Merge pull request #7 from GeoStat-Framework/sphinx_update

Sphinx update: Gallery

Author: MuellerSeb

.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

CHANGELOG.md

@@ -0,0 +1,63 @@
+# Changelog
+
+All notable changes to **welltestpy** will be documented in this file.
+
+
+## [1.0.0] - 2020-04
+
+### Enhancements
+- new estimators
+  - ExtTheis3D
+  - ExtTheis2D
+  - Neuman2004
+  - Theis
+  - ExtThiem3D
+  - ExtThiem2D
+  - Neuman2004Steady
+  - Thiem
+- better plotting
+- unit-tests run with py35-py38 on Linux/Win/Mac
+- coverage
+- sphinx gallery for examples
+
+### Bugfixes
+- estimation results stored as dict (order could alter before)
+
+### Changes
+- py2 support dropped
+
+
+## [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

README.md

@@ -2,8 +2,9 @@
 
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.1229051.svg)](https://doi.org/10.5281/zenodo.1229051)
 [![PyPI version](https://badge.fury.io/py/welltestpy.svg)](https://badge.fury.io/py/welltestpy)
-[![Build Status](https://travis-ci.org/GeoStat-Framework/welltestpy.svg?branch=master)](https://travis-ci.org/GeoStat-Framework/welltestpy)
-[![Documentation Status](https://readthedocs.org/projects/welltestpy/badge/?version=latest)](https://geostat-framework.readthedocs.io/projects/welltestpy/en/latest/?badge=latest)
+[![Build Status](https://travis-ci.com/GeoStat-Framework/welltestpy.svg?branch=master)](https://travis-ci.com/GeoStat-Framework/welltestpy)
+[![Coverage Status](https://coveralls.io/repos/github/GeoStat-Framework/welltestpy/badge.svg?branch=master)](https://coveralls.io/github/GeoStat-Framework/welltestpy?branch=master)
+[![Documentation Status](https://readthedocs.org/projects/welltestpy/badge/?version=stable)](https://geostat-framework.readthedocs.io/projects/welltestpy/en/stable/?badge=stable)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 <p align="center">
@@ -27,71 +28,20 @@ You can install the latest version with the following command:
 You can find the documentation under [geostat-framework.readthedocs.io][doc_link].
 
 
-### Example 1: Create a Campaign containing a pumping test
+### Example 1: A campaign containing a pumping test
 
-In the following a simple pumping test is created with artificial drawdown data
-generated by the Theis-solution.
+In the following, we will take a look at an artificial pumping test campaign,
+that is stored in a file called `Cmp_UFZ-campaign.cmp`.
 
 ```python
-# -*- coding: utf-8 -*-
-import numpy as np
 import welltestpy as wtp
-import anaflow as ana
-
-### create the field-site and the campaign
-field = wtp.data.FieldSite(name="UFZ", coordinates=[51.353839, 12.431385])
-campaign = wtp.data.Campaign(name="UFZ-campaign", fieldsite=field)
-
-### add 4 wells to the campaign
-campaign.add_well(name="well_0", radius=0.1, coordinates=(0.0, 0.0))
-campaign.add_well(name="well_1", radius=0.1, coordinates=(1.0, -1.0))
-campaign.add_well(name="well_2", radius=0.1, coordinates=(2.0, 2.0))
-campaign.add_well(name="well_3", radius=0.1, coordinates=(-2.0, -1.0))
-
-### generate artificial drawdown data with the Theis solution
-rate = -1e-4
-time = np.geomspace(10, 7200, 10)
-transmissivity = 1e-4
-storage = 1e-4
-rad = [
-    campaign.wells["well_0"].radius,  # well radius of well_0
-    campaign.wells["well_0"] - campaign.wells["well_1"],  # distance 0-1
-    campaign.wells["well_0"] - campaign.wells["well_2"],  # distance 0-2
-    campaign.wells["well_0"] - campaign.wells["well_3"],  # distance 0-3
-]
-drawdown = ana.theis(
-    time=time,
-    rad=rad,
-    storage=storage,
-    transmissivity=transmissivity,
-    rate=rate,
-)
-
-### create a pumping test at well_0
-pumptest = wtp.data.PumpingTest(
-    name="well_0",
-    pumpingwell="well_0",
-    pumpingrate=rate,
-    description="Artificial pump test with Theis",
-)
-
-### add the drawdown observation at the 4 wells
-pumptest.add_transient_obs("well_0", time, drawdown[:, 0])
-pumptest.add_transient_obs("well_1", time, drawdown[:, 1])
-pumptest.add_transient_obs("well_2", time, drawdown[:, 2])
-pumptest.add_transient_obs("well_3", time, drawdown[:, 3])
-
-### add the pumping test to the campaign
-campaign.addtests(pumptest)
-### optionally make the test steady
-# campaign.tests["well_0"].make_steady()
-
-### plot the well constellation and a test overview
+
+# create the field-site and the campaign
+campaign = wtp.load_campaign("Cmp_UFZ-campaign.cmp")
+
+# plot the well constellation and a test overview
 campaign.plot_wells()
 campaign.plot()
-
-### save the whole campaign
-campaign.save()
 ```
 
