Merge pull request #1047 from marscher/update_setup

[setup/recipe] updated dependencies, test against py36

.travis.yml

@@ -11,7 +11,7 @@ sudo: false
 env:
   global:
     - PATH=$HOME/miniconda/bin:$PATH
-    - common_py_deps="conda-build=2.1.2"
+    - common_py_deps="conda-build=2.1.4"
     - PACKAGENAME=pyemma
     - ORGNAME=omnia
     - PYTHONHASHSEED=0
@@ -21,20 +21,19 @@ env:
     - CONDA_PY=2.7 CONDA_NPY=1.11
     - CONDA_PY=3.4 CONDA_NPY=1.10
     - CONDA_PY=3.5 CONDA_NPY=1.11
+    - CONDA_PY=3.6 CONDA_NPY=1.11
 
 before_install:
 - devtools/ci/travis/install_miniconda.sh
 - conda config --set always_yes true
 - conda config --add channels omnia
-- conda config --add channels conda-forge
+#- conda config --add channels conda-forge
 - conda install -q $common_py_deps
 
 script:
 - conda build -q devtools/conda-recipe
 
 after_success:
 - pwd; ls -alh
-#- bash <(curl -s https://codecov.io/bash) -s $HOME
-- pip install codecov
-- codecov --file $HOME/coverage.xml
+- bash <(curl -s https://codecov.io/bash) -s $HOME -e CONDA_PY,CONDA_NPY
 

appveyor.yml

@@ -23,13 +23,17 @@ environment:
       CONDA_PY: "34"
       ARCH: "64"
 
+    - MINICONDA_PYTHON: "C:\\Miniconda3-x64"
+      CONDA_PY: "36"
+      ARCH: "64"
+
 install:
   - "SET PATH=%MINICONDA_PYTHON%;%MINICONDA_PYTHON%\\Scripts;%PATH%;"
 
   - conda config --set always_yes true 
   - conda config --add channels omnia 
-  - conda config --add channels conda-forge
-  - conda install -q conda-build=2.1.2 jinja2
+#  - conda config --add channels conda-forge
+  - conda install -q conda-build=2.1.4 jinja2
 
   # use agg backend in matplotlib to avoid gui popup, which can not be closed.
   - echo %userprofile%
@@ -40,7 +44,7 @@ build: false # Not a C# project, build stuff at the test step instead.
 
 test_script:
   # run testsuite and upload test results to AppVeyor; return exit code of testsuite
-  - conda build -q devtools/conda-recipe
+  - "%CMD_IN_ENV% conda build -q devtools/conda-recipe"
 
 #on_success:
 #  - devtools/ci/appveyor/after_success.bat  

circle.yml

@@ -15,7 +15,7 @@ checkout:
 dependencies:
   override:
     - devtools/ci/circle/install_miniconda.sh
-    - conda config --add channels conda-forge
+    - conda config --add channels omnia 
     - conda config --set always_yes true
     - conda install conda-build
 

devtools/conda-recipe/bld.bat

@@ -1,9 +1 @@
-if not defined APPVEYOR (
-    echo not on appveyor
-    "%PYTHON%" setup.py install
-) else ( 
-    echo on appveyor
-    cmd /E:ON /V:ON /C %APPVEYOR_BUILD_FOLDER%\devtools\ci\appveyor\run_with_env.cmd "%PYTHON%" setup.py install
-)
-set build_status=%ERRORLEVEL%
-if %build_status% == 1 exit 1
+%PYTHON% setup.py install --single-version-externally-managed --record record.txt

devtools/conda-recipe/build.sh

@@ -1,2 +1,6 @@
 #!/bin/bash
-$PYTHON setup.py install
+if [[ $OSTYPE == darwin* ]]; then
+     export CFLAGS="-headerpad_max_install_names"
+     export CXXFLAGS=$CFLAGS
+fi
+$PYTHON setup.py install --single-version-externally-managed --record record.txt

devtools/conda-recipe/meta.yaml

@@ -11,50 +11,34 @@ build:
 
