Merge pull request #106 from scicloj/2-beta4

2 beta4

CHANGELOG.md

@@ -1,6 +1,10 @@
 # Change Log
 All notable changes to this project will be documented in this file. This change log follows the conventions of [keepachangelog.com](http://keepachangelog.com/).
 
+## [2-beta4] - 2025-01-01
+- removed the Scicloj.ml.smile from the direct Noj dependencies (though it is still recommended to use with Noj)
+- updated deps (Metamorph.ml. Scicloj.ml.tribuo, Clay, Tableplot)
+
 ## [2-beta3] - 2024-12-24
 - updated deps (Libpython-clj, Tableplot, Clay)
 

build.clj

@@ -17,7 +17,7 @@
 
 
 (def lib 'org.scicloj/noj)
-(def version "2-beta3")
+(def version "2-beta4")
 (def snapshot (str version "-SNAPSHOT"))
 (def class-dir "target/classes")
 

deps.edn

@@ -6,13 +6,12 @@
         org.scicloj/kindly                        {:mvn/version "4-beta14"}
         generateme/fastmath                       {:mvn/version "3.0.0-alpha3"}
         aerial.hanami/aerial.hanami               {:mvn/version "0.20.1"}
-        org.scicloj/tableplot                     {:mvn/version "1-beta5"}
-        org.scicloj/scicloj.ml.smile              {:mvn/version "7.4.3"}
-        org.scicloj/metamorph.ml                  {:mvn/version "0.10.4"}
+        org.scicloj/tableplot                     {:mvn/version "1-beta6"}
+        org.scicloj/metamorph.ml                  {:mvn/version "0.11.1"}
         org.scicloj/sklearn-clj                   {:mvn/version "0.4.1"}
         org.scicloj/scicloj.ml.xgboost            {:mvn/version "6.2.0"}
 
-        org.scicloj/scicloj.ml.tribuo             {:mvn/version "0.1.4"}
+        org.scicloj/scicloj.ml.tribuo             {:mvn/version "0.1.6"}
 
         org.tribuo/tribuo-regression-liblinear    {:mvn/version "4.3.1"}
         org.tribuo/tribuo-regression-libsvm       {:mvn/version "4.3.1"}
@@ -36,7 +35,7 @@
         org.babashka/sci                          {:mvn/version "0.9.44"}
         org.mentat/emmy-viewers                   {:mvn/version "0.3.2"}
 
-        org.scicloj/clay                          {:mvn/version "2-beta26"}}
+        org.scicloj/clay                          {:mvn/version "2-beta27"}}
  :aliases
  {:gen-tests {:extra-paths ["build"]}
 
@@ -50,7 +49,8 @@
                       io.github.cognitect-labs/test-runner {:git/tag "v0.5.1" :git/sha "dfb30dd"}
                       org.slf4j/slf4j-nop {:mvn/version "2.0.16"}
                       org.scicloj/clay {:mvn/version "2-beta25"}
-                      clj-http/clj-http {:mvn/version "3.13.0"}}}
+                      clj-http/clj-http {:mvn/version "3.13.0"}
+                      org.scicloj/scicloj.ml.smile              {:mvn/version "7.4.3"}}}
 
   :model-integration-tests
   {:extra-paths ["model-integration-tests" "notebooks"]
@@ -60,12 +60,14 @@
                 org.bytedeco/arpack-ng-platform {:mvn/version "3.7.0-1.5.4"}
                 org.bytedeco/openblas {:mvn/version "0.3.10-1.5.4"}
                 org.bytedeco/javacpp {:mvn/version "1.5.4"}
+                org.scicloj/scicloj.ml.smile              {:mvn/version "7.4.3"}
 
                 com.taoensso/nippy {:mvn/version "3.4.2"}
 
                 org.slf4j/slf4j-nop {:mvn/version "2.0.16"}
                 org.slf4j/jul-to-slf4j {:mvn/version "2.0.16"}
-                io.github.cognitect-labs/test-runner {:git/tag "v0.5.1" :git/sha "dfb30dd"}}}
+                io.github.cognitect-labs/test-runner
+                {:git/tag "v0.5.1" :git/sha "dfb30dd"}}}
 
 
   :dev {:extra-paths ["notebooks"]
@@ -76,7 +78,8 @@
                      org.bytedeco/openblas {:mvn/version "0.3.10-1.5.4"}
                      org.bytedeco/javacpp {:mvn/version "1.5.4"}
                      com.oracle.labs.olcut/olcut-config-edn    {:mvn/version "5.1.4"}
-                     com.oracle.labs.olcut/olcut-config-json    {:mvn/version "5.1.4"}}}
+                     com.oracle.labs.olcut/olcut-config-json    {:mvn/version "5.1.4"}
+                     org.scicloj/scicloj.ml.smile              {:mvn/version "7.4.3"}}}
 
   :outdated {;; Note that it is `:deps`, not `:extra-deps`
              :deps {com.github.liquidz/antq {:mvn/version "RELEASE"}}

notebooks/noj_book/automl.clj

@@ -6,6 +6,10 @@
 ;;  validation to pick the best performing model automatically.
 ;;
 
