Merge pull request #2 from MolSSI/travis

Setting up Travis-CI, codecov, PyUp

.gitignore

@@ -1,13 +1,90 @@
+# -*- mode: gitignore; -*-
+
 # Other
 *.vscode
 *.swp
 scratch/
 
+## emacs: https://github.com/github/gitignore/blob/master/Global/Emacs.gitignore
+*~
+\#*\#
+/.emacs.desktop
+/.emacs.desktop.lock
+*.elc
+auto-save-list
+tramp
+.\#*
+
+# Org-mode
+.org-id-locations
+*_archive
+
+# flymake-mode
+*_flymake.*
+
+# eshell files
+/eshell/history
+/eshell/lastdir
+
+# elpa packages
+/elpa/
+
+# reftex files
+*.rel
+
+# AUCTeX auto folder
+/auto/
+
+# cask packages
+.cask/
+dist/
+
+# Flycheck
+flycheck_*.el
+
+# server auth directory
+/server/
+
+# projectiles files
+.projectile
+
+# directory configuration
+.dir-locals.el
+
+# network security
+/network-security.data
+## end of emacs
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
 *$py.class
 
+## macOS useful to ignore https://github.com/github/gitignore/blob/master/Global/macOS.gitignore
+*.DS_Store
+.AppleDouble
+.LSOverride
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+## end of macOS
+
 # C extensions
 *.so
 
@@ -70,6 +147,15 @@ instance/
 # Sphinx documentation
 docs/_build/
 
+# IntelliJ Idea family of suites
+.idea
+*.iml
+## File-based project format:
+*.ipr
+*.iws
+## mpeltonen/sbt-idea plugin
+.idea_modules/
+
 # PyBuilder
 target/
 

.pyup.yml

@@ -0,0 +1,64 @@
+# configure updates globally
+# default: all
+# allowed: all, insecure, False
+update: insecure
+
+# configure dependency pinning globally
+# default: True
+# allowed: True, False
+pin: False
+
+# set the default branch
+# default: empty, the default branch on GitHub
+# branch: dev
+
+# update schedule
+# default: empty
+# allowed: "every day", "every week", ..
+schedule: "every week on monday"
+
+# search for requirement files
+# default: True
+# allowed: True, False
+search: False
+
+# Specify requirement files by hand, default is empty
+# default: empty
+# allowed: list
+requirements:
+  - requirements_install.txt:
+      # update insecure only
+      update: insecure
+      pin: False
+  - requirements.txt:
+      # update all dependencies and pin them
+      update: all
+      pin: True
+  - requirements_dev.txt:
+      # update insecure only
+      update: insecure
+      pin: False
+
+# add a label to pull requests, default is not set
+# requires private repo permissions, even on public repos
+# default: empty
+# label_prs: update
+
+# assign users to pull requests, default is not set
+# requires private repo permissions, even on public repos
+# default: empty
+# assignees:
+#  - carl
+#  - carlsen
+
+# configure the branch prefix the bot is using
+# default: pyup-
+# branch_prefix: pyup/
+
+# set a global prefix for PRs
+# default: empty
+# pr_prefix: "Bug #12345"
+
+# allow to close stale PRs
+# default: True
+close_prs: True

