Make package for pypi (#12)

.gitignore

@@ -0,0 +1,6 @@
+# python stuff
+*.pyc
+*/__pycache__
+build/
+dist/
+mpl_chord_diagram.egg-info/

MANIFEST.in

@@ -0,0 +1,6 @@
+# Include the license file
+include LICENSE
+include Readme.md
+
+# include setup.py
+include setup.py

README.md

@@ -2,22 +2,25 @@
 
 Python module to plot chord diagrams with [matplotlib](https://matplotlib.org).
 
+Note that the repository has this structure (everything is on root level) to
+be able to be used more easily as a git submodule.
 
 ## Usage and requirements
 
-Add the module to your ``PYTHONPATH``, then, in python script or terminal:
+Install using
+
+    pip install mpl-chord-diagram
+
+then, in python script or terminal:
 
 ```python
 from mpl_chord_diagram import chord_diagram
 ```
 
-If you don't know how to change the ``PYTHONPATH``, use the ``example.py``
-file, it provides a workaround.
-
-The code requires ``numpy``, ``scipy`` and ``matplotlib``, you can install
-them by calling
+The code requires ``numpy``, ``scipy`` and ``matplotlib``, which should be
+installed automatically. If necessary, you can also install them by calling
 
-    pip install -r requirements.txt 
+    pip install -r requirements.txt
 
 
 ## Main plot function
@@ -66,35 +69,40 @@ An example can be found in file `example.py`.
 Here is what the diagrams look like (with and without gradient and gap,
 up and down are sorted respectively by domain size and distance):
 
-<img src="example_sort-size.png" width="390"
+<img src="images/example_sort-size.png" width="390"
      alt="Chord diagram without gradient, sorted by size"><img
-     src="example_gradient_sort-size.png" width="390"
+     src="images/example_gradient_sort-size.png" width="390"
      alt="Chord diagram without gradient, sorted by size">
 
-<img src="example_sort-distance.png" width="390"
+<img src="images/example_sort-distance.png" width="390"
      alt="Chord diagram without gradient, sorted by distance"><img
-     src="example_gradient_sort-distance.png" width="390"
+     src="images/example_gradient_sort-distance.png" width="390"
      alt="Chord diagram without gradient, dorted by distance">
 
 
 ## Contributors
 
 * Original author: [@fengwangPhysics](https://github.com/fengwangPhysics)
 * Refactoring (Tanguy Fardet, PRs
-  [#6](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/6) &
-  [#9](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/9))
+  [#6](https://github.com/Silmathoron/mpl_chord_diagram/pull/6),
+  [#9](https://github.com/Silmathoron/mpl_chord_diagram/pull/9) &
+  [#12](https://github.com/Silmathoron/mpl_chord_diagram/pull/12))
+* Support sparse matrices: Tanguy Fardet (PR
+  [#10](https://github.com/Silmathoron/mpl_chord_diagram/pull/10))
 * Improved color support:
-   - [@pakitochus](https://github.com/pakitochus) (PR [#1](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/1))
+   - [@pakitochus](https://github.com/pakitochus) (PR
+     [#1](https://github.com/Silmathoron/mpl_chord_diagram/pull/1))
    - Tanguy Fardet (PRs
-      [#4](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/4) for
+      [#4](https://github.com/Silmathoron/mpl_chord_diagram/pull/4) for
       colors/colormaps and
-      [#5](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/5) &
-      [#7](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/7) for
+      [#5](https://github.com/Silmathoron/mpl_chord_diagram/pull/5) &
+      [#7](https://github.com/Silmathoron/mpl_chord_diagram/pull/7) for
       gradients)
 * Improved arcs:
-   - [@cy1110](https://github.com/cy1110) (PR [#2](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/2))
+   - [@cy1110](https://github.com/cy1110) (PR
+     [#2](https://github.com/Silmathoron/mpl_chord_diagram/pull/2))
    - Tanguy Fardet (PRs
-     [#6](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/6) for
+     [#6](https://github.com/Silmathoron/mpl_chord_diagram/pull/6) for
      gap addition and
-     [#7](https://github.com/Silmathoron/matplotlib-chord-diagram/pull/7) for
+     [#7](https://github.com/Silmathoron/mpl_chord_diagram/pull/7) for
      adaptive curvature and sorting)

