Update master to Pastas 1.1.0 (#595)

pastas · May 12, 2023 · 5424a28 · 5424a28
2 parents 7302511 + a7b11cc
commit 5424a28
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diff --git a/.github/workflows/auto-author-assign.yml b/.github/workflows/auto-author-assign.yml
@@ -0,0 +1,15 @@
+# .github/workflows/auto-author-assign.yml
+name: Auto Author Assign
+
+on:
+  pull_request_target:
+    types: [opened, reopened]
+
+permissions:
+  pull-requests: write
+
+jobs:
+  assign-author:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: toshimaru/auto-author-assign@v1.6.2
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -1,8 +1,6 @@
-name: pastas
+name: CI
 
 on:
-  # Trigger the workflow on push or pull request on master,
-  # and also on dev branch
   push:
     branches:
       - master
@@ -29,15 +27,18 @@ jobs:
           - name: Test suite with py310-ubuntu
             python: "3.10"
             toxenv: py310
+          - name: Test suite with py311-ubuntu
+            python: "3.11"
+            toxenv: py311
           - 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
+          - name: Test suite for all unit tests including Notebooks
             python: "3.9"
-            toxenv: notebooks
+            toxenv: all
     env:
       # Color Output
       # Rich (pip)
@@ -68,30 +69,8 @@ jobs:
       - name: Test
         run: tox -e ${{ matrix.toxenv }} --skip-pkg-install
 
-      - name: Store coverage
-        uses: actions/upload-artifact@v3
-        with:
-          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' && success() }}
+        if: ${{ matrix.toxenv == 'all' && github.repository == 'pastas/pastas' && success() }}
         uses: codacy/codacy-coverage-reporter-action@master
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}

diff --git a/.github/workflows/test_benchmark_notebooks.yml b/.github/workflows/test_benchmark_notebooks.yml
@@ -0,0 +1,47 @@
+name: CI NB
+
+on:
+  pull_request:
+    branches:
+      - master
+
+jobs:
+  test:
+    name: ${{ matrix.name }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - name: Test suite for benchmark 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 }}
+        uses: actions/setup-python@v4
+        with:
+          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 tox
+
+      - name: Setup tox environment
+        run: tox -e ${{ matrix.toxenv }} --notest
+
+      - name: Test
+        run: tox -e ${{ matrix.toxenv }} --skip-pkg-install
diff --git a/README.rst b/README.rst
@@ -52,7 +52,7 @@ Get in Touch
 
 Quick installation guide
 ~~~~~~~~~~~~~~~~~~~~~~~~
-To install Pastas, a working version of Python 3.8, 3.9 or 3.10 has to be
+To install Pastas, a working version of Python 3.8, 3.9, 3.10, 3.11 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.
@@ -79,6 +79,7 @@ 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
+- `Metran <https://github.com/pastas/metran>`_ is a Python package to perform multivariate timeseries analysis using a technique called dynamic factor modelling.
 - `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.
 

diff --git a/doc/about/01_history.rst b/doc/about/01_history.rst
diff --git a/doc/about/03_citing.rst → doc/about/citing.rst b/doc/about/03_citing.rst → doc/about/citing.rst
diff --git a/doc/about/04_onsite_course.rst → doc/about/courses.rst b/doc/about/04_onsite_course.rst → doc/about/courses.rst
@@ -1,10 +1,9 @@
-On-site-courses
-===============
+Courses
+=======
 
-Every now and then on-site Pastas courses are held. Please check the `GitHub Discussion <https://github
+Every now and then (on-site) Pastas courses and workshops are held. Please check the `GitHub Discussion <https://github
 .com/pastas/pastas/discussions>`_ page for announcements of any public Pastas courses to be held. We can also provide
-private courses on request. To organize such a workshop please contact of the following.
+private courses on request. To organize such a workshop please contact one of the following:
 
 - For courses in the Netherlands, please contact Artesia (info[AT]artesia-water.nl)
 - For international courses, please contact Raoul Collenteur (Raoul.Collenteur[AT]eawag.ch)
-
diff --git a/doc/about/history.rst b/doc/about/history.rst
@@ -0,0 +1,47 @@
+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 <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!
+
+
diff --git a/doc/about/index.rst b/doc/about/index.rst
@@ -19,7 +19,12 @@ and their real-world applications.
 
 .. toctree::
     :hidden:
-    :maxdepth: 4
-    :glob:
+    :maxdepth: 1
 
-    ./*
+    history
+    team
+    related
+    citing
+    courses
+    publications
+    references
diff --git a/doc/about/05_publications.rst → doc/about/publications.rst b/doc/about/05_publications.rst → doc/about/publications.rst
diff --git a/doc/about/06_references.rst → doc/about/references.rst b/doc/about/06_references.rst → doc/about/references.rst
diff --git a/doc/about/related.rst b/doc/about/related.rst
@@ -0,0 +1,38 @@
+Related Packages
+================
+
+Pastas has grown in to a full `GitHub organisation
+<https://github.com/pastas>`_ with many useful tools to complement and improve
+the time series analysis experience. Important packages are:
+
+PastaStore
+----------
+
+`PastaStore <https://github.com/pastas/pastastore>`_ is a module that stores
+Pastas time series and models in a database. Storing time series and models in
+a database allows the user to manage time series and Pastas models on disk,
+which allows the user to pick up where they left off without having to reload
+everything. Additionally, PastaStore has a lot of tools to plot time series
+(spatially).
+
+Metran
+------
+
+While Pastas can only do univariate time series analysis, `Metran
+<https://github.com/pastas/metran>`_ can perform multivariate timeseries
+analysis using a technique called dynamic factor modelling. It can be used to
+describe the variation among many variables in terms of a few underlying but
+unobserved variables called factors.
+
+Others
+------
+
+There are also related packages which are not part of the Pastas organisation
+but depend on Pastas or can be of interest for users for their time series
+analysis workflow:
+
+* `traval <https://github.com/ArtesiaWater/traval>`_ for applying automatic error detection schemes to timeseries
+* `pyet <https://github.com/pyet-org/pyet>`_ for estimating potential/reference evaporation
+* `hydropandas <https://github.com/ArtesiaWater/traval>`_ for (automatically) loading observation data and time series from Dutch datasets
+* `SPEI <https://github.com/martinvonk/spei>`_ for calculating drought indices for time series such as the SPI, SPEI and SGI
+
diff --git a/doc/about/02_team.rst → doc/about/team.rst b/doc/about/02_team.rst → doc/about/team.rst
diff --git a/doc/benchmarks/autocorrelation.ipynb b/doc/benchmarks/autocorrelation.ipynb
diff --git a/doc/benchmarks/check_response_functions.ipynb b/doc/benchmarks/check_response_functions.ipynb
diff --git a/doc/benchmarks/noisemodel.ipynb b/doc/benchmarks/noisemodel.ipynb
diff --git a/doc/conf.py b/doc/conf.py
@@ -91,6 +91,14 @@
     "github_url": "https://github.com/pastas/pastas",
     "use_edit_page_button": True,
     "header_links_before_dropdown": 6,
+    "icon_links": [
+        {
+            "name": "GitHub",  # Label for this link
+            "url": "https://github.com/pastas/pastas",  # required
+            "icon": "fab fa-github-square",
+            "type": "fontawesome",  # Default is fontawesome
+        }
+    ],
 }
 
 html_context = {

diff --git a/doc/developers/index.rst b/doc/developers/index.rst
@@ -8,10 +8,12 @@ serves to document code conventions and quick how-to's for maintainers and devel
 
 .. toctree::
     :maxdepth: 1
-    :glob:
     :hidden:
 
-    ./*
+    code_style
+    contributing
+    new_release
+    roadmap
 
 Bug reports / Feature requests
 ------------------------------

diff --git a/doc/examples/04_adding_rivers.ipynb → doc/examples/adding_rivers.ipynb b/doc/examples/04_adding_rivers.ipynb → doc/examples/adding_rivers.ipynb
diff --git a/doc/examples/07_adding_trends.ipynb → doc/examples/adding_trends.ipynb b/doc/examples/07_adding_trends.ipynb → doc/examples/adding_trends.ipynb
diff --git a/doc/examples/05_adding_wells.ipynb → doc/examples/adding_wells.ipynb b/doc/examples/05_adding_wells.ipynb → doc/examples/adding_wells.ipynb
diff --git a/doc/examples/01_basic_model.ipynb → doc/examples/basic_model.ipynb b/doc/examples/01_basic_model.ipynb → doc/examples/basic_model.ipynb
@@ -262,7 +262,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:41:22) [MSC v.1929 64 bit (AMD64)]"
+   "version": "3.9.15"
   },
   "vscode": {
    "interpreter": {

diff --git a/doc/examples/03_calibration_options.ipynb → doc/examples/calibration_options.ipynb b/doc/examples/03_calibration_options.ipynb → doc/examples/calibration_options.ipynb
@@ -65,7 +65,7 @@
     "    .loc[\"1985\":\"2003\"]\n",
     ")\n",
     "\n",
-    "ps.plots.series(head, [evap, rain]);"
+    "ps.plots.series(head, [evap, rain], table=True);"
    ]
   },
   {
@@ -152,7 +152,7 @@
     "axes = ml.plots.results(\n",
     "    tmin=\"1975\", figsize=(10, 6)\n",
     ")  # Use tmin=1975 to show warmup period\n",
-    "axes[0].axvline(\"1986\", c=\"k\", linestyle=\"--\");  # Start of calibration"
+    "axes[0].axvline(pd.Timestamp(\"1986\"), c=\"k\", linestyle=\"--\");  # Start of calibration"
    ]
   },
   {
@@ -271,7 +271,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.15 | packaged by conda-forge | (main, Nov 22 2022, 08:41:22) [MSC v.1929 64 bit (AMD64)]"
+   "version": "3.9.15"
   },
   "vscode": {
    "interpreter": {

diff --git a/doc/examples/08_changing_responses.ipynb → doc/examples/changing_responses.ipynb b/doc/examples/08_changing_responses.ipynb → doc/examples/changing_responses.ipynb
@@ -278,7 +278,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "artesia",
+   "display_name": "pastas_dev",
    "language": "python",
    "name": "python3"
   },
@@ -292,11 +292,11 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.15"
   },
   "vscode": {
    "interpreter": {
-    "hash": "dace5e1b41a98a8e52d2a8eebc3b981caf2c12e7a76736ebfb89a489e3b62e79"
+    "hash": "29475f8be425919747d373d827cb41e481e140756dd3c75aa328bf3399a0138e"
    }
   }
  },