SoftwareUpgrades

This page contains notes about new software upgrades for the "default" environment.

2018-11-03

(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
(py3/new)
- Tensorflow Probability Lib, especially for edward2 (formerly edward)
- sklearn-porter: Transpile trained scikit-learn estimators to C, Java, JavaScript and others.
(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.
- Run sage_select in a terminal to change the default in a project.
- known issue: libhomfly not available, because it doesn't compile

(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_select to 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 ~/.bashrc.
(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-1 to get the 1.0.1 release.
(new) Ada programming language (Ada wikibook), including syntax highlighting of *.adb files
(upd) overall Linux software update, in particular OpenCV libraries and python-opencv
(new/lib) libopenblas-dev for building C/Fortran code on top of it
(new/bin) screen, powerline, glances, docsify, gnat (GNU Ada compiler)
(env) changing TERM=xterm-256color default environment variable
(env) global config file for htop
(new/py2,py3): prettytable
(chg) switching videochat from https://appear.in to https://meet.jit.si
(new/py3) 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 (https://leanprover.github.io/) 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/

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