Introduce CI, + other improvements (#43)

* #DC start

* #DC update travis.yml

* #DC update travis

* #DC add dep

* #DC update

* #DC update

* #DC add test

* #IM updates

* #DC update travis

* #DC update setup

* #DC update setup.py

* #BF add numpy

* #DC update

* #DC reduce number of python version

* #update setup.py

* #DC update setup.py

* #DC add numpy to req_dev

* #DC update tox

* #Dc update

* #DC typo

* #DC update tox

* #DC update

* flake8

* #IM update setup.cfg

* #DC change flake8

* #DC expand ignore list

* #DC ignore more flake8 rules

* #DC update Readme

* Add Codacy badge

* #DC update Readme

* #DC add codacy

* #DC update travis

* #DC update Readme

* #DC update

* #DC update readme

* Refactor CI (#5)

* Remove pytest cache from version control.

* Replace travisCI with github actions.

* Use setup.cfg as central configuration replacing requirements and setup.py

* Adjust tox.ini to new setup.cfg.

* Fix syntax error in gh yaml.

* Add badge and rename workflow name

* Ignore github actions if [skip ci] is contained in commit message

* Fix incorrect badge path in README [skip-ci]

* Remove obsolete version module.

* Move test data into subfolder and refactor conftest module.

* Add init module to test dir to allow coverage in local dev with pytest.

* Replace os.path with pathlib.Path. Convert `dumb_res` to fixture.

* #DC update various ...

* #DC add codacy

* #DC add contributing

* #DC update

* #DC update

* #DC add codacy

* #DC add environment variable

* #DC add conflicting file

* #DC update history

* #DC update readme

* #DC update Contributing.md

* #DC formatting oft setup.cfg

* #DC update links

* #DC update Contributing

* #DC remove requirements file

* #DC BE -> AE

* #DC comment out codacy

* DC update

Co-authored-by: The Codacy Badger <[email protected]>
Co-authored-by: Franz Wöllert <[email protected]>

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+source=hoggorm
+omit=
+[report]
+exclude_lines =
+    pragma: no cover
+    raise
+    except
+    register_parameter
+    warn

.github/workflows/ci.yml

@@ -0,0 +1,25 @@
+name: ci-build
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    if: "! contains(toJSON(github.event.commits.*.message), '[skip-ci]')"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: [3.6, 3.7, 3.8]
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v2
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install Tox and any other packages
+      run: pip install tox
+    - name: Run Tox
+      run: tox -e py
+      env:
+        CODACY_PROJECT_TOKEN: ${{ secrets.CODACY_PROJECT_TOKEN }}

CONTRIBUTING.md

@@ -0,0 +1,76 @@
+# Contributing to hoggorm
+
+If you are interested in contributing to hoggorm, your contributions will fall into three categories:
+
+1. You want to implement a new feature:
+....
+2. You want to fix a bug:
+    - Feel free to send a Pull Request any time you encounter a bug. Please provide a clear and concise description of what the bug was. If you are unsure about if this is a bug at all or how to fix, post about it in an issue.
+
+3. Improvement of documentation:
+
+Once you finish implementing a feature or bug-fix, please send a Pull Request to https://github.com/olivertomic/hoggorm
+
+## Developing hoggorm
+
+To develop hoggorm on your machine, here are some tips:
+
+1. Create and activate an environment for hoggorm
+
+```
+conda create -n envdevhoggorm python=3.6
+conda activate envdevhoggorm
+```
+
+2. Clone a copy of hoggorm from source:
+
+```
+git clone https://github.com/olivertomic/hoggorm.git 
+```
+
+4. Install hoggorm in `dev` and `test` mode:
+
+```
+cd hoggorm
+pip install -e .[dev,test]
+```
+
+5. Ensure that you have a working hoggorm installation by running the entire test suite with
+
+```
+python setup.py test
+```
+
+
+## Unit Testing
+
+hoggorm's testing is located under `test/`.
+Run the entire test suite with
+
+```
+python setup.py test
+```
+## Additional Comments
+ * American English is used
+ * We use Semantic Versioning (https://semver.org/)
+
+
+## Continuous Integration
+
+hoggorm uses [GitHub Action](https://github.com/andife/hoggorm/actions?query=workflow%3Aci-build) in combination with [CodeCov](https://codecov.io/github/andife/hoggorm?branch=hogCI) for continuous integration.
+
+Everytime you send a Pull Request, your commit will be built and checked against the hoggorm guidelines:
+
+1. Ensure that your code is formatted correctly by testing against the styleguides of [`flake8`](https://github.com/PyCQA/flake8) and [`pycodestyle`](https://github.com/PyCQA/pycodestyle):
+
+```
+pycodestyle hoggorm test examples
+flake8 hoggorm test examples
+```
+
+If you do not want to format your code manually, we recommend to use [`yapf`](https://github.com/google/yapf).
+
+
+```
+python setup.py test
+```

HISTORY.rst

@@ -0,0 +1,44 @@
+=======
+History
+=======
+
+
+0.14.X (2020-10-XX)
+-------------------
+TODO...
+* rework of README.rst (add colab and binder integration)
+* fix pytest 
+* Move test data into subfolder and refactor conftest module
+* reduce spelling errors
+* Introduce CONTRIBUTING 
+* Start use of "CII Best Practices"
+* New project structure based on cookiecutter
+* Introduce Continous Integration
+ * Use github actions for CI
+ * Integration of flake8 
+ * Integration of codecov 
+ * Integration of codacy
+
+
+0.13.3 (2019-07-11)
+-------------------
+
+Last reviewer requested change before publication of hoggorm package in Journal of Open Source Software:
+
+ * Updated usage example in readthedocs documentation in file quickstart.rst.
+
+
+0.13.2 (2019-07-06)
+-------------------
+
+* New and updated examples (Jupyter notebooks and executable scripts) for PCA, PLS1, PLS2 , PCR, SMI, RV and RV2
+* Updated documentation for ReadTheDocs
+* Updated tests
+* Updated license
+* Updated paper.md and paper.bib for publication of paper with Journal of Open Source Software (JOSS)
+
+
+0.12 (2019-01-21)
+-----------------
+
+* Git release matching PIP release from July 2018.

Makefile

@@ -0,0 +1,85 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache
+
+lint: ## check style with flake8
+	flake8 hoggorm tests
+
+test: ## run tests quickly with the default Python
+	pytest
+
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source hoggorm -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+docs: ## generate Sphinx HTML documentation, including API docs
+	rm -f docs/hoggorm.rst
+	rm -f docs/modules.rst
+	sphinx-apidoc -o docs/ hoggorm
+	$(MAKE) -C docs clean
+	$(MAKE) -C docs html
+	$(BROWSER) docs/_build/html/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: dist ## package and upload a release
+	twine upload dist/*
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install