+;; Note that this chapter reqiures `scicloj.ml.smile` as an additional
+;; dependency to Noj.
+;; [![Clojars Project](https://img.shields.io/clojars/v/org.scicloj/scicloj.ml.smile.svg)](https://clojars.org/org.scicloj/scicloj.ml.smile)
+
 (ns noj-book.automl
   (:require [noj-book.ml-basic :as ml-basic]
             [scicloj.kindly.v4.kind :as kind]
@@ -487,4 +491,4 @@ logistic-regression-specs
 ;; Nevertheless is some scenarios it is very useful to create a full transformation pipeline
 ;; as a metamorph pipeline. This would for example allow to perform very different transformation steps per model
 ;; and still only have a single seq of pipeline functions to manage,
-;; therefore having fully self contained pipelines.
+;; therefore having fully self contained pipelines.

notebooks/noj_book/known_issues.clj

@@ -29,6 +29,7 @@
 ;;
 ;; This can be used for reference or as a starting point to use Noj, if one desires.
 ;; ### scicloj.ml.smile
-;; Some of the Smile based models require native dependencies. This is documented in [Smile](https://github.com/haifengl/smile)
+;; Noj is often used together with `scicloj.ml.smile`, and
+;; some of the Smile based models require native dependencies. This is documented in [Smile](https://github.com/haifengl/smile)
 
 

notebooks/noj_book/recommended_libraries.clj

@@ -11,6 +11,7 @@
 ;; * [fitdistr](https://github.com/generateme/fitdistr) - fitting distributions
 ;; * [inferme](https://github.com/generateme/inferme) - Bayesian inference
 ;; * [cmdstan-clj](https://github.com/scicloj/cmdstan-clj) - bindings for [Stan](https://mc-stan.org/) Bayesian inference - 🛠 early stage
+;; * [scicloj.ml.smile](https://github.com/scicloj/scicloj.ml.smile) - [Smile](https://haifengl.github.io/) (v 2.6) machine learning models
 ;; * [fastmath-clustering](https://generateme.github.io/fastmath-clustering/) - a wrapper for [Smile](https://haifengl.github.io/) 2.6 clustering algorithms
 ;; * [clj-djl](https://github.com/scicloj/clj-djl) - bindings for [Deep Java Library](https://djl.ai/)
 ;; * [scicloj.ml.clj-djl](https://github.com/scicloj/scicloj.ml.clj-djl) - clj-djl models for [metamorph.ml](https://github.com/scicloj/metamorph.ml)

notebooks/noj_book/smile_classification.clj

@@ -1,5 +1,10 @@
 ;; # Smile classification models reference - DRAFT 🛠
 
+;; Note that this chapter reqiures `scicloj.ml.smile` as an additional
+;; dependency to Noj.
+;; [![Clojars Project](https://img.shields.io/clojars/v/org.scicloj/scicloj.ml.smile.svg)](https://clojars.org/org.scicloj/scicloj.ml.smile)
+
+
 (ns noj-book.smile-classification
   (:require
    [noj-book.utils.example-code :refer [iris-std]]

notebooks/noj_book/smile_others.clj

@@ -1,5 +1,9 @@
 ;; # Smile other models reference - DRAFT 🛠
 
+;; Note that this chapter reqiures `scicloj.ml.smile` as an additional
+;; dependency to Noj.
+;; [![Clojars Project](https://img.shields.io/clojars/v/org.scicloj/scicloj.ml.smile.svg)](https://clojars.org/org.scicloj/scicloj.ml.smile)
+
 ^:kindly/hide-code
 (ns noj-book.smile-others
   (:require

notebooks/noj_book/smile_regression.clj

@@ -1,5 +1,9 @@
 ;; # Smile regression models reference - DRAFT 🛠
 
+;; Note that this chapter reqiures `scicloj.ml.smile` as an additional
+;; dependency to Noj.
+;; [![Clojars Project](https://img.shields.io/clojars/v/org.scicloj/scicloj.ml.smile.svg)](https://clojars.org/org.scicloj/scicloj.ml.smile)
+
 ^:kindly/hide-code
 (require '[scicloj.ml.smile.regression]
          '[scicloj.ml.tribuo])

notebooks/noj_book/transformer_references.clj

@@ -1,5 +1,10 @@
 ;; # Transformer reference  - DRAFT 🛠
 
+;; Note that this chapter reqiures `scicloj.ml.smile` as an additional
+;; dependency to Noj.
+;; [![Clojars Project](https://img.shields.io/clojars/v/org.scicloj/scicloj.ml.smile.svg)](https://clojars.org/org.scicloj/scicloj.ml.smile)
+
+
 (ns noj-book.transformer-references
   (:require
    [scicloj.kindly.v4.api :as kindly]

notebooks/noj_book/underlying_libraries.clj

@@ -29,7 +29,6 @@
 ;; ## Machine learning
 ;; * [metamorph.ml](https://github.com/scicloj/metamorph.ml) - machine learning platform [(reference)](https://cljdoc.org/d/scicloj/metamorph.ml)
 ;; * [scicloj.ml.tribuo](https://github.com/scicloj/scicloj.ml.tribuo) - [Tribuo](https://tribuo.org/) machine learning models
-;; * [scicloj.ml.smile](https://github.com/scicloj/scicloj.ml.smile) - [Smile](https://haifengl.github.io/) (v 2.6) machine learning models
 ;; * [sklearn-clj](https://github.com/scicloj/sklearn-clj) - Plugin to use [sklearn](https://scikit-learn.org/) models in metamorph.ml
 
 ;; ## Visualization