Publish new version

.flake8

@@ -0,0 +1,4 @@
+[flake8]
+extend-ignore = E203
+max-line-length = 120
+exclude = doc,test,.git,.venv,__pycache__,venv

.github/workflows/automatic_test.yml

@@ -1,6 +1,7 @@
 name: unittest on push
 
 on:
+  pull_request:
   push:
     branches:
       - master
@@ -9,13 +10,16 @@ on:
 jobs:
   test:
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - name: Prepare the repo
-        uses: actions/checkout@master
-      - name: Set up Python 3.11
-        uses: actions/setup-python@v1
+        uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
         with:
-          python-version: 3.11
+          python-version: ${{ matrix.python-version }}
       - name: Install packages
         run: pip install -r test/unittest/test_requirements.txt
       - name: Test

.github/workflows/pre-commit.yaml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [master]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.11'
+    - uses: pre-commit/action@v3.0.1

.github/workflows/publish_to_pypi.yml

@@ -24,4 +24,4 @@ jobs:
     - name: Publish on PyPI
       uses: pypa/gh-action-pypi-publish@master
       with:
-        password: ${{ secrets.PYPI_ACCESS_TOKEN }}
+        password: ${{ secrets.PYPI_ACCESS_TOKEN }}

.gitignore

@@ -2,4 +2,4 @@
 build/
 dist/
 superflexpy.egg-info/
-**/.ipynb_checkpoints
+**/.ipynb_checkpoints

.pre-commit-config.yaml

@@ -0,0 +1,22 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-added-large-files
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8
+        exclude: ^(doc/|^test/)
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: ["--profile", "black", "--filter-files"]
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black

AUTHORS

@@ -4,4 +4,4 @@ Format: Name Surname, Affiliation, e-mail
 
 Marco Dal Molin, EAWAG, marco.dalmolin.1991@gmail.com
 Fabrizio Fenicia, EAWAG, fabrizio.fenicia@eawag.ch
-Dmitri Kavetski, University of Adelaide, dmitri.kavetski@adelaide.edu.au
+Dmitri Kavetski, University of Adelaide, dmitri.kavetski@adelaide.edu.au

README.md

@@ -11,4 +11,9 @@ flexible, conceptual, distributed hydrological models.
 Refer to the [documentation](https://superflexpy.readthedocs.io/) to learn to
 use the SuperflexPy, [install](https://pypi.org/project/superflexpy/) the
 package from here. [Examples](examples/) showing the basic usage of SuperflexPy
-are available.
+are available.
+
+## Development
+
+Please install all packages listed in the [requirements_dev.txt](requirements_dev.txt) file,
+the run `pre-commit install` to install the git hooks. This will enable code formatting and linting on every git commit.

doc/build_element_code.py

@@ -1,8 +1,7 @@
 import numba as nb
 import numpy as np
-from superflexpy.framework.element import ODEsElement
-from superflexpy.framework.element import LagElement
-from superflexpy.framework.element import ParameterizedElement
+
+from superflexpy.framework.element import LagElement, ODEsElement, ParameterizedElement
 
 # Implement a linear reservoir
 
@@ -27,22 +26,18 @@ class LinearReservoir(ODEsElement):
     """
 
     def __init__(self, parameters, states, approximation, id):
-
-        ODEsElement.__init__(self,
-                             parameters=parameters,
-                             states=states,
-                             approximation=approximation,
-                             id=id)
+        ODEsElement.__init__(self, parameters=parameters, states=states, approximation=approximation, id=id)
 
         self._fluxes_python = [self._fluxes_function_python]  # Used by get fluxes, regardless of the architecture
 
-        if approximation.architecture == 'numba':
+        if approximation.architecture == "numba":
             self._fluxes = [self._fluxes_function_numba]
-        elif approximation.architecture == 'python':
+        elif approximation.architecture == "python":
             self._fluxes = [self._fluxes_function_python]
         else:
-            message = '{}The architecture ({}) of the approximation is not correct'.format(self._error_message,
-                                                                                           approximation.architecture)
+            message = "{}The architecture ({}) of the approximation is not correct".format(
+                self._error_message, approximation.architecture
+            )
             raise ValueError(message)
 
     def set_input(self, input):
@@ -57,7 +52,7 @@ def set_input(self, input):
             1. Rainfall
         """
 
-        self.input = {'P': input[0]}
+        self.input = {"P": input[0]}
 
     def get_output(self, solve=True):
         """
@@ -72,65 +67,58 @@ def get_output(self, solve=True):
         """
 
         if solve:
-            self._solver_states = [self._states[self._prefix_states + 'S0']]
+            self._solver_states = [self._states[self._prefix_states + "S0"]]
             self._solve_differential_equation()
 
             # Update the state
-            self.set_states({self._prefix_states + 'S0': self.state_array[-1, 0]})
-
-        fluxes = self._num_app.get_fluxes(fluxes=self._fluxes_python,
-                                          S=self.state_array,
-                                          S0=self._solver_states,
-                                          dt=self._dt,
-                                          **self.input,
-                                          **{k[len(self._prefix_parameters):]: self._parameters[k] for k in self._parameters},
-                                          )
-        return [- fluxes[0][1]]
+            self.set_states({self._prefix_states + "S0": self.state_array[-1, 0]})
+
+        fluxes = self._num_app.get_fluxes(
+            fluxes=self._fluxes_python,
+            S=self.state_array,
+            S0=self._solver_states,
+            dt=self._dt,
+            **self.input,
+            **{k[len(self._prefix_parameters) :]: self._parameters[k] for k in self._parameters},
+        )
+        return [-fluxes[0][1]]
 
