old_contents: import os
  from setuptools import setup
  
  setup(
          name = "augur",
          version = "0.1.0",
          author = "nextstrain developers",
          author_email = "trevor@bedford.io, richard.neher@unibas.ch",
          description = ("Pipelines for real-time phylogenetic analysis"),
          license = "MIT",
          keywords = "nextstrain, molecular epidemiology",
          url = "https://github.com/nextstrain/augur",
          packages=['augur'],
          package_data={'augur': ['data/*']},
          install_requires = [
              "bcbio-gff >=0.6.4, ==0.6.*",
              "biopython >=1.69, ==1.*",
              "boto >=2.38, ==2.*",
              "cvxopt >=1.1.8, ==1.1.*",
              "ipdb >=0.10.1",
              "jsonschema ==3.0.0a1",
              "matplotlib >=2.0, ==2.*",
              "pandas >=0.17.1",
              "seaborn >=0.6.0, ==0.6.*",
              "snakemake >=5.1.5, ==5.*",
              "treetime ==0.4.1"
          ],
          extras_require={
              'dev': [
                  "pylint >=1.7.6, ==1.7.*",
                  "pytest >=3.2.1, ==3.*",
              ]
          },
          dependency_links = [
              "https://api.github.com/repos/neherlab/treetime/tarball/v0.4.1#egg=treetime-0.4.1",
              "git+https://github.com/Julian/jsonschema.git@9632422aa90cb1fbfbbb141954ef6d06437b0801#egg=jsonschema-3.0.0a1"
          ],
          classifiers=[
              "Development Status :: 3 - Alpha",
              "Topic :: Science",
              "License :: OSI Approved :: MIT License",
              ],
          scripts=['bin/augur']
          )
  
new_contents: import os
  from setuptools import setup
  
  setup(
          name = "augur",
          version = "0.1.0",
          author = "nextstrain developers",
          author_email = "trevor@bedford.io, richard.neher@unibas.ch",
          description = ("Pipelines for real-time phylogenetic analysis"),
          license = "MIT",
          keywords = "nextstrain, molecular epidemiology",
          url = "https://github.com/nextstrain/augur",
          packages=['augur'],
          package_data={'augur': ['data/*']},
          install_requires = [
              "bcbio-gff >=0.6.4, ==0.6.*",
              "biopython >=1.69, ==1.*",
              "boto >=2.38, ==2.*",
              "cvxopt >=1.1.8, ==1.1.*",
              "ipdb >=0.10.1",
              "jsonschema ==3.0.0a1",
              "matplotlib >=2.0, ==2.*",
              "pandas >=0.17.1",
              "seaborn >=0.6.0, ==0.6.*",
              "snakemake >=5.1.5, ==5.*",
              "treetime ==0.4.1"
          ],
          extras_require={
              'dev': [
                  "pylint >=1.7.6, ==1.7.*",
                  "pytest >=3.2.1, ==3.*",
              ]
          },
          dependency_links = [
              "https://api.github.com/repos/neherlab/treetime/tarball/v0.4.1#egg=treetime-0.4.1"
          ],
          classifiers=[
              "Development Status :: 3 - Alpha",
              "Topic :: Science",
              "License :: OSI Approved :: MIT License",
              ],
          scripts=['bin/augur']
          )
  
subject: Remove dependency link for jsonschema