Software Updates 2020¶
2020-12-09: materialize, hardlink, and updates¶
- Tools:
- (new) materialize – Materialize is a streaming database for real-time applications. Materialize accepts input data from a variety of streaming sources (e.g. Kafka) and files (e.g. CSVs), and lets you query them using SQL. Additionally
mzcli
is installed to interact with it. - (new) hardlink – consolidate duplicate files via hardlinks
- (new) materialize – Materialize is a streaming database for real-time applications. Materialize accepts input data from a variety of streaming sources (e.g. Kafka) and files (e.g. CSVs), and lets you query them using SQL. Additionally
- Python 3 (system-wide) and R:
- (upd) various packages updates
- System
- package updates
- npm 7, and also updating some node.js utils
2020-11-19 : Mathics, gprMax, and pybedtools¶
- Tools:
- (new) Mathics – a general-purpose computer algebra system (CAS). It is an open-source alternative to Mathematica.
- (new) file managers:
nnn
,ranger
, andlfm
- (upd) various system package updates
- Python 3 (system-wide):
- (new) gprMax – electromagnetic simulation software
- (new) pybedtools – is widely used for genomic interval manipulation or “genome algebra”
- (upd) various packages updates
2020-11-09 : RDkit, Matplotlib Venn and data8 datascience¶
- Python 3 (Anaconda 2020)
- (new) RDkit
2020.09.1
– Open-Source Cheminformatics Software - (new) matplotlib_venn
- (upd) various package updates
- (new) RDkit
- Python 3 (system-wide)
- (new) datascience by data8 – written for use in Berkeley’s DS 8 course and contains useful functionality for investigating and graphically displaying data.
- (upd) various package updates
- Linux system
- (upd) various package updates
2020-11-01: Sage 9.2¶
- SageMath 9.2 available now
- 9.2 Release Tour
- 9.2 example notebook
- To switch back to 9.1 as the default in your project, run
sage_select 9.1
in a Linux Terminal.
2020-10-28: Pandoc 2.11¶
- Utils:
- (upd) pandoc
2.11.0.1
– pandoc 2.11 release notes
- (upd) pandoc
- General:
- (upd) various Python 3 and Ubuntu Linux packages
2020-10-12: RPC info, PyCaret, R 4.0.3, …¶
- Utils:
- (new) rpcinfo – makes an RPC call to an RPC server and reports what it finds
- R:
- (upd) R
4.0.3
- various package updates
- (upd) R
- Python 3 (system-wide):
- (new) pycaret
2.1.2
– an open source, low-code machine learning library in Python that allows you to go from preparing your data to deploying your model within minutes in your choice of notebook environment - various package updates
- (new) pycaret
- Julia:
- (upd) Julia
1.5.2
- (upd) Julia
2020-09-28: aTSA, BERT and pyGIMLi¶
- Node.js:
- (upd) typescript
4.0.2
,prettier@2.1.1
,webpack@4.44.1
,coffeescript@2.5.1
,data-cli@0.10.1
,ijavascript@5.2.0
, …
- (upd) typescript
- R (system-wide):
- (new) aTSA – Contains some tools for testing, analyzing time series data and fitting popular time series models such as ARIMA, Moving Average and Holt Winters, etc.
- (upd) various packages
- Python 3 (system-wide):
- (upd) nbconvert
6.0.6
, matplotlib3.3.2
and various other packages
- (upd) nbconvert
- Utilities:
- (upd) heroku
7.43.0
- (upd) heroku
2020-09-12: Regular update¶
- Anaconda 2020:
- statsmodels
0.12.0
, pandas1.1.1
, matplotlib3.3.1
, dask/distributed2.25.0
, biopython1.78
, etc.
- statsmodels
- Python 3 (system-wide):
- pandas
1.1.2
, seaborn0.11.0
(to fix plotting issue #2194), …
- pandas
- Ubuntu 18.04:
- a couple of small updates, mostly system packages
2020-09-01: Julia 1.5.1¶
- Julia:
- updated to 1.5.1
- various package updates
- Python (system-wide):
- various package updates, including dask/distributed
2.25.0
, hypothesis5.29.1
- various package updates, including dask/distributed
- R (system-wide)
- various package updates
- Software
- (new) Asciidoctor
2.0.10
- CMake
3.18.2
- Haskell
ghc 8.10.2
- (new) Asciidoctor
2020-08-18: Ubuntu 20.04¶
The default environment for new projects changed: learn more …
2020-08-14/18.04: Regular update of Ubuntu 18.04¶
Cumulative updates to various software package environments.
2020-07-31: Cumulative Updates¶
Yet another round of cumulative updates to Linux, Python and R and a new tool grepcidr.
