Merge pull request #24 from scicloj/stabilize

Stabilize
scicloj · Aug 20, 2024 · bd52a6d · bd52a6d
2 parents 58c8051 + af39612
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,9 +1,9 @@
 # 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/).
 
-## [1-alpha35] - unreleased
-- avoding the unnecessary use of Reagent for Python plots
-- updated deps
+## [2-alpha1-SNAPSHOT] - unreleased
+- updating the set of depndencies: Fastmath 3-SNAPSHOT, the relevant metamorph.ml branch, kind-pyplot, hanamicloth, etc.
+- removing all Noj namespaces
 
 ## [1-alpha34] - 2024-04-15
 - removed the currently-unnecessary `calc-correlations-matrix` and `round` functions (#22) - thanks, @behrica

diff --git a/README.md b/README.md
@@ -1,6 +1,6 @@
 # scinojure (noj)
 
-![Noj logo](resources/Noj.svg)
+![Noj logo](notebooks/Noj.svg)
 
 The Noj library collects a few of the relevant Clojure data & science with additional documentation and convenience layers composing them together.
 

diff --git a/build.clj b/build.clj
@@ -15,7 +15,7 @@
             [deps-deploy.deps-deploy :as dd]))
 
 (def lib 'org.scicloj/noj)
-(def version "1-alpha34-SNAPSHOT")
+(def version "2-alpha1-SNAPSHOT")
 (def snapshot (str version "-SNAPSHOT"))
 (def class-dir "target/classes")
 

diff --git a/deps.edn b/deps.edn
@@ -1,19 +1,21 @@
 {:paths ["src" "resources"]
  :deps {org.clojure/clojure {:mvn/version "1.11.1"}
         scicloj/tablecloth {:mvn/version "7.029.2"}
-        org.scicloj/kindly {:mvn/version "4-beta4"}
-        generateme/fastmath {:mvn/version "2.4.0"}
+        org.scicloj/kindly {:mvn/version "4-beta6"}
+        generateme/fastmath {:mvn/version "3.0.0-SNAPSHOT"}
         aerial.hanami/aerial.hanami {:mvn/version "0.20.0"}
-        cljplot/cljplot {:mvn/version "0.0.3"}
-        scicloj/metamorph.ml {:mvn/version "0.8.2"}
-        scicloj/scicloj.ml.smile {:mvn/version "7.2"}
+        org.scicloj/hanamicloth {:mvn/version "1-alpha6-SNAPSHOT"}
+        scicloj/metamorph.ml {:git/url "https://github.com/scicloj/metamorph.ml"
+                              :git/sha "bb151eec256f0e4443cdb4f39be8609f6078a4ad"}
         scicloj/scicloj.ml.tribuo {:git/url "https://github.com/scicloj/scicloj.ml.tribuo"
-                                   :git/sha "1bde7c4"
-                                   :git/tag "v0.1.0"}
+                                   :git/sha "f4ebf1e1bb78eb99dd35ca886d75b9f65d800e8d"}
+        org.tribuo/tribuo-regression-sgd {:mvn/version "4.2.0"}
+        org.tribuo/tribuo-regression-tree {:mvn/version "4.2.0"}
+        org.tribuo/tribuo-classification-sgd {:mvn/version "4.2.0"}
+        org.tribuo/tribuo-classification-tree {:mvn/version "4.2.0"}
         clj-python/libpython-clj {:mvn/version "2.025"}
-        scicloj/clojisr {:mvn/version "1.0.0"}
-        org.scicloj/tempfiles {:mvn/version "1-alpha2"}
-        kixi/stats {:mvn/version "0.5.5"}}
+        org.scicloj/kind-pyplot {:mvn/version "1-beta1"}
+        scicloj/clojisr {:mvn/version "1.0.0"}}
  :aliases
  {:build {:deps {io.github.clojure/tools.build {:mvn/version "0.9.6"}
                  slipset/deps-deploy {:mvn/version "0.2.1"}}

diff --git a/docs/index.html b/docs/index.html
@@ -7,7 +7,7 @@
 <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes">
 
