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CHANGELOG.md

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Changelog

[Unreleased]

4.1.7

  • Install sklearn-pandas

4.1.6

  • standard: Add conda freetds package, to access MS SQL Server via ODBC.

4.1.5

  • r-ubuntu: Add bioconductor packages biomaRt and snpStats
  • r-ubuntu: Add plink
  • standard: Add six packages for bdaanccounting

4.1.4

  • Add mne

4.1.3

  • Fix: downgrade nbconvert to <6
  • Fix: revert nbgrader to before nbconvert 6.0 support
  • The above two are needed because my attempt at fixing nbgrader, jupyter/nbgrader#1405, has apparently failed. The changes in nbconvert to make feedback work and look good don't really work yet.

4.1.2

  • Fix: more nbgrader bugs (standard) This is not yet put into the base image, but should be.
  • Changed: add packages for bdaaccounting2021

4.1

4.0

  • Add viola to base packages
  • Change: Bump julia to 1.5.3
  • Change: Bump versions of various packages
  • Change: Bump base scipy notebook version
  • Change: Re-adjust installing keras, do it via pip only

[3.0.7] - r-ubuntu - 2020-11-19

Changed

  • Downgrade HTSeq to 0.11.1

[3.0.5] - r-ubuntu - 2020-10-23

Added

  • r-ubuntu: packages aods3 (CRAN) and (BiSeq, limma) (bioconductor)

[3.0.5] Standard - 2020-10-30

Changed

  • Changed JupyterLab staging directory permissions so that clients are able to build extensions manually

Fixed

  • Made sure that copied scripts have the executable bit set within the image after building

[3.0.4] r-umuntu - 2020-09-03

Added

  • Ubuntu packages libavfilter-dev and libmagick++-dev, for the below:
  • Add R packages av and magick

[3.0.3] r-ubuntu - 2020-08-27

Added

  • New packages: gifski ggforce ggrepel

[3.0.2] r-ubuntu - 2020-08-24

Added

  • New packages: StanHeaders, tweenr, gganimate

Changed

  • Updated CRAN snapshot date

[3.0.1] r-ubuntu - 2020-08-21

Added

  • New package: StanHeaders

[3.0.0] - 2020-07-14

Changed

  • Upgrade Python from 3.7.6 to 3.8.3
  • Upgrade CRAN snapshot to 2020-07-12
  • Upgrade nbgrader to version 26 Jun 2020 (b5ae9f8)
  • Upgrade scipy notebook to version 2020-07-05 (5197709e9f23)
  • Upgrade julia to v1.4.2
  • Bump package versions:
    • tensorflow 2.0 -> 2.2
    • keras 2.3 -> 2.4
    • pytorch 1.3 -> 1.5
    • torchvision 0.4 -> 0.6
    • rstudio 1.2.5001 -> 1.3.959

Fixed

  • Fix python-igraph unit test

[2.0.6] Standard - 2020-06-30

Added

  • Basic unit test for ortools package
  • New packages: inotify, configargparse, conda-tree

Changed

  • Made .bash_history persistent across server instances

[2.0.5] Standard - 2020-02-02

Added

  • New package: ortools

[2.0.4] Standard - 2020-01-16

Fixed

  • Fix nbgrader permissions problem

[2.0.3] Standard - 2020-01-15

Added

  • New packages: jupyter-matplotlib, ipympl

[2.0.2] Standard - 2020-01-13

Added

  • New package: opencv

[2.0.1] Standard - 2020-01-07

Added

  • New package: owslib

[2.0.0] - 2019-12-30

Changed

  • Upgrade jupyterlab to v1.2.4
  • Upgrade scipy notebook to version 12 Dec 2019
  • Upgrade nbgrader to version 12 Nov 2019 (4c5d6f6)
  • Downgrade gpflow to v2.0.0rc1
  • Upgrade julia to v1.3.0
  • Upgrade CRAN snapshot to 2019-12-29
  • Bump package versions:
    • tensorflow 2.0.0
    • keras 2.3
    • pytorch 1.3

Added

  • New package: pipdeptree

1.8.12 (standard)

