Merge pull request #22 from ArtesiaWater/dev

Update to 0.0.4

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     runs-on: ubuntu-18.04
     strategy:
       matrix:
-        python-version: [3.7]
+        python-version: [3.9]
 
     steps:
       - uses: actions/checkout@v2
@@ -43,23 +43,25 @@ jobs:
           flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
           # exit-zero treats all errors as warnings.
           flake8 . --count --exit-zero --max-complexity=10 --max-line-length=80 --statistics
-          
-      - name: Install pymake
-        shell: bash -l {0}
-        run: |
-          pip install https://github.com/modflowpy/pymake/zipball/master
             
       - name: Download executables needed for tests
         shell: bash -l {0}
         run: |
           python -c "import nlmod; nlmod.util.download_mfbinaries()"
             
       - name: Run notebooks
-        if: ${{ github.event_name == 'pull_request' }}
+        if: ${{ github.event_name == 'push' }}
         run: |
           py.test ./tests -m "notebooks"
       
       - name: Run tests only
-        if: ${{ github.event_name == 'push' }}
+        if: ${{ github.event_name == 'pull_request' }}
         run: |
           py.test ./tests -m "not notebooks"
+    
+
+      - name: Run codacy-coverage-reporter
+        uses: codacy/codacy-coverage-reporter-action@master
+        with:
+          project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
+          coverage-reports: coverage.xml

.github/workflows/python-publish.yml

@@ -0,0 +1,32 @@
+# This workflows will upload a Python Package using Twine when a release is created
+# For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [created]
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.8'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build setuptools wheel
+    - name: build binary wheel and a source tarball
+      run: |
+        python -m build --sdist --wheel --outdir dist/
+    - name: Publish a Python distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@main
+      with:
+        user: __token__
+        password: ${{ secrets.PYPI_API_TOKEN }}

.gitignore

@@ -20,7 +20,6 @@ parts/
 sdist/
 var/
 wheels/
-pip-wheel-metadata/
 share/python-wheels/
 *.egg-info/
 .installed.cfg
@@ -50,6 +49,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+cover/
 
 # Translations
 *.mo
@@ -72,6 +72,7 @@ instance/
 docs/_build/
 
 # PyBuilder
+.pybuilder/
 target/
 
 # Jupyter Notebook
@@ -82,7 +83,9 @@ profile_default/
 ipython_config.py
 
 # pyenv
-.python-version
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
 
 # pipenv
 #   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
@@ -128,6 +131,12 @@ dmypy.json
 # Pyre type checker
 .pyre/
 
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
 # vscode
 .vscode
 
@@ -136,5 +145,4 @@ bin/
 flowchartnlmod.pptx
 tests/data/
 examples/*/
-data/nhflo/
-
+data/nhflo/

.prospector.yaml

@@ -0,0 +1,27 @@
+pep257:
+  disable:
+    - D203
+    - D212
+    - D213
+    - D214
+    - D215
+    - D404
+    - D405
+    - D406
+    - D407
+    - D408
+    - D409
+    - D410
+    - D411
+    - D413
+    - D415
+    - D416
+    - D417
+
+pylint:
+  disable:
+    # Disable unnecessary else after return as it complains when returning in an else statement
+    # which is often more readable
+    - no-else-return
+    - too-many-arguments
+    - too-many-locals

.readthedocs.yml

@@ -0,0 +1,24 @@
+# .readthedocs.yml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Build documentation in the docs/ directory with Sphinx
+sphinx:
+  configuration: docs/source/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+  version: "3.7"
+  install:
+    - requirements: docs/requirements.txt
+    - method: pip
+      path: .
+
+build:
+  image: latest

LICENSE

@@ -0,0 +1,21 @@
+The MIT License (MIT)
+
+Copyright (c) 2020 O.E. Ebbens, D.A. Brakenhoff, R. Calje
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,13 +1,38 @@
+
 [![nlmod](https://github.com/ArtesiaWater/nlmod/actions/workflows/ci.yml/badge.svg?branch=main)](https://github.com/ArtesiaWater/nlmod/actions/workflows/ci.yml)
 
 # nlmod
 
-Python code to process, build and visualise MODFLOW models in the Netherlands. 
-Model data is stored in an xarray Datastore as much as possible.
+Python package with functions to process, build and visualise MODFLOW models in the Netherlands. 
+
+The functions in nlmod have three main objectives:
+1. Create and adapt the temporal and spatial discretization of a MODFLOW model using an xarray Dataset. These functions are contained in `nlmod.mdims`
+2. Read data from external sources, project this data on the modelgrid and add this data to an xarray Dataset. These functions are contained in `nlmod.read`
+3. Use data in an xarray Dataset to build modflow packages using flopy.  These functions are contained in `nlmod.mfpackages`
+
+External data sources that can be read are:
+- REGIS, subsurface model
+- Geotop, subsurface model
+- KNMI, precipitation and evaporation
+- Jarkus, bathymetry
+- Rijkswaterstaat, surface water polygons
 
 ## Installation
 
-The package is not (yet) available on PyPi. 
+Install the module with pip:
+
+`pip install nlmod`
+
+`nlmod` has many dependencies `xarray`, `flopy`, `rasterio`, `owslib`, `hydropandas`, `netcdf4`, `pyshp`, `rtree`, `openpyxl` and `matplotlib`.
+
+When using pip the dependencies are automatically installed. Some dependencies are notoriously hard to install on certain platforms. 
+Please see the [dependencies](https://github.com/ArtesiaWater/hydropandas#dependencies) section of the `hydropandas` package for more information on how to install these packages manually. 
+
+
+## Getting started
+If you are using nlmod for the first time you need to download the MODFLOW executables. You can easily download these executables by running this Python code:
+
+	import nlmod
+	nlmod.util.download_mfbinaries()
 
-You can install the package by cloning the repository and
-typing `pip install -e .` from the package root directory.
+After you've downloaded the executables you can run the Jupyter Notebooks in the examples folder. These notebooks illustrate how you to use the nlmod package. 

docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = source
+BUILDDIR      = build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

docs/make.bat

@@ -0,0 +1,35 @@
+@ECHO OFF
+
+pushd %~dp0
+
+REM Command file for Sphinx documentation
+
+if "%SPHINXBUILD%" == "" (
+	set SPHINXBUILD=sphinx-build
+)
+set SOURCEDIR=source
+set BUILDDIR=build
+
+if "%1" == "" goto help
+
+%SPHINXBUILD% >NUL 2>NUL
+if errorlevel 9009 (
+	echo.
+	echo.The 'sphinx-build' command was not found. Make sure you have Sphinx
+	echo.installed, then set the SPHINXBUILD environment variable to point
+	echo.to the full path of the 'sphinx-build' executable. Alternatively you
+	echo.may add the Sphinx directory to PATH.
+	echo.
+	echo.If you don't have Sphinx installed, grab it from
+	echo.http://sphinx-doc.org/
+	exit /b 1
+)
+
+%SPHINXBUILD% -M %1 %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+goto end
+
+:help
+%SPHINXBUILD% -M help %SOURCEDIR% %BUILDDIR% %SPHINXOPTS% %O%
+
+:end
+popd

docs/requirements.txt

@@ -0,0 +1,5 @@
+sphinx_rtd_theme
+Ipython
+ipykernel
+nbsphinx
+nbsphinx_link