BLD: General updates to the repository

.travis.yml

@@ -1,36 +1,57 @@
 language: python
 python:
-  - "2.7"
-  - "3.5"
-  - "3.6"
+  - 2.7
+  - 3.4
+  - 3.5
+  - 3.6
+  # also includes 3.7 (see below)
 env:
-  - NUMPY_VERSION=""  WITH_COVERAGE=1 # environment to test with the latest version of NumPy
+  - NUMPY_VERSION=""  # environment to test with the latest version of NumPy
   - NUMPY_VERSION="<1.13"
+
+matrix:
+  # support for python 3.7 is rather awkward via Travis CI
+  # https://github.com/travis-ci/travis-ci/issues/9815
+  include:
+    - python: 3.7
+      dist: xenial
+      sudo: true
+      env: NUMPY_VERSION=""
+    - python: 3.7
+      dist: xenial
+      sudo: true
+      env: NUMPY_VERSION="<1.13"
+  exclude:
+      # for older python versions only test the latest versions of NumPy
+      - python: 2.7
+        env: NUMPY_VERSION="<1.13"
+      - python: 3.4
+        env: NUMPY_VERSION="<1.13"
+      - python: 3.5
+        env: NUMPY_VERSION="<1.13"
+
 before_install:
-  - phantomjs --version
-  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh
-  - chmod +x miniconda.sh
+  - wget https://repo.continuum.io/miniconda/Miniconda2-latest-Linux-x86_64.sh -O miniconda.sh && chmod +x miniconda.sh
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda2/bin:$PATH
   # Update conda itself
   - conda update --yes conda
+
 install:
-  - conda create --yes -n env_name python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas nose flake8 pep8 jupyter
-  - source activate env_name
-  - pip install https://github.com/google/closure-linter/archive/master.zip
-  - pip install 'sphinx<1.6' sphinx-bootstrap-theme coverage coveralls
-  # install lockfile before to prevent a failure in travis
-  - pip install 'lockfile>=0.10.2'
+  - conda create --yes -n travis python=$TRAVIS_PYTHON_VERSION pip numpy${NUMPY_VERSION} 'scipy>=0.17.0' matplotlib pandas flake8 pep8 jupyter coverage cython
+  - source activate travis
+  - conda install -c conda-forge phantomjs --yes
+  # scikit-learn has to be pinned down due to a bug: https://github.com/scikit-learn/scikit-learn/issues/12671
+  - pip install https://github.com/google/closure-linter/archive/master.zip 'sphinx<1.6' sphinx-bootstrap-theme coveralls 'scikit-learn==0.19.2' --no-binary scikit-learn
   - pip install -e '.[all]' --verbose
   - npm install -g jsdoc
+
 script:
   - flake8 emperor/*.py tests/*.py scripts/*.py setup.py
   # we can only run gjslint in a python 2.7.x environment
   - if [[ $TRAVIS_PYTHON_VERSION == 2.7 ]]; then gjslint --custom_jsdoc_tags 'module,function,constructs,alias,default' 'emperor/support_files/js/*.js' 'tests/javascript_tests/*.js'; fi
-  # execute the full test suite
-  - python tests/all_tests.py
   # we just check coverage in the latest version of NumPy
-  - if [ ${WITH_COVERAGE} ]; then nosetests emperor --with-coverage --cover-package=emperor --cover-inclusive tests; fi
+  - coverage run tests/all_tests.py; coverage report
   - make -C doc html
 after_success:
   - coveralls

README.md

@@ -11,4 +11,10 @@ Before contributing code to Emperor, please familiarize yourself with the [contr
 