  • Install nltk

[1.8.11] r-ubuntu - 2019-11-21

Changed

  • Fix rtracklayer installation

1.8.8 (standard)

  • Install cma, pydub (intcompmedia)
  • Install nbgitpuller

1.8.7 (r-ubuntu)

Add htseq and samtools for htbioinformatics2019

1.8.6 (r-ubuntu)

fix tophat2 python interpreter, clean layers

1.8.5 (r-ubuntu)

  • add packages for htbioinformatics2019, including bioconductor and command-line tools

[1.8.4]

  • r-ubuntu: add markmyassignment

[1.8.3]

Changed

  • Update RStudio version

[1.8.1]

Changed

  • Add groups.sh hook create groups and set them as server requests

[1.8.0]

Changed

  • Try to make images work for bayesian data analysis course
    • Set clang as default compilers for R, or try to
    • Set CC and CXX to clang/clang++ in standard image
  • Combine standard layer creation to speed up build
  • Change location of clean-layer.sh, add some stuff to it
  • Updateto JupyterLab 1.1.3 ( (fixes file list with git-extension, jupyterlab/jupyterlab#7204)

[1.7.1] Standard - 2019-09-06

Added

  • Packages wordcloud and geopy for course datasci2019

[1.7.0] - 2019-08-26

Changed

  • Update scipy-notebook image to version 2ce7c06a61a1, version published Aug 11, 2019 03:40 AM

[1.6.1] R - 2019-08-26

Changed

  • Update jupyter-rsession-proxy

[1.6.1] Standard - 2019-08-26

Changed

  • Update qiskit to version 0.12.0

[1.6] Base - 2019-08-26

Changed

  • Update nbgrader to commit 49d2d1f

R [1.0.2] - 2019-08-23

Added

  • Add jupyterlab server proxy

Changed

  • Update CRAN to version 2019-07-05

[1.0.5] - 2019-08-22

Added

  • Add variable inspector to notebook and lab

Changed

  • Update nbgrader to commit db70a60

[1.0.4] - 2019-08-07

Changed

  • Add hub topbar button lab extension

[1.0.3] - 2019-08-05

Changed

  • Update scipy-notebook image to version 58169ec3cfd3, version published Aug 4, 2019 05:21 AM

[1.0.2] - 2019-08-05

Changed

  • Update nbgrader

[1.0.1] - 2019-07-26

Changed

  • Update scipy-notebook image to version 7a3e968dd212, version published on July 17, 2019 12:15 AM

Fixed

  • Stop pip from caching files

[1.0.0] - 2019-07-24

Updated images for JupyterHub 1.0

[0.5.19-1.0] - 2019-07-24

  • Improve image layer cache clearing

[0.5.18-1.0] - 2019-07-24

Changed

  • Update nbgrader to the latest commit

[0.5.17-1.0] - 2019-07-24

Changed

  • Update JupyterHub to version 1.0

[0.5.16] - 2019-07-23

  • Prepare for JupyterHub 1.0 upgrade

[0.5.15] - 2019-07-09

Fixed

  • Ensure that scripts are executable after copying

[0.5.14] - 2019-06-10

Updated

  • anaconda to version 4.6.14
  • the scipy image to version d4cbf2f80a2a, version published on June 2, 2019 03:45 AM

[0.5.13] - 2019-06-07

Added

  • qiskit

[0.5.12] - 2019-06-03

Added

  • calysto
  • metakernel

[0.5.11] - 2019-04-06

Added

  • tensorflow_hub

Updated

  • tensorflow

[0.5.10] - 2019-04-05

Fixed

  • cvxpy fixes

[0.5.9] - 2019-03-04

Added

  • julia

[0.5.8] - 2019-02-25

Added

  • gpflow

[0.5.7] - 2019-02-20

Added

  • cvxopt
  • lapack
  • cvxpy

Updated

  • nbgrader

[0.5.5] - 2019-01-28

Added

  • nbstripoutput

Updated

  • pytorch

[0.5.3] - 2019-01-06

Added

  • mlxetend
  • scikit-plot

[0.5.1] - 2019-01-02

Updated

  • nbgrader

[0.5.0] - 2018-12-29

Updated

  • Major update to latest notebook and software