testing badges

.github/workflows/python-package-conda.yml

@@ -27,16 +27,26 @@ jobs:
         # stop the build if there are Python syntax errors or undefined names
         flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
-        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+        flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --format=html --htmldir ./reports/flake8 --statistics --tee --output-file flake8stats.txt
     - name: Install HyVR-fork
       run: |
         pip install .
+    - name: Install genbadge
+      run: |
+        pip install genbadge
     - name: Test with pytest
       run: |
         conda install pytest
-        pytest
+        pytest --junitxml=reports/junit/junit.xml --html=reports/junit/report.html
     - name: Coverage tests
       run: |
         pip install coverage
         NUMBA_DISABLE_JIT=1 coverage run -m pytest
-        coverage html
+        coverage report -m
+        coverage xml -d reports/coverage
+        coverage html -d reports/coverage
+    - name: Generate badges
+      run: |
+        genbadge coverage
+        genbadge flake8
+        genbadge pytest

README.rst → README.md

@@ -1,81 +1,84 @@
-====================================================================
-Introduction
-====================================================================
-
-**HyVR**
-
-This is a fork from the original HyVR package with minimal implementation of
-the core features the idea to keep the original ideas alive, 
-but maintainable in the fast python development ecosystem.
-Thus, most of the non-essencial functionality, that is nowadays done much better in other packages, 
-has been dropped. The functionality is now focus on the creation of geobodies to grids.
-
-Eveything that could be done before is still doable, and more. But the user should understand a bit more about
-operating on arrays and using python.
-
-
-The Hydrogeological Virtual Reality simulation package (HyVR) is a Python module
-that helps researchers and practitioners generate sedimentary subsurface models with
-multiple scales of heterogeneity that are based on geological concepts. The
-simulation outputs can then be used to explore groundwater flow and solute
-transport behaviour, for example. The user must work with a previously created regular grid, which
-can be used directly in MODFLOW or interpolated to the simulation grid that the user will need.
-
-The original motivation for HyVR was the lack of tools for modelling sedimentary
-deposits that include bedding structure model outputs (i.e., dip and azimuth).
-Such bedding parameters were required to approximate full hydraulic-conductivity
-tensors for groundwater flow modelling. HyVR is able to simulate these bedding
-parameters and generate spatially distributed parameter fields, including full
-hydraulic-conductivity tensors. A documentation on the simplified HyVR is being built in: *TO BE ADDED*
-The original HyVR information is available in the online `technical documentation <https://driftingtides.github.io/hyvr/index.html>`_.
-
-For citation of the original software and development, please use the following reference:
-
-*HyVR can be attributed by citing the following journal article: Bennett, J. P.,
-Haslauer, C. P., Ross, M., & Cirpka, O. A. (2018). An open, object-based
-framework for generating anisotropy in sedimentary subsurface
-models. Groundwater.
-DOI:* `10.1111/gwat.12803 <https://onlinelibrary.wiley.com/doi/abs/10.1111/gwat.12803>`_.
-*A preprint version of the article is available* `here <https://github.com/driftingtides/hyvr/blob/master/docs/Bennett_GW_2018.pdf>`_.
-
-Installing the HyVR package
---------------------------------------
-
-Installing HyVR
-^^^^^^^^^^^^^^^
-
-The package should work whether you are using anaconda or another virtual environment.
-Your working environment should have updated installations of the following libraries:
-
-- numpy
-- numba
-- scipy
-
-Once you have activated your virtual environment, you can install HyVR
-using ``pip``. First git clone the repository,
-navigate to the root directory and type::
-
-    pip install .
-
-Alternatively, you can use the package without installing it by typing in your script::
-
-    sys.path.append("path where HyVR is") 
-
-Usage
------
-
