Merge branch 'dev' into 389-typehinting

pastas · Dec 27, 2022 · accf8e0 · accf8e0
2 parents c7f6b1e + de2b6ce
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diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -7,4 +7,4 @@ Add a short description describing the pull request (PR) here.
 - [ ] PEP8 compliant code
 - [ ] type hints for functions and methods
 - [ ] tests added / passed
-- [ ] Example Notebook (for new features)
+- [ ] Example Notebook (for new features)
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -19,10 +19,10 @@ jobs:
       matrix:
         python-version: ['3.7', '3.8', '3.9', '3.10']
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
 

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -13,9 +13,9 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v3
     - name: Set up Python
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: '3.x'
     - name: Install dependencies

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,6 +5,13 @@
 # Required
 version: 2
 
+
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
   configuration: doc/conf.py
@@ -14,11 +21,13 @@ sphinx:
 #  configuration: mkdocs.yml
 
 # Optionally build your docs in additional formats such as PDF and ePub
-formats: all
+#formats:
+#  - epub
+#  - pdf
 
 # Optionally set the version of Python and requirements required to build your docs
 python:
-  version: 3.7
+  system_packages: true
   install:
     - requirements: requirements.rtd.txt
     - requirements: requirements.ci.txt

diff --git a/CITATION.cff b/CITATION.cff
@@ -0,0 +1,37 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Collenteur"
+    given-names: "R.A."
+  - family-names: "Bakker"
+    given-names: "M"
+  - family-names: "Caljé"
+    given-names: "R"
+  - family-names: "Schaars"
+    given-names: "F"
+title: "Pastas: open-source software for the analysis of hydrogeological time series"
+version: 0.22.0
+doi: 10.5281/zenodo.1465866
+date-released: 2022-08-02
+url: "https://github.com/pastas/pastas"
+preferred-citation:
+  type: article
+  authors:
+    - family-names: "Collenteur"
+      given-names: "R.A."
+      orcid: "https://orcid.org/0000-0001-7843-1538"
+    - family-names: "Caljé"
+      given-names: "R"
+    - family-names: "Klop"
+      given-names: "S.A."
+    - family-names: "Schaars"
+      given-names: "F"
+    - family-names: "Bakker"
+      given-names: "M"
+      orcid: "https://orcid.org/0000-0002-5629-2861"
+  doi: "10.1111/gwat.12925"
+  journal: "Groundwater"
+  month: 7
+  title: "Pastas: open source software for the analysis of groundwater time series"
+  volume: 57
+  year: 2019
diff --git a/README.rst b/README.rst
@@ -35,15 +35,10 @@ built-in optimization, visualisation, and statistical analysis tools.
 Documentation & Examples
 ~~~~~~~~~~~~~~~~~~~~~~~~
 - Documentation is provided on a dedicated website: http://pastas.readthedocs.io/
-- Examples can be found on the `examples directory on the documentation website <https://pastas.readthedocs.io/en/dev/examples/index.html>`_.
+- Examples can be found on the `examples directory on the documentation website <https://pastas.readthedocs.io/en/dev/examples/index.html>`_
 - View and edit a working example notebook of a Pastas model in `MyBinder <https://mybinder.org/v2/gh/pastas/pastas/master?filepath=examples%2Fnotebooks%2F1_basic_model.ipynb>`_
 - A list of Publications that used Pastas is available in a `dedicated GitHub repo <https://github.com/pastas/pastas_research>`_
 
-Related packages
-~~~~~~~~~~~~~~~~
-- Pastastore is a package for managing multiple timeseries and pastas models: https://github.com/pastas/pastastore
-- Hydropandas can be used to obtain Dutch observation datasets: https://github.com/ArtesiaWater/hydropandas
-
 Get in Touch
 ~~~~~~~~~~~~
 - Questions on Pastas can be asked and answered on `Github Discussions <https://github.com/pastas/pastas/discussions>`_.
@@ -78,7 +73,13 @@ Developers
 To get the latest development version, use::
 
    pip install git+https://github.com/pastas/pastas.git@dev#egg=pastas
-  
+
+Related packages
+~~~~~~~~~~~~~~~~
+- `Pastastore <https://github.com/pastas/pastastore>`_ is a Python package for managing multiple timeseries and pastas models 
+- `Hydropandas <https://github.com/ArtesiaWater/hydropandas/blob/master/examples/03_hydropandas_and_pastas.ipynb>`_ can be used to obtain Dutch timeseries (KNMI, Dinoloket, ..)
+- `PyEt <https://github.com/phydrus/pyet>`_ can be used to compute potential evaporation from meteorological variables.
+
 Dependencies
 ~~~~~~~~~~~~
 Pastas depends on a number of Python packages, of which all of the necessary

diff --git a/concepts/armamodel.ipynb b/concepts/armamodel.ipynb
diff --git a/concepts/autocorrelation.ipynb b/concepts/autocorrelation.ipynb
diff --git a/concepts/handling_timeseries.ipynb b/concepts/handling_timeseries.ipynb
diff --git a/concepts/hantush_response.ipynb b/concepts/hantush_response.ipynb
diff --git a/concepts/noisemodel.ipynb b/concepts/noisemodel.ipynb
diff --git a/concepts/pastas_synthetic.ipynb b/concepts/pastas_synthetic.ipynb
diff --git a/concepts/pastas_timeseries.ipynb b/concepts/pastas_timeseries.ipynb
diff --git a/concepts/response_functions.ipynb b/concepts/response_functions.ipynb