     @staticmethod
     def _fluxes_function_python(S, S0, ind, P, k, dt):
-
         if ind is None:
             return (
                 [
                     P,
-                    - k * S,
+                    -k * S,
                 ],
                 0.0,
-                S0 + P * dt
+                S0 + P * dt,
             )
         else:
             return (
                 [
                     P[ind],
-                    - k[ind] * S,
+                    -k[ind] * S,
                 ],
                 0.0,
                 S0 + P[ind] * dt[ind],
-                [
-                    0.0,
-                    - k[ind]
-                ]
+                [0.0, -k[ind]],
             )
 
     @staticmethod
-    @nb.jit('Tuple((UniTuple(f8, 2), f8, f8))(optional(f8), f8, i4, f8[:], f8[:], f8[:])',
-            nopython=True)
+    @nb.jit("Tuple((UniTuple(f8, 2), f8, f8))(optional(f8), f8, i4, f8[:], f8[:], f8[:])", nopython=True)
     def _fluxes_function_numba(S, S0, ind, P, k, dt):
-
         return (
             (
                 P[ind],
-                - k[ind] * S,
+                -k[ind] * S,
             ),
             0.0,
             S0 + P[ind] * dt[ind],
-            (
-                0.0,
-                - k[ind]
-            )
+            (0.0, -k[ind]),
         )
 
+
 # Implement lag function
 
 
@@ -152,33 +140,31 @@ class TriangularLag(LagElement):
     """
 
     def _build_weight(self, lag_time):
-
         weight = []
 
         for t in lag_time:
             array_length = np.ceil(t)
             w_i = []
 
             for i in range(int(array_length)):
-                w_i.append(self._calculate_lag_area(i + 1, t)
-                           - self._calculate_lag_area(i, t))
+                w_i.append(self._calculate_lag_area(i + 1, t) - self._calculate_lag_area(i, t))
 
             weight.append(np.array(w_i))
 
         return weight
 
     @staticmethod
     def _calculate_lag_area(bin, len):
-
         if bin <= 0:
             value = 0
         elif bin < len:
-            value = (bin / len)**2
+            value = (bin / len) ** 2
         else:
             value = 1
 
         return value
 
+
 # Implement a parametrized splitter
 
 
@@ -214,7 +200,7 @@ def set_input(self, input):
             1. Incoming flow
         """
 
-        self.input = {'Q_in': input[0]}
+        self.input = {"Q_in": input[0]}
 
     def get_output(self, solve=True):
         """
@@ -233,9 +219,6 @@ def get_output(self, solve=True):
 
         # solve is not needed but kept in the interface
 
-        split_par = self._parameters[self._prefix_parameters + 'split-par']
+        split_par = self._parameters[self._prefix_parameters + "split-par"]
 
-        return [
-            self.input['Q_in'] * split_par,
-            self.input['Q_in'] * (1 - split_par)
-        ]
+        return [self.input["Q_in"] * split_par, self.input["Q_in"] * (1 - split_par)]

doc/case_studies.rst

@@ -155,4 +155,4 @@ We can now run the model and access its output (see :ref:`demo_network` for deta
 .. literalinclude:: model_thur_hess2020.py
    :language: python
    :lines: 262
-   :linenos:
+   :linenos:

doc/changelog.rst

@@ -1,18 +1,8 @@
-.. note:: Last update 25/11/2023
+.. note:: Last update 29/11/2021
 
 Change log
 ==========
 
-Version 1.3.2
--------------
-
-Minor changes
-.............
-
-- `Pull request <https://github.com/dalmo1991/superflexPy/pull/9>`_ from
-  `alessandro-mariotti-zupit <https://github.com/alessandro-mariotti-zupit>`_
-  that upgrades python and packages versions.
-
 Version 1.3.1
 -------------
 
@@ -126,4 +116,4 @@ Minor changes to existing components
 New code
 ........
 
-- Added :code:`hymod` elements
+- Added :code:`hymod` elements

doc/components.rst

@@ -217,7 +217,7 @@ In the schematic, element E3 receives 3 input fluxes, which are indexed based
 on their order: red (index 0), black (index 1), and blue (index 2). The red flux
 comes from both upstream elements (index 0 and 1, respectively); the black flux
 comes only from element E1 (index 1); the blue flux comes only from element E2
-(index 2). This information is represented by the direction matrix
+(index 0). This information is represented by the direction matrix
 :math:`\mathbf{D}` as follows:
 
 .. math::

doc/components_code.py

@@ -1,8 +1,8 @@
-e1 = Element(parameters={'p1': 0.1}, states={'S': 10.0})
+e1 = Element(parameters={"p1": 0.1}, states={"S": 10.0})
 
 u1 = Unit([e1])
 u2 = Unit([e1])
 
-e1.set_parameters({'e1_p1': 0.2})
-u1.set_parameters({'u1_e1_p1': 0.3})
-u2.set_parameters({'u2_e1_p1': 0.4})
+e1.set_parameters({"e1_p1": 0.2})
+u1.set_parameters({"u1_e1_p1": 0.3})
+u2.set_parameters({"u2_e1_p1": 0.4})