Change Log

All notable changes to this project will be documented in this file. This change log follows the conventions of keepachangelog.com.

[1.0.0]

• require-r creates namespace as r.namespace, also namespace as an alias
• dependencies update, TMD 7.029
• SVG plots are annotated with kind/html
• documentation migrated to Clay (partially)

[1.0.0-BETA22 - 2023-11-26]

• dependencies update, TMD 7.021

[1.0.0-BETA21 - 2022-12-28]

• dependencies update
• plotting to svg tries to load svglite by default and use it (#86, #69), there is an option to switch between both implementations (default and svglite)
• defr implemented

[1.0.0-BETA20 - 2022-08-13]

• dependencies update (all libraries)
• REngine updated (by using https://github.com/scicloj/clojisr-rengine)
• warn-on-reflection removed

[1.0.0-BETA19 - 2020-04-05]

• depdendency updates (clojure: "1.10.2", tech.ml.dataset: "5.15")

[1.0.0-BETA18 - 2020-02-19]

• updating the tech.ml.dataset dependency to version "5.00-beta-28" (minor adaptation was required)

[1.0.0-BETA17 - 2020-01-27]

• updating the tech.ml.dataset dependency to version "5.00-beta-27"

[1.0.0-BETA16]

• updated the tech.ml.dataset version (latest 5.0 beta)
• removed the Specter dependency
• removed Renjin -- it will be supported in a separate library -- discussion here
• ADDED vrksasna draft for session management
• a very minor extension of clojisr internals to support that
• removed GCReference (and tech.resource dependency) - replaced by proxy object.
• added clojure.async latest dependency

[1.0.0-BETA15] - 2020-07-12

• [hot fix] datasets are not transfered as data.frame due to implementation of map interfaces in t.m.ds 3.01

[1.0.0-BETA14] - 2020-07-11

• clojisr.v1.rserve and clojisr.v1.renjin namespaces are deprecated now
• setting default session type moved to clojisr.v1.r/set-default-session-type! function
• refactoring of RServe process spawn and connection to mitigate (#62)
• abandoned sessions/R processes cleaning fixes
• tech.ml/dataset bumped to 3.01 version

[1.0.0-BETA13] - 2020-07-09

• regresion with quote (#61), changed to use :!wrap hint
• datetime conversion to string fixes
• tech.ml.dataset bumped to 2.15 version
• (experimental) turned off pomegranate dynamic dep loading for renjin

[1.0.0-BETA12] - 2020-07-08

Note: quote function doesn't work properly

• refactored data and dataset transition between clojure and R backend as described here (#14)
• tech.ml.dataset bumped to 2.13 version
• removed java->naive-clj and added java->native-clj
• require-r is moved to clojisr.v1.r (direct call to clojisr.v1.require/require-r is possible but deprecated)
• reflection warnings mitigation
• integer transition (#73)
• ##Inf/##-Inf transition (#72)
• wrapping into () and {} (#61)
• unary operator wraps next form into parentheses (#59)
• missing path is created when plotting (#56)
• operators wrapped into % (like %chin%) are treated as binary operators (#55)

[1.0.0-BETA11] - 2020-05-20

• updates in exception handling
• updated tech.datatype, tech.ml.dataset dependency versions with some small code adaptation (#64)
• notespace is no longer a dependency
• rsymbol introduced
• moved to lein-tools-deps and all deps are defined in deps.edn now

[1.0.0-BETA10] - 2020-03-29

• new forms added: if, do, for and while
• more binary operators: %%, %/%, ** and %in%
• sequences beginning with command as backticked string are now callable (eg. '("^" 2 4))
• vector starting with :!code is callable
• JVM shutdown hook is registered to clean all R processes which are run when closing java process bra, brabra, bra<-, brabra<- can accept nil as empty-symbol now.
• data function introduced (to load data from package)
• removed empty-symbol (use nil in brackets) and na (use just 'NA)
• picking a random free port as the default Rserve port
• updating notespace dep version
• updating tech.ml.dataset dep version

[1.0.0-BETA9] - 2020-03-21

• changed logging to clojure/tools.logging
• major breaking change: a new set of code-generation rules

[1.0.0-BETA8] - 2020-02-24

• bugfix for plotting (to draw a chart print should be called instead of plot)
• tech.ml libraries bumped
• deps updated
• bugfix: recognizing S4 functions ("standardGeneric")
• bugfix: handling session-args carefully on r->clj data conversion
• Clojure working directory is now set on R side
• print-loop bound to session (#42)
• RConnection locking revisited (#40)
• GC rewritten (#25)
• More careful session management (all atoms are now defonce, closed? depends on processes state)
• fixed rmarkdown bug (wrong usage of gc)

[1.0.0-BETA7] - 2020-02-16

• require-r:
  • :arglists tag added for required R functions
  • warning when package is not found
• bugfix for problems when dynamically loading renjin jar:
  • using pomegranate directly, rather than alembic (to suppoert Java newer than Java 8)
  • handling classloaders carefully
• a new API for data visualization, with more rendering options

[1.0.0-BETA6] - 2020-02-08

• bugfix of a problem with using Alembic (making sure https is used)
• change in the setup API of backends: requiring the main namesapce of a backend (renjin/rserve) sets default session-type, if no other default has been set yet;

[1.0.0-BETA5] - 2020-02-07

• require-r can :refer :all now
• REXPList, REXPNull are supported in data conversion
• changed the API for setting up and switching backends ("session-types")
• also fixed #27 by loading the renjin Jar on-the-fly with the proper repository into

[1.0.0-BETA4] - 2020-02-05

The main changes on the user side are the fact that R functions are Clojure functions, and the initial suppoort for a Renjin backend. Details below:

• performance improvement: using an R environment rather than an R list for session memory
• some refactoring to allow other kinds of R backends, in particular exending the Session protocol to take care of details such as printing and package in spection
• more careful id management of sessions
• checking the object class on creation of R objects
• being careful when printing objects of lost sessions
• R objects now extend the IFn inerface, so that R functions are Clojure functions
• bugfix in regreshing objects across sessions
• simplified the implementation of require-r -- functions can now be handled as regular objects
• handling of strange symbols/keywords: refactored a bit, added some filtering
• initial support of a Renjin (pure-JVM R) backend
• handling failures in require-r
• changes in logging

[1.0.0-BETA3] - 2020-01-28

• handling unhandled cases in java->naive-clj conversion
• loading data, not only functions, at require-r
• require-r optimization: all underlying robjects are created once, then bound to namespaces
• more careful handling of data conversion of list names: names with reader special characters are not converted to keywords

[1.0.0-BETA2] - 2020-01-21

• added '$ as binary operator
• performance bugfix: using native double array and type hint when conferting integer R vectors with missing values to clj
• recognizing reticulate python functions as functions
• bugfix in overriding default session args

[1.0.0-BETA1] - 2020-01-07

Initial v1 version.

Main developments since earlier versions:

• code generation
• changes in error handling, printing, etc.
• requiring of R packages inspired by the python interop story (though less sophisticated)
• function call syntax a bit different (no detailed function signatures yet)
• documentation and tests using notespace

[0.0.1-SNAPSHOT] - Sep. 2019 - Dec. 2019

Initial draft version