Support Python 3.12, numpy >= 1.24 and pytest 8.0.x.

.github/workflows/build-docs.yml

@@ -16,7 +16,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v5
         with:
-          python-version: '3.11'
+          python-version: '3.12'
       - name: Install dependencies
         run: |
           pip install .

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest, windows-latest]
-        python-version: ['3.9', '3.11']
+        python-version: ['3.9', '3.12']
 
     steps:
       - uses: actions/checkout@v4

.readthedocs.yaml

@@ -12,7 +12,7 @@ sphinx:
 build:
   os: "ubuntu-22.04"
   tools:
-    python: "3.11"
+    python: "3.12"
 
 python:
   install:

docs/conf.py

@@ -158,7 +158,7 @@
     'xarray': ('https://docs.xarray.dev/en/stable/', None),
     'numpy': ('https://numpy.org/doc/stable/', None),
     'scipy': ('https://docs.scipy.org/doc/scipy/', None),
-    'pytest': ('https://docs.pytest.org/en/7.1.x/', None),
+    'pytest': ('https://docs.pytest.org/en/8.0.x/', None),
     'openpyxl': ('https://openpyxl.readthedocs.io/en/stable', None)
 }
 

docs/installation.rst

@@ -41,7 +41,7 @@ PySD requires **Python 3.9** or above.
 
 PySD builds on the core Python data analytics stack, and the following third party libraries:
 
-* Numpy < 1.24
+* Numpy >= 1.23
 * Scipy
 * Pandas (with Excel support: `pip install pandas[excel]`)
 * Parsimonious
@@ -65,7 +65,7 @@ In order to plot model outputs as shown in :doc:`Getting started <../getting_sta
 
 * Matplotlib
 
-To export data to netCDF (*.nc*) files:
+To export data to netCDF (*.nc*) files or to serialize external objects:
 
 * netCDF4
 

docs/whats_new.rst

@@ -1,5 +1,34 @@
 What's New
 ==========
+v3.13.3 (2024/02/02)
+--------------------
+New Features
+~~~~~~~~~~~~
+
+Breaking changes
+~~~~~~~~~~~~~~~~
+
+Deprecations
+~~~~~~~~~~~~
+
+Bug fixes
+~~~~~~~~~
+
+Documentation
+~~~~~~~~~~~~~
+- Improve documentation for :py:mod:`netCDF4` dependency. (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+
+Performance
+~~~~~~~~~~~
+
+Internal Changes
+~~~~~~~~~~~~~~~~
+- Support for Python 3.12. (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+- Support for :py:mod:`numpy` >= 1.24. (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+- Correct some warnings management in the tests. (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+- Fix :py:mod:`numpy` requirements to >= 1.23 to follow `NEP29 <https://numpy.org/neps/nep-0029-deprecation_policy.html>`_. (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+- Custom error messages when :py:mod:`netCDF4` is missing (:issue:`435`). (`@enekomartinmartinez <https://github.com/enekomartinmartinez>`_)
+
 v3.13.2 (2024/01/09)
 --------------------
 New Features

pysd/_version.py

@@ -1 +1 @@
-__version__ = "3.13.2"
+__version__ = "3.13.3"

pysd/builders/python/python_expressions_builder.py

@@ -460,10 +460,9 @@ def build_not_implemented(self, arguments: dict) -> BuildAST:
         """
         final_subscripts = self.reorder(arguments)
         warnings.warn(
-            "\n\nTrying to translate '"
-            + self.function.upper().replace("_", " ")
+            "Trying to translate '" + self.function.upper().replace("_", " ")
             + "' which it is not implemented on PySD. The translated "
-            + "model will crash... "
+            + "model will crash..."
         )
         self.section.imports.add("functions", "not_implemented_function")
 

pysd/py_backend/allocation.py

@@ -106,7 +106,11 @@ def get_functions(cls, q0, pp, kind):
             interval = interval.union(i)
 
