diff --git a/.gitattributes b/.gitattributes index 9030923a..4d42c31f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1 +1,3 @@ -*.ipynb linguist-vendored \ No newline at end of file +*.ipynb linguist-vendored +# *.png filter=lfs diff=lfs merge=lfs -text +# *.jpg filter=lfs diff=lfs merge=lfs -text diff --git a/.shippable.yml b/.shippable.yml deleted file mode 100644 index f1e1de21..00000000 --- a/.shippable.yml +++ /dev/null @@ -1,45 +0,0 @@ -# After changing this file, check it on: -# http://yaml-online-parser.appspot.com/ - -language: python - -sudo: true - -python: - - 2.7 - - 3.5 - -cache: pip - -env: - - CI_REPORTS=shippable/testresults COVERAGE_REPORTS=shippable/codecoverage CODACY_PROJECT_TOKEN=43ac6a06566f42968e919830ee28de4d - -build: - ci: - - echo $CI_REPORTS && mkdir -p $CI_REPORTS - - echo $COVERAGE_REPORTS && mkdir -p $COVERAGE_REPORTS - - DISPLAY="" - -before_install: - - apt-get update # --fix-missing - - apt-get install freetype* - - apt-get install python-dev python-tk python3-dev python3-tk - - apt-get install pkg-config - - apt-get install openslide-tools - - pip install --upgrade pip - -install: - - pip install -r requirements.txt - - pip install -r ./tests/requirements.txt - - pip --version ; pip freeze - -script: - - mkdir results - # - nosetests --with-xunit --xunit-file=shippable/testresults/nosetests.xml - - nosetests -v --exe --with-doctest --with-coverage --with-xunit --cover-package=birl --xunit-file=shippable/testresults/nosetests.xml - -after_success: - - codecov - - coverage xml -o $COVERAGE_REPORTS/coverage.xml - - python-codacy-coverage -r $COVERAGE_REPORTS/coverage.xml - - coverage report diff --git a/.travis.yml b/.travis.yml index 76a30d7e..e163044c 100644 --- a/.travis.yml +++ b/.travis.yml @@ -8,8 +8,6 @@ # this file is *not* meant to cover or endorse the use of travis, but rather to # help confirm pull requests to this project. -dist: xenial # Ubuntu 16.04 - env: global: - DISPLAY="" @@ -18,23 +16,52 @@ language: python matrix: include: - - python: 2.7 + - os: osx + osx_image: xcode9.4 + language: generic + env: TOXENV=py36 + addons: + homebrew: + # update: true + packages: python3.6 + before_install: + # - brew update && brew install git-lfs + - pip3 install virtualenv + - virtualenv -p python3 ~/venv + - source ~/venv/bin/activate + #before_script: + # - git lfs install + # - git lfs pull + - os: linux + python: 2.7 + dist: xenial # Ubuntu 16.04 env: TOXENV=py27 - - python: 3.5 + - os: linux + python: 3.5 + dist: xenial # Ubuntu 16.04 env: TOXENV=py35 - - python: 3.6 + - os: linux + python: 3.6 + dist: bionic # Ubuntu 18.04 env: TOXENV=py36 - - python: 3.7 + - os: linux + python: 3.7 + dist: bionic # Ubuntu 18.04 env: TOXENV=py37 # See http://docs.travis-ci.com/user/caching/#pip-cache cache: pip +before_install: + - if [ "$TRAVIS_OS_NAME" = "osx" ]; then + brew install openslide ; + else + sudo apt-get install openslide-tools ; + fi + install: - - sudo apt-get install openslide-tools - pip install -r requirements.txt - pip install -r ./tests/requirements.txt - - pip install tox - pip --version ; pip list script: diff --git a/appveyor.yml b/appveyor.yml index 3a6dc757..5719d83f 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -11,25 +11,25 @@ environment: # a later point release. # See: http://www.appveyor.com/docs/installed-software#python - - PYTHON: "C:\\Python27" - PYTHON_VERSION: "2.7.x" - PYTHON_ARCH: "32" - TOXENV: "py27" + #- PYTHON: "C:\\Python27" + # PYTHON_VERSION: "2.7.x" + # PYTHON_ARCH: "32" + # TOXENV: "py27" - PYTHON: "C:\\Python27-x64" PYTHON_VERSION: "2.7.x" PYTHON_ARCH: "64" TOXENV: "py27" - - PYTHON: "C:\\Python35" - PYTHON_VERSION: "3.5.x" - PYTHON_ARCH: "32" - TOXENV: "py35" + #- PYTHON: "C:\\Python35" + # PYTHON_VERSION: "3.5.x" + # PYTHON_ARCH: "32" + # TOXENV: "py35" - - PYTHON: "C:\\Python35-x64" - PYTHON_VERSION: "3.5.x" - PYTHON_ARCH: "64" - TOXENV: "py35" + #- PYTHON: "C:\\Python35-x64" + # PYTHON_VERSION: "3.5.x" + # PYTHON_ARCH: "64" + # TOXENV: "py35" - PYTHON: "C:\\Python36-x64" PYTHON_VERSION: "3.6.x" diff --git a/circle.yml b/circle.yml index f10af66e..2a929f3b 100644 --- a/circle.yml +++ b/circle.yml @@ -6,7 +6,8 @@ references: run: name: Install Packages command: | - sudo apt-get update + sudo apt-get update -qq + # sudo apt-get install git-lfs sudo apt-get install tk-dev pkg-config python-dev python-tk tree sudo apt-get install openslide-tools @@ -91,23 +92,19 @@ references: jobs: - Py2: + Py3-Tests: docker: - - image: circleci/python:2.7 - steps: &steps + - image: circleci/python:3.6 + steps: &steps_tests - checkout # INSTALLATION - *install_deps + #- run: git lfs pull - *install_pips # TESTING - *test_coverage # DOCUMENTATION - *make_docs - # EXPERIMENTS - - *run_dataset - - *run_experiment - - *run_bUnwarpJ - - *run_RVSS # PASSING - run: @@ -121,15 +118,37 @@ jobs: - store_artifacts: path: test-reports - Py3: + Py3-Experiments: docker: - image: circleci/python:3.6 - steps: *steps + steps: &steps_expts + - checkout + # INSTALLATION + - *install_deps + #- run: git lfs pull + - *install_pips + # EXPERIMENTS + - *run_dataset + - *run_experiment + - *run_bUnwarpJ + - *run_RVSS + + Py2-Tests: + docker: + - image: circleci/python:2.7 + steps: *steps_tests + + Py2-Experiments: + docker: + - image: circleci/python:2.7 + steps: *steps_expts workflows: version: 2 build: jobs: - - Py2 - - Py3 + - Py2-Tests + - Py3-Tests + - Py2-Experiments + - Py3-Experiments diff --git a/requirements.txt b/requirements.txt index b4b68dc5..34c7307a 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -numpy>=1.8.2,<1.16.0 # version 1.16 breaks skimage 0.14 +numpy>=1.8.2 scipy>=0.10.0 pandas>=0.17.1 six>=1.7.3 diff --git a/tests/requirements.txt b/tests/requirements.txt index 25f3780e..00ddc219 100644 --- a/tests/requirements.txt +++ b/tests/requirements.txt @@ -6,4 +6,5 @@ pytest-cov flake8 check-manifest codacy-coverage -parameterized \ No newline at end of file +parameterized +tox \ No newline at end of file