Style switch to ruff format

.github/workflows/rtc-tools.yml

@@ -28,7 +28,10 @@ jobs:
     timeout-minutes: 30
     steps:
     - uses: actions/checkout@v4.1.0
-    - run: python setup.py sdist bdist_wheel
+    - run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - run: python -m build
     - uses: actions/upload-artifact@v4
       if: success()
       with:
@@ -50,13 +53,15 @@ jobs:
         - '3.9'
         - '3.10'
         - '3.11'
+        - '3.12'
+        - '3.13'
     steps:
     - uses: actions/checkout@v4
     - run: pip install tox
     - run: tox -vv
 
   coverage:
-    needs: test-linux
+    needs: build
     runs-on: ubuntu-latest
     container:
       image: python:3.9
@@ -71,7 +76,7 @@ jobs:
   #   - run: codecov --token=$CODECOV_TOKEN
 
   examples-linux:
-    needs: coverage
+    needs: build
     runs-on: ubuntu-latest
     container:
       image: python:${{ matrix.version }}
@@ -85,22 +90,36 @@ jobs:
         - '3.9'
         - '3.10'
         - '3.11'
+        - '3.12'
+        - '3.13'
     steps:
     - uses: actions/checkout@v4.1.0
     - run: pip install tox
     - run: tox -vv
 
-  # deploy:
-  #   needs: examples-linux
-  #   runs-on: ubuntu-latest
-  #   container:
-  #     image: python:3.9
-  #   if: (github.ref == 'refs/tags//^2\..*$/') && !(startsWith(github.ref, 'refs/heads'))
-  #   timeout-minutes: 30
-  #   steps:
-  #   - uses: actions/checkout@v4.1.0
-  #   - uses: actions/download-artifact@v4.1.0
-  #     with:
-  #       name: "${{ github.job }}"
-  #   - run: pip install twine
-  #   - run: twine upload -u $PYPI_USER -p $PYPI_PASSWORD dist/*
+  deploy:
+    needs: [test-linux, coverage, examples-linux]
+    runs-on: ubuntu-latest
+    if: ${{ github.event_name == 'push' && startsWith(github.ref, 'refs/tags/2.')  }}
+    permissions:
+      id-token: write  # Required for OIDC PyPI publishing
+      contents: read
+    steps:
+      - name: Check out code
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.x'
+
+      - name: Install build dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+
+      - name: Build package
+        run: python -m build
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.pre-commit-config.yaml

@@ -5,13 +5,9 @@ exclude: |
     versioneer.py
   )$
 repos:
-  # Using this mirror lets us use mypyc-compiled black, which is about 2x faster
-  - repo: https://github.com/psf/black-pre-commit-mirror
-    rev: 23.9.1
-    hooks:
-      - id: black
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.1.3
+    rev: v0.9.4
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
+      - id: ruff-format

CONTRIBUTING.md

@@ -72,7 +72,7 @@ Commit messages should have the following structure:
 
 To set up your development environment, you will need:
 
-- Python 3.8 or higher
+- Python 3.9 or higher
 - Git
 
 You can clone the repository and install it from source:
@@ -104,12 +104,11 @@ pip install pytest
 pytest tests
 ```
 
-To build the documentation, you will need Sphinx amd the sphnix-rtd-theme:
+To build the documentation, you will need matploblib, sphinx and sphinx-rtd-theme:
 
