Merge pull request #8 from GeoStat-Framework/develop

Release v1

.coveragerc

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

.gitignore

@@ -1,11 +1,125 @@
-*.pyc
-*.orig
-*~
-.spyproject/
+# Byte-compiled / optimized / DLL files
 __pycache__/
-docs/build/
-#_build
-#_static
-#_templates
-#docs/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+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
+
+# 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/
+
+# Cython generated C code
+*.c
+*.cpp
+
+
+# generated docs
+docs/source/examples/
+docs/source/generated/
+examples/Cmp_UFZ-campaign.cmp
+
+*.DS_Store
+
+*.zip
+
+*.vtu
+*.vtr

.travis.yml

@@ -1,53 +1,82 @@
 language: python
+python: 3.8
 
-matrix:
-  include:
-    # use macOS for py2 since building pandas wheels takes ages on linux
-    # and matplotlib is not installing on linux
-    - name: "MacOS py27"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp27-*"
-        - COVER="off"
-
-    # use macOS for py3 since building matplotlib is not working on linux
-    - name: "MacOS py36"
-      os: osx
-      language: generic
-      env:
-        - PIP=pip2
-        - CIBW_BUILD="cp36-*"
-        - COVER="on"
+# setuptools-scm needs all tags in order to obtain a proper version
+git:
+  depth: false
 
 env:
   global:
+    # Note: TWINE_PASSWORD is set in Travis settings
     - TWINE_USERNAME=geostatframework
-
-script:
-  # create wheels
-  - sudo $PIP install cibuildwheel==0.10.1
-  - cibuildwheel --output-dir wheelhouse
-  # create source dist for pypi and create coverage (only once for linux py3.6)
-  - |
-    if [[ $COVER == "on" ]]; then
-      rm -rf dist
-      python setup.py sdist
-    fi
-
-after_success:
-  # pypi upload (test allways and official on TAG)
-  - python -m pip install twine
-  - python -m twine upload --skip-existing --repository-url https://test.pypi.org/legacy/ wheelhouse/*.whl
-  - python -m twine upload --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*.tar.gz
-  - |
-    if [[ $TRAVIS_TAG ]]; then
-      python -m twine upload --skip-existing wheelhouse/*.whl
-      python -m twine upload --skip-existing dist/*.tar.gz
-    fi
+    - CIBW_BUILD="cp35-* cp36-* cp37-* cp38-*"
+    - CIBW_SKIP="*_i686"  # skip linux 32bit for matplotlib
+    # update setuptools to latest version
+    - CIBW_BEFORE_BUILD="pip install -U setuptools"
+    # testing with cibuildwheel
+    - CIBW_TEST_REQUIRES=pytest
+    - CIBW_TEST_COMMAND="pytest -v {project}/tests"
 
 notifications:
   email:
     recipients:
     - [email protected]
+
+before_install:
+  - |
+    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 tmp_dist
+
+stages:
+  - test
+  - coverage
+  - name: deploy
+    if: (NOT type IN (pull_request)) AND (repo = GeoStat-Framework/welltestpy)
+
+jobs:
+  include:
+    - stage: test
+      name: Test on Linux
+      services: docker
+    - stage: test
+      name: Test on MacOS
+      os: osx
+      language: generic
+    - stage: test
+      name: Test on Windows
+      os: windows
+      language: shell
+
+    - stage: coverage
+      name: Coverage on Linux
+      services: docker
+      install: python3 -m pip install .[test] coveralls
+      script:
+        - python3 -m pytest --cov welltestpy --cov-report term-missing -v tests/
+        - python3 -m coveralls
+
+    # Test Deploy source distribution
+    - stage: deploy
+      name: Test Deploy
+      install: python3 -m pip install -U setuptools wheel twine
+      script: python3 setup.py sdist --formats=gztar bdist_wheel
+      after_success:
+       - python3 -m twine upload --verbose --skip-existing --repository-url https://test.pypi.org/legacy/ dist/*
+
+    # Deploy source distribution
+    - stage: deploy
+      name: Deploy to PyPI
+      if: tag IS present
+      install: python3 -m pip install -U setuptools wheel twine
+      script: python3 setup.py sdist --formats=gztar bdist_wheel
+      after_success: python3 -m twine upload --verbose --skip-existing dist/*

