Update setup.py and test/deploy scripts

- drop pbr
- update setuptools to >= 30.3
- specify requirements and tests_require in setup.cfg
- refer to smif package under src
- update travis install method
- specify (CLI) entry_points in setup.py
- sprinkle tests with __init__.py  following pytest good
  practises recommendation
  https://docs.pytest.org/en/latest/goodpractices.html
- remove unused features for behave (BDD testing)
- simplify .environment.yml
  - this is used by ReadTheDocs to build smif docs
  - dependencies are commented if for #dev #test or #docs,
    with the idea that dev and test dependencies are handy
    to have here for a developer setting up a new conda
    environment.
  - no version numbers (only pinning numbers in requirements.txt)
- sort requirements.txt, relax versions to >=X.Y
- specify stages for travis, and skip cleanup on deploy
  - skip_cleanup means the web assets built by  are left
    in place for the python package to include
  - build stages allow travis to run multiple jobs in parallel, then
    the next stage after those are complete - for us, that could mean
    testing several python versions then deploying just once
- remove apt (git and pip) requirements for travis
- specify data files in MANIFEST

Author: tomalrussell

.coveragerc

@@ -1,8 +1,7 @@
 # .coveragerc to control coverage.py
 [run]
 branch = True
-source = smif
-# omit = bad_file.py
+source = src/smif
 
 [report]
 # Regexes for lines to exclude from consideration

.environment.yml

@@ -1,101 +1,28 @@
 # Conda environment specification
-# 1. to export (recommend editing before checking in to git):
-#    conda env export > .environment.yml
-# 2. to import/create a copy of the environment:
+# To import/create a copy of the environment:
 #    conda env create -f .environment.yml
 name: smif
 channels:
 - conda-forge
 - defaults
 dependencies:
-- backports=1.0=py35_1
-- backports.functools_lru_cache=1.4=py35_1
-- ca-certificates=2017.11.5=0
-- certifi=2017.11.5=py35_0
-- click=6.7=py35_0
-- click-plugins=1.0.3=py35_0
-- cligj=0.4.0=py35_0
-- curl=7.55.1
-- cycler=0.10.0=py35_0
-- expat=2.1.0
-- fiona=1.7.10=py35_2
-- freetype=2.7
-- freexl=1.0.2
-- gdal=2.1.3
-- geos=3.6.2
-- hdf4=4.2.13
-- hdf5=1.10.1
-- icu=58.2
-- jpeg=9b
-- kealib=1.4.7
-- krb5=1.14.2
-- libiconv=1.14
-- libnetcdf=4.4.1.1
-- libpng=1.6.28
-- libpq=9.6.3
-- libspatialindex=1.8.5
-- libspatialite=4.3.0a
-- libssh2=1.8.0
-- libtiff=4.0.9
-- libxml2=2.9.5
-- matplotlib=2.1.0=py35_1
-- munch=2.2.0=py35_0
-- openjpeg=2.1.2
-- openssl=1.0.2l
-- pcre=8.39
-- pip=9.0.1=py35_0
-- proj4=4.9.3
-- pyparsing=2.2.0=py35_0
-- pyqt=5.6.0=py35_4
-- python=3.5.4=1
-- python-dateutil=2.6.1=py35_0
-- pytz=2017.3=py_2
-- pyyaml=3.12=py35_1
-- qt=5.6.2
-- rtree=0.8.3=py35_0
-- scikit-optimize=0.3=py35_0
-- setuptools=37.0.0=py35_0
-- shapely=1.6.2=py35_1
-- sip=4.18=py35_1
-- six=1.11.0=py35_1
-- sqlite=3.13.0
-- tornado=4.5.2=py35_0
-- wheel=0.30.0
-- xerces-c=3.2.0
-- yaml=0.1.6
-- zlib=1.2.11
-- mkl=2017.0.3=0
-- numpy=1.13.1=py35_0
-- scikit-learn=0.19.0=np113py35_0
-- scipy=0.19.1=np113py35_0
+- python=3.6
+- codecov  # test
+- fiona
+- flask
+- isodate
+- networkx
+- numpy
+- pint
+- pylint  # dev
+- pytest  # test
+- pytest-cov  # test
+- python-dateutil
+- pyyaml
+- rtree
+- scikit-optimize
+- shapely
+- sphinx  # docs
 - pip:
-  - alabaster==0.7.10
-  - aspy.yaml==1.0.0
-  - babel==2.5.3
-  - backports.functools-lru-cache==1.4
-  - better-apidoc==0.1.2
-  - cached-property==1.3.1
-  - chardet==3.0.4
-  - colorama==0.3.9
-  - decorator==4.1.2
-  - docutils==0.14
-  - flask==0.12.2
-  - identify==1.0.7
-  - idna==2.6
-  - imagesize==0.7.1
-  - isodate==0.6.0
-  - itsdangerous==0.24
-  - jinja2==2.10
-  - markupsafe==1.0
-  - networkx==1.11
-  - nodeenv==1.2.0
-  - pint==0.8.1
-  - pre-commit==1.4.1
-  - pygments==2.2.0
-  - requests==2.18.4
-  - snowballstemmer==1.2.1
-  - sphinx==1.6.6
-  - sphinxcontrib-websupport==1.0.1
-  - urllib3==1.22
-  - virtualenv==15.1.0
-  - werkzeug==0.12.2
+  - better-apidoc  # docs
+  - pre-commit  # dev