 ```bash
-pip install sphinx
-pip install sphnix-rtd-theme
-cd docs
+pip install matplotlib sphinx sphinx-rtd-theme
+cd doc
 make html
 ```
 

README.md

@@ -1,8 +1,14 @@
 # Deltares RTC-Tools
 
-[![Pipeline](https://gitlab.com/deltares/rtc-tools/badges/master/pipeline.svg)](https://gitlab.com/deltares/rtc-tools/commits/master)
-[![Coverage](https://codecov.io/gl/deltares/rtc-tools/branch/master/graph/badge.svg)](https://codecov.io/gl/deltares/rtc-tools)
+[![Pipeline](https://github.com/deltares/rtc-tools/actions/workflows/rtc-tools.yml/badge.svg)](
+    https://github.com/deltares/rtc-tools/actions/workflows/rtc-tools.yml
+)
+[![Coverage](https://codecov.io/gl/deltares/rtc-tools/branch/master/graph/badge.svg)](
+    https://codecov.io/gl/deltares/rtc-tools
+)
 
+> **NOTE** The rtc-tools repository has been migrated from gitlab to here;
+see [migration from gitlab](#migration-from-gitlab).
 
 RTC-Tools is an open-source Python package for simulation and optimization of cyber-physical systems.  It can be used for model-predictive control and operational decision making of water and energy systems.  It is developed and maintained by Deltares, in collaboration with partners.
 
@@ -45,6 +51,19 @@ pip install rtc-tools
 Documentation and examples can be found on [readthedocs](https://rtc-tools.readthedocs.io).
 
 
+## Migration from GitLab
+
+The rtc-tools repository has been migrated from gitlab (https://gitlab.com/deltares/rtc-tools)
+to here.
+To change the git remote url, run
+
+`git remote set-url origin https://github.com/Deltares/rtc-tools.git`
+
+and
+
+`git remote set-url --push origin https://github.com/Deltares/rtc-tools.git`.
+
+
 ## License
 RTC-Tools is licensed under the **[GNU Lesser General Public License v3.0](https://gitlab.com/deltares/rtc-tools/-/blob/guidelines_contributions/COPYING)**, and can be used free of charge. Deltares offers support packages for users who require assistance.
 

doc/conf.py

@@ -20,7 +20,6 @@
 import os
 import re
 
-import sphinx_rtd_theme
 from rtctools._version import get_versions
 
 # -- General configuration ------------------------------------------------
@@ -77,7 +76,7 @@
 #
 # This is also used if you do content translation via gettext catalogs.
 # Usually you set "language" from the command line for these cases.
-language = None
+language = "en"
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
@@ -139,8 +138,6 @@
 # html_theme_options = {}
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
-
 html_static_path = ["_static"]
 
 html_css_files = [

doc/examples/optimization/ensemble.rst

@@ -243,6 +243,9 @@ should print out the following lines::
 This is the same output as the output for :doc:`mixed_integer`, except
 now the output for each ensemble is printed.
 
+
+.. _ensemble-results:
+
 Extracting Results
 ------------------
 
@@ -254,9 +257,6 @@ matplotlib:
 .. plot:: examples/pyplots/ensemble_results.py
    :include-source:
 
-
-.. _ensemble-results:
-
 This plots the inflow and release values in two different ways: the middle graph 
 depicts them in the same way you have seen until now (and this is how they truly 
 should be interpreted). The lower plot shows the same points, but connected with 

doc/examples/pyplots/basic_results.py

@@ -6,9 +6,13 @@
 
 # Import Data
 output_data_path = "../../../examples/basic/reference_output/timeseries_export.csv"
-results = np.recfromcsv(output_data_path, encoding=None)
+results = np.genfromtxt(
+    output_data_path, delimiter=",", encoding=None, dtype=None, names=True, case_sensitive="lower"
+)
 input_data_path = "../../../examples/basic/input/timeseries_import.csv"
-input_data = np.recfromcsv(input_data_path, encoding=None)
+input_data = np.genfromtxt(
+    input_data_path, delimiter=",", encoding=None, dtype=None, names=True, case_sensitive="lower"
+)
 
 # Get times as datetime objects
 times = [datetime.strptime(x, "%Y-%m-%d %H:%M:%S") for x in results["time"]]

doc/examples/pyplots/cascading_channels_results.py

@@ -6,7 +6,9 @@
 
 # Import Data
 data_path = "../../../examples/cascading_channels/reference_output/timeseries_export.csv"
-record = np.recfromcsv(data_path, encoding=None)
+record = np.genfromtxt(
+    data_path, delimiter=",", encoding=None, dtype=None, names=True, case_sensitive="lower"
+)
 
 # Get times as datetime objects
 times = [datetime.strptime(x, "%Y-%m-%d %H:%M:%S") for x in record["time"]]

doc/examples/pyplots/channel_pulse_results.py

@@ -9,17 +9,46 @@
 output_dir = Path("../../../examples/channel_pulse/reference_output/").resolve()
 
 # Import Data
-rtc_tools_record = np.recfromcsv(output_dir / "timeseries_export_inertial_wave.csv", encoding=None)
-rtc_tools_semi_impl_record = np.recfromcsv(
-    output_dir / "timeseries_export_inertial_wave_semi_implicit.csv", encoding=None
+rtc_tools_record = np.genfromtxt(
+    output_dir / "timeseries_export_inertial_wave.csv",
+    delimiter=",",
+    encoding=None,
+    dtype=None,
+    names=True,
+    case_sensitive="lower",
 )
-rtc_tools_conv_acc_record = np.recfromcsv(
-    output_dir / "timeseries_export_saint_venant.csv", encoding=None
+rtc_tools_semi_impl_record = np.genfromtxt(
+    output_dir / "timeseries_export_inertial_wave_semi_implicit.csv",
+    delimiter=",",
+    encoding=None,
+    dtype=None,
+    names=True,
+    case_sensitive="lower",
 )
-rtc_tools_conv_acc_upwind_record = np.recfromcsv(
-    output_dir / "timeseries_export_saint_venant_upwind.csv", encoding=None
+rtc_tools_conv_acc_record = np.genfromtxt(
+    output_dir / "timeseries_export_saint_venant.csv",
+    delimiter=",",
+    encoding=None,
+    dtype=None,
+    names=True,
+    case_sensitive="lower",
+)
+rtc_tools_conv_acc_upwind_record = np.genfromtxt(
+    output_dir / "timeseries_export_saint_venant_upwind.csv",
+    delimiter=",",
+    encoding=None,
+    dtype=None,
+    names=True,
+    case_sensitive="lower",
+)
+hec_ras_record = np.genfromtxt(
+    output_dir / "HEC-RAS_export.csv",
+    delimiter=",",
+    encoding=None,
+    dtype=None,
+    names=True,
+    case_sensitive="lower",
 )
-hec_ras_record = np.recfromcsv(output_dir / "HEC-RAS_export.csv", encoding=None)
 
 # Get times as datetime objects
 times = [datetime.strptime(x, "%Y-%m-%d %H:%M:%S") for x in rtc_tools_record["time"]]