Merge pull request #2 from GeoStat-Framework/develop

1.0.0 release

.coveragerc

@@ -0,0 +1,11 @@
+[run]
+source = anaflow
+omit = *docs*, *examples*, *tests*
+
+[report]
+exclude_lines =
+    pragma: no cover
+    if __name__ == '__main__':
+    def __repr__
+    def __str__
+

.travis.yml

@@ -1,54 +1,81 @@
 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 py36"
-      sudo: required
-      language: python
-      python: 3.6
-      services: docker
-      env:
-        - PIP=pip
-        - 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
-  - $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-*"
+    # 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/AnaFlow)
+
+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 anaflow --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

@@ -3,16 +3,22 @@
 All notable changes to **AnaFlow** will be documented in this file.
 
 
-## [Unreleased]
+## [1.0.0] - 2020-03-22
 
 ### Enhancements
 - new TPL Solution
-- new tools module
+- new tools sub-module
 - using pentapy to solve LES in laplace space
 - solution for aparent transmissivity from neuman 2004
 - added extended GRF model
 - convenient functions for (inverse-)laplace transformation
 
+### Bugfixes
+- `lat_ext` was ignored by ext_theis_3d
+
+### Changes
+- py2.7 support dropped
+
 
 ## [0.4.0] - 2019-03-07
 
@@ -63,7 +69,7 @@ Containing:
 - lap_transgwflow_cyl - Solution for a diskmodel in laplace inversion
 
 
-[Unreleased]: https://github.com/GeoStat-Framework/gstools/compare/v0.4.0...HEAD
+[1.0.0]: https://github.com/GeoStat-Framework/gstools/compare/v0.4.0...v1.0.0
 [0.4.0]: https://github.com/GeoStat-Framework/gstools/compare/v0.3.0...v0.4.0
 [0.3.0]: https://github.com/GeoStat-Framework/gstools/compare/v0.2.4...v0.3.0
 [0.2.4]: https://github.com/GeoStat-Framework/gstools/compare/v0.1...v0.2.4

LICENSE

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2019 Sebastian Mueller
+Copyright (c) 2019 - 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 +1,9 @@
+include README.md
 include MANIFEST.in
 include setup.py
+include setup.cfg
 recursive-include anaflow *.py
+recursive-include tests *.py
 recursive-include docs/source *
 include docs/Makefile docs/requirements.txt
 include LICENSE

README.md

@@ -2,8 +2,8 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1135723.svg)](https://doi.org/10.5281/zenodo.1135723)
 [![PyPI version](https://badge.fury.io/py/anaflow.svg)](https://badge.fury.io/py/anaflow)
-[![Build Status](https://travis-ci.org/GeoStat-Framework/AnaFlow.svg?branch=master)](https://travis-ci.org/GeoStat-Framework/AnaFlow)
-[![Documentation Status](https://readthedocs.org/projects/docs/badge/?version=latest)](https://anaflow.readthedocs.io/en/latest/)
+[![Build Status](https://travis-ci.com/GeoStat-Framework/AnaFlow.svg?branch=master)](https://travis-ci.com/GeoStat-Framework/AnaFlow)
+[![Documentation Status](https://readthedocs.org/projects/docs/badge/?version=stable)](https://anaflow.readthedocs.io/en/stable/)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 <p align="center">
@@ -90,7 +90,7 @@ inverse laplace-transformation of a given function
 
 - [NumPy >= 1.14.5](https://www.numpy.org)
 - [SciPy >= 1.1.0](https://www.scipy.org)
-- [pentapy](https://github.com/GeoStat-Framework/pentapy)
+- [pentapy >= 1.1.0](https://github.com/GeoStat-Framework/pentapy)
 
 
 ## Contact
@@ -100,7 +100,7 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[MIT][mit_link] © 2019
+[MIT][mit_link] © 2019 - 2020
 