 #### This will give the following plots:
@@ -104,8 +54,6 @@ campaign.save()
 <img src="https://raw.githubusercontent.com/GeoStat-Framework/welltestpy/master/docs/source/pics/01_pumptest.png" alt="Pumptest" width="600px"/>
 </p>
 
-And the campaign is stored to a file called `Cmp_UFZ-campaign.cmp`
-
 
 ### Example 2: Estimate transmissivity and storativity
 
@@ -115,7 +63,7 @@ transmissivity and storativity.
 ```python
 import welltestpy as wtp
 
-campaign = wtp.data.load_campaign("Cmp_UFZ-campaign.cmp")
+campaign = wtp.load_campaign("Cmp_UFZ-campaign.cmp")
 estimation = wtp.estimate.Theis("Estimate_theis", campaign, generate=True)
 estimation.run()
 ```
@@ -158,12 +106,12 @@ welltestpy.tools     # Subpackage with miscellaneous tools
 
 ## Requirements
 
-- [NumPy >= 1.13.0](https://www.numpy.org)
-- [SciPy >= 0.19.1](https://www.scipy.org)
-- [Pandas >= 0.20.3](https://pandas.pydata.org)
-- [Matplotlib >= 2.0.2](https://matplotlib.org)
-- [AnaFlow](https://github.com/GeoStat-Framework/AnaFlow)
-- [SpotPy](https://github.com/thouska/spotpy)
+- [NumPy >= 1.14.5](https://www.numpy.org)
+- [SciPy >= 1.1.0](https://www.scipy.org)
+- [Pandas >= 0.23.2](https://pandas.pydata.org)
+- [AnaFlow >= 1.0.0](https://github.com/GeoStat-Framework/AnaFlow)
+- [SpotPy >= 1.5.0](https://github.com/thouska/spotpy)
+- [Matplotlib >= 3.0.0](https://matplotlib.org)
 
 
 ## Contact
@@ -173,7 +121,7 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[MIT][license_link] © 2018-2019
+[MIT][license_link] © 2018-2020
 
 [license_link]: https://github.com/GeoStat-Framework/welltestpy/blob/master/LICENSE
-[doc_link]: https://geostat-framework.readthedocs.io/projects/welltestpy/en/latest/
+[doc_link]: https://welltestpy.readthedocs.io

docs/Makefile

@@ -4,7 +4,7 @@
 # You can set these variables from the command line.
 SPHINXOPTS    =
 SPHINXBUILD   = python3 -msphinx
-SPHINXPROJ    = GeoStatTools
+SPHINXPROJ    = welltestpy
 SOURCEDIR     = source
 BUILDDIR      = build
 

docs/requirements_doc.txt

@@ -1 +1,2 @@
 numpydoc
+sphinx-gallery