:
    • ipywidgets support in CoCalc’s Jupyter notebooks. This isn’t 100% done, but suitable for all basic applications. The coolest part? It syncs across all collaborators of the same notebook!

      ../_images/cocalc-ipywidgets-sync-2019-05-08.gif
  • R:
    • Due to blowups of image sizes, we switched the default graphics format to PNG. To continue plotting SVG images, please run

      options(jupyter.plot_mimetypes = c('image/svg+xml'))
      

      in your notebook.

  • Python 3:

    • (upd) Qiskit 0.10.1 and deps: fastdtw-0.3.2, pyeda-0.28.0, pylatexenc-1.4, qiskit-aer-0.2.0, qiskit-aqua-0.5.0, qiskit-chemistry-0.5.0, qiskit-ibmq-provider-0.2.2, qiskit-ignis-0.1.1, qiskit-terra-0.8.0
    • (upd) VQE Playground and PyGame 1.9.6
  • Anaconda 5 environment:

    • Adding RDKit, updating matplotlib, …:

      The following NEW packages will be INSTALLED:
        lame               conda-forge/linux-64::lame-3.100-h14c3975_1001
        matplotlib-base    conda-forge/linux-64::matplotlib-base-3.0.3-py36h5f35d83_1
        pycairo            conda-forge/linux-64::pycairo-1.18.1-py36h438ddbb_0
        rdkit              conda-forge/linux-64::rdkit-2019.03.1-py36h9c20d5c_0
      
      The following packages will be UPDATED:
        cairo                               1.14.12-h80bd089_1005 --> 1.16.0-ha4e643d_1000
        dbus                    pkgs/main::dbus-1.13.2-h714fa37_1 --> conda-forge::dbus-1.13.6-he372182_0
        ffmpeg                                   4.0.2-ha0c5888_2 --> 4.1.3-h167e202_0
        glib                                 2.56.2-had28632_1001 --> 2.58.3-hf63aee3_1001
        gnutls                                  3.5.19-h2a4e5f8_1 --> 3.6.5-hd3a4fd2_1002
        gst-plugins-base   pkgs/main::gst-plugins-base-1.14.0-hb~ --> conda-forge::gst-plugins-base-1.14.4-hdf3bae2_1001
        gstreamer          pkgs/main::gstreamer-1.14.0-hb453b48_1 --> conda-forge::gstreamer-1.14.4-h66beb1c_1001
        harfbuzz                              1.9.0-he243708_1001 --> 2.4.0-h37c48d4_0
        libxml2                                  2.9.8-h422b904_5 --> 2.9.9-h13577e0_0
        matplotlib                           2.2.3-py36h8e2386c_0 --> 3.0.3-py36_1
        nettle                                              3.3-0 --> 3.4.1-h1bed415_1002
        opencv               3.4.4-py36_blas_openblashbbbf1d5_201 --> 3.4.4-py36_blas_openblash641cfe3_1205
        pango                               1.40.14-hf0c64fd_1003 --> 1.40.14-h4ea9474_1004
        pyqt                                 5.6.0-py36h8210e8a_7 --> 5.9.2-py36hcca6a23_0
        qt                         pkgs/main::qt-5.6.3-h8bf5577_3 --> conda-forge::qt-5.9.7-h52cfd70_1
        sip                                 4.18.1-py36hfc679d8_0 --> 4.19.8-py36hf484d3e_1000
        x264                            1!152.20180717-h470a237_1 --> 1!152.20180806-h14c3975_0
      
      The following packages will be DOWNGRADED:
        poppler                              0.67.0-h2fc8fa2_1002 --> 0.67.0-h2ad7f00_6
      

2019-05-04

  • Python 3:
    • (upd) PyGame 1.9.4
    • (upd) pip-19.1
    • (upd) Dask 1.2.0, dask-ml-0.12.0 and distributed-1.27.0
    • (upd) rpy2-2.8.6 (the latest release)
    • (upd) selenium-3.141.0 in combination with chromedriver
  • R:
  • Node.js: (upd) chromedriver@74.0.0
  • Linux package updates: fenics 1:2019.1.0, gcc 8.3, and gcc 7.4 for g++ and gfortran , …

2019-04-27

  • Software
    • (upd) Nodejs 10, including all system-wide node packages
    • (upd) QGIS 3.6.2
    • (upd) Gradle 4.4.1
    • … and various Linux libraries
  • Python 3:
    • (upd) arctic 1.74.0 to fix a pandas incompatibility

2019-04-21

  • Python 3:
    • (upd) pandas 0.24.2: check pandas release notes for changes since 0.23.
    • (new) umap-learn (UMAP example): Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
  • R:
    • (new) Seurat 3.0.0: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. <https://satijalab.org/seurat/>
    • (new) bibliometrix <https://cran.r-project.org/package=bibliometrix>: An R-Tool for Comprehensive Science Mapping Analysis
  • Software:
    • (new) ttf-mscorefonts Linux package to provide more fonts, primarily for XeLaTeX.
    • (upd) routine Linux package update, including xpra-2.5.1.

