Update master to Pastas 0.23.0, last release before 1.0. (#477)

Co-authored-by: Martin Vonk <66305055+martinvonk@users.noreply.github.com> Co-authored-by: Davíd Brakenhoff <d.brakenhoff@artesia-water.nl> Co-authored-by: Martin Vonk <vonk.mart@gmail.com> Co-authored-by: Mark Bakker <markbak@gmail.com> Co-authored-by: Ruben Caljé <r.calje@artesia-water.nl>
pastas · Jan 30, 2023 · b7c66ba · b7c66ba
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -0,0 +1,5 @@
+# .git-blame-ignore-revs
+# apply isort, black and docformatter to code base
+6a9346b581883b4f29982c8ef1102a4b1a102664
+# apply isort, black, docformatter to submodules in pastas
+9f58ed52e0151a525e7ad67e14bfd9217f4aa773
diff --git a/.gitattributes b/.gitattributes
@@ -0,0 +1,7 @@
+# linguist settings based on linguist overrides.md
+# controls the GitHub language
+
+# ignore .pas files since they are recognized as Pascal
+*.pas linguist-vendored
+# count Jupyter Notebooks as Python files
+*.ipynb linguist-language=Python
diff --git a/.github/ISSUE_TEMPLATE/development.md b/.github/ISSUE_TEMPLATE/development.md
@@ -1,7 +1,7 @@
 ---
 name: Development
 about: Suggest new features to implement into Pastas
-title: "[Development]"
+title: "[DEVELOPMENT]"
 labels: development
 assignees: ''
 

diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -4,6 +4,8 @@ Add a short description describing the pull request (PR) here.
 # Checklist before PR can be merged:
 - [ ] closes issue #xxxx
 - [ ] is documented
-- [ ] PEP8 compliant code
+- [ ] Format code with [Black formatting](https://black.readthedocs.io)
+- [ ] type hints for functions and methods
 - [ ] tests added / passed
 - [ ] Example Notebook (for new features)
+- [ ] Remove output for all notebooks with changes
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -17,7 +17,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10']
     steps:
       - uses: actions/checkout@v3
 
@@ -29,20 +29,14 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          if [ -f requirements.ci.txt ]; then pip install -r requirements.ci.txt; fi
-          pip install flake8 pytest
-          pip install codecov
-          pip install pytest-cov
-          pip install codacy-coverage
-          pip install -e .
-      
-      - name: Lint with flake8
-        run: |
-          # 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=80 --statistics
+          pip install -e .[ci]
       
+      - name: Lint with black
+        uses: psf/black@stable
+        with:
+          options: "--check"
+          jupyter: true
+
       - name: Run tests and notebooks
         if: ${{ github.event_name == 'pull_request' }}
         run: |

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
@@ -21,11 +21,11 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install setuptools wheel twine
+        pip install wheel twine build
     - name: Build and publish
       env:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        python setup.py sdist bdist_wheel
-        twine upload dist/*
+        python3 -m build
+        python3 -m twine upload --repository pypi dist/*
diff --git a/.gitignore b/.gitignore
@@ -7,6 +7,8 @@
 
 *.so
 
+*.coverage*
+
 pastas.egg-info
 pastas/gui/settings
 

diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -5,8 +5,6 @@
 # Required
 version: 2
 
-
-
 build:
   os: ubuntu-22.04
   tools:
@@ -29,7 +27,8 @@ sphinx:
 python:
   system_packages: true
   install:
-    - requirements: requirements.rtd.txt
-    - requirements: requirements.ci.txt
     - method: pip
       path: .
+      extra_requirements:
+        - ci
+        - rtd
diff --git a/README.rst b/README.rst
@@ -12,8 +12,8 @@ Pastas: Analysis of Groundwater Time Series
 .. image:: https://img.shields.io/pypi/l/pastas.svg
    :target: https://mit-license.org/
 .. image:: https://img.shields.io/pypi/pyversions/pastas
-   :target: https://pypi.python.org/pypi/pastas      
-.. image:: https://api.codacy.com/project/badge/Grade/952f41c453854064ba0ee1fa0a0b4434    
+   :target: https://pypi.python.org/pypi/pastas
+.. image:: https://api.codacy.com/project/badge/Grade/952f41c453854064ba0ee1fa0a0b4434
    :target: https://www.codacy.com/gh/pastas/pastas
 .. image:: https://api.codacy.com/project/badge/Coverage/952f41c453854064ba0ee1fa0a0b4434
    :target: https://www.codacy.com/gh/pastas/pastas
@@ -26,7 +26,7 @@ Pastas: Analysis of Groundwater Time Series
 
 Pastas: what is it?
 ~~~~~~~~~~~~~~~~~~~
-Pastas is an open source python package for processing, simulating and analyzing 
+Pastas is an open source python package for processing, simulating and analyzing
 groundwater time series. The object oriented structure allows for the quick
 implementation of new model components. Time series models can be created,
 calibrated, and analysed with just a few lines of python code with the
@@ -66,8 +66,8 @@ Update
 ------
 To update pastas, use::
 
-  pip install pastas --upgrade  
-  
+  pip install pastas --upgrade
+
 Developers
 ----------
 To get the latest development version, use::
@@ -76,7 +76,7 @@ To get the latest development version, use::
 
 Related packages
 ~~~~~~~~~~~~~~~~
-- `Pastastore <https://github.com/pastas/pastastore>`_ is a Python package for managing multiple timeseries and pastas models 
+- `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.
 
@@ -91,10 +91,9 @@ Pastas
 - matplotlib>=3.1
 - pandas>=1.1
 - scipy>=1.3
+- numba>=0.51
 
-Apart from this, is is highly recommended to install Numba (>0.51) to
-gain significant speed-ups. To install Numba (and another optional 
-dependency LmFit) at the same time with Pastas use::
+To install the most important optional dependencies (solver LmFit and function visualisation Latexify) at the same time with Pastas use::
 
    pip install pastas[full]
 

diff --git a/doc/Makefile b/doc/Makefile
@@ -52,7 +52,6 @@ clean:
 	rm -rf $(BUILDDIR)/*
 
 html:
-	$ python convert_nb.py
 	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
 	@echo
 	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."

diff --git a/doc/api/index.rst b/doc/api/index.rst
@@ -10,18 +10,18 @@ left-hand menu you will find the different categories of the API documentation.
 .. autosummary::
     :toctree: ./generated
     :nosignatures:
-    :recursive:
 
     model.Model
-    modelplots.Plotting
-    timeseries.TimeSeries
     stressmodels
-    recharge
     noisemodels
     transform
     rfunc
+    recharge
     solver
+    modelplots.Plotting
+    timeseries.TimeSeries
     utils
+    timeseries_utils
     plots
     stats
 

diff --git a/doc/api/read.rst b/doc/api/read.rst
@@ -1,5 +1,5 @@
-pastas.io / read
-================
+pastas.io
+=========
 
 This section lists all the read methods that are available in Pastas to
 import time series and the input/output methods to store and load Pastas
@@ -15,21 +15,6 @@ IO Methods
 
    load
 
-Read Methods
-------------
-
-.. currentmodule:: pastas.read
-
-.. autosummary::
-   :nosignatures:
-   :toctree: ./generated
-
-   read_dino
-   read_meny
-   read_knmi
-   read_waterbase
-   read_dino_level_gauge
-
 Using Pandas
 ------------
 While Pastas provides a few basic methods for reading time series data, we