CI, Build and DOC updates (#142)

* tests on top-level; run against installed version * make matplotlib optional * add req files * add cov file * update travis * update dependencies * add scipy to build_wheel deps * MacOS ssl fix attempt * test: skip erroneous drift test (on win) * update setup to use scm; demand cython * setup: readme type rst * update doc reqs * rename doc->docs * restructure doc * adopt geostat doc style pt 1 * setup update docs path * drop py2 support; __doc__ update * add logo * resize log (rst images not rendered correctly on GH) * ignore auto-generated version file * eliminate some doc errors * tackle logo issue * build doc against installed again * travis: install wheel for cibuildwheel on linux * travis: update packages * travis: update wheel * remove py2 rfs * auditwheel bug needs to be fixed by manylinux * bigger logo * cok: use scipy blas and lapack directly * remove lapack module; use scipy instead * dont use raw in Readme * tests: skip edk test only on windows * DOC: update use of recommonmark [skip-ci]
GeoStat-Framework · MuellerSeb · Apr 4, 2020 · Mar 25, 2020 · Mar 27, 2020 · Mar 27, 2020
commit 39f70971d5e8459e9cd21acd98e349e65906b64a
diff --git a/.coveragerc b/.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__
diff --git a/.gitignore b/.gitignore
@@ -108,6 +108,7 @@ tags
 
 # own stuff
 info/
+pykrige/_version.py
 
 # Cython generated C code
 *.c

diff --git a/.travis.yml b/.travis.yml
@@ -1,49 +1,99 @@
 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"
+    - 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
+  - |
+    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
+
 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
+  - python3 -m pip install cibuildwheel==1.3.0
+  - 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: "sdist and coverage"
+      services: docker
+      script:
+        - python3 -m pip install -U setuptools pytest-cov coveralls scikit-learn
+        - python3 -m pip install -U numpy==1.17.3 cython==0.29.14
+        - python3 -m pip install -r requirements.txt
+        - 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-*"
diff --git a/doc/release_notes.md → CHANGELOG.md b/doc/release_notes.md → CHANGELOG.md
@@ -1,55 +1,65 @@
-# Release notes
+Changelog
+=========
 
-### Version 1.4.1
+
+Version 1.4.1
+-------------
 *January 13, 2019*
 
-#### New features
-* Added method to obtain variogram model points. PR[#94](https://github.com/bsmurphy/PyKrige/pull/94) by [Daniel Mejía Raigosa](https://github.com/Daniel-M)
+**New features**
 
-#### Bug fixes
-* Fixed OrdinaryKriging readme example. PR[#107](https://github.com/bsmurphy/PyKrige/pull/107) by [Harry Matchette-Downes](https://github.com/harrymd)
-* Fixed kriging matrix not being calculated correctly for geographic coordinates. PR[99](https://github.com/bsmurphy/PyKrige/pull/99) by [Mike Rilee](https://github.com/michaelleerilee)
+* Added method to obtain variogram model points. PR[#94](https://github.com/GeoStat-Framework/PyKrige/pull/94) by [Daniel Mejía Raigosa](https://github.com/Daniel-M)
+
+**Bug fixes**
+
+* Fixed OrdinaryKriging readme example. PR[#107](https://github.com/GeoStat-Framework/PyKrige/pull/107) by [Harry Matchette-Downes](https://github.com/harrymd)
+* Fixed kriging matrix not being calculated correctly for geographic coordinates. PR[99](https://github.com/GeoStat-Framework/PyKrige/pull/99) by [Mike Rilee](https://github.com/michaelleerilee)
 