 ## Usage
 
-You can start using Emperor through [QIIME2](https://qiime2.org)'s [interfaces](https://docs.qiime2.org/2.0.6/interfaces/) (the command line interface or the graphical user interface), or alternatively using the Python interface (compatible with the Jupyter notebook, see [this example](http://nbviewer.jupyter.org/github/biocore/emperor/blob/new-api/examples/keyboard.ipynb)). For more detalis, refer to our [online documentation](http://emperor.microbio.me/uno/).
+You can start using Emperor through [QIIME2](https://qiime2.org)'s [interfaces](https://docs.qiime2.org/2018.8/interfaces/) (the command line interface or the graphical user interface), or alternatively using the Python interface (compatible with the Jupyter notebook, see [this example](http://nbviewer.jupyter.org/github/biocore/emperor/blob/new-api/examples/keyboard.ipynb)). For more detalis, refer to our [online documentation](http://emperor.microbio.me/uno/).
+
+## Publications
+
+- [EMPeror: a tool for visualizing high-throughput microbial community data](https://www.ncbi.nlm.nih.gov/pubmed/24280061). GigaScience, 2013.
+
+- [Bringing the Dynamic Microbiome to Life with Animations](https://www.ncbi.nlm.nih.gov/pubmed/28081445). Cell Host & Microbe, 2016.

setup.py

@@ -9,8 +9,7 @@
 
 import sys
 
-from distutils.core import setup
-from glob import glob
+from setuptools import setup, find_packages
 
 __version__ = "1.0.0beta18-dev"
 __maintainer__ = "Emperor development team"
@@ -25,6 +24,9 @@
     Programming Language :: Python
     Programming Language :: Python :: 2.7
     Programming Language :: Python :: 3.4
+    Programming Language :: Python :: 3.5
+    Programming Language :: Python :: 3.6
+    Programming Language :: Python :: 3.7
     Programming Language :: Python :: Implementation :: CPython
     Operating System :: OS Independent
     Operating System :: POSIX
@@ -33,19 +35,15 @@
 
 classifiers = [s.strip() for s in classes.split('\n') if s]
 
-long_description = """Emperor: a tool for visualizing high-throughput microbial community data
-
-EMPeror: a tool for visualizing high-throughput microbial community data.
-Vazquez-Baeza Y, Pirrung M, Gonzalez A, Knight R.
-Gigascience. 2013 Nov 26;2(1):16.
-"""
+with open('README.md') as f:
+    long_description = f.read()
 
 skbio_2 = "scikit-bio >= 0.4.1, < 0.5.0"
 skbio_3 = "scikit-bio >= 0.4.1"
 base = ["numpy >= 1.7", "scipy >= 0.17.0", "click", "pandas",
         skbio_2, "jinja2 >= 2.9", "future"]
 doc = ["Sphinx < 1.6", "sphinx-bootstrap-theme"]
-test = ["nose >= 0.10.1", "pep8", "flake8"]
+test = ["pep8", "flake8"]
 all_deps = base + doc + test
 
 # prevent python2 from trying to install skbio >= 0.5.0 (which only works in
@@ -63,8 +61,8 @@
     maintainer=__maintainer__,
     maintainer_email=__email__,
     url='http://github.com/biocore/emperor',
-    packages=['emperor', 'emperor.qiime_backports'],
-    scripts=glob('scripts/*py'),
+    packages=find_packages(),
+    scripts=['scripts/make_emperor.py'],
     package_data={
         'emperor': ['support_files/vendor/js/three.js-plugins/*.js',
                     'support_files/vendor/js/*.js',
@@ -84,5 +82,6 @@
     install_requires=base,
     extras_require={'doc': doc, 'test': test, 'all': all_deps},
     long_description=long_description,
+    long_description_content_type='text/markdown',
     license='BSD-3-Clause',
     classifiers=classifiers)

tests/all_tests.py

@@ -14,14 +14,12 @@
 dde2a06f2d990db8b09da65764cd27fc047db788
 """
 
-import re
 import sys
 import click
 import subprocess
 
-from os import walk
-from glob import glob
-from os.path import join, abspath, dirname, split
+from os.path import join, abspath, dirname
+from unittest import TestLoader, TextTestRunner
 
 from emperor import __version__
 
@@ -66,43 +64,15 @@ def test(suppress_unit_tests, suppress_javascript_unit_tests, unittest_glob):
                                "run.")
 
