Migrate

.editorconfig

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+# EditorConfig helps developers define and maintain consistent
+# coding styles between different editors and IDEs
+# editorconfig.org
+
+root = true
+
+
+[*]
+
+# Change these settings to your own preference
+indent_style = space
+indent_size = 2
+
+# We recommend you to keep these unchanged
+end_of_line = lf
+charset = utf-8
+trim_trailing_whitespace = true
+insert_final_newline = true
+
+[*.md]
+trim_trailing_whitespace = false

.gitattributes

@@ -0,0 +1,126 @@
+# These settings are for any web project
+
+# Handle line endings automatically for files detected as text
+# and leave all files detected as binary untouched.
+* text=auto
+
+#
+# The above will handle all files NOT found below
+#
+
+#
+## These files are text and should be normalized (Convert crlf => lf)
+#
+
+# source code
+*.php text
+*.css text
+*.sass text
+*.scss text
+*.less text
+*.styl text
+*.js text
+*.ts text
+*.coffee text
+*.json text
+*.htm text
+*.html text
+*.xml text
+*.txt text
+*.ini text
+*.inc text
+*.pl text
+*.rb text
+*.py text
+*.scm text
+*.sql text
+*.sh text eof=LF
+*.bat text
+
+# templates
+*.hbt text
+*.jade text
+*.haml text
+*.hbs text
+*.dot text
+*.tmpl text
+*.phtml text
+
+# server config
+.htaccess text
+
+# git config
+.gitattributes text
+.gitignore text
+
+# code analysis config
+.jshintrc text
+.jscsrc text
+.jshintignore text
+.csslintrc text
+
+# misc config
+*.yaml text
+*.yml text
+.editorconfig text
+
+# build config
+*.npmignore text
+*.bowerrc text
+
+# Heroku
+Procfile text
+.slugignore text
+
+# Documentation
+*.md text
+LICENSE text
+AUTHORS text
+
+
+#
+## These files are binary and should be left untouched
+#
+
+# (binary is a macro for -text -diff)
+*.png binary
+*.jpg binary
+*.jpeg binary
+*.gif binary
+*.ico binary
+*.mov binary
+*.mp4 binary
+*.mp3 binary
+*.flv binary
+*.fla binary
+*.swf binary
+*.gz binary
+*.zip binary
+*.7z binary
+*.ttf binary
+*.pyc binary
+*.pdf binary
+
+# Source files
+# ============
+*.pxd		text
+*.py 		text
+*.py3 		text
+*.pyw 		text
+*.pyx  		text
+*.sh        text eol=lf
+*.json      text
+
+# Binary files
+# ============
+*.db		binary
+*.p 		binary
+*.pkl 		binary
+*.pyc 		binary
+*.pyd		binary
+*.pyo 		binary
+
+# Note: .db, .p, and .pkl files are associated
+# with the python modules ``pickle``, ``dbm.*``,
+# ``shelve``, ``marshal``, ``anydbm``, & ``bsddb``
+# (among others).

.gitignore

@@ -1 +1,19 @@
+# general things to ignore
+/.tscache
+/.idea
+/build/
+/dist/
+*.egg-info/
+*.egg
+*.py[cod]
+__pycache__/
+*.so
+*~
+*.log
+*.pot
 *.pyc
+*.swp
+*.lock
+# due to using tox and pytest
+.tox
+.cache

.travis.yml

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+language: python
+sudo: required
+env:
+  - TOXENV=py27
+  - TOXENV=py34
+
+install:
+  - (!(test -f docker_packages.txt) || (cat docker_packages.txt | xargs sudo apt-get install -y))
+  - pip install -r requirements_dev.txt
+  - pip install -r requirements.txt
+
+script: npm run dist
+
+deploy:
+  provider: releases
+  api_key:
+    secure: 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
+  file_glob: true
+  file: dist/phovea_clustering*.egg
+  on:
+    tags: true
+
+notifications:
+  slack:
+    secure: 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
+    on_success: change
+    on_failure: always