-### Version 1.4.0
-*April 24, 2018*
 
-#### New features
+Version 1.4.0
+-------------
+*April 24, 2018*
 
-* Regression kriging algotithm. PR [#27](https://github.com/bsmurphy/PyKrige/pull/27) by [Sudipta Basaks](https://github.com/basaks).
-* Support for spherical coordinates. PR [#23](https://github.com/bsmurphy/PyKrige/pull/23) by [Malte Ziebarth](https://github.com/mjziebarth)
-* Kriging parameter tuning with scikit-learn. PR [#24](https://github.com/bsmurphy/PyKrige/pull/24) by [Sudipta Basaks](https://github.com/basaks).
-* Variogram model parameters can be specified using a list or a dict. Allows for directly feeding in the partial sill rather than the full sill. PR [#47](https://github.com/bsmurphy/PyKrige/pull/47) by [Benjamin Murphy](https://github.com/bsmurphy).
+**New features**
 
-#### Enhancements
+* Regression kriging algotithm. PR [#27](https://github.com/GeoStat-Framework/PyKrige/pull/27) by [Sudipta Basaks](https://github.com/basaks).
+* Support for spherical coordinates. PR [#23](https://github.com/GeoStat-Framework/PyKrige/pull/23) by [Malte Ziebarth](https://github.com/mjziebarth)
+* Kriging parameter tuning with scikit-learn. PR [#24](https://github.com/GeoStat-Framework/PyKrige/pull/24) by [Sudipta Basaks](https://github.com/basaks).
+* Variogram model parameters can be specified using a list or a dict. Allows for directly feeding in the partial sill rather than the full sill. PR [#47](https://github.com/GeoStat-Framework/PyKrige/pull/47) by [Benjamin Murphy](https://github.com/GeoStat-Framework).
 
-* Improved memory usage in variogram calculations. PR [#42](https://github.com/bsmurphy/PyKrige/pull/42) by [Sudipta Basaks](https://github.com/basaks).
-* Added benchmark scripts. PR [#36](https://github.com/bsmurphy/PyKrige/pull/36) by [Roman Yurchak](https://github.com/rth)
-* Added an extensive example using the meusegrids dataset. PR [#28](https://github.com/bsmurphy/PyKrige/pull/28) by [kvanlombeek](https://github.com/kvanlombeek).
+**Enhancements**
 
-#### Bug fixes
+* Improved memory usage in variogram calculations. PR [#42](https://github.com/GeoStat-Framework/PyKrige/pull/42) by [Sudipta Basaks](https://github.com/basaks).
+* Added benchmark scripts. PR [#36](https://github.com/GeoStat-Framework/PyKrige/pull/36) by [Roman Yurchak](https://github.com/rth)
+* Added an extensive example using the meusegrids dataset. PR [#28](https://github.com/GeoStat-Framework/PyKrige/pull/28) by [kvanlombeek](https://github.com/kvanlombeek).
 
-* Statistics calculations in 3D kriging. PR [#45](https://github.com/bsmurphy/PyKrige/pull/45) by [Will Chang](https://github.com/whdc).
-* Automatic variogram estimation robustified. PR [#47](https://github.com/bsmurphy/PyKrige/pull/47) by [Benjamin Murphy](https://github.com/bsmurphy).
+**Bug fixes**
 
+* Statistics calculations in 3D kriging. PR [#45](https://github.com/GeoStat-Framework/PyKrige/pull/45) by [Will Chang](https://github.com/whdc).
+* Automatic variogram estimation robustified. PR [#47](https://github.com/GeoStat-Framework/PyKrige/pull/47) by [Benjamin Murphy](https://github.com/GeoStat-Framework).
 
 
-### Version 1.3.1
+Version 1.3.1
+-------------
 *December 10, 2016*
 
 * More robust setup for building Cython extensions
 
 
-### Version 1.3.0
+Version 1.3.0
+-------------
 *October 23, 2015*
 
 * Added support for Python 3.
 * Updated the setup script to handle problems with trying to build the Cython extensions. If the appropriate compiler hasn't been installed on Windows, then the extensions won't work (see [this discussion of using Cython extensions on Windows] for how to deal with this problem). The setup script now attempts to build the Cython extensions and automatically falls back to pure Python if the build fails. **NOTE that the Cython extensions currently are not set up to work in Python 3** (see [discussion in issue #10]), so they are not built when installing with Python 3. This will be changed in the future.
 
