Remove graph-tool from doc requirements

docs/conf.py

@@ -69,9 +69,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.0.0'
+version = '2.0.2'
 # The full version, including alpha/beta/rc tags.
-release = '2.0.0'
+release = '2.0.2'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/setup.py

@@ -0,0 +1,76 @@
+#!/usr/bin/env python
+# vim: set fileencoding=<utf-8> :
+
+from setuptools import setup, find_packages
+from codecs import open
+from os import path
+import os
+import re
+import io
+
+
+def read(*names, **kwargs):
+    with io.open(
+        os.path.join(os.path.dirname(__file__), *names),
+        encoding=kwargs.get("encoding", "utf8")
+    ) as fp:
+        return fp.read()
+
+
+def find_version(*file_paths):
+    version_file = read(*file_paths)
+    version_match = re.search(r"^__version__ = ['\"]([^'\"]*)['\"]",
+                              version_file, re.M)
+    if version_match:
+        return version_match.group(1)
+    raise RuntimeError("Unable to find version string.")
+
+
+here = path.abspath(path.dirname(__file__))
+
+
+with open(path.join(here, 'README.md'), encoding='utf-8') as f:
+    long_description = f.read()
+
+setup(
+    name='poppunk',
+    version=find_version("PopPUNK/__init__.py"),
+    description='PopPUNK (POPulation Partitioning Using Nucleotide Kmers)',
+    long_description=long_description,
+    long_description_content_type='text/markdown',
+    url='https://github.com/johnlees/PopPUNK',
+    author='John Lees and Nicholas Croucher',
+    author_email='john@johnlees.me',
+    license='Apache Software License',
+    classifiers=[
+        'Development Status :: 4 - Beta',
+        'Intended Audience :: Science/Research',
+        'Topic :: Scientific/Engineering :: Bio-Informatics',
+        'License :: OSI Approved :: Apache Software License',
+        'Programming Language :: Python :: 3.8',
+    ],
+    python_requires='>=3.7.0',
+    keywords='bacteria genomics population-genetics k-mer',
+    packages=['PopPUNK'],
+    entry_points={
+        "console_scripts": [
+            'poppunk = PopPUNK.__main__:main',
+            'poppunk_prune = PopPUNK.prune_db:main',
+            'poppunk_references = PopPUNK.reference_pick:main',
+            'poppunk_tsne = PopPUNK.tsne:main'
+            ]
+    },
+    scripts=['scripts/poppunk_calculate_rand_indices.py',
+             'scripts/poppunk_extract_components.py',
+             'scripts/poppunk_calculate_silhouette.py',
+             'scripts/poppunk_extract_distances.py'],
+    install_requires=['numpy',
+                      'scipy',
+                      'scikit-learn',
+                      'DendroPy',
+                      'pandas',
+                      'graph-tool',
+                      'matplotlib',
+                      'hdbscan'],
+    test_suite="test",
+)

readthedocs.yml

@@ -18,5 +18,5 @@ python:
    install:
       - requirements: docs/requirements.txt
       - method: setuptools
-        path: .
+        path: docs
    system_packages: true

requirements.txt

@@ -1,10 +1 @@
-Cython>=0.26.1
-DendroPy>=4.3.0
-h5py>=2.10.0
-hdbscan>=0.8.13
-matplotlib>=2.1.2
-graph-tool>=2.31
-numpy>=1.14.1
-pandas>=0.22.0
-scikit-learn>=0.19.1
-scipy>=1.0.0
+Cython>=0.26.1

setup.py

@@ -60,9 +60,9 @@ def find_version(*file_paths):
             'poppunk_tsne = PopPUNK.tsne:main'
             ]
     },
-    scripts=['scripts/poppunk_calculate_rand_indices.py', 
+    scripts=['scripts/poppunk_calculate_rand_indices.py',
              'scripts/poppunk_extract_components.py',
-             'scripts/poppunk_calculate_silhouette.py', 
+             'scripts/poppunk_calculate_silhouette.py',
              'scripts/poppunk_extract_distances.py'],
     install_requires=['numpy',
                       'scipy',