Merge pull request #10 from univieCUBE/dev

Merge dev into master

.appveyor.yml

@@ -0,0 +1,80 @@
+# based on https://github.com/ogrisel/python-appveyor-demo/
+# Thanks to Olivier Grisel for the template!
+
+environment:
+  global:
+    # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the
+    # /E:ON and /V:ON options are not enabled in the batch script intepreter
+    # See: http://stackoverflow.com/a/13751649/163740
+    CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\appveyor\\run_with_env.cmd"
+
+  matrix:
+    - PYTHON: "C:\\Python37-x64"
+      PYTHON_VERSION: "3.7.x" # currently 3.7.?
+      PYTHON_ARCH: "64"
+
+install:
+  # If there is a newer build queued for the same PR, cancel this one.
+  # The AppVeyor 'rollout builds' option is supposed to serve the same
+  # purpose but it is problematic because it tends to cancel builds pushed
+  # directly to master instead of just PR builds (or the converse).
+  # credits: JuliaLang developers.
+  - ps: if ($env:APPVEYOR_PULL_REQUEST_NUMBER -and $env:APPVEYOR_BUILD_NUMBER -ne ((Invoke-RestMethod `
+        https://ci.appveyor.com/api/projects/$env:APPVEYOR_ACCOUNT_NAME/$env:APPVEYOR_PROJECT_SLUG/history?recordsNumber=50).builds | `
+        Where-Object pullRequestId -eq $env:APPVEYOR_PULL_REQUEST_NUMBER)[0].buildNumber) { `
+          throw "There are newer queued builds for this pull request, failing early." }
+  - ECHO "Filesystem root:"
+  - ps: "ls \"C:/\""
+
+  - ECHO "Installed SDKs:"
+  - ps: "ls \"C:/Program Files/Microsoft SDKs/Windows\""
+
+  # Install Python (from the official .msi of https://python.org) and pip when
+  # not already installed.
+  - ps: if (-not(Test-Path($env:PYTHON))) { & appveyor\install.ps1 }
+
+  # Prepend newly installed Python to the PATH of this build (this cannot be
+  # done from inside the powershell script as it would require to restart
+  # the parent CMD process).
+  - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%"
+
+  # Check that we have the expected version and architecture for Python
+  - "python --version"
+  - "python -c \"import struct; print(struct.calcsize('P') * 8)\""
+
+  # Upgrade to the latest version of pip to avoid it displaying warnings
+  # about it being out of date.
+  - "python -m pip install --upgrade pip"
+
+  # Install the build dependencies of the project. If some dependencies contain
+  # compiled extensions and are not provided as pre-built wheel packages,
+  # pip will build them from source using the MSVC compiler matching the
+  # target Python version and architecture
+  - "python -m pip install wheel pytest"
+  - "python -m pip install -r requirements.txt"
+
+build_script:
+  # Build the compiled extension
+  - "python setup.py build"
+
+test_script:
+  # Run the project tests
+  - "pytest"
+
+after_test:
+  # If tests are successful, create binary packages for the project.
+  - "python setup.py bdist_wheel"
+  - "python setup.py bdist_wininst"
+  - "python setup.py bdist_msi"
+  - ps: "ls dist"
+
+artifacts:
+  # Archive the generated packages in the ci.appveyor.com build report.
+  - path: dist\*
+
+#on_success:
+#  - TODO: upload the content of dist/*.whl to a public wheelhouse
+#
+
+cache:
+  - '%LOCALAPPDATA%\pip\Cache -> appveyor.yml'

.flake8

@@ -0,0 +1,2 @@
+[flake8]
+max-line-length = 120

.gitattributes

@@ -1,2 +1 @@
-pica/dev_scripts/* linguist-documentation
 pica/docs/* linguist-documentation

.gitignore

@@ -102,3 +102,4 @@ ENV/
 .mypy_cache/
 /.idea/
 /.github/
+/PICA2.iml

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/conf.py
+
+# Build documentation with MkDocs
+#mkdocs:
+#  configuration: mkdocs.yml
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: 3.7
+  install:
+    - requirements: requirements-rtd.txt
+  system_packages: false

