Software Updates 2019

2019-12-15: SymPy 1.5

2019-12-07: Design of Experiment Generator

2019-11-29: Julia 1.3

  • Julia

    • (new) Julia 1.3 now available: run julia-1.3 or the corresponding Jupyter kernel. It will become the default version soon!

    • (dep) Julia 1.2 is deprecated.

  • SageMath

    • (new) optional package pynormaliz – Normaliz backend for polyhedral computations:

      sage: P = Polyhedron(vertices=[[0,0],[0,1],[1,0]], backend="normaliz"); P
A 2-dimensional polyhedron in ZZ^2 defined as the convex hull of 3 vertices

sage: P.ehrhart_series()
1/(-t^3 + 3*t^2 - 3*t + 1)
  • Python 3 (system-wide)

    • (new) adtk 0.4.1 - Anomaly Detection Toolkit (ADTK) is a Python package for unsupervised / rule-based time series anomaly detection.

    • (upd) pint 0.9 – makes units easy

    • (upd) bokeh 1.4.0

  • Python 3 (Anaconda 2019)
  • Software

    • (upd) git-lfs 2.9.1, bazel 1.2.1, Python 3.6.9

    • (upd) rust rustc +nightly: 1.41.0-nightly (412f43ac5 2019-11-24)

2019-11-23: various Python 3 package updates

2019-11-19: improved support for Rust

  • Software

    • (new/upd) Rust available in stable, beta and nightly channels and code formatting (red arrow below) via rustfmt!

    ~$ rustc --version
rustc 1.39.0 (4560ea788 2019-11-04)
~$ rustc +beta --version
rustc 1.40.0-beta.2 (2a0ba54fa 2019-11-16)
~$ rustc +nightly --version
rustc 1.41.0-nightly (5c5b8afd8 2019-11-16)
    https://storage.googleapis.com/cocalc-extra/rust.png

    Rust in a frame-editor, side-by-side with a Terminal

  • Python 3

2019-11-16

  • Python 3

    • (new) periodictable 1.5.1 – The periodictable package provides an extensible periodic table of the elements prepopulated with data important to neutron and X-ray scattering experiments

    • (new) teneto 0.4.6 – various tools for analyzing temporal network data

    • (new) python-highcharts 0.4.2 – a simple translation layer between Python and Javascript for Highcharts projects (highcharts, highmaps, and highstocks)

    • (upd) scipy 1.3.2, numpy 1.17.4, dask/distributed 2.7.0

    • (upd) data science libs: sklearn-porter 0.7.3, sklearn-pandas 1.6.0, scikit-image 0.16.2 scikit-posthocs 0.6.1

    • (upd) scikit-surprise 1.1.0 – a Python scikit building and analyzing recommender systems that deal with explicit rating data

    • (upd) Pandas related: pandas 0.25.3, pandas-bokeh 0.4, pandas-datareader 0.8.1, pandas-gbq 0.11.0

    • (upd) Google GCP libs: google-api-core 1.14.3, google-cloud-bigquery 1.21.0, google-cloud-core 1.0.3, google-cloud-storage 1.22.0, googleapis-common-protos 1.6.0

2019-11-09

  • Platform:
  • Software:

    • (upd) Jupyter Lab 1.1.4

    • (upd) Node.js related coffeescript@2.4.1, typescript@3.7.2, and npm@6.13.0

  • Python3:

    • (upd) Tensorflow 2 tensorflow-2.0.0, tensorboard-2.0.1, tensorflow-estimator-2.0.1, … (Tensorflow 1 is still available in the Anaconda 2019 kernel)

    • (new) ortools 7.4.7247 – a fast and portable software for combinatorial optimization

    • (upd) Cython 0.29.14, joblib 0.14, numpy 1.17.3, h5py 2.10.0, keras 2.3.1

  • SageMath:

    • (upd) Development version 9.0.beta4

2019-10-25

  • Platform

    • (new) Sytnax highlighting for Verilog files (.v and .vh)

    • (enh) TimeTravel opens up in a frame

  • Software
  • SageMath:

    • (fix) hotfix for viewing plot3d renderings in the Jupyter Notebook – issue #28648

2019-10-19

  • SageMath

    • (upd) SageMath 8.9 including many extra packages and libs. This also implies an update of SageTeX to 3.3.

