Update master-branch to Pastas 1.0: Arrabiata (#529)

.github/workflows/ci.yml

@@ -14,41 +14,84 @@ on:
 
 jobs:
   test:
+    name: ${{ matrix.name }}
     runs-on: ubuntu-latest
     strategy:
+      fail-fast: false
       matrix:
-        python-version: ['3.8', '3.9', '3.10']
+        include:
+          - name: Test suite with py38-ubuntu
+            python: "3.8"
+            toxenv: py38
+          - name: Test suite with py39-ubuntu
+            python: "3.9"
+            toxenv: py39
+          - name: Test suite with py310-ubuntu
+            python: "3.10"
+            toxenv: py310
+          - name: Formatting with black + isort
+            python: "3.9"
+            toxenv: format
+          - name: Linting with flake8
+            python: "3.9"
+            toxenv: lint
+          - name: Test suite for Jupyter Notebooks
+            python: "3.9"
+            toxenv: notebooks
+    env:
+      # Color Output
+      # Rich (pip)
+      FORCE_COLOR: 1
+      # Tox
+      PY_COLORS: 1
+      # Pytest
+      PYTEST_ADDOPTS: "--color=yes"
     steps:
       - uses: actions/checkout@v3
 
-      - name: Set up Python ${{ matrix.python-version }}
+      - name: Set up Python ${{ matrix.python }}
         uses: actions/setup-python@v4
         with:
-          python-version: ${{ matrix.python-version }}
-
+          python-version: ${{ matrix.python }}
+          check-latest: true
+          cache: "pip"
+          cache-dependency-path: pyproject.toml
+
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-          pip install -e .[ci]
-      
-      - name: Lint with black
-        uses: psf/black@stable
+          pip install tox
+
+      - name: Setup tox environment
+        run: tox -e ${{ matrix.toxenv }} --notest
+
+      - name: Test
+        run: tox -e ${{ matrix.toxenv }} --skip-pkg-install
+
+      - name: Store coverage
+        uses: actions/upload-artifact@v3
         with:
-          options: "--check"
-          jupyter: true
-
-      - name: Run tests and notebooks
-        if: ${{ github.event_name == 'pull_request' }}
-        run: |
-          py.test ./tests
-      
-      - name: Run tests only
-        if: ${{ github.event_name == 'push' }}
-        run: |
-          py.test ./tests -m "not notebooks"
-      
+          name: coverage
+          path: coverage.xml
+          if-no-files-found: ignore
+
+  coverage:
+    name: Coverage
+    runs-on: ubuntu-latest
+    needs: test
+    steps:
+      - name: Set up Python ${{ matrix.python }}
+        uses: actions/setup-python@v4
+        with:
+          check-latest: true
+
+      - name: Get coverage
+        uses: actions/download-artifact@v3
+        with:
+          name: coverage
+
       - name: Run codacy-coverage-reporter
-        if: github.repository == 'pastas/pastas'
+        if: ${{ github.repository == 'pastas/pastas' && success() }}
         uses: codacy/codacy-coverage-reporter-action@master
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

.gitignore

@@ -16,6 +16,7 @@ examples/notebooks/.ipynb_checkpoints/
 gui/settings
 build
 dist
+.tox
 
 .idea/.name
 .cache/v/cache/lastfailed
@@ -32,3 +33,7 @@ dist
 
 .DS_Store
 /doc/api/generated/
+Test_Model.pdf
+test.pas
+doc/about/publications.bib
+doc/about/references.bib

README.rst

@@ -13,16 +13,18 @@ Pastas: Analysis of Groundwater Time Series
    :target: https://mit-license.org/
 .. image:: https://img.shields.io/pypi/pyversions/pastas
    :target: https://pypi.python.org/pypi/pastas
+.. image:: https://img.shields.io/pypi/dm/pastas
+   :target: https://pypi.org/project/pastas/
+.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1465866.svg
+   :target: https://doi.org/10.5281/zenodo.1465866
 .. 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
-.. image:: https://zenodo.org/badge/DOI/10.5281/zenodo.1465866.svg
-   :target: https://doi.org/10.5281/zenodo.1465866
-.. image:: https://mybinder.org/badge_logo.svg
-   :target: https://mybinder.org/v2/gh/pastas/pastas/master?filepath=examples%2Fnotebooks%2F1_basic_model.ipynb
 .. image:: https://readthedocs.org/projects/pastas/badge/?version=latest
    :target: https://pastas.readthedocs.io/en/latest/?badge=latest
+.. image:: https://mybinder.org/badge_logo.svg
+   :target: https://mybinder.org/v2/gh/pastas/pastas/master?filepath=examples%2Fnotebooks%2F1_basic_model.ipynb
 