2019-04-14

  • SageMath 8.7
    • (new) package plot3D in Sage’s R, along with tidyverse and dplyr
../_images/sage-R-plot3d.png
  • Anaconda 5:
    • (new) additionally to hoomod blue, freud-1.0.0, fresnel-0.8.0, embree3-3.5.2, and gsd-1.6.1
  • Python 3:
    • (upd) SymPy 1.4
    • (new) Orange 3: Open source machine learning and data visualization for novice and expert.
    • (upd) Qiskit related: qiskit-0.8.0, qiskit-aer-0.1.1, qiskit-ignis-0.1.0, qiskit-terra-0.7.1
  • Library:
    • all entries are updated to their latest upstream version
    • adding VQE Playground: gaining intuition about Variational Quantum Eigensolver
  • R:
    • (upd) also updating tidyverse and dplyr

2019-04-07

  • SageMath 8.7 is the default sage.
    • You can still use the previous one via sage-8.6, select the appropriate kernel, or switch it in your project by running sage_select 8.6 in a Linux Terminal.
    • SnapPy tests do not pass, I don’t know why …
  • R (R-Project):
    • (upd) bioconductor packages, in particular affy, limma, puma, etc.
  • Python:
  • Software:
    • Spyder IDE 3.3.4 (via X11) and Python 3 deps: PyQt5-sip-4.19.15, pyqt5-5.12.1, pyqtwebengine-5.12.1, qtawesome-0.5.7, qtpy-1.7.0, spyder-kernels-0.4.3, and wurlitzer-1.0.2.
    • VS Code 1.33
    • Gyoto

2019-03-31

2019-03-23

  • (UI/LaTeX) LaTeX editor: “shell-escape” mode to e.g. draw plots using Gnuplot
  • (UI/Chat) @Mention a project collaborator in a chat to ping her/him via email.
  • (new) ROOT Kernel: ROOT is a modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualization and storage. ROOT example Jupyter worksheet
  • (new) rclonersync for cloud storage
  • R: installing qdap library and updating a couple of other ones …
  • Python 3: Sphinx 1.8.5
  • Julia 1.1: adding Images and updating various packages like JuMP 0.19!
  • Linux: various package updates, in particular bazel 0.23.2, xpra 2.5, git-lfs 2.7.1, and code 1.32
  • (upd) SageMath Development version 8.7.rc0

2019-03-11

  • Python:
  • Software:
    • ts-node to run TypeScript files from the command line more easily
    • updating npm to version 6.9.0
  • Disabling jupyter lab drawio, because it didn’t build correctly

2019-03-02

2019-02-23

2019-02-16

2019-02-09

  • (Linux)
    • new: Cantera 2.4.0 for Python 2 and Python 3
    • updates: macaulay2 1.13, bazel 0.22, chrome and firefox, and various other packages
  • (Python3)
    • new: pyfftw 0.11.1, pymp-pypi 0.4.2
    • updates: dask-1.1.1
  • (Node): npm 6.7.0
  • (Julia): making Julia 1.1.0 the default (v1.1.0 release notes) and removing older, no longer maintained versions. Maybe cleanup the build cache, by running rm -rf ~/.julia in the Terminal/Miniterm.
  • (Anaconda 5): various updates to packages
  • (Sage) Development version 8.7 beta 3 (Python 3)

2019-01-26

  • (sage): Sage 8.6 is the default! (use sage_select 8.4 to switch back). Enjoy the shorter startup time, which also speeds up compiling SageTeX documents!
    • A Python3 version of Sage 8.6 is also available: sage-8.6-py3 or in a Jupyter Notebook: sagemath-8.6-python3.ipynb. (this is experimental)
  • (py3):
    • new:
      • ipyvolume 0.5.1 (demo notebook, requires the plain jupyter server!)
      • qiskit-chemistry 0.4.2 – a set of tools, algorithms and software to use for quantum chemistry research
      • PySCF – a simple, light-weight, and efficient platform for quantum chemistry calculations
    • updated:
      • pip3 19.0.1
      • qiskit 0.7.2, qiskit-aqua 0.4.1
      • scikit-bio 0.5.5
      • dask 1.1.0
      • nbgrader 0.5.5
      • ipython 6.5.0
      • Cython 0.29.2
      • setuptools 40.6.3
      • tensorboard 1.12.2
      • tmuxp 1.4.2
      • axelrod 4.4.0
  • (R):
    • new:
    • updated: knitr 1.21, ggplot 3.1.0, data.table 1.20.0, dplyr 0.7.8, Rcpp 1.0, rlang 0.3.1, forecast 8.5, psych 1.8.12, plotly 4.8, yaml 2.2
  • (Julia): new: D4M packageDynamic Distributed Dimensional Data Model
  • (node/upd): npm 6.6.0, TypeScript 3.2.4, tslint 5.12.1, forever 0.15.3, CoffeeScript 2.3.2, reveal-md 2.4.1, prettier 1.16.0, tldr 3.2.6, docsify-cli 4.3.0, chromedriver 2.45.0
  • (Linux) various system packages, noteworthy: xpra 2.4.3

2019-01-20

  • (new) SageMath version 8.6 (sage-8.6) + Jupyter Kernel available (not the default yet!)

  • (new) Cadabra2 _”a field-theory motivated approach to computer algebra”_ available via cadabra2 or in an X11 desktop as cadabra2-gtk (screenshot)

  • (chg) As announced previously, Julia version 1 is the default now. Symlink ~/bin/julia to julia-0.7 if you need to switch back.

  • (new): Julia 1 packages: SymPy, Combinatorics, UnicodePlots, Bokeh and Nemo

  • (py3):

2019-01-12

2019-01-06

  • Julia 1.0.3: comes with packages PyPlot, Plots, DifferentialEquations, Compat, LinearAlgebra, GLM, etc. now!
  • Sage development version 8.6.rc0