 requirements:
   build:
+    - cython
+    - mdtraj
+    - numpy x.x
     - python
-    - setuptools
-    - cython >=0.20
-    - bhmm >=0.6,<0.7
-    - joblib >0.8.4
-    - matplotlib
-    - mdtraj >=1.7
-    - mock
-    - funcsigs
-    - msmtools >=1.1.3
-    - thermotools >=0.2.3
-    - nose
-    - numpy x.x 
-    - pyyaml
     - scipy
-    - six
-    - psutil >=3.1.1
-    - decorator >=4.0.0
-    - progress_reporter <=1.2
-
-  run:
-    - python
     - setuptools
+  run:
     - bhmm >=0.6,<0.7
+    - decorator >=4.0.0
     - joblib >0.8.4
     - matplotlib
-    - mdtraj >=1.7
+    - mdtraj
     - mock
-    - funcsigs
-    - msmtools >=1.1.3
-    - thermotools >=0.2.3
+    - msmtools >=1.2
     - numpy x.x
+    - progress_reporter <=1.2
+    - psutil >3.1
+    - python
     - pyyaml
     - scipy
+    - setuptools
     - six >=1.10
-    - psutil >=3.1.1
-    - decorator >=4.0.0
-    - progress_reporter <=1.2
+    - thermotools >=0.2.3
 
 test:
   requires:
     - pytest 
     - pytest-cov
-    #- pytest-xdist
   imports:
     - pyemma
 

pyemma/conftest.py

@@ -7,28 +7,3 @@ def no_progress_bars():
     import pyemma
     pyemma.config.show_progress_bars = False
     pyemma.config.use_trajectory_lengths_cache = False
-
-
-def static_var(name, value):
-    def decorate(func):
-        setattr(func, name, value)
-        return func
-    return decorate
-
-
-def get_extension_names():
-    import json, pkg_resources
-    extensions_file = pkg_resources.resource_filename('pyemma', '_extensions.json')
-    with open(extensions_file) as f:
-        inp = json.load(f)
-    extension_stubs = [e.split('.')[-1] for e in inp]
-    return extension_stubs
-
-
-# this hook should ignore setuptools generated stub loaders for extension,
-# because they cause PathMismatch errors in pytest during discovery.
-@static_var('extension_stubs', get_extension_names())
-def pytest_ignore_collect(path, config):
-
-    if any(path.basename.startswith(e) for e in pytest_ignore_collect.extension_stubs):
-        return True

setup.py

@@ -219,23 +219,6 @@ def run_tests(self):
 
     versioneer_cmds['test'] = PyTest
 
-    from setuptools.command.egg_info import egg_info
-
-    class extensions_json(egg_info):
-        def run(self):
-            f = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'pyemma', '_extensions.json')
-            print("Generating {}".format(f))
-            extension_names = [e.name for e in extensions()]
-
-            with open(f, 'wb') as fp:
-                import json
-                s = json.dumps(extension_names).encode('ascii')
-                fp.write(s)
-
-            egg_info.run(self)
-
-    versioneer_cmds['egg_info'] = extensions_json
-
     return versioneer_cmds
 
 
@@ -262,9 +245,9 @@ def run(self):
     # runtime dependencies
     install_requires=['numpy>=1.7.0',
                       'scipy>=0.11',
-                      'mdtraj>=1.7.0',
+                      'mdtraj>=1.8.0',
                       'matplotlib',
-                      'msmtools>=1.1.4',
+                      'msmtools>=1.2',
                       'thermotools>=0.2.3',
                       'bhmm>=0.6,<0.7',
                       'joblib>0.8.4',
@@ -293,7 +276,7 @@ def run(self):
                                   ]
 
     metadata['package_data'] = {
-                                'pyemma': ['pyemma.cfg', 'logging.yml', '_extensions.json', 'setup.cfg'],
+                                'pyemma': ['pyemma.cfg', 'logging.yml', 'setup.cfg'],
                                 'pyemma.coordinates.tests': ['data/*'],
                                 'pyemma.msm.tests': ['data/*'],
                                 'pyemma.datasets': ['*.npz'],