.travis.yml

@@ -1,51 +1,78 @@
 language: python
-
-# Run jobs on container-based infrastructure, can be overridden per job
-
-matrix:
-  include:
-    # Extra includes for OSX since python language is not available by default on OSX
-    - os: osx
-      language: generic
-      env: PYTHON_VER=3.6
-    - os: osx
-      language: generic
-      env: PYTHON_VER=3.7
-
-
-    - os: linux
-      language: generic  # No need to set Python version since its conda
-      env: PYTHON_VER=3.6
-    - os: linux
-      language: generic
-      env: PYTHON_VER=3.7
-
-
 before_install:
-    # Additional info about the build
-  - uname -a
-  - df -h
-  - ulimit -a
-
-    # Install the Python environment
-  - source devtools/travis-ci/before_install.sh
-  - python -V
-
+- uname -a
+- df -h
+- ulimit -a
+- source devtools/travis-ci/before_install.sh
+- python -V
 install:
-
-    # Create test environment for package
-  - python devtools/scripts/create_conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/test_env.yaml
-    # Activate the test environment
-  - conda activate test
-    # Build and install package
-  - python setup.py develop --no-deps
-
-
-script:
-  - pytest -v --cov=reference_handler reference_handler/tests/
-
+- python devtools/scripts/create_conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/test_env.yaml
+- conda activate test
+- pip install -e .
+- conda list
+- pip freeze
+matrix:
+  fast_finish: true
 notifications:
-    email: false
-
-after_success:
-  - codecov
+  email: false
+stages:
+- lint
+- test
+- deploy
+jobs:
+  include:
+  - stage: lint
+    name: Check formatting of code for PEP-8
+    os: linux
+    language: generic
+    env: PYTHON_VER=3.7
+    script:
+    - flake8 reference_handler
+    - yapf --diff --recursive  reference_handler
+  - stage: test
+    name: Tests on MacOS Python 3.6
+    script:
+    - pytest -v reference_handler/tests/
+    os: osx
+    language: generic
+    env: PYTHON_VER=3.6
+  - stage: test
+    name: Tests on MacOS Python 3.7
+    script:
+    - pytest -v reference_handler/tests/
+    os: osx
+    language: generic
+    env: PYTHON_VER=3.7
+  - stage: test
+    name: Tests on Linux Python 3.6
+    script:
+    - pytest -v reference_handler/tests/
+    os: linux
+    language: generic
+    env: PYTHON_VER=3.6
+  - stage: test
+    name: Tests and coverage on Linux Python 3.7
+    script:
+    - pytest -v --cov=reference_handler reference_handler/tests/
+    after_success:
+    - codecov
+    os: linux
+    language: generic
+    env: PYTHON_VER=3.7
+  - stage: deploy
+    name: Deploy to PyPi
+    if: tag IS present
+    dist: xenial
+    python: 3.7
+    script: skip
+    deploy:
+      provider: pypi
+      distributions: sdist bdist_wheel
+      skip_existing: true
+      on:
+        condition: "$TRAVIS_OS_NAME = linux"
+        repo: molssi/reference_handler
+        tags: true
+      user: seamm
+      password:
+        secure: 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

.yapfignore

@@ -0,0 +1 @@
+packmol_step/_version.py

Makefile

@@ -49,19 +49,17 @@ clean-test: ## remove test and coverage artifacts
 	find . -name '.pytype' -exec rm -fr {} +
 
 lint: ## check style with yapf
-	yapf --diff --recursive  reference_handler tests
-	flake8  reference_handler tests
+	yapf --diff --recursive  reference_handler
+	flake8  reference_handler
 
 flake: ## check the style with flake8
-	flake8  reference_handler tests
+	flake8  reference_handler reference_handler/tests
 
 format: ## reformat with with yapf and isort
-	yapf --recursive --in-place  reference_handler tests
-	#isort --recursive --atomic  reference_handler tests
+	yapf --recursive --in-place  reference_handler
 
 typing: ## check typing
 	pytype reference_handler_ff_util
-#	mypy -p reference_handler_ff_util
 
 test: ## run tests quickly with the default Python
 	pytest

README.md

@@ -1,9 +1,9 @@
 reference_handler
 ==============================
 [//]: # (Badges)
-[![Travis Build Status](https://travis-ci.org/REPLACE_WITH_OWNER_ACCOUNT/reference_handler.png)](https://travis-ci.org/REPLACE_WITH_OWNER_ACCOUNT/reference_handler)
-[![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/REPLACE_WITH_APPVEYOR_LINK/branch/master?svg=true)](https://ci.appveyor.com/project/REPLACE_WITH_OWNER_ACCOUNT/reference_handler/branch/master)
-[![codecov](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/reference_handler/branch/master/graph/badge.svg)](https://codecov.io/gh/REPLACE_WITH_OWNER_ACCOUNT/reference_handler/branch/master)
+[![Travis Build Status](https://travis-ci.org/molssi/reference_handler.png)](https://travis-ci.org/molssi/reference_handler)
+[![AppVeyor Build status](https://ci.appveyor.com/api/projects/status/REPLACE_WITH_APPVEYOR_LINK/branch/master?svg=true)](https://ci.appveyor.com/project/molssi/reference_handler/branch/master)
+[![codecov](https://codecov.io/gh/molssi/reference_handler/branch/master/graph/badge.svg)](https://codecov.io/gh/molssi/reference_handler/branch/master)
 
 A Python package that creates a consolidated list of references (BibTex, RIS) of scientific material 
 used in a Python package.

devtools/conda-envs/test_env.yaml

@@ -6,11 +6,14 @@ dependencies:
   - pip
 
     # Testing
+  - coverage
+  - flake8
   - pytest
   - pytest-cov
-  - codecov
+  - pytest-runner
 
     # Pip-only installs
-  #- pip:
-  #  - codecov
+  - pip:
+      # Testing
+    - yapf
 

reference_handler/__init__.py

@@ -4,7 +4,7 @@
 """
 
 # Add imports here
-from .reference_handler import Reference_Handler
+from .reference_handler import Reference_Handler  # noqa: F401
 
 # Handle versioneer
 from ._version import get_versions