Merge pull request #10 from GeoStat-Framework/develop

1.1.0 release

.gitignore

@@ -111,3 +111,6 @@ info/
 
 # JOSS stuff
 paper/compile
+
+# setuptools_scm generated version files
+pentapy/_version.py

.travis.yml

@@ -1,137 +1,66 @@
 language: python
+python: 3.8
 
-matrix:
-  include:
-    - name: "Linux py27"
-      sudo: required
-      language: python
-      python: 2.7
-      services: docker
-      env:
-        - PIP=pip
-        - CIBW_BUILD="cp27-*"
-        - COVER="off"
-
-    - name: "Linux py34"
-      sudo: required
-      language: python
-      python: 3.4
-      services: docker
-      env:
-        - PIP=pip
-        - CIBW_BUILD="cp34-*"
-        - COVER="off"
-
-    - name: "Linux py35"
-      sudo: required
-      language: python
-      python: 3.5
-      services: docker
-      env:
-        - PIP=pip
-        - CIBW_BUILD="cp35-*"
-        - COVER="off"
-
-    # py36 for coverage and sdist
-    - name: "Linux py36"
-      sudo: required
-      language: python
-      python: 3.6
-      services: docker
-      env:
-        - PIP=pip
-        - CIBW_BUILD="cp36-*"
-        - COVER="on"
-
-    # https://github.com/travis-ci/travis-ci/issues/9815
-    - name: "Linux py37"
-      sudo: required
-      language: python
-      python: 3.7
-      dist: xenial
-      services: docker
-      env:
-        - PIP=pip
-        - CIBW_BUILD="cp37-*"
-        - COVER="off"
-
-    - name: "MacOS py27"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp27-*"
-        - COVER="off"
-
-    - name: "MacOS py34"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp34-*"
-        - COVER="off"
-
-    - name: "MacOS py35"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp35-*"
-        - COVER="off"
-
-    - name: "MacOS py36"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp36-*"
-        - COVER="off"
-
-    - name: "MacOS py37"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp37-*"
-        - COVER="off"
+# 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==1.14.5 cython==0.28.3"
-    - CIBW_TEST_REQUIRES=pytest-cov
-    # inplace cython build and test run
-    - CIBW_TEST_COMMAND="cd {project} && python setup.py build_ext --inplace && py.test --cov pentapy --cov-report term-missing -v {project}/tests"
+    - CIBW_BEFORE_BUILD="pip install numpy==1.17.3 cython==0.29.14 setuptools"
+    - CIBW_TEST_REQUIRES=pytest
+    - CIBW_TEST_COMMAND="pytest -v {project}/tests"
+    - CIBW_BUILD="cp35-* cp36-* cp37-* cp38-*"
 
-script:
-  # create wheels
-  - $PIP install cibuildwheel==0.11.1
-  - cibuildwheel --output-dir wheelhouse
-  # create source dist for pypi and create coverage (only once for linux py3.6)
+before_install:
   - |
-    if [[ $COVER == "on" ]]; then
-      rm -rf dist
-      python -m pip install -U numpy==1.14.5 cython==0.28.3 setuptools
-      python -m pip install pytest-cov coveralls
-      python -m pip install -r docs/requirements.txt
-      python setup.py sdist
-      python setup.py build_ext --inplace
-      python -m pytest --cov pentapy --cov-report term-missing -v tests/
-      python -m coveralls
+    if [[ "$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:
-  # pypi upload ("test" allways and "official" on TAG)
-  - python -m pip install twine
-  - python -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ wheelhouse/*.whl
-  - python -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*.tar.gz
   - |
-    if [[ $TRAVIS_TAG ]]; then
-      python -m twine upload --verbose --skip-existing wheelhouse/*.whl
-      python -m twine upload --verbose --skip-existing dist/*.tar.gz
+    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:
-    - info@geostat-framework.org
+      - info@geostat-framework.org
+
+jobs:
+  include:
+    - name: "sdist and coverage"
+      services: docker
+      script:
+        - python3 -m pip install -U setuptools pytest-cov coveralls
+        - 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 pentapy --cov-report term-missing -v tests/
+        - python3 -m coveralls
+
+    - name: "Linux py35-py38"
+      services: docker
+
+    - name: "MacOS py35-py38"
+      os: osx
+      language: shell
+
+    - name: "Win py35-py38"
+      os: windows
+      language: shell