     test_dir = abspath(dirname(__file__))
-
-    unittest_good_pattern = re.compile(r'OK\s*$')
-    application_not_found_pattern = re.compile(b'ApplicationNotFoundError')
-    python_name = 'python'
     bad_tests = []
-    missing_application_tests = []
 
     # Run through all of Emperor's unit tests, and keep track of any files
     # which fail unit tests, note that these are the unit tests only
     if not suppress_unit_tests:
-        unittest_names = []
-        if not unittest_glob:
-            for root, dirs, files in walk(test_dir):
-                for name in files:
-                    if name.startswith('test_') and name.endswith('.py'):
-                        unittest_names.append(join(root, name))
-        else:
-            for fp in glob(unittest_glob):
-                fn = split(fp)[1]
-                if fn.startswith('test_') and fn.endswith('.py'):
-                    unittest_names.append(abspath(fp))
-
-        unittest_names.sort()
-
-        for unittest_name in unittest_names:
-            print("Testing %s:\n" % unittest_name)
-            command = '%s %s -v' % (python_name, unittest_name)
-            stdout, stderr, return_value = console(command)
-            print(stderr.decode("utf-8"))
-            if not unittest_good_pattern.search(stderr.decode("utf-8")):
-                if application_not_found_pattern.search(stderr):
-                    missing_application_tests.append(unittest_name)
-                else:
-                    bad_tests.append(unittest_name)
+        res = TextTestRunner().run(TestLoader().discover(start_dir=test_dir))
 
     if not suppress_javascript_unit_tests:
-        print("JavaScript Test Suite")
+        click.echo("JavaScript Test Suite")
         runner = join(test_dir, 'javascript_tests', 'runner.js')
         index = join(test_dir, 'javascript_tests', 'index.html')
 
@@ -117,35 +87,29 @@ def test(suppress_unit_tests, suppress_javascript_unit_tests, unittest_glob):
     else:
         javascript_tests_passed = True
 
-    print("==============\nResult summary\n==============")
+    click.echo("==============\nResult summary\n==============")
 
     if not suppress_unit_tests:
-        print("\nUnit test result summary\n------------------------\n")
-        if bad_tests:
-            print("\nThe following unit tests failed.\n%s"
-                  % '\n'.join(bad_tests))
-
-        if missing_application_tests:
-            print("\nThe following unit tests failed, in part or whole due "
-                  "to missing external applications.\nDepending on the "
-                  "Emperor features you plan to use, this may not be "
-                  "critical.\n%s" % '\n'.join(missing_application_tests))
-
-        if not(missing_application_tests or bad_tests):
-            print("\nAll unit tests passed.\n")
+        click.echo("\nUnit test result summary\n------------------------\n")
+        if not res.wasSuccessful():
+            bad_tests = [i[0].id() for i in res.failures + res.errors]
+            click.echo("\nThe following unit tests failed:\n%s"
+                       % '\n'.join(bad_tests))
+        else:
+            click.echo("\nAll unit tests passed.\n")
 
     if not suppress_javascript_unit_tests:
-        print('\nJavaScript unit tests result summary\n'
-              '------------------------------------\n')
+        click.echo('\nJavaScript unit tests result summary\n'
+                   '------------------------------------\n')
         if javascript_tests_passed:
-            print('All JavaScript unit tests passed.\n')
+            click.echo('All JavaScript unit tests passed.\n')
         else:
-            print('JavaScript unit tests failed, check the summary above.')
+            click.echo('JavaScript unit tests failed, check the summary '
+                       'above.')
 
     # In case there were no failures of any type, exit with a return code of 0
     return_code = 1
-    if (len(bad_tests) == 0 and len(missing_application_tests) == 0 and
-       javascript_tests_passed):
+    if (len(bad_tests) == 0 and javascript_tests_passed):
         return_code = 0
 
     exit(return_code)