.travis.yml

@@ -1,26 +1,76 @@
-# Config file for automatic testing at travis-ci.org
+lanuage: python
 
-language: python
 python:
-  - 3.7
-
-# Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
-install: pip install -U tox-travis
-
-# Command to run tests, e.g. python setup.py test
-script: tox
-
-# Assuming you have installed the travis-ci CLI tool, after you
-# create the Github repo and add it to Travis, run the
-# following command to finish PyPI deployment setup:
-# $ travis encrypt --add deploy.password
-deploy:
-  provider: pypi
-  distributions: sdist bdist_wheel
-  user: LokiLuciferase
-  password:
-    secure: PLEASE_REPLACE_ME
-  on:
-    tags: true
-    repo: LokiLuciferase/pica
-    python: 3.6
+  - '3.7'
+
+matrix:
+  include:
+    - os: linux
+      dist: xenial
+      sudo: false
+    - os: osx
+      # osx_image: xcode10.2
+      sudo: true
+
+env:
+  global:
+  - CACHE_DIR="$HOME/virtualenv"
+  - MINICONDA_DIR="$HOME/miniconda"
+  - PYTHONIOENCODING=UTF8
+
+before_install:
+  - bash travis/install-conda.sh
+  - export PATH="$MINICONDA_DIR/bin:$PATH"
+  - hash -r
+  - bash travis/install-pip.sh
+
+install:
+  - python setup.py build
+  - python setup.py install
+
+before_script:
+  - flake8 --exit-zero .
+
+script:
+  - pytest --cov=pica
+
+after_success:
+  - codecov
+
+cache:
+  - pip
+  - ccache
+  - packages
+  - directories:
+      - "$HOME/.cache/pip"
+      - "$HOME/virtualenv"
+      - "$HOME/miniconda"
+
+branches:
+  only:
+  - master
+  - develop
+  - dev
+
+# TODO enable tox usage as originial intended
+#
+## Command to install dependencies, e.g. pip install -r requirements.txt --use-mirrors
+#install: pip install -U tox-travis
+#
+## Command to run tests, e.g. python setup.py test
+#script: tox
+#
+## Assuming you have installed the travis-ci CLI tool, after you
+## create the Github repo and add it to Travis, run the
+## following command to finish PyPI deployment setup:
+## $ travis encrypt --add deploy.password
+#deploy:
+#  provider: pypi
+#  distributions: sdist bdist_wheel
+#  user: LokiLuciferase
+#  password:
+#    secure: PLEASE_REPLACE_ME
+#  on:
+#    tags: true
+#    repo: LokiLuciferase/pica
+#    python: 3.6

AUTHORS.rst

@@ -5,4 +5,10 @@ Credits
 Development Lead
 ----------------
 
-* Lukas Lueftinger <[email protected]>
+* Lukas Lüftinger <[email protected]>
+
+Contributors
+------------
+
+* Patrick Hyden <[email protected]>
+* Roman Feldbauer <[email protected]>

README.rst

@@ -1,21 +1,27 @@
-====
-PICA
-====
+
+PICA2
+=====
 
 
 .. image:: https://img.shields.io/pypi/v/pica.svg
         :target: https://pypi.python.org/pypi/pica
 
-.. image:: https://img.shields.io/travis/LokiLuciferase/pica.svg
-        :target: https://travis-ci.org/LokiLuciferase/pica
+.. image:: https://travis-ci.com/univieCUBE/PICA2.svg?branch=master
+    :target: https://travis-ci.com/univieCUBE/PICA2
+
+.. image:: https://codecov.io/gh/univieCUBE/PICA2/branch/master/graph/badge.svg
+  :target: https://codecov.io/gh/univieCUBE/PICA2
 
