python: Add conda env and minor

python/README.org

@@ -11,8 +11,15 @@
 
 The ~Python~ interface calls the ~Julia~ ~SG-t-SNE-Π~ library, through the
 ~PyJulia~ package. Please follow the [[https://pyjulia.readthedocs.io/en/latest/installation.html][official installation instructions]]
-to get ~PyJulia~ working. You can verify that your installation is valid
-by issuing the following command. More details are available in the
+to get ~PyJulia~ working. 
+To verify that your installation is completed succesfully try to issue the following command.
+
+#+begin_src python
+from julia import Base
+Base.sind(90)
+#+end_src
+
+More details on the PyJulia package are available in the
 [[https://pyjulia.readthedocs.io/en/latest/usage.html][official usage tutorial]].
 
 You need to do either one of the following for ~PyJulia~ to work:
@@ -26,13 +33,34 @@ You need to do either one of the following for ~PyJulia~ to work:
   python-jl
   #+end_src
   which is bundled in PyJulia. 
-
-You can verify your installation by issuing  
-#+begin_src python
-from julia import Base
-Base.sind(90)
+
+To install the python wrapper of SG-t-SNE-Π to your python virtual environment or a conda environment follow the instructions below:
+
+To install using Conda:
+
+#+begin_src bash
+git clone https://github.com/fcdimitr/sgtsnepi.git
+cd sgtsnepi
+conda env create -f python/environment.yml
+source activate sgtsnepi
+python-jl python/test_digits.py
+#+end_src
+
+To install to a new python virtual environment:
+
+#+begin_src bash
+python3 -m venv /path/to/new/virtual/environment
+source /path/to/new/virtual/environment/bin/activate
+git clone https://github.com/fcdimitr/sgtsnepi.git
+cd sgtsnepi
+pip install -r python/requirements.txt
+python-jl python/test_digits.py
 #+end_src
 
+
+
+
+
 * SG-t-SNE-Π usage
 
 The ~SG-t-SNE-Π~ Python module is now ready to be used. Simply import the module and call ~SG-t-SNE-Π~ on a sparse, CSC matrix.

python/__init__.py

@@ -0,0 +1 @@
+from .sgtsnepi import * # noqa

python/environment.yml

@@ -0,0 +1,8 @@
+name: sgtsnepi
+channels:
+  - defaults
+  - conda-forge
+dependencies:
+  - pip
+  - pip:
+    - -r file:requirements.txt

python/sgtsnepi.py

@@ -2,12 +2,14 @@
 from julia import Main
 from julia import Pkg
 
+
 # load packages in Julia
-Pkg.add( "SparseArrays" )
-Pkg.add( Pkg.PackageSpec(name="SGtSNEpi", version="0.2.1") )
+Pkg.add("SparseArrays")
+Pkg.add(Pkg.PackageSpec(name="SGtSNEpi", version="0.2.1"))
 
 from julia import SGtSNEpi
 
+
 # prepare Julia wrappers
 Main.eval("""
   using SparseArrays, SGtSNEpi
@@ -22,7 +24,9 @@
   sgtsnepi( A::PyObject ; kwargs... ) = sgtsnepi( scipyCSC_to_julia(A) ; kwargs... )
 """)
 
-# setup Python function
+__all__ = ['sgtsnepi']
+
 
-def sgtsnepi( A, **kwargs ):
-    return SGtSNEpi.sgtsnepi( A, **kwargs )
+# Setup Python function
+def sgtsnepi(A, **kwargs):
+    return SGtSNEpi.sgtsnepi(A, **kwargs)

python/test_digits.py

@@ -1,65 +1,68 @@
 ## test_digits.py
 # Test 3D SG-t-SNE embedding 
 
-## download the matrix and label file from Tim Davids' matrix collection
+from julia.api import Julia
 import requests
-url = "https://suitesparse-collection-website.herokuapp.com/MM/ML_Graph/optdigits_10NN.tar.gz"
-r = requests.get(url, allow_redirects=True)
-open('optdigits_10NN.tar.gz', 'wb').write(r.content)
+from scipy.io import mmread
+from scipy.sparse import csc_matrix
+import sys
+import os.path
+from os import path
+import tarfile
+import matplotlib.pyplot as plt
+from matplotlib.colors import ListedColormap
 