         # Full allocation function -> function to solve
-        def full_allocation(x): return np.sum([func(x) for func in functions])
+        def full_allocation(x):
+            if isinstance(x, np.ndarray):
+                # Fix to solve issues in the newest numpy versions
+                x = x.squeeze()[()]
+            return np.sum([func(x) for func in functions])
 
         def_intervals = []
         for subinterval in interval:

pysd/py_backend/model.py

@@ -516,6 +516,11 @@ def initialize_external_data(self, externals=None):
         --------
         :func:`pysd.py_backend.model.Macro.serialize_externals`
 
+        Note
+        ----
+        To load externals from a netCDF file you need to have installed
+        the optional dependency `netCDF4`.
+
         """
 
         if not externals:
@@ -534,7 +539,11 @@ def initialize_external_data(self, externals=None):
         if not externals.is_file():
             raise FileNotFoundError(f"Invalid file path ({str(externals)})")
 
-        ds = xr.open_dataset(externals)
+        try:
+            ds = xr.open_dataset(externals)
+        except ValueError:  # pragma: no cover
+            raise ModuleNotFoundError("No module named 'netCDF4'")
+
 
         for ext in self._external_elements:
             if ext.py_name in ds.data_vars.keys():
@@ -607,6 +616,11 @@ def serialize_externals(self, export_path="externals.nc",
         --------
         :func:`pysd.py_backend.model.Macro.initialize_external_data`
 
+        Note
+        ----
+        To run this function you need to have installed the optional
+        dependency `netCDF4`.
+
         """
         data = {}
         metadata = {}
@@ -679,7 +693,10 @@ def serialize_externals(self, export_path="externals.nc",
         for key, values in metadata.items():
             ds[key].attrs = values
 
-        ds.to_netcdf(export_path)
+        try:
+            ds.to_netcdf(export_path)
+        except KeyError:  # pragma: no cover
+            raise ModuleNotFoundError("No module named 'netCDF4'")
 
     def __include_for_serialization(self, ext, py_name_clean, data, metadata,
                                     lookup_dims, data_dims):
@@ -1125,12 +1142,6 @@ def _set_components(self, params, new):
                 new_function = self._constant_component(value, dims)
                 self._dependencies[func_name] = {}
 
-            # this won't handle other statefuls...
-            if '_integ_' + func_name in dir(self.components):
-                warnings.warn("Replacing the equation of stock "
-                              "'{}' with params...".format(key),
-                              stacklevel=2)
-
             # copy attributes from the original object to proper working
             # of internal functions
             new_function.__name__ = func_name

pysd/py_backend/output.py

@@ -386,7 +386,7 @@ def make_flat_df(df, return_addresses, flatten=False):
             if is_dataarray and values[0].size == 1:
                 # some elements are returned as 0-d arrays, convert
                 # them to float
-                values = [float(x) for x in values]
+                values = [x.squeeze().values[()] for x in values]
                 is_dataarray = False
 
             if flatten and is_dataarray:

requirements.txt

@@ -1,4 +1,4 @@
-numpy<1.24
+numpy>=1.23
 pandas[excel]
 parsimonious
 xarray>=2023.9

setup.py

@@ -25,6 +25,7 @@
         'Programming Language :: Python :: 3.9',
         'Programming Language :: Python :: 3.10',
         'Programming Language :: Python :: 3.11',
+        'Programming Language :: Python :: 3.12',
     ],
     install_requires=open('requirements.txt').read().strip().split('\n'),
     package_data={

tests/conftest.py

@@ -53,5 +53,8 @@ def ignore_warns():
     # warnings to be ignored in the integration tests
     return [
         "numpy.ndarray size changed, may indicate binary incompatibility.",
-        "Creating an ndarray from ragged nested sequences.*"
+        "Creating an ndarray from ragged nested sequences.*",
+        "datetime.datetime.* is deprecated and scheduled for removal in a "
+        "future version. Use timezone-aware objects to represent datetimes "
+        "in UTC.*",
     ]

