Merge pull request #11 from GeoStat-Framework/develop

Release v1.0.3

Author: MuellerSeb

.github/workflows/main.yml

@@ -0,0 +1,89 @@
+name: Continuous Integration
+
+on:
+  push:
+    branches:
+      - "master"
+      - "develop"
+    tags:
+      - "*"
+  pull_request:
+    branches:
+      - "develop"
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+env:
+  # needed by coveralls
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+jobs:
+  build_sdist:
+    name: sdist on ${{ matrix.os }} with py ${{ matrix.python-version }}
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, windows-latest, macos-latest]
+        python-version: [3.5, 3.6, 3.7, 3.8, 3.9]
+
+    steps:
+      - uses: actions/checkout@v2
+        with:
+          fetch-depth: '0'
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions\setup-python@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install -U wheel
+          pip install -r requirements_setup.txt
+          pip install -r requirements.txt
+          pip install -r requirements_test.txt
+          pip install coveralls>=3.0.0
+
+      - name: Build sdist
+        run: |
+          python setup.py sdist --formats=gztar bdist_wheel -d dist
+
+      - name: Run tests
+        run: |
+          python -m pytest --cov welltestpy --cov-report term-missing -v tests/
+          python -m coveralls --service=github
+
+      - uses: actions/upload-artifact@v2
+        if: matrix.os == 'ubuntu-latest' && matrix.python-version == '3.9'
+        with:
+          path: dist
+
+  upload_to_pypi:
+    needs: [build_sdist]
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/download-artifact@v2
+        with:
+          name: artifact
+          path: dist
+
+      - name: Publish to Test PyPI
+        # only if working on develop
+        if: github.ref == 'refs/heads/master' || github.ref == 'refs/heads/develop'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.test_pypi_password }}
+          repository_url: https://test.pypi.org/legacy/
+          skip_existing: true
+
+      - name: Publish to PyPI
+        # only if tagged
+        if: startsWith(github.ref, 'refs/tags')
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          user: __token__
+          password: ${{ secrets.pypi_password }}

.travis.yml

@@ -2,6 +2,19 @@
 
 All notable changes to **welltestpy** will be documented in this file.
 
+## [1.0.3] - 2021-02
+
+### Enhancements
+- Estimations: run method now provides `plot_style` keyword to control plotting
+
+### Changes
+- Fit plot style for transient pumping tests was updated
+
+### Bugfixes
+- Estimations: run method was throwing an Error when setting `run=False`
+- Plotter: all plotting routines now respect setted font-type from matplotlib
+
+
 ## [1.0.2] - 2020-09-03
 
 ### Bugfixes
@@ -78,6 +91,7 @@ All notable changes to **welltestpy** will be documented in this file.
 
 First alpha release of welltespy.
 
+[1.0.3]: https://github.com/GeoStat-Framework/welltestpy/compare/v1.0.2...v1.0.3
 [1.0.2]: https://github.com/GeoStat-Framework/welltestpy/compare/v1.0.1...v1.0.2
 [1.0.1]: https://github.com/GeoStat-Framework/welltestpy/compare/v1.0.0...v1.0.1
 [1.0.0]: https://github.com/GeoStat-Framework/welltestpy/compare/v0.3.2...v1.0.0

CHANGELOG.md

@@ -1,6 +1,6 @@
 The MIT License (MIT)
 
-Copyright (c) 2020 Sebastian Mueller
+Copyright (c) 2021 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

LICENSE

@@ -2,9 +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.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)
+[![Build Status](https://github.com/GeoStat-Framework/welltestpy/workflows/Continuous%20Integration/badge.svg?branch=develop)](https://github.com/GeoStat-Framework/welltestpy/actions)
+[![Coverage Status](https://coveralls.io/repos/github/GeoStat-Framework/welltestpy/badge.svg?branch=develop)](https://coveralls.io/github/GeoStat-Framework/welltestpy?branch=develop)
+[![Documentation Status](https://readthedocs.org/projects/welltestpy/badge/?version=latest)](https://geostat-framework.readthedocs.io/projects/welltestpy/en/latest/?badge=latest)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/ambv/black)
 
 <p align="center">
@@ -25,7 +25,7 @@ You can install the latest version with the following command:
 
 ## Documentation for welltestpy
 
-You can find the documentation under [geostat-framework.readthedocs.io][doc_link].
+You can find the documentation under [https://welltestpy.readthedocs.io][doc_link].
 
 
 ### Example 1: A campaign containing a pumping test
@@ -121,7 +121,7 @@ You can contact us via <[email protected]>.
 
 ## License
 
-[MIT][license_link] © 2018-2020
+[MIT][license_link] © 2018-2021
 
 [license_link]: https://github.com/GeoStat-Framework/welltestpy/blob/master/LICENSE
 [doc_link]: https://welltestpy.readthedocs.io

README.md

@@ -263,9 +263,9 @@ def setup(app):
     # only show "print" output as output
     "capture_repr": (),
     # path to your examples scripts
-    "examples_dirs": ["../../examples",],
+    "examples_dirs": ["../../examples"],
     # path where to save gallery generated examples
-    "gallery_dirs": ["examples",],
+    "gallery_dirs": ["examples"],
     # Pattern to search for example files
     "filename_pattern": "/.*.py",
     "ignore_pattern": r"03_estimate_hetero\.py",

docs/source/conf.py

@@ -300,6 +300,7 @@ def run(
         fittingplotname=None,
         interactplotname=None,
         estname=None,
+        plot_style="WTP",
     ):
         """Run the estimation.
 