 Pastas: what is it?
 ~~~~~~~~~~~~~~~~~~~
@@ -34,10 +36,10 @@ built-in optimization, visualisation, and statistical analysis tools.
 
 Documentation & Examples
 ~~~~~~~~~~~~~~~~~~~~~~~~
-- Documentation is provided on a dedicated website: http://pastas.readthedocs.io/
+- Documentation is provided on the dedicated website `pastas.dev <http://www.pastas.dev/>`_
 - 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>`_
+- A list of publications that use Pastas is available in a `dedicated Zotero group <https://www.zotero.org/groups/4846685/pastas/items/32FS5PTW/item-list>`_
 
 Get in Touch
 ~~~~~~~~~~~~
@@ -50,7 +52,7 @@ Get in Touch
 
 Quick installation guide
 ~~~~~~~~~~~~~~~~~~~~~~~~
-To install Pastas, a working version of Python 3.7, 3.8 or 3.9 has to be
+To install Pastas, a working version of Python 3.8, 3.9 or 3.10 has to be
 installed on your computer. We recommend using the `Anaconda Distribution
 <https://www.continuum.io/downloads>`_ as it includes most of the python
 package dependencies and the Jupyter Notebook software to run the notebooks.
@@ -90,7 +92,7 @@ Pastas
 - numpy>=1.7
 - matplotlib>=3.1
 - pandas>=1.1
-- scipy>=1.3
+- scipy>=1.8
 - numba>=0.51
 
 To install the most important optional dependencies (solver LmFit and function visualisation Latexify) at the same time with Pastas use::

doc/about/01_history.rst

@@ -0,0 +1,36 @@
+History
+=======
+
+The Development of Pastas started in the spring of 2016 at the TU Delft and Artesia in the Netherlands. Researchers
+at the TU Delft required a flexible framework that could support future research on time series analysis of
+groundwater data. Consulting company `Artesia <https://www.artesia-water.nl>`_ on the other hand, needed a tool
+that allowed them to perform more complex analyses in a scripted environment. As such, Pastas was developed under
+a fruitful partnership between academia and private industry, a collaboration that continues to this day.
+
+.. figure:: ./../_static/history_initial.jpg
+    :figwidth: 600px
+
+    Drawing the initial design of Pastas on a whiteboard (5th of April, 2016)
+
+Python was chosen as the programming language for Pastas, being a flexible and open-source language that allows for
+quick prototyping. Moreover, many if not most hydrologists learn Python during their education, making the software
+available to many. From the start, all code was made completely open-source under MIT license, embracing open science
+and FAIR (Findability, Accessibility, Interoperability, and Reuse) data practices.
+
+International use of Pastas and research grew substantially after the publication of the Pastas article in the
+international journal Groundwater :cite:p:`collenteur_pastas_2019`. In addition, the University of Graz in Austria
+and now the Swiss research institute Eawag employed one of the maintainers, further pushing the international use and
+development of Pastas. Since its inception, Pastas has been applied in over a dozen countries worldwide. Supporting
+international research continues to be an important goal of Pastas. For a list of peer-reviewed publications using
+Pastas please see the :doc:`Publications page <05_publications>`.
+
+Pastas 1.0
+----------
+
+In february 2023, Pastas version 1.0 was released, the celebration of 7 years of research and development of Pastas.
+Pastas was already operational for a couple of years, but the a lot of features were still changing. In Pastas 1.0
+focus lies on Pastas main goal: time series analysis on groundwater levels. This was done by improving the
+documentation, removing unused features, unifying the API and relying more on high quality Python packages such as
+Pandas, NumPy and Numba. With version 1.0, Pastas is ready for further future developments!
+
+