tests/pytest.ini

@@ -2,4 +2,6 @@
 python_files = pytest_*/**/*.py pytest_*/*.py
 filterwarnings =
     error
-    ignore:numpy.ndarray size changed, may indicate binary incompatibility.:RuntimeWarning
+    always:numpy.ndarray size changed, may indicate binary incompatibility.:RuntimeWarning
+    always::DeprecationWarning
+    always::PendingDeprecationWarning

tests/pytest_builders/pytest_python.py

@@ -1,6 +1,7 @@
-import pytest
 from pathlib import Path
 
+import pytest
+
 from pysd.builders.python.namespace import NamespaceManager
 from pysd.builders.python.subscripts import SubscriptManager
 from pysd.builders.python.python_model_builder import\
@@ -147,13 +148,13 @@ def test_referencebuilder_subscripts_warning(self, component,
         component.section.subscripts.mapping = {
             dim: [] for dim in subscripts}
         component.section.namespace.namespace = namespace
-        warning_message =\
+        warn_message =\
             f"The reference to '{origin_name}' in variable 'My Var' has "\
             r"duplicated subscript ranges\. If mapping is used in one "\
             r"of them, please, rewrite reference subscripts to avoid "\
             r"duplicates\. Otherwise, the final model may crash\.\.\."\
 
-        with pytest.warns(UserWarning, match=warning_message):
+        with pytest.warns(UserWarning, match=warn_message):
             ReferenceBuilder(reference_str, component)
 
     @pytest.mark.parametrize(

tests/pytest_integration/pytest_integration_vensim_pathway.py

@@ -564,6 +564,7 @@
         "file": "test_subscripted_round.mdl",
         "warns": [
             "Variable '.*' is defined with different .*types: '.*'",
+            "invalid value encountered in cast"
         ]
     },
     "subscripted_smooth": {

tests/pytest_pysd/pytest_errors.py

@@ -1,6 +1,8 @@
-import pytest
+import re
 import shutil
 
+import pytest
+
 from pysd import read_vensim, read_xmile, load
 
 
@@ -92,13 +94,21 @@ def test_loading_error(loader, model_path, raise_type, error_message):
     ]
 )
 def test_not_implemented_and_incomplete(model_path):
-    with pytest.warns(UserWarning) as ws:
+    with pytest.warns() as record:
         model = read_vensim(model_path)
-        assert "'incomplete var' has no equation specified"\
-            in str(ws[0].message)
-        assert "Trying to translate 'MY FUNC' which it is not implemented"\
-            " on PySD. The translated model will crash..."\
-            in str(ws[1].message)
+
+    warn_message = "'incomplete var' has no equation specified"
+    assert any([
+        re.match(warn_message, str(warn.message))
+        for warn in record
+    ]), f"Couldn't match warning:\n{warn_message}"
+
+    warn_message = "Trying to translate 'MY FUNC' which it is "\
+        "not implemented on PySD. The translated model will crash..."
+    assert any([
+        re.match(warn_message, str(warn.message))
+        for warn in record
+    ]), f"Couldn't match warning:\n{warn_message}"
 
     with pytest.warns(RuntimeWarning,
          match="Call to undefined function, calling dependencies "

tests/pytest_pysd/pytest_functions.py

@@ -574,7 +574,7 @@ def test_get_time_value_errors(self, measure, relativeto,
                 lambda: 0, relativeto, np.random.randint(-100, 100), measure)
 
     def test_vector_select(self):
-        warning_message =\
+        warn_message =\
             r"Vensim's help says that numerical_action=5 computes the "\
             r"product of selection_array \^ expression_array\. But, in fact,"\
             r" Vensim is computing the product of expression_array \^ "\
@@ -584,7 +584,7 @@ def test_vector_select(self):
         array = xr.DataArray([3, 10, 2], {'dim': ["A", "B", "C"]})
         sarray = xr.DataArray([1, 0, 2], {'dim': ["A", "B", "C"]})
 