 
-<title>Noj Documentation</title>
+<title>Scinojure Documentation</title>
 <style>
 code{white-space: pre-wrap;}
 span.smallcaps{font-variant: small-caps;}
@@ -30,7 +30,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./noj_book.prepare_for_ml.html" rel="next">
+<link href="./noj_book.ml_basic.html" rel="next">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -96,7 +96,7 @@
   <nav id="quarto-sidebar" class="sidebar collapse collapse-horizontal quarto-sidebar-collapse-item sidebar-navigation floating overflow-auto">
     <div class="pt-lg-2 mt-2 text-left sidebar-header">
     <div class="sidebar-title mb-0 py-0">
-      <a href="./">Noj Documentation</a> 
+      <a href="./">Scinojure Documentation</a> 
     </div>
       </div>
         <div class="mt-2 flex-shrink-0 align-items-center">
@@ -114,14 +114,14 @@
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./noj_book.prepare_for_ml.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Machine learning specific functionality in <code>tech.ml.dataset</code></span></span></a>
+  <a href="./noj_book.ml_basic.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Machine learning</span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./noj_book.ml_basic.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Machine learning</span></span></a>
+  <a href="./noj_book.prepare_for_ml.html" class="sidebar-item-text sidebar-link">
+ <span class="menu-text"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">Machine learning specific functionality in <code>tech.ml.dataset</code></span></span></a>
   </div>
 </li>
         <li class="sidebar-item">
@@ -141,47 +141,11 @@
   <a href="./noj_book.datasets.html" class="sidebar-item-text sidebar-link">
  <span class="menu-text"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">Datasets</span></span></a>
   </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.python.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Python (experimental 🛠)</span></span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.statistics.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">8</span>&nbsp; <span class="chapter-title">Statistics (experimental 🛠)</span></span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.visualization.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">9</span>&nbsp; <span class="chapter-title">Visualization (too be deprecated 🛠)</span></span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.statistical_visualization.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">10</span>&nbsp; <span class="chapter-title">Statistical Visualization (to be depracated 🛠)</span></span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.more_visualization.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">11</span>&nbsp; <span class="chapter-title">More visualization examples (to be deprecated 🛠)</span></span></a>
-  </div>
 </li>
         <li class="sidebar-item">
   <div class="sidebar-item-container"> 
   <a href="./noj_book.visualizing_correlation_matrices.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">12</span>&nbsp; <span class="chapter-title">Visualizing correlation matrices (experimental 🛠) - DRAFT</span></span></a>
-  </div>
-</li>
-        <li class="sidebar-item">
-  <div class="sidebar-item-container"> 
-  <a href="./noj_book.known_issues.html" class="sidebar-item-text sidebar-link">
- <span class="menu-text"><span class="chapter-number">13</span>&nbsp; <span class="chapter-title">Known Issues ❗</span></span></a>
+ <span class="menu-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Visualizing correlation matrices (experimental 🛠) - DRAFT</span></span></a>
   </div>
 </li>
     </ul>
@@ -207,7 +171,7 @@ <h2 id="toc-title">Table of contents</h2>
 
 <header id="title-block-header" class="quarto-title-block default">
 <div class="quarto-title">
-<h1 class="title">Noj Documentation</h1>
+<h1 class="title">Scinojure Documentation</h1>
 </div>
 