.zenodo.json

@@ -0,0 +1,19 @@
+{
+    "license": "MIT",
+    "language": "eng",
+    "keywords": [
+        "linear algebra",
+        "equation systems",
+        "pentadiagonal matrices",
+        "math",
+        "Python",
+        "GeoStat-Framework"
+    ],
+    "creators": [
+        {
+            "orcid": "0000-0001-9060-4008",
+            "affiliation": "Helmholtz Centre for Environmental Research - UFZ",
+            "name": "Sebastian M\u00fcller"
+        }
+    ]
+}

CHANGELOG.md

@@ -0,0 +1,54 @@
+# Changelog
+
+All notable changes to **pentapy** will be documented in this file.
+
+
+## [1.1.0] - 2020-03-22
+
+### Enhancements
+- Python 3.8 support
+
+### Changes
+- python only builds are no longer available
+- Python 2.7 and 3.4 support dropped
+
+
+## [1.0.3] - 2019-11-10
+
+### Enhancements
+- the algorithms `PTRANS-I` and `PTRANS-II` now raise a warning when they can not solve the given system
+- there are now switches to install scipy and umf solvers as extra requirements
+
+### Bugfixes
+- multiple minor bugfixes
+
+
+## [1.0.0] - 2019-09-18
+
+### Enhancements
+- the second algorithm `PTRANS-II` from *Askar et al. 2015* is now implemented and can be used by `solver=2`
+- the package is now tested and a coverage is calculated
+- there are now pre-built binaries for Python 3.7
+- the documentation is now available under https://geostat-framework.readthedocs.io/projects/pentapy
+
+### Changes
+- pentapy is now licensed under the MIT license
+
+
+## [0.1.1] - 2019-03-08
+
+### Bugfixes
+- MANIFEST.in was missing in the 0.1.0 version
+
+
+## [0.1.0] - 2019-03-07
+
+This is the first release of pentapy, a python toolbox for solving pentadiagonal linear equation systems.
+The solver is implemented in cython, which makes it really fast.
+
+
+[1.1.0]: https://github.com/GeoStat-Framework/gstools/compare/v1.0.3...v1.1.0
+[1.0.3]: https://github.com/GeoStat-Framework/gstools/compare/v1.0.0...v1.0.3
+[1.0.0]: https://github.com/GeoStat-Framework/gstools/compare/v0.1.1...v1.0.0
+[0.1.1]: https://github.com/GeoStat-Framework/gstools/compare/v0.1...v0.1.1
+[0.1.0]: https://github.com/GeoStat-Framework/gstools/releases/tag/v0.1

MANIFEST.in

@@ -1,6 +1,9 @@
+include README.md
 include MANIFEST.in
 include setup.py
+include setup.cfg
 recursive-include pentapy *.py *.pyx *.c
+recursive-include tests *.py
 recursive-include docs/source *
 include docs/Makefile docs/requirements.txt
 include LICENSE

