Merge pull request #17 from ottogroup/develop

Develop

.travis.yml

@@ -1,23 +1,28 @@
 language: python
 python:
-  - "3.3"
   - "3.4"
+  - "3.5"
 env:
   - TRAVIS=yes
 before_install:
+  # update R version
+  - codename=$(lsb_release -c -s)
+  - echo "deb https://cran.rstudio.com/bin/linux/ubuntu $codename/" | sudo tee -a /etc/apt/sources.list > /dev/null
+  - sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
+  - sudo add-apt-repository -y ppa:marutter/rdev
   - sudo apt-get update -qq
   - sudo apt-get install -qq libatlas-dev libatlas-base-dev liblapack-dev gfortran r-base
   - wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh -O miniconda.sh
   - chmod +x miniconda.sh
   - ./miniconda.sh -b
-  - export PATH=/home/travis/miniconda/bin:$PATH
+  - export PATH=/home/travis/miniconda2/bin:$PATH
   - conda update --yes conda
   - travis_retry conda install --yes python=$TRAVIS_PYTHON_VERSION --file requirements.txt
+  - sudo rm /home/travis/miniconda2/lib/libgfortran* # get rid of conflicting lib (rpy2/R)
   - pip install pytest pytest-cov
   - pip install coveralls
 install:
-  - if [[ $TRAVIS_PYTHON_VERSION == 3.3* ]]; then conda config --add channels https://conda.binstar.org/asmeurer; conda install --yes singledispatch; fi
-  - travis_retry pip install rpy2==2.5.2
+  - travis_retry pip install rpy2==2.7.8
   - travis_retry python setup.py dev
 script: travis_wait py.test --runslow
 after_success:

CHANGES.txt

@@ -1,3 +1,15 @@
+v1.0.1.dev1 - 2016-03-04
+========================
+
+- Updated requirements in order to use newer versions of dependencies
+
+- Added information about virtual memory size (vms) to /alive entry
+  point
+
+- Added Python 3.5 to and removed Python 3.3 from Travis CI test
+  settings
+
+
 v1.0 - 2015-07-01
 =================
 

README.rst

@@ -75,9 +75,14 @@ enterprise contexts for setting up productive services – like
 pluggable decorator lists** in the configuration file of a service,
 keeping track of service calls and corresponding permissions.
 
+Everyone is welcome to contribute to Palladium. More information on
+how to to contribute can be found in the FAQ section of the
+`Palladium documentation <http://palladium.readthedocs.org>`_.
+
 Links
 -----
 
 - Source code repository at GitHub: https://github.com/ottogroup/palladium
 - Documentation including installation instructions and tutorial: http://palladium.readthedocs.org
+- Mailing list: https://groups.google.com/forum/#!forum/pld-list
 - Maintainer: `Andreas Lattner <https://github.com/alattner>`_

VERSION

@@ -0,0 +1 @@
+1.0.1

addons/docker/palladium_base_image/Dockerfile

@@ -13,8 +13,8 @@ RUN conda config --add channels https://conda.binstar.org/ottogroup \
     && conda config --set ssl_verify false \
     && conda update --yes conda
 
-RUN wget --no-check-certificate https://raw.githubusercontent.com/ottogroup/palladium/1.0/requirements.txt
+RUN wget --no-check-certificate https://raw.githubusercontent.com/ottogroup/palladium/1.0.1/requirements.txt
 
 RUN conda install --yes --file requirements.txt
 
-RUN conda install --no-deps palladium==1.0
+RUN conda install --no-deps palladium==1.0.1

docs/conf.py

@@ -68,6 +68,11 @@ class Dummy(object):
 
 base.BaseEstimator = Dummy
 
+# Retrieve version from file
+doc_dir = os.path.dirname(os.path.abspath(__file__))
+project_dir = os.path.dirname(doc_dir)
+version_filename = os.path.join(project_dir, 'VERSION')
+
 #  on_rtd is whether we are on readthedocs.org, this line of code grabbed
 #  from docs.readthedocs.org
 on_rtd = os.environ.get('READTHEDOCS', None) == 'True'
@@ -108,16 +113,16 @@ class Dummy(object):
 
 # General information about the project.
 project = 'Palladium'
-copyright = '2015, Otto Group BI'
+copyright = '2016, Otto Group BI'
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 #
 # The short X.Y version.
-version = '1.0'
+version = open(version_filename).read().strip()
 # The full version, including alpha/beta/rc tags.
-release = '1.0'
+release = version
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -52,6 +52,14 @@ enterprise contexts for setting up productive services – like
 pluggable decorator lists** in the configuration file of a service,
 keeping track of service calls and corresponding permissions.
 
+Links
+-----
+
+- Source code repository at GitHub: https://github.com/ottogroup/palladium
+- Documentation including installation instructions and tutorial: http://palladium.readthedocs.org
+- Mailing list: https://groups.google.com/forum/#!forum/pld-list
+- Maintainer: `Andreas Lattner <https://github.com/alattner>`_
+
 User's Guide
 ------------
 

docs/user/deployment.rst

@@ -127,9 +127,9 @@ Run ``docker build`` in your terminal:
 
 .. code-block:: bash
 
-  sudo docker build -t myname/palladium-base:1.0 .
+  sudo docker build -t myname/palladium-base:1.0.1 .
 