2020-07-16: Minor/Bugfixes¶
This is a cumulative update with several small changes and bugfixes. For example a dependency problem for PyTorch. A noteworthy new library is Epidemics-on-Networks for Python 3 (system-wide), e.g. EoN example test.
2020-06-20: Updating SnapPy in SageMath¶
- Python 3 (system-wide)
- (upd) tensorflow
2.2.0
, Cython0.29.20
, dask2.18.1
, dask2.19.0
, distributed2.19.0
, pandas1.0.5
- (upd) qiskit related packages and pyscf
1.7.3
- (upd) tensorflow
- Sage 9.1
- (upd) snappy
2.8
, spherogram1.8.3
, plink2.3.1
- (upd) snappy
- Sage 8.9
- (upd) plink
2.3.1
, snappy2.8
, spherogram1.8.3
- (upd) plink
- Software
- various system-wide updates, including R packages
2020-06-06: Prophet and pmdarima¶
- Python 3 (system-wide)
2020-05-27: Sage 9.1 and Node.js 12¶
- SageMath 9.1 available now
- Julia
- (upd) Julia
1.4.2
- (upd) Julia
- Python 3 (system-wide)
- (upd) scikit-learn, sympy
1.6.0
, mxnet1.6.0
- (upd) scikit-learn, sympy
2020-05-20¶
- Software
- (new) mathlibtools
0.0.6
for LEAN
- (new) mathlibtools
- Python 3 (system-wide)
- (upd) scikit-learn
0.23.0
, imageio2.8.0
, PyLaTeX1.3.2
, obspy1.2.1
- (upd) scikit-learn
- Julia 1.4
- (new) FFTW
2020-05-12: Octave 5.2.0¶
- Expanded the list of pre-installed Octave packages
- Updated the Octave Jupyter kernel
- Made it a first class citizen
2020-05-10: QuSpin and RmdFormats¶
- Python 3 (Anaconda 2019):
- (new) QuSpin
0.3.4
– Python package for exact diagonalization and quantum dynamics of arbitrary boson, fermion and spin many-body systems. QuSpin supports the use of various (user-defined) symmetries for one and higher-dimensional lattice systems, (imaginary) time evolution following arbitrary user-specified driving protocols, and constrained Hilbert spaces.
- (new) QuSpin
- Python 3 (system-wide)
- (fix) the
/ext/bin/tensorboard
wrapper script works again - (upd) dask/distributed
2.16.0
- (fix) the
- R (system-wide)
- (new) rmdformats – provides several HTML output formats of unique and attractive styles for RMarkdown
- various package updates …
2020-05-08: Fixing Keras¶
- Python 3 (system-wide)
- (fix) keras in tensorflow by downgrading tensorflow-estimator (issue tf #37525)
- Software
- (upd) npm
6.14.5
, typescript3.8.3
- (upd) npm
2020-05-04: Stellargraph¶
- Python 3 (system-wide)
- (new) stellargraph
0.11.1
– software for network graph analytics - (upd) tensorflow-estimator
2.2.0
, tensorflow-probability0.9.0
, dask2.15.0
, distributed2.15.1
, statsmodels0.11.1
- (new) stellargraph
- R (system-wide)
- (new) genlasso
1.4
– Provides fast algorithms for computing the solution path for generalized lasso problems - (new) coronavirus
0.1
– Provides a daily summary of the Coronavirus (COVID-19) cases by state/province - many additional packages and updates
- (new) genlasso
- Jupyter Notebooks:
- (rem) disabling deprecated and little useful kernels:
- Julia 1.3: use Julia 1.4
- Sage’s Python 2: use Sage’s Python mode. also, starting with 9.0 it’s Python 3
- Sage’s R: use R (system-wide), there is no reason left to use this one
2020-04-25: R 3.6.3
and Julia 1.4.1
¶
- R (system-wide)
- (upd) Upgrading R to
3.6.3 -- "Holding the Windsock"
and many R packages - (rem) Removing
r-cran-bvs
,r-cran-haplo.ccs
, andr-cran-haplo.stats
, because they were holding back updating R
- (upd) Upgrading R to
- Julia
- (upd) to 1.4.1
- (new) adding several packages: see Julia Packages on CoCalc
2020-04-16 COBOL (GnuCOBOL)¶
- Software:
- (new) COBOL via GnuCOBOL – an acronym for “common business-oriented language”). Created in the 1960’s, it is a compiled English-like computer programming language designed for business use. It is imperative, procedural and, since 2002, object-oriented. – cobol example file
- (upd) Rust
rustc +stable: 1.42.0
rustc +beta: 1.43.0-beta.5
rustc +nightly: 1.44.0-nightly
- (new) Intel MKL
intel-mkl-64bit-2020.1-102
– The Fastest and Most-Used Math Library for Intel®-Based Systems - use via
export LD_LIBRARY_PATH=/opt/intel/mkl/lib/intel64
- use via
- (new) Intel MKL
- Python 3 (system-wide):
- (upd) numpy
1.18.2
- (upd) numpy
- SageMath:
- (upd) development version
9.1.rc0
- (upd) development version
2020-04-08: healpy 1.13¶
2020-03-30: Julia 1.4¶
- Julia:
- (new) Julia 1.4 release notes – please update from 1.3 to 1.4 soon, since 1.3 is deprecated.