.yo-rc.json

@@ -0,0 +1,52 @@
+{
+  "generator-phovea": {
+    "type": "slib",
+    "name": "phovea_clustering",
+    "author": "The Caleydo Team",
+    "githubAccount": "phovea",
+    "modules": [
+      "phovea_server"
+    ],
+    "extensions": [],
+    "sextensions": [
+      {
+        "type": "clustering",
+        "id": "caleydo-clustering-kmeans",
+        "module": "clustering_kmeans",
+        "extras": {}
+      },
+      {
+        "type": "clustering",
+        "id": "caleydo-clustering-hierarchical",
+        "module": "clustering_hierarchical",
+        "extras": {}
+      },
+      {
+        "type": "clustering",
+        "id": "caleydo-clustering-affinity",
+        "module": "clustering_affinity",
+        "extras": {}
+      },
+      {
+        "type": "clustering",
+        "id": "caleydo-clustering-fuzzy",
+        "module": "clustering_fuzzy",
+        "extras": {}
+      },
+      {
+        "type": "namespace",
+        "id": "caleydo-clustering",
+        "module": "clustering_api",
+        "extras": {
+          "namespace": "/api/clustering"
+        }
+      }
+    ],
+    "libraries": [],
+    "unknown": {
+      "requirements": [],
+      "dockerPackages": []
+    },
+    "today": "Fri, 23 Dec 2016 03:02:24 GMT"
+  }
+}

ISSUE_TEMPLATE.md

@@ -0,0 +1,17 @@
+* Release number or git hash: 
+* Web browser version and OS: 
+* Environment (local or deployed): 
+
+### Steps to reproduce
+
+1. 
+2. 
+
+### Observed behavior
+* Any unexpected output or action (or lack of expected output or action)
+* Web browser console errors (including tracebacks)
+* Server errors (relevant messages and tracebacks)
+* Static or animated images showing the UI behavior
+
+### Expected behavior
+* 

LICENSE

@@ -0,0 +1,22 @@
+Copyright (c) 2016, The Caleydo Team
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without modification,
+are permitted provided that the following conditions are met:
+
+  Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
+
+  Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
+
+  Neither the name of the Caleydo Software nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR
+ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+(INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
+ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+(INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

README.md

@@ -1,23 +1,44 @@
-Caleydo Clustering
-==================
-
-This repository is a server-side plugin for Caleydo to apply clustering algorithms on arbitrary matrices.
-
-Supported Algorithms:
---------------------
-- K-Means (Init methods: Forgy, Uniform, Random, Kmeans++)
-- Hierarchical Clustering (Single, Complete, Weighted, Median)
-- Affinity Propagation
-- Fuzzy Clustering
-- Various Distance Measurements(Euclidean, Chebyshef, Manhattan, Pearson, Spearman, ...)
-
-General Information:
--------------------
-- All these algorithms expect the input as matrix (or 2D numpy array)
-- It is assumed that the matrix is dense (no sparse matrix support right now)
-- NaN values will be converted to zero
-
-Future Work:
+phovea_clustering [![Phovea][phovea-image]][phovea-url] [![NPM version][npm-image]][npm-url] [![Build Status][travis-image]][travis-url] [![Dependency Status][daviddm-image]][daviddm-url]
+=====================
+
+
+
+Installation
 ------------
-- Improvement of algorithms
-- Combination of several clustering results
+
+```
+git clone https://github.com/phovea/phovea_clustering.git
+cd phovea_clustering
+npm install
+```
+
+Testing
+-------
+
+```
+npm test
+```
+
+Building
+--------
+
+```
+npm run build
+```
+
+
+
+***
+
+<a href="https://caleydo.org"><img src="http://caleydo.org/assets/images/logos/caleydo.svg" align="left" width="200px" hspace="10" vspace="6"></a>
+This repository is part of **[Phovea](http://phovea.caleydo.org/)**, a platform for developing web-based visualization applications. For tutorials, API docs, and more information about the build and deployment process, see the [documentation page](http://caleydo.org/documentation/).
+
+
+[phovea-image]: https://img.shields.io/badge/Phovea-Server%20Plugin-10ACDF.svg
+[phovea-url]: https://phovea.caleydo.org
+[npm-image]: https://badge.fury.io/js/phovea_clustering.svg
+[npm-url]: https://npmjs.org/package/phovea_clustering
+[travis-image]: https://travis-ci.org/phovea/phovea_clustering.svg?branch=master
+[travis-url]: https://travis-ci.org/phovea/phovea_clustering
+[daviddm-image]: https://david-dm.org/phovea/phovea_clustering.svg?theme=shields.io
+[daviddm-url]: https://david-dm.org/phovea/phovea_clustering