-        with pytest.warns(UserWarning, match=warning_message):
+        with pytest.warns(UserWarning, match=warn_message):
             assert vector_select(sarray, array, ["dim"], np.nan, 5, 1)\
                 == 12
 

tests/pytest_pysd/pytest_output.py

@@ -116,7 +116,7 @@ class EmptyHandler(OutputHandlerInterface):
 
     @pytest.mark.parametrize("model_path", [test_model_look])
     def test_invalid_output_file(self, model):
-        error_message = "expected str, bytes or os.PathLike object, not int"
+        error_message = ".* str.* os.PathLike object.*"
         with pytest.raises(TypeError, match=error_message):
             model.run(output_file=1234)
 

tests/pytest_pysd/pytest_pysd.py

@@ -1,3 +1,4 @@
+import re
 from pathlib import Path
 
 import pytest
@@ -140,13 +141,13 @@ def test_run_return_timestamps(self, model):
 
         # assert one timestamp is not returned because is not multiple of
         # the time step
-        warning_message =\
+        warn_message =\
             "The returning time stamp '%s' seems to not be a multiple "\
             "of the time step. This value will not be saved in the output. "\
             "Please, modify the returning timestamps or the integration "\
             "time step to avoid this."
         # assert that return_timestamps works with float error
-        with pytest.warns(UserWarning, match=warning_message % 0.55):
+        with pytest.warns(UserWarning, match=warn_message % 0.55):
             stocks = model.run(
                 time_step=0.1, return_timestamps=[0.3, 0.1, 0.55, 0.9])
         assert 0.1 in stocks.index
@@ -155,7 +156,7 @@ def test_run_return_timestamps(self, model):
         assert 0.55 not in stocks.index
 
         with pytest.warns(UserWarning,
-                          match=warning_message % "(0.15|0.55|0.95)"):
+                          match=warn_message % "(0.15|0.55|0.95)"):
             stocks = model.run(
                 time_step=0.1, return_timestamps=[0.3, 0.15, 0.55, 0.95])
         assert 0.15 not in stocks.index
@@ -348,13 +349,19 @@ def test_set_component_with_real_name(self, model):
     @pytest.mark.parametrize("model_path", [test_model])
     def test_set_components_warnings(self, model):
         """Addresses https://github.com/SDXorg/pysd/issues/80"""
-        warn_message = r"Replacing the equation of stock "\
-                       r"'Teacup Temperature' with params\.\.\."
-        with pytest.warns(UserWarning, match=warn_message):
+        warn_message = r"Replacing the value of Stateful variable with "\
+            r"an expression\. To set initial conditions use "\
+            r"`set_initial_condition` instead\.\.\."
+        with pytest.warns() as record:
             model.set_components(
                 {"Teacup Temperature": 20, "Characteristic Time": 15}
             )  # set stock value using params
 
+        assert any([
+            re.match(warn_message, str(warn.message))
+            for warn in record
+        ]), f"Couldn't match warning:\n{warn_message}"
+
     @pytest.mark.parametrize("model_path", [test_model])
     def test_set_components_with_function(self, model):
         def test_func():
@@ -967,12 +974,17 @@ def test_set_initial_value_subscripted_value_with_numpy_error(self, model):
 
     @pytest.mark.parametrize("model_path", [test_model])
     def test_replace_stateful(self, model):
-        warn_message = "Replacing the value of Stateful variable with "\
-                       "an expression. To set initial conditions use "\
-                       "`set_initial_condition` instead..."
-        with pytest.warns(UserWarning, match=warn_message):
+        warn_message = r"Replacing the value of Stateful variable with "\
+            r"an expression\. To set initial conditions use "\
+            r"`set_initial_condition` instead\.\.\."
+        with pytest.warns() as record:
             model.components.teacup_temperature = 3
 
+        assert any([
+            re.match(warn_message, str(warn.message))
+            for warn in record
+        ]), f"Couldn't match warning:\n{warn_message}"
+
         stocks = model.run()
         assert np.all(stocks["Teacup Temperature"] == 3)