- Python 3 (system-wide)
- (upd) geopandas
0.7.0
, rasterio1.1.3
, isochrones2.1
, cython0.29.16
, matplotlib3.2.1
, pandas1.0.3
, ipykernel5.2.0
, nipype1.4.2
- (upd) geopandas
- Python 3 (Anaconda 2019)
- (upd) matplotlib
3.2.1
, numba0.48.0
, numpy1.18.1
, statsmodels0.11.1
, geopandas0.7.0
, pandas1.0.3
- (upd) matplotlib
- Node.js
- (upd) coffeescript
2.5.1
, typescript3.8.3
, npm6.14.4
, data-cli0.9.6
, ijavascript5.2.0
(for the JavaScript kernel), chromedriver80.0.1
, prettier2.0.2
, lerna3.20.2
, webpack4.42.1
- (upd) coffeescript
- Software
- (upd) various Linux package updates, including
qgis
related ones to3.12.1
- (upd) various Linux package updates, including
2020-03-20:¶
- Python 3 Anaconda 2019
- (upd) scikit-learn
0.22.2.post1
, matplotlib3.2.0
- (upd) scikit-learn
- Python 3 system-wide
- (new) ccdproc
2.1.0
– an Astropy affiliated package for basic data reductions of CCD images - (upd) matplotlib
3.2.0
, dask/distributed2.12
, scikit-learn0.22.2.post1
- (new) ccdproc
- Software
- (new)
libnetcdff6 (4.4.4+ds-3)
andlibnetcdff-dev (4.4.4+ds-3)
- (new)
- R (system-wide)
- (new)
markovchain 0.8.4
- (upd) various packages …
- (new)
2020-02-29: Async I/O in Jupyter Notebooks¶
- Python 3
(upd) various Jupyter libs: jupyter-client
6.0.0
, jupyter-console6.1.0
, jupyterhub1.1.0
, jupyterlab1.2.6
, ipykernel5.1.4
, ipython7.12.0
, …This means you work seamlessly with Python 3’s async/await coroutines in the system-wide Python3 kernel:
import asyncio async def main(): print('hello') await asyncio.sleep(1) print('world') await main()
(new) folium
0.10.1
– maps of the world. tryimport folium; folium.Map(location=[45.523, -122.675], width=750, height=500)
(upd) requests
2.23.0
, cython0.29.15
, numba0.48.0
, numpy1.17.5
, curio1.0
, nest-asyncio1.2.3
, biopython1.76
(upd) PyTest related:
pytest-5.3.5
,pytest-doctestplus-0.5.0
,pytest-forked-1.1.3
,pytest-html-2.0.1
,pytest-mock-2.0.0
,pytest-pylint-0.15.0
,hypothesis-5.5.4
,pytest-astropy-0.8.0
- Software
- (upd) qgis
3.12
- (upd) typescript
3.8.2
- (upd) qgis
- LEAN
- (upd) mathlib
2020-02-27
nightly build (LEAN 3.6.0 and mathlib aren’t compatible yet, hence no update of LEAN itself)
- (upd) mathlib
- R
- (new) mltools
0.3.5
– A collection of machine learning helper functions, particularly assisting in the Exploratory Data Analysis phase.
- (new) mltools
2020-02-21: LEAN 3.5.1 and JavaScript Kernel¶
- LEAN, the open source theorem prover:
Update to 3.5.1, the most recent LEAN community edition
Latest mathlib build
- Try it:
- LEAN maths challenges (open this link, then click “Edit” to copy the files into a new project where you can run the programs)
- Natural numbers example:
- Jupyter:
- (new) You can run JavaScript in a Jupyter Notebook, powered by Node.js – ijavascript example notebook.
- Software:
- (upd) pandoc
2.9.2
– pandoc 2.9.2 release notes - (new) fractint – in an X11 desktop, run
xfractint
- (new) surface evolver
2.70
– an interactive program for the modelling of liquid surfaces shaped by various forces and constraints (runevolver
in an X11 desktop)
- (upd) pandoc
- Python
- (upd) protobuf
3.11.3
, dask2.11.0
and distributed2.11.0
, spacy2.2.3
, nilearn0.6.1
- (upd) protobuf
2020-02-16: Pandas 1.0 and Octave 5.2.0¶
- Python 3:
- (upd) pandas
1.0
– Pandas 1.0 release notes. This is a major release which might break some libs. Please let us know about any issues. You can always switch back to the previous release inSettings
→Project Control
→Software Environment
and selectPrevious
. - (upd) updating Pandas reverse dependencies: Mesa
0.8.6
, Orange33.24.1
, Quandl3.5.0
, TPOT0.11.1
, adtk0.5.2
, altair4.0.1
, arctic1.79.3
, arviz0.6.1
, bqplot0.12.3
, cobra0.17.1
, dask-ml1.2.0
, empyrical0.5.3
, isochrones2.0.1
, linearmodels4.17
, mlxtend0.17.1
, openTSNE0.3.12
, optlang1.4.4
, pandas-bokeh0.4.2
, pandas-profiling2.4.0
, pdpipe0.0.41
, pysal2.1.0
, qgrid1.2.0
, scikit-rf0.15.1
, tabulate0.8.6
, tellurium2.1.5
, teneto0.5.0
, xarray0.15.0
- (upd) pandas
- Anaconda Python:
- (new) ocaml
4.06.1
– an industrial strength programming language supporting functional, imperative and object-oriented styles - (upd) various package updates, including numpy, scipy, scikit learn, statsmodels, etc.
- (new) ocaml
2020-02-03: AstroPy 4.0¶
- Python 3:
- (upd) astropy
4.0
, astroplan0.6
– what’s new in AstroPY 4.0 - (upd) mypy
0.761
, pygments2.5.2
, yapf0.29.0
, dask2.10.0
, matplotlib3.1.2
, rpy23.2.5
, statsmodels0.11.0
, pip20.0.2
- (upd) astropy
- SageMath (8.9 and 9.0):
- (upd) admcycles
1.0
, a major release update!
- (upd) admcycles
- Software:
- (new) openscad (available as
openscad-nightly
) together with support packagesmeshlab
,geomview
andlibrecad
- (upd) various Linux system packags, including R libs
- (new) openscad (available as
2020-01-29 Rust 1.40
¶
- Software:
- (upd) a round of updating Rust:
- stable:
1.40.0
- beta:
1.41.0-beta.2
- nightly:
1.42.0-nightly
- stable:
- Python 3 and Anaconda 2019:
- (new) pgmpy
0.1.9
– a python library for working with Probabilistic Graphical Models
- (new) pgmpy
- Python 3:
- (new) okpy
1.14.19
– OK autogrades programming assignments, facilitates submission, composition feedback, and analytics for your class. It’s installed for the Linux Terminal and runok --help
for more info. - (new) pyreadstat
0.2.9
– read and write sas (sas7bdat, sas7bcat, xport), spps (sav, zsav, por) and stata (dta) data files into/from pandas dataframes - (new) bitarray
1.2.1
– efficient arrays of booleans - (new) ifsFractals
1.17.4
– fast IFS fractal generation (ifs fractals example) - (upd) PyTorch
1.3.1
, joblib0.14.1
, drive-cli2.1.0
, seaborn0.10.0
, numba0.47.0
- (new) okpy
2020-01-19: SentimentAnalysis R package¶
- R Software:
- (new) SentimentAnalysis – package introduces a powerful toolchain facilitating the sentiment analysis of textual contents in R.
- Python 3:
- (upd) sympy
1.5.1
, tensorflow2.1.0
, tensorflow-estimator2.1.0
, dask/distributed2.9.2/.3
- (upd) sympy
2020-01-05: SageMath 9.0 based on Python 3¶
- SageMath:
(new)
sage-9.0
and associated Jupyter Kernel available. This release marks a significant change, because the era of Python 2 ends and Python 3 starts – finally.Note
Please read about the changes in Sage 9.0 regarding Python 3 or more general, consult the Python 3 porting guide!
- Julia:
- new year cleanup: only supporting
1.0 LTS
and newer versions – currently1.3.1
– which is the default Julia on CoCalc now. - (upd) re-installing all packages will lead to various updates
- (new) ApproxFun and SpecialMatrices in
1.3.1
- new year cleanup: only supporting
- Python 3:
- (new) kplr
0.2.2
– A Python interface to the Kepler data - (upd)
six 1.13
, numpy1.17.4
, scipy1.4.1
,ansi2html-1.5.2
,markdown2-2.3.8
,pylint-2.4.4
, pillow6.2.1
, imageio2.6.1
, pywavelets1.1.1
, scikit-learn0.22.1
, tpot0.11.0
- (new) kplr
- Python 2:
- Python 2 is still available, but w/o maintenance.
- If you require specific setups for old libraries and python 2, we can setup a custom software environment.
- R:
- (new) DeclareDesign
0.20.0
and DesignLibrary0.1.4
- (new) DeclareDesign