Added CI setup files. Added rules to Makefile. Added test requirements.

Signed-off-by: Daniel Scheffler <danschef@gfz-potsdam.de>

Makefile

@@ -45,13 +45,17 @@ clean-pyc: ## remove Python file artifacts
 	find . -name '__pycache__' -exec rm -fr {} +
 
 clean-test: ## remove test and coverage artifacts
+	coverage erase
 	rm -fr .tox/
 	rm -f .coverage
 	rm -fr htmlcov/
-	rm -fr .pytest_cache
+	rm -fr nosetests.html
+	rm -fr nosetests.xml
 
 lint: ## check style with flake8
-	flake8 pyrsr tests
+	flake8 --max-line-length=120 pyrsr tests > ./tests/linting/flake8.log
+	pycodestyle pyrsr --exclude="*.ipynb,*.ipynb*" --max-line-length=120 > ./tests/linting/pycodestyle.log
+	-pydocstyle pyrsr > ./tests/linting/pydocstyle.log
 
 test: ## run tests quickly with the default Python
 	python setup.py test
@@ -60,10 +64,18 @@ test-all: ## run tests on every Python version with tox
 	tox
 
 coverage: ## check code coverage quickly with the default Python
-	coverage run --source pyrsr setup.py test
+	coverage run --source pyrsr --source bin setup.py test
+	coverage combine 	# must be called in order to make coverage work in multiprocessing
 	coverage report -m
 	coverage html
-	$(BROWSER) htmlcov/index.html
+	# $(BROWSER) htmlcov/index.html
+
+nosetests: clean-test ## Runs nosetests with coverage, xUnit and nose-html-output
+	## - puts the coverage results in the folder 'htmlcov'
+	## - generates 'nosetests.html' (--with-html)
+	## - generates 'nosetests.xml' (--with-xunit) which is currently not visualizable by GitLab
+	nosetests -vv --with-coverage --cover-package=pyrsr --cover-package=bin --cover-erase --cover-html \
+		--cover-html-dir=htmlcov --with-html --with-xunit --rednose --force-color
 
 docs: ## generate Sphinx HTML documentation, including API docs
 	rm -f docs/pyrsr.rst
@@ -85,4 +97,8 @@ dist: clean ## builds source and wheel package
 	ls -l dist
 
 install: clean ## install the package to the active Python's site-packages
+	pip install -r requirements.txt
 	python setup.py install
+
+gitlab_CI_docker:  ## Build a docker image for CI use within gitlab
+	cd ./tests/CI_docker/; bash ./build_testsuite_image.sh

setup.py

@@ -41,7 +41,7 @@ requirements = ['numpy', 'pandas', 'matplotlib', 'scipy']
 
 setup_requirements = []
 
-test_requirements = []
+test_requirements = ['coverage', 'nose', 'nose-htmloutput', 'rednose']
 
 setup(
     author="Daniel Scheffler",

tests/CI_docker/build_testsuite_image.sh

+#!/usr/bin/env bash
+
+context_dir="./context"
+dockerfile="pyrsr_ci.docker"
+tag="spechomo_ci:0.0.1"
+gitlab_runner="spechomo_gitlab_CI_runner"
+
+echo "#### Build runner docker image"
+sudo docker rmi ${tag}
+sudo docker build -f ${context_dir}/${dockerfile} -m 20G -t ${tag} ${context_dir}
+# sudo docker build -f ./context/pyrsr_ci.docker -m 20G -t spechomo_ci:0.7.0 ./context --no-cache
+
+echo "#### Create gitlab-runner (daemon) container with tag; ${tag}"
+sudo docker stop ${gitlab_runner}
+sudo docker rm ${gitlab_runner}
+sudo docker run -d --name ${gitlab_runner} --restart always \
+-v /var/run/docker.sock:/var/run/docker.sock gitlab/gitlab-runner:latest
+
+echo "#### Register container at gitlab, get token here https://gitext.gfz-potsdam.de/geomultisens/spechomo/settings/ci_cd"
+read -p "Please enter gitlab token: " token
+echo ""
+read -p "Please enter gitlab runner name: " runner_name
+echo "New gitlab runner image will named  ${gitlab_runner}"
+sudo docker exec -it ${gitlab_runner} /bin/bash -c "export RUNNER_EXECUTOR=docker && gitlab-ci-multi-runner register -n \
+  --url 'https://gitext.gfz-potsdam.de/ci' \
+  --registration-token '${token}' \
+  --run-untagged=true \
+  --locked=true \
+  --tag-list  spechomo_client \
+  --description '${runner_name}' \
+  --docker-image '${tag}' "

tests/CI_docker/context/environment_pyrsr.yml

+name: pyrsr
+
+channels: &id1
+  - http://conda.anaconda.org/conda-forge
+
+dependencies:
+  - python=3.*.*
+  - matplotlib
+  - numpy
+  - pandas
+
+  - pip:
+    - scipy
+
+    # test and doc dependencies
+    - coverage
+    - flake8
+    - nose
+    - nose2
+    - nose-htmloutput
+    - pycodestyle
+    - pylint
+    - pydocstyle
+    - rednose
+    - sphinx-argparse

tests/CI_docker/context/pyrsr_ci.docker

+FROM gms_base_centos:0.2
+
+# copy some needed stuff to /root
+COPY *.yml /root/
+
+# update the ci_env environment (that already contains all packages installed via 'docker_pyenvs' repo)
+RUN /bin/bash -i -c "\
+    source /root/miniconda3/bin/activate ; \
+    source activate ci_env; \
+    conda env update -n ci_env -f /root/environment_pyrsr.yml"