-[closed issue #2]: https://github.com/bsmurphy/PyKrige/issues/2
-[this discussion of using Cython extensions on Windows]: https://github.com/cython/cython/wiki/CythonExtensionsOnWindows
-[discussion in issue #10]: https://github.com/bsmurphy/PyKrige/issues/10
+* [closed issue #2]: https://github.com/GeoStat-Framework/PyKrige/issues/2
+* [this discussion of using Cython extensions on Windows]: https://github.com/cython/cython/wiki/CythonExtensionsOnWindows
+* [discussion in issue #10]: https://github.com/GeoStat-Framework/PyKrige/issues/10
+
 
-### Version 1.2.0
+Version 1.2.0
+-------------
 *August 1, 2015*
 
 * Updated the execution portion of each class to streamline processing and reduce redundancy in the code.
@@ -60,7 +70,8 @@
 * Added support for three-dimensional universal kriging. The previous three-dimensional kriging class has been renamed OrdinaryKriging3D within module ok3d, and the new class is called UniversalKriging3D within module uk3d. See `UniversalKriging3D.__doc__` for usage information. A regional linear drift ('regional_linear') is the only code-internal drift that is currently supported, but the 'specified' and 'functional' generic drift capabilities are also implemented here (see above). The regional linear drift is applied in all three spatial dimensions.
 
 
-### Version 1.1.0
+Version 1.1.0
+-------------
 *May 25, 2015*
 
 * Added support for two different approaches to solving the entire kriging problem. One approach solves for the specified grid or set of points in a single vectorized operation; this method is default. The other approach loops through the specified points and solves the kriging system at each point. In both of these techniques, the kriging matrix is set up and inverted only once. In the vectorized approach, the rest of the kriging system (i.e., the RHS matrix) is set up as a single large array, and the whole system is solved with a single call to `numpy.dot()`. This approach is faster, but it can consume a lot of RAM for large datasets and/or large grids. In the looping approach, the rest of the kriging system (the RHS matrix) is set up at each point, and the kriging system at that point is solved with a call to `numpy.dot()`. This approach is slower, but it does not take as much memory. The approach can be specified by using the `backend` kwarg in the `execute()` method: `'vectorized'` (default) for the vectorized approach, `'loop'` for the looping approach. Thanks to Roman Yurchak for these changes and optimizations.
@@ -69,13 +80,16 @@
 * Added support for 3D kriging. This is now available as class `Krige3D` in `pykrige.k3d`. The usage is essentially the same as with the two-dimensional kriging classes, except for a few extra arguments that must be passed during instantiation and when calling `Krige3D.execute()`. See `Krige3D.__doc__` for more information.
 
 
-### Version 1.0.3
+Version 1.0.3
+-------------
 *February 15, 2015*
 
 * Fixed a problem with the tests that are performed to see if the kriging system is to be solved at a data point. (Tests are completed in order to determine whether to force the kriging solution to converge to the true data value.)
 * Changed setup script.
 
-### Version 1.0
+
+Version 1.0
+-----------
 *January 25, 2015*
 
 * Changed license to New BSD.
@@ -87,14 +101,17 @@
 * Fixed slight problem with `read_asc_grid()` function in `kriging_tools`. Also made some code improvements to both the `write_asc_grid()` and `read_asc_grid()` functions in `kriging_tools`.
 
 
-### Version 0.2.0
+Version 0.2.0
+-------------
 *November 23, 2014*
 
 * Consolidated backbone functions into a single module in order to reduce redundancy in the code. `OrdinaryKriging` and `UniversalKriging` classes now import and call the `core` module for the standard functions.
 * Fixed a few glaring mistakes in the code.
 * Added more documentation.
 