.pre-commit-config.yaml

@@ -8,6 +8,7 @@
     -   id: check-xml
     -   id: debug-statements
     -   id: end-of-file-fixer
+    -   id: requirements-txt-fixer
     -   id: flake8
         args:
         - --exclude=docs/conf.py --ignore F401,F811 tests

.travis.yml

@@ -1,44 +1,46 @@
 sudo: false
 language: python
-virtualenv:
-  system_site_packages: true
+notifications:
+  email: false
+
 cache:
   pip: true
   directories:
-    - smif/app/node_modules
+    - src/smif/app/node_modules
 before_cache:
   - rm -f $HOME/.cache/pip/log/debug.log
+
 env:
   global:
-  - SKIP_GENERATE_AUTHORS=1
-  - SKIP_WRITE_GIT_CHANGELOG=1
+    - SKIP_GENERATE_AUTHORS=1
+    - SKIP_WRITE_GIT_CHANGELOG=1
+    - DISTRIB="conda"
   matrix:
-  - DISTRIB="conda" PYTHON_VERSION="3.5" COVERAGE="false"
-  - DISTRIB="conda" PYTHON_VERSION="3.6" COVERAGE="true"
-install:
-- source tests/travis_install.sh
-- pip install -r test-requirements.txt -r requirements.txt
-- python setup.py develop
-- nvm install 6.11.4
-- nvm use 6.11.4
-- cd $TRAVIS_BUILD_DIR/smif/app && npm install
+    - PYTHON_VERSION="3.5" COVERAGE="false"
+    - PYTHON_VERSION="3.6" COVERAGE="true"
+
+install: source $TRAVIS_BUILD_DIR/ci/install.sh
 script:
-- cd $TRAVIS_BUILD_DIR && python setup.py test
-- cd $TRAVIS_BUILD_DIR/smif/app && npm test
-after_success:
-- cd $TRAVIS_BUILD_DIR
-- if [[ "$COVERAGE" == "true" ]]; then bash <(curl -s https://codecov.io/bash) -cF python || echo "failed"; fi
-- cd $TRAVIS_BUILD_DIR/smif/app && npm run-script report
-- if [[ "$COVERAGE" == "true" ]]; then bash <(curl -s https://codecov.io/bash) -cF javascript || echo "failed"; fi
-notifications:
-  email: false
-before_deploy:
-  cd $TRAVIS_BUILD_DIR/smif/app && npm run build
-deploy:
-  provider: pypi
-  user: willu47
-  password:
-    secure: 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
-  on:
-    tags: true
-    all_branches: true
+  - cd $TRAVIS_BUILD_DIR && python setup.py test
+  - cd $TRAVIS_BUILD_DIR/src/smif/app && npm test
+after_success: $TRAVIS_BUILD_DIR/ci/coverage.sh
+
+jobs:
+  include:
+    - stage: PyPI release
+      if: tag =~ ^v
+      env: PYTHON_VERSION="3.6" COVERAGE="false"
+      install: source $TRAVIS_BUILD_DIR/ci/install.sh
+      script: echo "Deploying to PyPI"
+      before_deploy:
+        - cd $TRAVIS_BUILD_DIR/src/smif/app && npm run build
+        - cd $TRAVIS_BUILD_DIR
+      deploy:
+        provider: pypi
+        user: willu47
+        password:
+          secure: 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
+        on:
+          tags: true
+          all_branches: true
+        skip_cleanup: true