@@ -348,11 +349,13 @@ def run(
             If ``None``, it will be the current time +
             ``"_estimate"``.
             Default: ``None``
+        plot_style : str, optional
+            Plot stlye. The default is "WTP".
         """
         if self.setup.dummy:
             raise ValueError(
                 "Estimate: for parameter estimation"
-                + " you can't use a dummy paramter."
+                " you can't use a dummy paramter."
             )
         act_time = timemodule.strftime("%Y-%m-%d_%H-%M-%S")
 
@@ -405,42 +408,45 @@ def run(
         else:
             rank = 0
 
+        # initialize the sampler
+        sampler = spotpy.algorithms.sceua(
+            self.setup,
+            dbname=dbname,
+            dbformat="csv",
+            parallel=parallel,
+            save_sim=True,
+            db_precision=np.float64,
+        )
+        # start the estimation with the sce-ua algorithm
         if run:
-            # initialize the sampler
-            sampler = spotpy.algorithms.sceua(
-                self.setup,
-                dbname=dbname,
-                dbformat="csv",
-                parallel=parallel,
-                save_sim=True,
-                db_precision=np.float64,
-            )
-            # start the estimation with the sce-ua algorithm
             sampler.sample(rep, ngs=10, kstop=100, pcento=1e-4, peps=1e-3)
 
-            if rank == 0:
-                # save best parameter-set
+        if rank == 0:
+            if run:
                 self.result = sampler.getdata()
-                para_opt = spotpy.analyser.get_best_parameterset(
-                    self.result, maximize=False
+            else:
+                self.result = np.genfromtxt(
+                    dbname + ".csv", delimiter=",", names=True
                 )
-                void_names = para_opt.dtype.names
-                para = []
-                header = []
-                for name in void_names:
-                    para.append(para_opt[0][name])
-                    header.append(name[3:])
-                    self.estimated_para[header[-1]] = para[-1]
-                np.savetxt(paraname, para, header=" ".join(header))
-
-        if rank == 0:
+            para_opt = spotpy.analyser.get_best_parameterset(
+                self.result, maximize=False
+            )
+            void_names = para_opt.dtype.names
+            para = []
+            header = []
+            for name in void_names:
+                para.append(para_opt[0][name])
+                header.append(name[3:])
+                self.estimated_para[header[-1]] = para[-1]
+            np.savetxt(paraname, para, header=" ".join(header))
             # plot the estimation-results
             plotter.plotparatrace(
                 result=self.result,
                 parameternames=paranames,
                 parameterlabels=paralabels,
                 stdvalues=self.estimated_para,
                 plotname=traceplotname,
+                style=plot_style,
             )
             plotter.plotfit_steady(
                 setup=self.setup,
@@ -450,8 +456,11 @@ def run(
                 radnames=self.radnames,
                 extra=self.extra_kw_names,
                 plotname=fittingplotname,
+                style=plot_style,
+            )
+            plotter.plotparainteract(
+                self.result, paralabels, interactplotname, style=plot_style
             )
-            plotter.plotparainteract(self.result, paralabels, interactplotname)
 
     def sensitivity(
         self,
@@ -462,6 +471,7 @@ def sensitivity(
         plotname=None,
         traceplotname=None,
         sensname=None,
+        plot_style="WTP",
     ):
         """Run the sensitivity analysis.
 
@@ -501,11 +511,13 @@ def sensitivity(
             If ``None``, it will be the current time +
             ``"_estimate"``.
             Default: ``None``
+        plot_style : str, optional
+            Plot stlye. The default is "WTP".
         """
         if len(self.setup.para_names) == 1 and not self.setup.dummy:
             raise ValueError(
                 "Sensitivity: for estimation with only one parameter"
-                + " you have to use a dummy paramter."
+                " you have to use a dummy paramter."
             )
         if rep is None:
             rep = spotpylib.fast_rep(
@@ -592,11 +604,14 @@ def sensitivity(
             header = " ".join(paranames)
             np.savetxt(sensname, sens_est["ST"], header=header)
             np.savetxt(sensname1, sens_est["S1"], header=header)
-            plotter.plotsensitivity(paralabels, sens_est, plotname)
+            plotter.plotsensitivity(
+                paralabels, sens_est, plotname, style=plot_style
+            )
             plotter.plotparatrace(
                 data,
                 parameternames=paranames,
                 parameterlabels=paralabels,
                 stdvalues=None,
                 plotname=traceplotname,
+                style=plot_style,
             )