  • Software
  • Python 3:

    • (ann) soon, Tensorflow will be version 2 – this has breaking changes

    • (new) tpot 0.10.2 – is a Python Automated Machine Learning tool that optimizes machine learning pipelines using genetic programming.

    • (new) scikit-mdr 0.4.4 – a scikit-learn-compatible Python implementation of Multifactor Dimensionality Reduction (MDR) for feature construction.

    • (new) scikit-rebate – 0.6 a scikit-learn-compatible Python implementation of ReBATE, a suite of Relief-based feature selection algorithms for Machine Learning

    • (upd) dask/distributed 2.6.0, numba 0.46.0, textract 1.6.3, beautifulsoup4 4.8.0, pytables 3.5.2, xgboost 0.90 and pip 19.3

  • Anaconda 2019:

2019-10-11

2019-10-05

  • Platform

    • (new) The $MPLBACKEND environment variable is set for matplotlib based on the terminal type. This means you can plot to a file or to a graphical window in X11 without having to explicitly set it (ticket #4120).

  • SageMath

    • (new) SageMath 8.9 rollout on CoCalc, including additional packages and extensions. Try the “Sage 8.9” Jupyter Kernel! Soon, it will become the default version for running Sage. Sage Worksheets currently do not support Sage 8.9.

  • Anaconda Python 3:

    • (new) DEAP 1.3.0 a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent.

    • (new) simanneal 0.4.2 This module performs simulated annealing optimization to find the optimal state of a system.

  • Python 3:

2019-09-30

  • Software

    • (upd) Jupytext 1.2.4 – a command-line tool to convert ipynb files to markdown, Rmarkdown, etc.

    • (fix) Updating Jupyter Console, because the previous update broke it.

  • Julia:

    • (upd) 1.0.5 Long Term Release

    • (upd) various packages for 1.2.0

2019-09-28

  • CoCalc platform:

    • CoCalc’s Jupyter Notebook’s nbgrader toolbar inserts templates for automatically graded answers and corresponding tests for Python, R and Julia. This makes creating new test cells for your course assignments much easier!

  • Software:

    • (new) IPOPT interior point solver, stand-alone binary:

      ~$ ipopt --version
Ipopt 3.12.12 (Linux x86_64), ASL(20160307)
  • Anaconda 2019:
  • Python 3:

2019-09-21

  • Python 3
  • R (system-wide)

    • (upd) various packages, including BioConductor

    • (new) installing oligo 1.48.0 and some other BioConductor packages

  • Sage Development version 8.9.rc0

  • Custom Software Environments:

    • (upd) ModSimPy to enable ipynb to PDF exports

2019-09-09

  • Software:

    • (upd) TypeScript 3.6.2

    • (upd) prettier 1.18.2

    • (upd) Selenium 4, ChromeDriver 76, GeckoDriver 1.16.2

    • (upd) Spyder 3.3.6

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

  • Python 3:

    • (new) arch 4.9.1: Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance)

    • (new) linearmodels 4.13: Linear (regression) models for Python. Extends statsmodels with Panel regression, instrumental variable estimators, system estimators and models for estimating asset prices.

    • (upd) pip 19.2.3

    • (upd) pandas 0.25.1 and pandas-datareader-0.7.4

    • (upd) psycopg2 2.8.3

    • (upd) numpy 1.17.2

    • (upd) matplotlib 3.1.1

    • (upd) pytest 5.1.2 + associated libraries

    • (rem) axelrod blocks updates, use Anaconda 2019

  • Anaconda 2019:

    • (new) contextily 1.0rc2 + geopy 1.20.0

2019-08-28

  • Python 3:

    • (new) pomegranate: implements fast and flexible probabilistic models ranging from individual probability distributions to compositional models such as Bayesian networks and hidden Markov models

    • (upd) Cython 0.29.13

    • (upd) RISE 5.5.1

  • Julia 1.2:
  • Jupyter Classic:

    • (fix) re-enabling nbextensions configurator

2019-08-25

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 4.0.0 – Plotly 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 0.14.9 – package 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) rclone – rsync 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 package – Dynamic 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