.zenodo.json

@@ -0,0 +1,20 @@
+{
+    "license": "MIT",
+    "language": "eng",
+    "keywords": [
+        "Groundwater flow equation",
+        "Groundwater",
+        "Pumping test",
+        "Pump test",
+        "Aquifer analysis",
+        "Python",
+        "GeoStat-Framework"
+    ],
+    "creators": [
+        {
+            "orcid": "0000-0001-9060-4008",
+            "affiliation": "Helmholtz Centre for Environmental Research - UFZ",
+            "name": "Sebastian M\u00fcller"
+        }
+    ]
+}

CHANGELOG.md

@@ -0,0 +1,75 @@
+# Changelog
+
+All notable changes to **welltestpy** will be documented in this file.
+
+
+## [1.0.0] - 2020-04-09
+
+### Enhancements
+- new estimators
+  - ExtTheis3D
+  - ExtTheis2D
+  - Neuman2004
+  - Theis
+  - ExtThiem3D
+  - ExtThiem2D
+  - Neuman2004Steady
+  - Thiem
+- better plotting
+- unit-tests run with py35-py38 on Linux/Win/Mac
+- coverage calculation
+- sphinx gallery for examples
+- allow style setting in plotting routines
+
+### Bugfixes
+- estimation results stored as dict (order could alter before)
+
+### Changes
+- py2 support dropped
+- `Fieldsite.coordinates` now returns a `Variable`; `Fieldsite.pos` as shortcut
+- `Fieldsite.pumpingrate` now returns a `Variable`; `Fieldsite.rate` as shortcut
+- `Fieldsite.auqiferradius` now returns a `Variable`; `Fieldsite.radius` as shortcut
+- `Fieldsite.auqiferdepth` now returns a `Variable`; `Fieldsite.depth` as shortcut
+- `Well.coordinates` now returns a `Variable`; `Well.pos` as shortcut
+- `Well.welldepth` now returns a `Variable`; `Well.depth` as shortcut
+- `Well.wellradius` added and returns the radius `Variable`
+- `Well.aquiferdepth` now returns a `Variable`
+- `Fieldsite.addobservations` renamed to `Fieldsite.add_observations`
+- `Fieldsite.delobservations` renamed to `Fieldsite.del_observations`
+- `Observation` has changed order of inputs/outputs. Now: `observation`, `time`
+
+
+## [0.3.2] - 2019-03-08
+
+### Bugfixes
+- adopt AnaFlow API
+
+
+## [0.3.1] - 2019-03-08
+
+### Bugfixes
+- update travis workflow
+
+
+## [0.3.0] - 2019-02-28
+
+### Enhancements
+- added documentation
+
+
+## [0.2.0] - 2018-04-25
+
+### Enhancements
+- added license
+
+
+## [0.1.0] - 2018-04-25
+
+First alpha release of welltespy.
+
+[1.0.0]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.3.2...v1.0.0
+[0.3.2]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.3.1...v0.3.2
+[0.3.1]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.3.0...v0.3.1
+[0.3.0]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.2...v0.3.0
+[0.2.0]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.1...v0.2
+[0.1.0]: https://github.com/GeoStat-Framework/welltestpy/releases/tag/v0.1

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2019 Sebastian Mueller
+Copyright (c) 2020 Sebastian Mueller
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

MANIFEST.in

@@ -1,6 +1,12 @@
+include README.md
 include MANIFEST.in
 include setup.py
+include setup.cfg
 recursive-include welltestpy *.py
+recursive-include tests *.py
 recursive-include docs/source *
-include docs/Makefile docs/requirements.txt
+include docs/Makefile docs/requirements.txt docs/requirements_doc.txt
 include LICENSE
+include requirements.txt
+include requirements_setup.txt
+include requirements_test.txt