MANIFEST.in

@@ -0,0 +1,2 @@
+include src/smif/app/dist/*
+recursive-include smif/sample_project/

ci/coverage.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+# This script is meant to be called by the "after_success" step defined in
+# .travis.yml. See http://docs.travis-ci.com/ for more details.
+
+set -e # exit on error
+set -x # echo commands
+
+if [[ "$COVERAGE" == "true" ]]; then
+    cd $TRAVIS_BUILD_DIR
+
+    # Upload python coverage
+    bash <(curl -s https://codecov.io/bash) -cF python || echo "failed"
+
+    # Run node coverage
+    cd $TRAVIS_BUILD_DIR/src/smif/app && npm run-script report
+
+    # Upload javascript coverage
+    bash <(curl -s https://codecov.io/bash) -cF javascript || echo "failed"
+fi

tests/travis_install.sh ci/install.sh

@@ -6,7 +6,6 @@
 #
 # This script is taken from Scikit-Learn (http://scikit-learn.org/)
 #
-# THIS SCRIPT IS SUPPOSED TO BE AN EXAMPLE. MODIFY IT ACCORDING TO YOUR NEEDS!
 
 set -e
 
@@ -27,14 +26,29 @@ if [[ "$DISTRIB" == "conda" ]]; then
     # Configure the conda environment and put it in the path using the
     # provided versions
     conda config --add channels conda-forge
-    conda create -n testenv --yes python=$PYTHON_VERSION pip numpy pyyaml fiona rtree shapely scikit-optimize
+    conda create -n testenv --yes python=$PYTHON_VERSION \
+        fiona \
+        flask \
+        isodate \
+        networkx \
+        numpy \
+        pint \
+        pytest \
+        pytest-cov \
+        python-dateutil \
+        pyyaml \
+        rtree \
+        scikit-optimize \
+        shapely
     source activate testenv
-
-elif [[ "$DISTRIB" == "ubuntu" ]]; then
-    # Use standard ubuntu packages in their default version
-    echo ubuntu
 fi
 
-if [[ "$COVERAGE" == "true" ]]; then
-    pip install coverage coveralls
-fi
+# Pip install by default
+pip install -r requirements.txt
+python setup.py develop
+
+# Install node and npm dependencies
+nvm install 6.11.4
+nvm use 6.11.4
+cd $TRAVIS_BUILD_DIR/src/smif/app && npm install
+cd $TRAVIS_BUILD_DIR

docs/conf.py

@@ -1,7 +1,12 @@
 # -*- coding: utf-8 -*-
 #
 # This file is execfile()d with the current directory set to its containing dir.
-#
+
+# To run the docs build directly, generate module index:
+#   rm -r docs/api ; sphinx-apidoc -f -M -o docs/api smif
+# Then build docs:
+#   rm -r docs/_build ; sphinx-build -b html docs docs/_build/html
+
 # Note that not all possible configuration values are present in this
 # autogenerated file.
 #
@@ -24,7 +29,6 @@
 import os
 import sys
 
-# from sphinx import apidoc
 import better_apidoc
 
 # add these directories to sys.path here. If the directory is relative to the
@@ -35,9 +39,14 @@
 __location__ = os.path.join(os.getcwd(), os.path.dirname(
     inspect.getfile(inspect.currentframe())))
 
-output_dir = os.path.join(__location__, "../docs/api")
-module_dir = os.path.join(__location__, "../smif")
-templates_dir = os.path.join(__location__, "../docs/_templates")
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+sys.path.insert(0, os.path.join(__location__, '../src'))
+
+output_dir = os.path.join(__location__, "api")
+module_dir = os.path.join(__location__, "../src/smif")
+templates_dir = os.path.join(__location__, "_templates")
 
 better_apidoc.main([
     'better-apidoc',

requirements.txt

@@ -1,12 +1,14 @@
-# Add your requirements here like:
-numpy
-pyyaml>=3.12
-networkx~=1.11
-python-dateutil==2.6.0
-isodate
+# Add your pinned requirements so that they can be easily installed with:
+# pip install -r requirements.txt
+# Remember to also add them in setup.cfg and environment.yml but unpinned.
 fiona>=1.7
-shapely>=1.3
+Flask>=0.12
+isodate>=0.6
+networkx>=1.11
+numpy>=1.11
+Pint>=0.8
+python-dateutil>=2.6
+pyyaml>=3.12
 Rtree>=0.7
-Pint==0.8.1
-Flask==0.12.2
-scikit-optimize==0.3
+scikit-optimize>=0.3
+shapely>=1.3