doc/about/02_team.rst

@@ -0,0 +1,110 @@
+Pastas Team
+===========
+
+Active maintainers
+------------------
+
+Core team
+~~~~~~~~~
+The following people are part of the core team of Pastas and can merge pull requests on the Pastas GitHub.
+
+
+.. grid:: 1 2 3 4
+
+    .. grid-item::
+
+        .. figure:: https://avatars2.githubusercontent.com/u/12051167?s=460&u=ad0baaa3520ab942c93af44ea8e296b44ea459ac&v=4
+            :figwidth: 150px
+            :target: https://github.com/raoulcollenteur
+
+            Raoul Collenteur
+            (Eawag)
+
+    .. grid-item::
+        .. figure:: https://avatars3.githubusercontent.com/u/1363400?s=460&u=8d34d0824bd0f43a63f29c0b71fbfae435a15565&v=4
+            :figwidth: 150px
+            :target: https://github.com/mbakker7
+
+            Mark Bakker
+            (TU Delft)
+
+    .. grid-item::
+        .. figure:: https://avatars3.githubusercontent.com/u/18527362?s=460&u=3e1faab416c86e141ff0860017a5a02133830b08&v=4
+            :figwidth: 150px
+            :target: https://github.com/rubencalje
+
+            Ruben Caljé
+            (Artesia)
+
+    .. grid-item::
+        .. figure:: https://avatars1.githubusercontent.com/u/6552225?s=460&u=ba73dc4a63fe3d5707a2da9276143d16672ad413&v=4
+            :figwidth: 150px
+            :target: https://github.com/dbrakenhoff
+
+            Davíd Brakenhoff
+            (Artesia)
+
+Developers
+~~~~~~~~~~
+
+The following people are part of the development team of Pastas and help develop new features.
+
+.. grid:: 1 2 3 4
+
+    .. grid-item::
+        .. figure:: https://avatars.githubusercontent.com/u/10562903?v=4
+            :figwidth: 120px
+            :target: https://github.com/OnnoEbbens
+
+            Onno Ebbens
+            (Artesia)
+
+    .. grid-item::
+        .. figure:: https://avatars.githubusercontent.com/u/66305055?v=4
+            :figwidth: 120px
+            :target: https://github.com/martinvonk
+
+            Martin Vonk
+            (Artesia & TU Delft)
+
+All the people who have contributed code to the Pastas project can be found on `GitHub Contributor list <https://github
+.com/pastas/pastas/graphs/contributors>`_.
+
+
+Institutional partners
+----------------------
+Institutional partners are companies and universities that support the project by employing maintainers and developers.
+Current institutional partners include:
+
+.. grid:: 1 2 3 3
+
+    .. grid-item-card::
+
+
+        .. figure:: ./../_static/Eawag_logo.png
+            :figwidth: 150px
+            :target: https://www.eawag.ch/en/
+
+    .. grid-item-card::
+
+        .. figure:: ./../_static/TUD_logo.png
+            :figwidth: 150px
+            :target: https://www.tudelft.nl
+
+    .. grid-item-card::
+
+        .. figure:: ./../_static/Art_logo.jpg
+            :figwidth: 150px
+            :target: http://www.artesia-water.nl
+
+Past Institutional support
+--------------------------
+The following institutions have employed maintainers in the past or past maintainers:
+
+.. grid:: 1 2 3 3
+
+    .. grid-item-card::
+
+        .. figure:: ./../_static/logo_graz.png
+            :figwidth: 150px
+            :target: https://erdwissenschaften.uni-graz.at/en/

doc/about/03_citing.rst

@@ -0,0 +1,73 @@
+Citing and logo
+===============
+
+If you find Pastas useful in your work, please cite the `Pastas article published in Groundwater journal <https://doi.org/10.1111/gwat.12925>`_:
+
+Collenteur, R., Caljé, R., Klop, S., Schaars, F., & Bakker, M. (2019). Pastas: open source software for the analysis of groundwater time series. Groundwater, 57. https://doi.org/10.1111/gwat.12925
+
+.. code-block:: text
+
+    @article{Collenteur_Pastas_open_source_2019,
+      author        = {Collenteur, R.A. and
+                       Caljé, R. and
+                       Klop, S.A. and
+                       Schaars, F. and
+                       Bakker, M.},
+      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}
+    }
+
+To cite a specific version of Pastas, you can cite `one of the releases on Zenodo <https://doi.org/10.5281/zenodo
+.7585471>`_:
+
+.. code-block:: text
+
+    @software{raoul_collenteur_2023_7585471,
+      author        = {Raoul Collenteur and
+                       Mark Bakker and
+                       Ruben Caljé and
+                       Frans Schaars},
+      title         = {{Pastas: open-source software for the analysis of
+                        hydrogeological time series}},
+      month         = jan,
+      year          = 2023,
+      publisher     = {Zenodo},
+      version       = {v1.0.0},
+      doi           = {10.5281/zenodo.7585471},
+      url           = {https://doi.org/10.5281/zenodo.7585471}
+    }
+
+Naming
+------
+
+Pastas is written as one, non-capitalized word: "Pastas".
+
+Logo
+----
+
+.. figure::
+    ./../_static/logo.png
+    :figwidth: 200px
+
+Color
+-----
+
+.. raw:: html
+
+    <table class="table">
+        <tr>
+            <td style="text-align: center;">
+                <svg xmlns="http://www.w3.org/2000/svg" width="100" height="100">
+                    <circle cx="50" cy="50" r="50" fill="#009BE0"/>
+                </svg>
+                <br/>
+                <b style="color: #009BE0;">Pastas Blue</b><br/>
+                RGB: R0 G155 B224<br/>
+                HEX: #009BE0
+            </td>
+        </tr>
+    </table>