Software Updates 2018¶
This is an archive of older updates of the Default environment.
- (py3) - new: nbval for unit-testing Jupyter Notebooks
- (x11) - new: sqlitebrowser - updated: OpenModelica 1.14
- SageMath development version 8.5.rc1
- we have
sqlite(version 2) and
sqlite3(version 3) command line interface on board - Updated Rust to 1.30 - broad Linux package update
- (node/upd): npm 6.50, TypeScript 3.2.2, prettier from 1.11 to 1.15.3, …
- (julia): removing deprecated 0.6 Jupyter kernel
- (software/new): ROOT version 6.14/06, released 2018-11-05. To work with graphical interface: first, open up an X11 environment, then start ROOT by calling
start-rootin the terminal.
- (Sage/upd) Sage Development updated to 8.5.rc0
Note about future updates:
- We will remove Julia 0.6.x (0.7 and 1.0 remains for now)
- Make the
python2jupyter kernel choice more explicit (System’s global version vs. SageMath’s)
- (Julia/upd) Julia 1.0.2 (
julia-1) and packages CSV, DataFrames, Gadfly, Statistics, LinearAlgebra and GLM in default julia 0.7
- (Software/new) sqlline, JDBC for PostgreSQL and MySQL – issue #3400
- (Linux/upd) various updates, only minor version number changes
kgraphviewerand additional launcher buttons
- (Py3/upd) graphviz 0.10.1, mxnet 1.3.1, tellurium 2.1.3, jinja2 2.9.6, pymc3 3.5, scikit-image 0.14.1
- (Py2&3/new) hmmlearn 0.2.1
- (Library) new entry Scikit Image Tutorial and updates of several entries
- (Sage/upd) Sage Development updated to 8.5.beta5
- (Linux/upd) noteworthy minor updates: vs code: 1.29.1, bazel: 0.19.2, idle: 3.6.7, python3: 3.6.7, postgresql: 11.1
- (Py3/new) NOAA SDK
- (Py3/upd) yapf 0.25, tensorflow 1.12, tensorboard 1.12, tensorflow-probability 0.5, scikit-learn 0.20.1, numba 0.40.1, arctic 1.73 (also Py2)
(py2/py3 updates): Bokeh 1.0, Sphinx 1.8.1, Plotly 3.3.0, tensorflow 1.11 (py3 only), Pip 18.1
(Sage/upd) Sage Development version updated to 8.5.beta2
(x11) xdotool, xclip, xvfb update
(linux/upd) broad Linux update, in particular rustc 1.28, cargo 0.29, bazel 0.19, …
(node.js/upd) noteworthy are typescript 3.1.4, coffeescript 2.3.2, prettier 1.14.3, reveal-md 2.3.0 and tldr 3.2.5
(R/upd) updating some packages like dplyr, knitr, data.table, plotly, etc.
(R/new) export package
(R/new) installing “swirl” courses globally for R. Create an “X11 Desktop” file, run R, and then start it:
> require(swirl) > swirl_options(swirl_data_dir = "/home/user/swirl") > swirl()
- (upd) SageMath 8.4 as the new default Sage version.
sage_selectin a terminal to change the default in a project.
- known issue:
libhomflynot available, because it doesn’t compile
- (upd) SageMath development version 8.5.beta0
- (new) Tellurium in Python 2 and 3. example worksheet
- (new) X11 releated: nteract.io, atom editor (to e.g. be able to install juno for julia in your project), Avogadro, etc.
- (py2/py3) monty library and pivottablejs
- (new) Sage 8.4 (default still 8.3). Use
sage_selectto switch it, test it, and maybe give us feedback.
- (new) PostgreSQL 11 (default still 10). It’s in
/usr/lib/postgresql/11/bin/. To use it, fix your path, e.g. via
path-remove "/usr/lib/postgresql/10/bin"; path-append "/usr/lib/postgresql/11/bin"in your
- (upd) overall Linux software update. notable: * git (1:2.17.1-1ubuntu0.3`_ * texlive-binaries (2017.20170613.44572-8ubuntu0.1)
- (new) xpra/websockify
- (new) couple of X11 related software, like PSPP, Gimp, LibreOffice, …
- (fix) relaxing policies for ImageMagick to be able to run convert on PDF files.
- (upd/enh) Julia 1.0.1 and associated Julia Jupyter kernel
- in a terminal, run
julia-1to get the 1.0.1 release.