 
@@ -234,32 +198,28 @@ <h1 class="title">Noj Documentation</h1>
 </style>
 <script src="index_files/md-default0.js" type="text/javascript"></script>
 <script src="index_files/md-default1.js" type="text/javascript"></script>
+<svg fill="none" height="128" stroke-linecap="round" stroke-linejoin="round" stroke-width="31" viewbox="-128 -128 256 256" width="128" xmlns="http://www.w3.org/2000/svg"><circle cx="0" cy="0" fill="#2F4179" r="128" stroke="none"></circle><g stroke-linecap="butt"><path d="M -128,0 Q -112,0 -112,20 -100,100 -20,112 0,112 0,128" stroke="#62B132"></path><path d="M 128,0 Q 112,0 112,-20 100,-100 20,-112  0,-112 0,-128" stroke="#5881D8"></path></g><g fill="#FFCD52" id="north star"><path d="M 0 -80 L 8 0 0 80 -8 0 Z"></path><path d="M -80 0 L 0 8 80 0 0 -8 Z"></path><path d="M -40.0 -40.0 L -8 0 40.0 40.0 8 0 Z"></path><path d="M -40.0 40.0 L -8 0 40.0 -40.0 8 0 Z"></path></g></svg>
+
 <section id="preface" class="level1" data-number="1">
 <h1 data-number="1"><span class="header-section-number">1</span> Preface</h1>
-<p>Noj (scinojure) is an opinionated way to use the emerging Clojure data stack.</p>
-<p>It collects a few of the main dependencies together with functions allowing to conveniently use them together.</p>
+<p>Scinojure is an entry point to the Clojure stack for data &amp; science.</p>
+<p>It collects a few of the main libraries and documents common ways to use them together.</p>
 <p><strong>Source:</strong> <a href="https://github.com/scicloj/noj"><img src="https://img.shields.io/badge/github-%23121011.svg?style=for-the-badge&amp;logo=github&amp;logoColor=white" class="img-fluid" alt="(GitHub repo)"></a></p>
 <p><strong>Artifact:</strong> <a href="https://clojars.org/org.scicloj/noj"><img src="https://img.shields.io/clojars/v/org.scicloj/noj.svg" class="img-fluid" alt="(Clojars coordinates)"></a></p>
-<p><strong>Status:</strong> Some parts of the underlying libraries are stable. Some part of Noj are still experimental, and the API will change. These details should be clarified soon.</p>
+<p><strong>Status:</strong> Mos of the underlying libraries are stable. The experimental parts are marked as such.</p>
 <section id="getting-started" class="level2" data-number="1.1">
 <h2 data-number="1.1" class="anchored" data-anchor-id="getting-started"><span class="header-section-number">1.1</span> Getting started</h2>
-<p>See the standalone repo example: <a href="https://scicloj.github.io/noj-getting-started/">Noj - getting started - from raw data to a blog post</a></p>
+<p>coming soon</p>
 </section>
 <section id="existing-chapters-in-this-book" class="level2" data-number="1.2">
 <h2 data-number="1.2" class="anchored" data-anchor-id="existing-chapters-in-this-book"><span class="header-section-number">1.2</span> Existing chapters in this book:</h2>
 <ul>
-<li><p><a href="noj_book.prepare_for_ml.html">Machine learning specific functionality in <code>tech.ml.dataset</code></a></p></li>
 <li><p><a href="noj_book.ml_basic.html">Machine learning</a></p></li>
+<li><p><a href="noj_book.prepare_for_ml.html">Machine learning specific functionality in <code>tech.ml.dataset</code></a></p></li>
 <li><p><a href="noj_book.automl.html">AutoML using metamorph pipelines</a></p></li>
 <li><p><a href="noj_book.interactions_ols.html">Ordinary least squares with interactions</a></p></li>
 <li><p><a href="noj_book.datasets.html">Datasets</a></p></li>
-<li><p><a href="noj_book.python.html">Python (experimental 🛠)</a></p></li>
-<li><p><a href="noj_book.statistics.html">Statistics (experimental 🛠)</a></p></li>
-<li><p><a href="noj_book.visualization.html">Visualization (too be deprecated 🛠)</a></p></li>
-<li><p><a href="noj_book.statistical_visualization.html">Statistical Visualization (to be depracated 🛠)</a></p></li>
-<li><p><a href="noj_book.more_visualization.html">More visualization examples (to be deprecated 🛠)</a></p></li>
 <li><p><a href="noj_book.visualizing_correlation_matrices.html">Visualizing correlation matrices (experimental 🛠) - DRAFT</a></p></li>
-<li><p><a href="noj_book.known_issues.html">Known Issues ❗</a></p></li>
 </ul>
 <div style="background-color:grey;height:2px;width:100%;"></div>
 <div><pre><small><small>source: <a href="https://github.com/scicloj/noj/blob/main/notebooks/index.clj">notebooks/index.clj</a></small></small></pre></div>
@@ -693,8 +653,8 @@ <h2 data-number="1.2" class="anchored" data-anchor-id="existing-chapters-in-this
   <div class="nav-page nav-page-previous">
   </div>
   <div class="nav-page nav-page-next">
-      <a href="./noj_book.prepare_for_ml.html" class="pagination-link" aria-label="Machine learning specific functionality in `tech.ml.dataset`">
-        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Machine learning specific functionality in <code>tech.ml.dataset</code></span></span> <i class="bi bi-arrow-right-short"></i>
+      <a href="./noj_book.ml_basic.html" class="pagination-link" aria-label="Machine learning">
+        <span class="nav-page-text"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Machine learning</span></span> <i class="bi bi-arrow-right-short"></i>
       </a>
   </div>
 </nav>