-.. image:: https://readthedocs.org/projects/pica/badge/?version=latest
-        :target: https://pica.readthedocs.io/en/latest/?badge=latest
+.. image:: https://ci.appveyor.com/api/projects/status/iursmhw1wocfgpua?svg=true
+  :target: https://ci.appveyor.com/project/VarIr/pica2
+
+.. image:: https://readthedocs.org/projects/pica2-test/badge/?version=latest
+        :target: https://pica2_test.readthedocs.io/en/latest/?badge=latest
         :alt: Documentation Status
 
 
 Microbial Phenotype Prediction, re-implemented with Python 3.7 and scikit-learn
 
-
+* Supported platforms: Linux, MacOS, Windows
 * Free software: MIT license
 

docs/conf.py

@@ -73,18 +73,18 @@
 exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
 
 # The name of the Pygments (syntax highlighting) style to use.
-pygments_style = 'sphinx'
+pygments_style = 'monokai'
 
 # If true, `todo` and `todoList` produce output, else they produce nothing.
 todo_include_todos = False
 
-
-# -- Options for HTML output -------------------------------------------
+# -- Options for HTML output -------------------------------------------------
 
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'alabaster'
+html_theme = 'nature'
+
 
 # Theme options are theme-specific and customize the look and feel of a
 # theme further.  For a list of options available for each theme, see the
@@ -95,8 +95,11 @@
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,
 # so a file named "default.css" will overwrite the builtin "default.css".
-html_static_path = ['_static']
+# See: https://www.sphinx-doc.org/en/master/usage/configuration.html#confval-html_static_path
 
+# If we don't use any static files, we shouldn't include this here
+# html_static_path = ['_static']
+html_static_path = []
 
 # -- Options for HTMLHelp output ---------------------------------------
 

docs/index.rst

@@ -1,5 +1,5 @@
-Welcome to PICA's documentation!
-================================
+Welcome to the PICA2 documentation!
+===================================
 
 .. toctree::
    :maxdepth: 2

docs/installation.rst

@@ -8,13 +8,13 @@ Installation
 Stable release
 --------------
 
-To install PICA, run this command in your terminal:
+To install PICA2, run this command in your terminal:
 
 .. code-block:: console
 
     $ pip install pica
 
-This is the preferred method to install PICA, as it will always install the most recent stable release.
+This is the preferred method to install PICA2, as it will always install the most recent stable release.
 
 If you don't have `pip`_ installed, this `Python installation guide`_ can guide
 you through the process.
@@ -26,19 +26,19 @@ you through the process.
 From sources
 ------------
 
-The sources for PICA can be downloaded from the `Github repo`_.
+The sources for PICA2 can be downloaded from the `Github repo`_.
 
 You can either clone the public repository:
 
 .. code-block:: console
 
-    $ git clone git://github.com/LokiLuciferase/pica
+    $ git clone git://github.com/univieCUBE/PICA2
 
 Or download the `tarball`_:
 
 .. code-block:: console
 
-    $ curl  -OL https://github.com/LokiLuciferase/pica/tarball/master
+    $ curl  -OL https://github.com/univieCUBE/PICA2/tarball/master
 
 Once you have a copy of the source, you can install it with:
 
@@ -47,5 +47,5 @@ Once you have a copy of the source, you can install it with:
     $ python setup.py install
 
 
-.. _Github repo: https://github.com/LokiLuciferase/pica
-.. _tarball: https://github.com/LokiLuciferase/pica/tarball/master
+.. _Github repo: https://github.com/univieCUBE/PICA2
+.. _tarball: https://github.com/univieCUBE/PICA2/tarball/master

docs/modules.rst

@@ -0,0 +1,7 @@
+pica
+====
+
+.. toctree::
+   :maxdepth: 4
+
+   pica

docs/pica.io.rst

@@ -0,0 +1,22 @@
+pica.io package
+===============
+
+Submodules
+----------
+
+pica.io.io module
+-----------------
+
+.. automodule:: pica.io.io
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+
+Module contents
+---------------
+
+.. automodule:: pica.io
+   :members:
+   :undoc-members:
+   :show-inheritance: