Merge pull request #145 from GeoStat-Framework/develop

v1.5.0

Author: MuellerSeb

.coveragerc

@@ -0,0 +1,10 @@
+[run]
+source = pykrige
+omit = *docs*, *examples*, *tests*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if __name__ == '__main__':
+    def __repr__
+    def __str__

.gitignore

@@ -1,16 +1,123 @@
-*.pyc
-*.egg-info/
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
 build/
-doc/_build/
-*.swp
-.idea/*
-dist/*
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+docs/output.txt
+docs/source/examples/
+docs/source/generated/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+tags
+/test_*
+
+# own stuff
+info/
+pykrige/_version.py
+
+# Cython generated C code
 *.c
-*.so
-.cache/
-doc/examples/
-doc/generated/
-doc/modules/
+*.cpp
 
+# special
+*.DS_Store
+*.zip
+*.vtu
+*.vtr
 examples/meuse_example_data/*
 *.ipynb_checkpoints/*

.travis.yml

@@ -1,49 +1,107 @@
 language: python
-sudo: required
-services:
-  - xvfb
-matrix:
-    include:
-    - python: "3.6"
-      env: DEPS="numpy scipy cython nose matplotlib scikit-learn gstools"
-    - python: "3.5"
-      env: DEPS="numpy scipy=0.18 cython nose matplotlib scikit-learn=0.18.1"
-    - python: "2.7"
-      env: DEPS="numpy=1.10.4 scipy=0.17 cython nose matplotlib scikit-learn=0.17.1"
-
-# setup adapted from https://github.com/soft-matter/trackpy/blob/master/.travis.yml
+python: 3.8
+
+# setuptools-scm needs all tags in order to obtain a proper version
+git:
+  depth: false
+
+env:
+  global:
+    - TWINE_USERNAME=geostatframework
+    - CIBW_BEFORE_BUILD="pip install numpy==1.17.3 scipy==1.3.2 cython==0.29.14 setuptools"
+    - CIBW_TEST_REQUIRES="pytest scikit-learn gstools"
+    - CIBW_TEST_COMMAND="pytest -v {project}/tests"
+
 before_install:
-    - wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
-    - chmod +x miniconda.sh
-    - ./miniconda.sh -b
-    - export PATH=/home/travis/miniconda3/bin:$PATH
-    - conda update --yes conda
-    - conda info -a
-    - conda config --add channels conda-forge
-
-install:
-    - conda create -q -n krige-env -y $DEPS pip pytest-cov pytest python=${TRAVIS_PYTHON_VERSION}
-    - source activate krige-env
-    - which pip
-    - pip install coveralls
-    - pip install -e .
-
-before_script:
-  - "export DISPLAY=:99.0"
-
-# command to run tests
-script:
-    - source activate krige-env
-    - pytest -sv ./pykrige/ --cov=pykrige
-    - |
-        # run examples
-        # scikit-learn needed by the regression kriging example
-        # conda install -y scikit-learn gstools
-        set -x
-        for f in examples/*.py; do
-           python $f 2>&1 | tee -a ~/log.txt
-        done
-        if grep -q "Traceback (most recent call last):" ~/log.txt; then false; else true; fi
-
-#after_success:
-#    coveralls
+  - |
+    if [[ "$TRAVIS_OS_NAME" = windows ]]; then
+        choco install python --version 3.8.0
+        export PATH="/c/Python38:/c/Python38/Scripts:$PATH"
+        # make sure it's on PATH as 'python3'
+        ln -s /c/Python38/python.exe /c/Python38/python3.exe
+    fi
+
+install: python3 -m pip install cibuildwheel==1.3.0
+
+script: python3 -m cibuildwheel --output-dir dist
+
+after_success:
+  - |
+    if [[ $TRAVIS_PULL_REQUEST == 'false' ]]; then
+      python3 -m pip install twine
+      python3 -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*
+      if [[ $TRAVIS_TAG ]]; then python3 -m twine upload --verbose --skip-existing dist/*; fi
+    fi
+
+notifications:
+  email:
+    recipients:
+      - [email protected]
+
+jobs:
+  include:
+    - name: "black check"
+      services: docker
+      install: python3 -m pip install black
+      script: python3 -m black --check pykrige/ examples/ tests/
+      after_success: echo "all files formatted correctly"
+      after_failure: echo "some files not formatted correctly"
+
+    - name: "sdist and coverage"
+      services: docker
+      install:
+        - python3 -m pip install -r requirements_setup.txt
+        - python3 -m pip install -r requirements_test.txt
+        - python3 -m pip install -r requirements.txt
+      script:
+        - python3 setup.py sdist -d dist
+        - python3 setup.py build_ext --inplace
+        - python3 -m pytest --cov pykrige --cov-report term-missing -v tests/
+        - python3 -m coveralls
+
+    - name: "Linux py35"
+      services: docker
+      env: CIBW_BUILD="cp35-*"
+    - name: "Linux py36"
+      services: docker
+      env: CIBW_BUILD="cp36-*"
+    - name: "Linux py37"
+      services: docker
+      env: CIBW_BUILD="cp37-*"
+    - name: "Linux py38"
+      services: docker
+      env: CIBW_BUILD="cp38-*"
+
+    - name: "MacOS py35"
+      os: osx
+      language: shell
+      env: CIBW_BUILD="cp35-*"
+    - name: "MacOS py36"
+      os: osx
+      language: shell
+      env: CIBW_BUILD="cp36-*"
+    - name: "MacOS py37"
+      os: osx
+      language: shell
+      env: CIBW_BUILD="cp37-*"
+    - name: "MacOS py38"
+      os: osx
+      language: shell
+      env: CIBW_BUILD="cp38-*"
+
+    - name: "Win py35"
+      os: windows
+      language: shell
+      env: CIBW_BUILD="cp35-*"
+    - name: "Win py36"
+      os: windows
+      language: shell
+      env: CIBW_BUILD="cp36-*"
+    - name: "Win py37"
+      os: windows
+      language: shell
+      env: CIBW_BUILD="cp37-*"
+    - name: "Win py38"
+      os: windows
+      language: shell
+      env: CIBW_BUILD="cp38-*"

.zenodo.json

@@ -0,0 +1,62 @@
+{
+    "license": "BSD-3-Clause",
+    "contributors": [
+        {
+            "type": "Other",
+            "name": "Malte Ziebarth"
+        },
+        {
+            "type": "Other",
+            "name": "Sudipta Basak"
+        },
+        {
+            "type": "Other",
+            "name": "Matthew Peveler"
+        },
+        {
+            "type": "Other",
+            "name": "kvanlombeek"
+        },
+        {
+            "type": "Other",
+            "name": "Will Chang"
+        },
+        {
+            "type": "Other",
+            "name": "Harry Matchette-Downes"
+        },
+        {
+            "type": "Other",
+            "name": "Daniel Mej\u00eda Raigosa"
+        }
+    ],
+    "language": "eng",
+    "keywords": [
+        "kriging",
+        "ordinary kriging",
+        "universal kriging",
+        "external drift kriging",
+        "regression kriging",
+        "variogram",
+        "geostatistics",
+        "Python",
+        "GeoStat-Framework"
+    ],
+    "creators": [
+        {
+            "orcid": "0000-0001-7636-3711",
+            "affiliation": "United State Geological Survey: Golden, CO, US",
+            "name": "Benjamin Murphy"
+        },
+        {
+            "orcid": "0000-0002-2565-4444",
+            "affiliation": "Symerio",
+            "name": "Roman Yurchak"
+        },
+        {
+            "orcid": "0000-0001-9060-4008",
+            "affiliation": "Helmholtz Centre for Environmental Research - UFZ",
+            "name": "Sebastian M\u00fcller"
+        }
+    ]
+}