+# SG-tSNE-Π setup
+# Setup julia
+jl = Julia(compiled_modules=False)
 
-## unzip to the current folder
-import tarfile
+current_dir = os.path.dirname(os.path.abspath(__file__))
+sys.path.insert(0, current_dir)  # Add path
 
-tar = tarfile.open('./optdigits_10NN.tar.gz', 'r:gz')
-tar.extractall()
-tar.close()
+from sgtsnepi import sgtsnepi
 
-## reading out the matrix and the label
-from scipy.io import mmread
-from scipy.sparse import csc_matrix
+if path.exists("optdigits_10NN.tar.gz"):
+    pass
+else:
+    print("Downloading and extracting file")
+    # Download the matrix and label file from Tim Davids' matrix collection
+    url = "https://suitesparse-collection-website.herokuapp.com/MM/ML_Graph/optdigits_10NN.tar.gz"
+    r = requests.get(url, allow_redirects=True)
+    open('optdigits_10NN.tar.gz', 'wb').write(r.content)
+
+    # Unzip to the current folder
+    tar = tarfile.open('./optdigits_10NN.tar.gz', 'r:gz')
+    tar.extractall()
+    tar.close()
+
+# Reading out the matrix and the label
 
 A = mmread('./optdigits_10NN/optdigits_10NN.mtx')
 A = csc_matrix(A)
 L = mmread('./optdigits_10NN/optdigits_10NN_label.mtx')
 L = csc_matrix(L).toarray()
 
-## SG-tSNE-Π setup
-# setup julia
-from julia.api import Julia
-jl = Julia(compiled_modules=False)
-
-# add current path
-import sys
-sys.path.insert(0,"./")
-
 # generate the embedding
-from sgtsnepi import sgtsnepi
-Y = sgtsnepi(A, d = 3, λ = 10, max_iter = 500)
-
-# visualization -- require matplotlib package
-import matplotlib.pyplot as plt
-from matplotlib.colors import ListedColormap
-import numpy as np
+Y = sgtsnepi(A, d = 3, λ = 10, max_iter=500)
 
 # distinguishable color map (10 clusters)
 cmap = [[0.3000, 0.3000, 1.0000],
-[0.3000, 1.0000, 0.3000],
-[1.0000, 0.3000, 0.3000],
-[1.0000, 0.8552, 0.3000],
-[0.3000, 0.3000, 0.4931],
-[1.0000, 0.3000, 0.8069],
-[0.3000, 0.5655, 0.3000],
-[0.5897, 0.3966, 0.3000],
-[0.3000, 1.0000, 0.9034],
-[0.3000, 0.7586, 1.0000]];
+        [0.3000, 1.0000, 0.3000],
+        [1.0000, 0.3000, 0.3000],
+        [1.0000, 0.8552, 0.3000],
+        [0.3000, 0.3000, 0.4931],
+        [1.0000, 0.3000, 0.8069],
+        [0.3000, 0.5655, 0.3000],
+        [0.5897, 0.3966, 0.3000],
+        [0.3000, 1.0000, 0.9034],
+        [0.3000, 0.7586, 1.0000]]
 newcmap = ListedColormap(cmap)
 
 # draw scatter plot (3D)
 fig = plt.figure()
 ax = fig.add_subplot(projection='3d')
 
-ax.scatter(Y[:,0], Y[:,1], Y[:,2], c=L, marker='.', cmap=newcmap)
+ax.scatter(Y[:, 0], Y[:, 1], Y[:, 2], c=L, marker='.', cmap=newcmap)
 
 ax.set_xlabel('X')
 ax.set_ylabel('Y')

setup.py

@@ -0,0 +1,22 @@
+import setuptools
+
+with open("README.md", "r") as fh:
+    long_description = fh.read()
+
+
+setuptools.setup(
+     name='sgtsnepi',  
+     version='0.1',
+     author="Dimitris Floros",
+     author_email="  ",
+     description="A Docker and AWS utility package",
+     long_description=long_description,
+   long_description_content_type="text/markdown",
+     url="https://github.com/fcdimitr/sgtsnepi",
+     packages=setuptools.find_packages(),
+     classifiers=[
+         "Programming Language :: Python :: 3",
+         "License :: OSI Approved :: MIT License",
+         "Operating System :: OS Independent",
+     ],
+ )