-See the documentation and the examples folder for usage.
-
-Development
------------
-
-The orgininal HyVR has been developed by Jeremy Bennett (`website <https://jeremypaulbennett.weebly.com>`_)
-as part of his doctoral research at the University of Tübingen and by Samuel
-Scherrer as a student assistant.
-
-The current version is maintained by Vitor Cantarella (`website <https://vcantarella.gitub.io>`_)
-
-Problems, Bugs, Unclear Documentation
--------------------------------------
-
-please use the Issues page for bugs.
+# Status
+
+[![Coverage Status](./reports/coverage/coverage-badge.svg?dummy=8484744)](./reports/coverage/index.html)
+
+[![Tests Status](./reports/junit/junit-badge.svg?dummy=8484744)](./reports/junit/report.html)
+
+[![Flake8 Status](./reports/flake8/flake8-badge.svg?dummy=8484744)](./reports/flake8/index.html)
+
+# Introduction
+
+**HyVR**
+
+This is a fork from the original HyVR package with minimal implementation of
+the core features the idea to keep the original ideas alive, 
+but maintainable in the fast python development ecosystem.
+Thus, most of the non-essencial functionality, that is nowadays done much better in other packages, 
+has been dropped. The functionality is now focus on the creation of geobodies to grids.
+
+Eveything that could be done before is still doable, and more. But the user should understand a bit more about
+operating on arrays and using python.
+
+
+The Hydrogeological Virtual Reality simulation package (HyVR) is a Python module
+that helps researchers and practitioners generate sedimentary subsurface models with
+multiple scales of heterogeneity that are based on geological concepts. The
+simulation outputs can then be used to explore groundwater flow and solute
+transport behaviour, for example. The user must work with a previously created regular grid, which
+can be used directly in MODFLOW or interpolated to the simulation grid that the user will need.
+
+The original motivation for HyVR was the lack of tools for modelling sedimentary
+deposits that include bedding structure model outputs (i.e., dip and azimuth).
+Such bedding parameters were required to approximate full hydraulic-conductivity
+tensors for groundwater flow modelling. HyVR is able to simulate these bedding
+parameters and generate spatially distributed parameter fields, including full
+hydraulic-conductivity tensors. A documentation on the simplified HyVR is being built in: *TO BE ADDED*
+The original HyVR information is available in the online `technical documentation <https://driftingtides.github.io/hyvr/index.html>`_.
+
+For citation of the original software and development, please use the following reference:
+
+* HyVR can be attributed by citing the following journal article: Bennett, J. P.,
+    Haslauer, C. P., Ross, M., & Cirpka, O. A. (2018). An open, object-based
+    framework for generating anisotropy in sedimentary subsurface
+    models. Groundwater.
+    DOI:* [10.1111/gwat.12803](https://onlinelibrary.wiley.com/doi/abs/10.1111/gwat.12803>).
+*   A preprint version of the article is available* [here](https://github.com/driftingtides/hyvr/blob/master/docs/Bennett_GW_2018.pdf) .
+
+## Installing the HyVR package
+--------------------------------------
+
+The package should work whether you are using anaconda or another virtual environment.
+Your working environment should have updated installations of the following libraries:
+
+- numpy
+- numba
+- scipy
+
+Once you have activated your virtual environment, you can install HyVR
+using `pip`. First git clone the repository,
+navigate to the root directory and type::
+
+```    pip install .```
+
+Alternatively, you can use the package without installing it by typing in your script::
+
+```    sys.path.append("path where HyVR is")``` 
+
+## Usage
+-----
+
+See the documentation and the examples folder for usage.
+
+## Development
+-----------
+
+The orgininal HyVR has been developed by Jeremy Bennett ([website](https://jeremypaulbennett.weebly.com))
+as part of his doctoral research at the University of Tübingen and by Samuel
+Scherrer as a student assistant.
+
+The current version is maintained by Vitor Cantarella ([website](https://vcantarella.gitub.io))
+
+## Problems, Bugs, Unclear Documentation
+-------------------------------------
+
+please use the Issues page for bugs.