-A Docker image with the name ``myname/palladium-base:1.0`` should now
+A Docker image with the name ``myname/palladium-base:1.0.1`` should now
 be created. You can check this with:
 
 .. code-block:: bash

docs/user/faq.rst

@@ -7,6 +7,28 @@ Frequently asked questions
 .. contents::
    :local:
 
+How do I contribute to Palladium?
+=================================
+
+Everyone is welcome to contribute to Palladium.  You can help us
+to improve Palladium when you:
+
+- Use Palladium and give us feedback or submit bug reports to GitHub.
+
+- Improve existing code or documentation and send us a pull request on
+  GitHub.
+
+- Suggest a new feature, and possibly send a pull request for it.
+
+In case you intend to improve or to add code to Palladium, we kindly ask you to:
+
+- Include documentation and tests for new code.
+
+- Ensure that all existing tests still run successfully.
+
+- Ensure backward compatibility in the general case.
+
+
 How do I configure where output is logged to?
 =============================================
 

docs/user/installation.rst

@@ -4,7 +4,7 @@
 Installation
 ============
 
-Palladium requires Python 3.3 or better to run. If you are currently using
+Palladium requires Python 3.4 or better to run. If you are currently using
 an older version of Python, you might want to check the :ref:`FAQ
 entry about virtual environments <virtual-env>`.  Some of Palladium's
 dependencies such as ``numpy``, ``scipy`` and ``scikit-learn`` may

palladium/server.py

@@ -212,10 +212,12 @@ def alive(alive=None):
     if alive is None:
         alive = {}
 
+    mem, mem_vms = memory_usage_psutil()
     info = {
-        'memory_usage': int(memory_usage_psutil()),
+        'memory_usage': mem,  # rss, resident set size
+        'memory_usage_vms': mem_vms,  # vms, virtual memory size
         'palladium_version': __version__,
-        }
+    }
 
     info['service_metadata'] = get_config().get('service_metadata', {})
 

palladium/tests/test_server.py

@@ -287,6 +287,7 @@ def test_empty_process_state(self, config, flask_client):
         resp_data = json.loads(resp.get_data(as_text=True))
 
         assert sorted(resp_data.keys()) == ['memory_usage',
+                                            'memory_usage_vms',
                                             'palladium_version',
                                             'service_metadata']
         assert resp_data['service_metadata'] == config['service_metadata']

palladium/util.py

@@ -279,8 +279,9 @@ def memory_usage_psutil():
     """Return the current process memory usage in MB.
     """
     process = psutil.Process(os.getpid())
-    mem = process.get_memory_info()[0] / float(2 ** 20)
-    return mem
+    mem = process.memory_info()[0] / float(2 ** 20)
+    mem_vms = process.memory_info()[1] / float(2 ** 20)
+    return mem, mem_vms
 
 
 def version_cmd(argv=sys.argv[1:]):  # pragma: no cover

requirements-dev.txt

@@ -1,4 +1,4 @@
-cov-core==1.14.0
-coverage==3.7.1
-pytest==2.6.4
-pytest-cov==1.8.0
+cov-core==1.15.0
+coverage==4.0.3
+pytest==2.8.5
+pytest-cov==2.2.1

requirements.txt

@@ -1,20 +1,19 @@
 Flask==0.10.1
-Jinja2==2.7.3
+Jinja2==2.8
 MarkupSafe==0.23
-Werkzeug==0.10.4
+Werkzeug==0.11.4
 docopt==0.6.2
 itsdangerous==0.24
 joblib==0.8.4
 # julia==0.1.1
-numpy==1.9.2
-pandas==0.16.2
-psutil==2.2.1
+numpy==1.10.4
+pandas==0.17.1
+psutil==3.4.2
 python-dateutil==2.4.2
-pytz==2015.4
-# rpy2==2.5.2
-scikit-learn==0.16.1
-scipy==0.15.1
-# singledispatch==3.4.0.3  # for Python 3.3
-six==1.9.0
-sqlalchemy==1.0.5
-ujson==1.33
+pytz==2015.7
+# rpy2==2.7.8
+scikit-learn==0.17.1
+scipy==0.17.0
+six==1.10.0
+sqlalchemy==1.0.11
+ujson==1.35

setup.cfg

@@ -4,6 +4,6 @@ docs = develop easy_install palladium[docs]
 
 [pytest]
 addopts =
-  -p pytest_cov --cov=palladium --cov-report=term-missing --cov-config .coveragerc
+  --cov=palladium --cov-report=term-missing --cov-config .coveragerc
   palladium/ examples/
 python_files = test*py

setup.py

@@ -1,7 +1,7 @@
 import os
 from setuptools import setup, find_packages
 
-version = '1.0'
+version = open('VERSION').read().rstrip()
 
 install_requires = [
     'docopt',
@@ -47,8 +47,8 @@
           'Development Status :: 5 - Production/Stable',
           'Intended Audience :: Developers',
           'License :: OSI Approved :: Apache Software License',
-          'Programming Language :: Python :: 3.3',
           'Programming Language :: Python :: 3.4',
+          'Programming Language :: Python :: 3.5',
       ],
       packages=find_packages(),
       include_package_data=True,