-### Version 0.1.2
+
+Version 0.1.2
+-------------
 *October 27, 2014*
 
 * First complete release.
diff --git a/LICENSE.txt → LICENSE b/LICENSE.txt → LICENSE
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -1,18 +1,7 @@
-include LICENSE.txt
 include README.md
-include CHANGELOG.md
-include setup.cfg
+include MANIFEST.in
 include setup.py
-recursive-include pykrige *.py
-recursive-include pykrige *.pyx
-recursive-include pykrige *.pxd
-include pykrige/tests/test_data/test_data.txt
-include pykrige/tests/test_data/test1_answer.asc
-include pykrige/tests/test_data/test1_settings.txt
-include pykrige/tests/test_data/test2_answer.asc
-include pykrige/tests/test_data/test2_settings.txt
-include pykrige/tests/test_data/test3_answer.asc
-include pykrige/tests/test_data/test3_dem.asc
-include pykrige/tests/test_data/test3_settings.txt
-include pykrige/tests/test_data/test3d_answer.txt
-include pykrige/tests/test_data/test3d_data.txt
+include setup.cfg
+recursive-include pykrige *.py *.pyx *.pxd
+recursive-include tests *.py *.txt *.asc
+include LICENSE
diff --git a/README.rst b/README.rst
@@ -1,25 +1,27 @@
 PyKrige
 =======
 
-Kriging Toolkit for Python
-
-.. image:: https://img.shields.io/pypi/v/pykrige.svg
-    :target: https://pypi.python.org/pypi/pykrige
-
-.. image:: https://anaconda.org/conda-forge/pykrige/badges/version.svg
-  :target: https://github.com/conda-forge/pykrige-feedstock
-
+.. image:: https://badge.fury.io/py/PyKrige.svg
+   :target: https://badge.fury.io/py/PyKrige
+.. image:: https://img.shields.io/conda/vn/conda-forge/pykrige.svg
+   :target: https://anaconda.org/conda-forge/pykrige
 .. image:: https://readthedocs.org/projects/pykrige/badge/?version=latest
-    :target: http://pykrige.readthedocs.io/en/latest/?badge=latest
-    :alt: Documentation Status
+   :target: http://pykrige.readthedocs.io/en/latest/?badge=latest
+   :alt: Documentation Status
+.. image:: https://travis-ci.com/GeoStat-Framework/PyKrige.svg?branch=master
+   :target: https://travis-ci.com/GeoStat-Framework/PyKrige
 
-.. image:: https://travis-ci.org/bsmurphy/PyKrige.svg?branch=master
-    :target: https://travis-ci.org/bsmurphy/PyKrige
 
-.. image:: https://ci.appveyor.com/api/projects/status/github/bsmurphy/PyKrige?branch=master&svg=true
-    :target: https://ci.appveyor.com/project/bsmurphy/pykrige
+.. figure:: https://github.com/GeoStat-Framework/GeoStat-Framework.github.io/raw/master/docs/source/pics/PyKrige_250.png
+   :align: center
+   :alt: PyKrige
+   :figclass: align-center
 
 
+Kriging Toolkit for Python.
+
+Purpose
+^^^^^^^
 
 The code supports 2D and 3D ordinary and universal kriging. Standard variogram models
 (linear, power, spherical, gaussian, exponential) are built in, but custom variogram models can also be used.
@@ -36,14 +38,14 @@ See the documentation at `http://pykrige.readthedocs.io/ <http://pykrige.readthe
 Installation
 ^^^^^^^^^^^^
 
-PyKrige requires Python 2.7 or 3.5+ as well as numpy, scipy and matplotlib. It can be installed from PyPi with,
+PyKrige requires Python 3.5+ as well as numpy, scipy. It can be installed from PyPi with,
 
 .. code:: bash
 
     pip install pykrige
 
 scikit-learn is an optional dependency needed for parameter tuning and regression kriging.
-
+matplotlib is an optional dependency needed for plotting.
 
 If you use conda, PyKrige can be installed from the `conda-forge` channel with,
-Original file line number
+Diff line change
@@ Expand Up / @@ -108,6 +108,7 @@ tags @@
     # own stuff
     info/
+    pykrige/_version.py
     # Cython generated C code
     *.c
@@ Expand Down @@