__init__.py

@@ -6,3 +6,8 @@
 """
 
 from .chord_diagram import chord_diagram
+
+
+__version__ = "0.1.0"
+
+__author__ = "Tanguy Fardet"

chord_diagram.py

@@ -19,7 +19,7 @@
 LW = 0.3
 
 
-def chord_diagram(mat, names=None, width=0.1, pad=2., gap=0., chordwidth=0.7,
+def chord_diagram(mat, names=None, width=0.1, pad=2., gap=0.03, chordwidth=0.7,
                   ax=None, colors=None, cmap=None, alpha=0.7,
                   use_gradient=False, show=False, **kwargs):
     """

example.py

@@ -13,10 +13,11 @@
 
 # flux matrix
 
-flux = np.array([[11975,  5871, 8916, 2868],
-  [ 1951, 10048, 2060, 6171],
-  [ 8010, 16145, 81090, 8045],
-  [ 1013,   990,  940, 6907]
+flux = np.array([
+    [11975,  5871, 8916, 2868],
+    [ 1951, 10048, 2060, 6171],
+    [ 8010, 16145, 81090, 8045],
+    [ 1013,   990,  940, 6907]
 ])
 
 names = ['non-crystal', 'FCC', 'HCP', 'BCC']
@@ -30,8 +31,10 @@
 for grd, gap, sort in zip(gradients, gaps, sorts):
     chord_diagram(flux, names, gap=gap, use_gradient=grd, sort=sort)
 
+    str_grd = "_gradient" if grd else ""
+
     plt.savefig(
-        "example{}_sort-{}.png".format("_gradient" if grd else "", sort),
+        "images/example{}_sort-{}.png".format(str_grd, sort),
                 dpi=600, transparent=True, bbox_inches='tight',
                 pad_inches=0.02)
 

setup.cfg

@@ -0,0 +1,5 @@
+[bdist_wheel]
+# This flag says that the code is written to work on both Python 2 and Python
+# 3. If at all possible, it is good practice to do this. If you cannot, you
+# will need to generate wheels for each Python version that you support.
+universal=1

setup.py

@@ -0,0 +1,84 @@
+import os, errno
+from setuptools import setup, find_packages
+
+
+# create directory
+setup_dir = os.path.abspath(os.path.dirname(__file__))
+directory = setup_dir + '/mpl_chord_diagram/'
+
+try:
+    os.makedirs(directory)
+except OSError as e:
+    if e.errno != errno.EEXIST:
+        raise
+
+
+# move important files
+move = (
+    '__init__.py',
+    'LICENSE',
+    'chord_diagram.py',
+    'gradient.py',
+    'utilities.py',
+    'example.py',
+)
+
+
+for fname in move:
+    try:
+        os.rename(fname, directory + fname)
+    except Exception as e:
+        print(e)
+
+
+from mpl_chord_diagram import __version__
+
+long_descr = '''
+The module enables to plot chord diagrams with matplotlib from lists,
+numpy or scipy sparse matrices.
+It provides tunable parameters such as arc sorting based on size or distance,
+and supports gradients to better visualize source and target regions.
+'''
+
+
+try:
+    # install
+    setup(
+        name = 'mpl_chord_diagram',
+        version = __version__,
+        description = 'Python module to plot chord diagrams with matplotlib.',
+        package_dir = {'': '.'},
+        packages = find_packages('.'),
+
+        # Include the non python files:
+        package_data = {'': ['LICENSE', '*.md']},
+
+        # Requirements
+        install_requires = ['numpy', 'scipy', 'matplotlib'],
+
+        # Metadata
+        url = 'https://github.com/Silmathoron/mpl_chord_diagram',
+        author = 'Tanguy Fardet',
+        author_email = '[email protected]',
+        license = 'MIT',
+        keywords = 'chord diagram matplotlib plotting',
+        long_description = long_descr,
+        classifiers = [
+            'Development Status :: 5 - Production/Stable',
+            'Intended Audience :: Science/Research',
+            'License :: OSI Approved :: MIT License',
+            'Natural Language :: English',
+            'Programming Language :: Python :: 3',
+            'Operating System :: OS Independent',
+            'Topic :: Scientific/Engineering :: Visualization',
+            'Framework :: Matplotlib',
+        ]
+    )
+except:
+    pass
+finally:
+    for fname in move:
+        try:
+            os.rename(directory + fname, fname)
+        except:
+            pass