 [mit_link]: https://github.com/GeoStat-Framework/AnaFlow/blob/master/LICENSE
-[doc_link]: https://geostat-framework.readthedocs.io/projects/anaflow/en/latest/
+[doc_link]: https://anaflow.readthedocs.io

anaflow/__init__.py

@@ -83,10 +83,6 @@
 
 
 """
-from __future__ import absolute_import
-
-from anaflow._version import __version__
-
 from anaflow.flow import (
     thiem,
     theis,
@@ -112,6 +108,12 @@
     specialrange_cut,
 )
 
+try:
+    from anaflow._version import __version__
+except ModuleNotFoundError:  # pragma: nocover
+    # package is not installed
+    __version__ = "0.0.0.dev0"
+
 __all__ = ["__version__"]
 __all__ += [
     "thiem",

anaflow/flow/__init__.py

@@ -58,8 +58,6 @@
    ext_grf
    ext_grf_steady
 """
-from __future__ import absolute_import
-
 from anaflow.flow.homogeneous import thiem, theis, grf
 from anaflow.flow.heterogeneous import (
     ext_thiem_2d,

anaflow/flow/ext_grf_model.py

@@ -11,8 +11,6 @@
    ext_grf_steady
 """
 # pylint: disable=C0103
-from __future__ import absolute_import, division, print_function
-
 import numpy as np
 from scipy.integrate import quad as integ
 

anaflow/flow/heterogeneous.py

@@ -19,8 +19,6 @@
    neuman2004_steady
 """
 # pylint: disable=C0103
-from __future__ import absolute_import, division, print_function
-
 import functools as ft
 
 import numpy as np
@@ -287,7 +285,7 @@ def ext_thiem_3d(
     # derive the result
     res = np.exp(-chi) * (np.log(rad) - np.log(r_ref))
     res += sub21 * np.sinh(chi) + sub22 * (1.0 - np.cosh(chi))
-    res *= -rate / (2.0 * np.pi * K_efu)
+    res *= -rate / (2.0 * np.pi * K_efu * lat_ext)
     res += h_ref
 
     return res

anaflow/flow/homogeneous.py

@@ -12,8 +12,6 @@
    grf
 """
 # pylint: disable=C0103
-from __future__ import absolute_import, division, print_function
-
 import numpy as np
 
 from anaflow.tools.special import well_solution, grf_solution

anaflow/flow/laplace.py

@@ -10,8 +10,6 @@
    grf_laplace
 """
 # pylint: disable=C0103
-from __future__ import absolute_import, division, print_function
-
 import warnings
 
 import numpy as np

anaflow/tools/__init__.py

@@ -67,8 +67,6 @@
    get_lap
    get_lap_inv
 """
-from __future__ import absolute_import
-
 from anaflow.tools.mean import (
     annular_fmean,
     annular_amean,

anaflow/tools/coarse_graining.py

@@ -18,8 +18,6 @@
    TPL_CG_error
 """
 # pylint: disable=C0103
-from __future__ import absolute_import, division, print_function
-
 import numpy as np
 from scipy.optimize import root
 

anaflow/tools/laplace.py

@@ -13,9 +13,6 @@
    lap_trans
    stehfest
 """
-
-from __future__ import absolute_import, division, print_function
-
 from math import floor, factorial
 import numpy as np
 from scipy.integrate import quad

anaflow/tools/mean.py

@@ -15,8 +15,6 @@
    annular_pmean
 """
 # pylint: disable=E1137, C0103
-from __future__ import absolute_import, division, print_function
-
 import numpy as np
 
 from scipy.integrate import quad as integ

anaflow/tools/special.py

@@ -21,8 +21,6 @@
    neuman2004_trans
 """
 
-from __future__ import absolute_import, division, print_function
-
 import numpy as np
 from scipy.special import gamma, gammaincc, exp1, expn, hyp2f1
 

docs/requirements.txt

@@ -1,5 +1,3 @@
-#required for readthedocs.org
-numpy>=1.14.5
-scipy>=1.1.0
-pentapy
-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
 
@@ -95,8 +96,9 @@ def setup(app):
 master_doc = "contents"
 
 # General information about the project.
+curr_year = datetime.datetime.now().year
 project = "AnaFlow"
-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