- in a terminal, run
- (new) Ada programming language (Ada wikibook), including syntax highlighting of
- (upd) overall Linux software update, in particular OpenCV libraries and
libopenblas-devfor building C/Fortran code on top of it
- (new/bin) screen, powerline <https://powerline.readthedocs.io/en/latest/usage/shell-prompts.html), `glances, docsify, gnat (GNU Ada compiler)
- (env) changing TERM=xterm-256color default environment variable
- (env) global config file for htop
- (chg) switching videochat from https://appear.in to https://meet.jit.si
- (new/py3) jupytext <https://github.com/mwouts/jupytext/), [notedown, control, and slycot
- (upd/py3) jupyter nbconvert (just 5.3.1 to 5.4.0, but there could be noticeable changes)
- (bug/py) there are known issues with
mpl_toolkits/Basemap– please use Ubuntu’s Python 3 environment.
- (upd) broad Linux software packages update, including minor updates to bazel, chrome, curl and python3.6
- (upd/py3) “pip3” 18.0, seaborn 0.9.0, geopandas 0.4.0, and scikit-learn 0.20.0
- (upd/py2) “pip2” 18.0, seaborn 0.9.0, tensorflow 1.10.1
- (rem/ac5) removing broken pandas-datareader from anaconda5 (no update available yet, use Ubuntu’s Python 3)
- (new/npm) tldr pages
- (upd) broad round of updating Anaconda 5 packages
- (rem) Removal of PostgreSQL 9.6. We provide the 10.x series by default.
- for the purpose of upgrading, the old install is kept in
/usr/lib/postgresql/9.6/for a little while.
- (fix) pandas-datareader incompatibility resolved
- (upd/py3) dask/distributed, SymPy 1.3, Numba 0.38.1/llvmlite, and pandas-datareader 0.7.0
- (upd/py2) pandas 0.23.4 and pandas-datareader 0.7.0
- (upd) LEAN mathlib to rev d0f1b21a9df64f, located in /ext/lean/lean-3.4.1-linux/mathlib/.
- (new/py2+py3) pyLADvis
- (new) C++ 17 Jupyter kernel via xeus-cling
- (upd) SageMath release 8.4.beta6 2018-09-22
- (new) R packages: roperators and a couple from R Views 2018-07
- (upd) bazel 0.17.1
- (upd) nodejs 8.12 (+ npm package updates)
- (upd) relaxing browser compatibility check specifically for newest Firefox 60.2 ESR
- (upd) major changes in handling RMarkdown files
- (new) support for automatically processing PythonTeX code in LaTeX documents
- (new) additional Library entries for RMarkdown and LaTeX/PythonTeX examples
- (new) first iteration to support LEAN
- (upd) SageMath 8.4.beta5 (released on 2018-07-16)
- (fix) irregularities with man-pages introduces in previous update
- (compat) Firefox 62 was released, which works well again with CoCalc’s websocket over Cloudflare
- (upd/py3) tensorflow 1.10.1
- (upd/node) npm 5.6.0 → 6.4.1, typescript 3.0.3, CoffeeScript 2.3.1 and a couple other global node packages
- (upd/linux) headless chrome 69, and a couple of linux system libs
- (upd/sage) SageMath development 8.4beta4 available
- (upd/anaconda) broad package upgrade of Anaconda5 environment
- (chg) Jupyter plots done via R in Sage output SVG by default
- (new) stapler python tool, a successor of pdftk (which is discontinued) – https://github.com/hellerbarde/stapler
- (new) julia 0.7 upgrade: either keep the existing 0.6 line, or select 0.7
- (old) you can still select a 0.6 kernel or run julia-0.6
- for 0.7, only a few global libraries installed, i.e. those where precompiling works without errors
- upon opening a jupyter file, you have to explicitly select the version
- (upd) isochrones library: upgraded, and primarily updated a lot of datasets into $ISOCHRONES for dartmouth, but also some for “mist” – https://isochrones.readthedocs.io/en/latest/
- (fix) no man/doc pages were installed. this is fixed now.
- (new) giac wrapper script to expose sage’s binary globally in $EXT/bin/giac. Therefore cocalc provides giac again. https://www-fourier.ujf-grenoble.fr/~parisse/giac.html
- (enh) web client: tightening browser requirements to inform affected users about https://bugzilla.mozilla.org/show_bug.cgi?id=1453204
- (exp) experimental support for LEAN – https://leanprover.github.io/