README.md

@@ -3,10 +3,9 @@
 [![status](https://joss.theoj.org/papers/57c3bbdd7b7f3068dd1e669ccbcf107c/status.svg)](https://joss.theoj.org/papers/57c3bbdd7b7f3068dd1e669ccbcf107c)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2587158.svg)](https://doi.org/10.5281/zenodo.2587158)
 [![PyPI version](https://badge.fury.io/py/pentapy.svg)](https://badge.fury.io/py/pentapy)
-[![Build Status](https://travis-ci.org/GeoStat-Framework/pentapy.svg?branch=master)](https://travis-ci.org/GeoStat-Framework/pentapy)
-[![Build status](https://ci.appveyor.com/api/projects/status/yyfgn9dgxcoolp97/branch/master?svg=true)](https://ci.appveyor.com/project/GeoStat-Framework/pentapy/branch/master)
+[![Build Status](https://travis-ci.com/GeoStat-Framework/pentapy.svg?branch=master)](https://travis-ci.com/GeoStat-Framework/pentapy)
 [![Coverage Status](https://coveralls.io/repos/github/GeoStat-Framework/pentapy/badge.svg?branch=master)](https://coveralls.io/github/GeoStat-Framework/pentapy?branch=master)
-[![Documentation Status](https://readthedocs.org/projects/pentapy/badge/?version=latest)](https://geostat-framework.readthedocs.io/projects/pentapy/en/latest/?badge=latest)
+[![Documentation Status](https://readthedocs.org/projects/pentapy/badge/?version=stable)](https://geostat-framework.readthedocs.io/projects/pentapy/en/stable/?badge=stable)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 
@@ -41,6 +40,15 @@ following extra argument:
 Instead of "all" you can also typ "scipy" or "umfpack" to get one of these specific packages.
 
 
+## Citation
+
+If you use `pentapy` in your publication, please cite it:
+
+> Müller, (2019). pentapy: A Python toolbox for pentadiagonal linear systems. Journal of Open Source Software, 4(42), 1759, https://doi.org/10.21105/joss.01759
+
+To cite a certain release, have a look at the Zenodo site: https://doi.org/10.5281/zenodo.2587158
+
+
 ## References
 
 The solver is based on the algorithms PTRANS-I and PTRANS-II
@@ -95,7 +103,7 @@ The implementations of pentapy are almost one order of magnitude faster than the
 scipy algorithms for banded or sparse matrices.
 
 The performance plot was created with [``perfplot``](https://github.com/nschloe/perfplot).
-Have a look at the script: [``examples/04_perform_simple.py``](https://github.com/GeoStat-Framework/pentapy/blob/master/examples/04_perform_simple.py).
+Have a look at the script: [``examples/03_perform_simple.py``](https://github.com/GeoStat-Framework/pentapy/blob/master/examples/03_perform_simple.py).
 
 
 
@@ -115,10 +123,10 @@ You can contact us via <info@geostat-framework.org>.
 
 ## License
 
-[MIT][licence_link] © 2019
+[MIT][licence_link] © 2019 - 2020
 
 [ref_link]: http://dx.doi.org/10.1155/2015/232456
 [pip_link]: https://pypi.org/project/pentapy
 [winpy_link]: https://winpython.github.io/
 [licence_link]: https://github.com/GeoStat-Framework/pentapy/blob/master/LICENSE
-[doc_link]: https://geostat-framework.readthedocs.io/projects/pentapy/en/latest/
+[doc_link]: https://pentapy.readthedocs.org

docs/requirements.txt

@@ -1,4 +1,3 @@
-#required for readthedocs.org
-cython>=0.28.3
-numpy>=1.14.5
-numpydoc
+-r requirements_doc.txt
+-r ../requirements_setup.txt
+-r ../requirements.txt

docs/requirements_doc.txt

@@ -0,0 +1 @@
+numpydoc

docs/source/conf.py

@@ -20,6 +20,7 @@
 # NOTE:
 # pip install sphinx_rtd_theme
 # is needed in order to build the documentation
+import datetime
 import os
 import sys
 
@@ -94,8 +95,9 @@ def setup(app):
 master_doc = "contents"
 
 # General information about the project.
+curr_year = datetime.datetime.now().year
 project = "pentapy"
-copyright = "2019, Sebastian Mueller"
+copyright = "2019 - {}, Sebastian Mueller".format(curr_year)
 author = "Sebastian Mueller"
 
 # The version info for the project you're documenting, acts as replacement for

docs/source/index.rst

@@ -109,4 +109,4 @@ Optional
 License
 =======
 
-`MIT <https://github.com/GeoStat-Framework/pentapy/blob/master/LICENSE>`_ © 2019
+`MIT <https://github.com/GeoStat-Framework/pentapy/blob/master/LICENSE>`_

examples/03_compare.py → examples/02_compare.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 """
-3. Example.
+2. Example.
 
 Here we compare the outcome of the PTRANS-I and PTRANS-II algorithm for
 a random input.