Release 0.1.1a12

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
       - uses: pre-commit/action@v3.0.1
 
   test:
@@ -26,7 +26,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ ubuntu-latest, macos-latest, windows-latest ]
-        python-version: [ "3.10", "3.11", "3.12", "3.13"]
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
     - uses: actions/checkout@v4
@@ -36,9 +36,9 @@ jobs:
         python-version: ${{ matrix.python-version }}
 
     - name: Install Poetry
-      uses: abatilo/actions-poetry@v4.0.0
-      with:
-        poetry-version: 1.5.1
+      run: |
+        pipx install poetry --python python${{ matrix.python-version }}
+        poetry --version
 
     - name: Install dependencies
       run: poetry install
@@ -53,7 +53,7 @@ jobs:
              github.event.pull_request.user.login == 'pre-commit-ci[bot]'
             ) && (
              matrix.os == 'ubuntu-latest' && 
-             matrix.python-version == '3.10'
+             matrix.python-version == '3.11'
             )
           }}
       uses: codecov/codecov-action@v5
@@ -68,13 +68,13 @@ jobs:
       - uses: actions/checkout@v4
       - uses: actions/setup-python@v5
         with:
-          python-version: "3.10"
+          python-version: "3.11"
 
       - name: Install Poetry
-        uses: abatilo/actions-poetry@v4.0.0
-        with:
-          poetry-version: 1.5.1
-
+        run: |
+          pipx install poetry --python python3.11
+          poetry --version
+      
       - name: Install dependencies
         run: poetry install
 

docs/source/conf.py

@@ -144,6 +144,7 @@ class MyReferenceStyle(AuthorYearReferenceStyle):
     ("py:class", "dataclasses.InitVar"),
     ("py:class", "Quantity"),
     ("py:class", "numpy._typing._array_like._ScalarType_co"),
+    ("py:class", "numpy._typing._array_like._ScalarT"),
     # God only knows why this is needed. We don't refer to pint.util.Quantity and it
     # isn't in the pint objects.inv, so why the hell is intersphinx trying to build
     # references to it.

docs/source/using_the_ve/virtual_ecosystem_in_static_mode.md

@@ -163,14 +163,11 @@ Once the baseline run is complete, you can set up the experiment with default
 
 # Generate the static config file programmatically
 import sys
+import tomllib
 from pathlib import Path
 
 import tomli_w
 
-if sys.version_info[:2] >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib
 
 # Create output directory
 output_dir = Path("/tmp/ve_example/HydroDefault_out/")

pyproject.toml

@@ -1,16 +1,16 @@
-[tool.poetry]
+[project]
 authors = [
-  "Rob Ewers <r.ewers@imperial.ac.uk>",
-  "David Orme <d.orme@imperial.ac.uk>",
-  "Jacob Cook <j.cook17@imperial.ac.uk>",
-  "Vivienne Groner <v.groner@imperial.ac.uk>",
-  "Taran Rallings <t.rallings@imperial.ac.uk>",
-  "Olivia Daniel <olivia.daniel08@imperial.ac.uk>",
-  "Jaideep Joshi <joshi@iiasa.ac.at>",
-  "Anna Rallings <a.rallings@imperial.ac.uk>",
-  "Priyanga Amarasekare <pamarasekare@gmail.com>",
-  "Diego Alonso Alvarez <d.alonso-alvarez@imperial.ac.uk>",
-  "Alex Dewar <a.dewar@imperial.ac.uk>",
+  {name = "Rob Ewers", email = "r.ewers@imperial.ac.uk"},
+  {name = "David Orme", email = "d.orme@imperial.ac.uk"},
+  {name = "Jacob Cook", email = "j.cook17@imperial.ac.uk"},
+  {name = "Vivienne Groner", email = "v.groner@imperial.ac.uk"},
+  {name = "Taran Rallings", email = "t.rallings@imperial.ac.uk"},
+  {name = "Olivia Daniel", email = "olivia.daniel08@imperial.ac.uk"},
+  {name = "Jaideep Joshi", email = "joshi@iiasa.ac.at"},
+  {name = "Anna Rallings", email = "a.rallings@imperial.ac.uk"},
+  {name = "Priyanga Amarasekare", email = "pamarasekare@gmail.com"},
+  {name = "Diego Alonso Alvarez", email = "d.alonso-alvarez@imperial.ac.uk"},
+  {name = "Alex Dewar", email = "a.dewar@imperial.ac.uk"},
 ]
 classifiers = [
   "Development Status :: 2 - Pre-Alpha",
@@ -19,33 +19,40 @@ classifiers = [
   "Topic :: Scientific/Engineering",
 ]
 description = """An holistic ecosystem simulation model."""
-homepage = "https://virtual-ecosystem.readthedocs.io/"
 license = "BSD-3-Clause"
+license-files = ["LICENSE"]
 name = "virtual_ecosystem"
 readme = "README.md"
-repository = "https://github.com/ImperialCollegeLondon/virtual_ecosystem"
-version = "0.1.1a11"
+version = "0.1.1a12"
+
+requires-python = ">=3.11"
+
+dependencies = [
+  "Shapely (>2.0)",
+  "dask (>2023.6)",
+  "dpath (>2.0)",
+  "jsonschema (>4.14)",
+  "netcdf4 (>1.6)",
+  "numpy  (>2.0)",
+  "openpyxl (>3.1)",
+  "pint (>0.24)",
+  "pyrealm (>=2.0.0rc5)",
+  "scipy (>1.12)",
+  "tomli-w  (>1.0)",
+  "tqdm (>4.66)",
+  "xarray (>2024.6)",
+  "types-tabulate (>0.9)",
+]
 
-[tool.poetry.scripts]
+[project.scripts]
 ve_run = "virtual_ecosystem.entry_points:ve_run_cli"
 
-[tool.poetry.dependencies]
-Shapely = "^2.0"
-dask = ">=2023.6,<2026.0"
-dpath = "^2.0.6"
-jsonschema = "^4.14.0"
-netcdf4 = "^1.6.5"
-numpy = "^2.0"
-openpyxl = "^3.1.5"
-pint = "^0.24.1"
-pyrealm = {git = "https://github.com/ImperialCollegeLondon/pyrealm.git", branch = "develop"}
-python = ">=3.10,<3.14"
-scipy = "^1.9.0"
-tomli = {version = "^2.0.1", python = "<3.11"}
-tomli-w = "^1.0.0"
-tqdm = "^4.66.2"
-xarray = ">=2024.6,<2026.0"
-types-tabulate = "^0.9.0.20241207"
+[project.urls]
+homepage = "https://virtual-ecosystem.readthedocs.io/"
+repository = "https://github.com/ImperialCollegeLondon/virtual_ecosystem"
+
+[tool.poetry]
+requires-poetry = ">=2.0"
 
 [tool.poetry.group.types.dependencies]
 types-dataclasses = "^0.6.6"
@@ -104,7 +111,7 @@ python_files = 'test_*.py'
 testpaths = ['tests']
 
 [tool.ruff]
-target-version = "py310"
+target-version = "py311"
 
 [tool.ruff.lint]
 # Enable all `pydocstyle` rules, limiting to those that adhere to the

tests/core/test_variables.py

@@ -1,14 +1,7 @@
 """Tests for the virtual_ecosystem.core.variables module."""
 
-import sys
-
 import pytest
 
-if sys.version_info[:2] >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib  # noqa: F401
-
 
 @pytest.fixture(autouse=True)
 def known_variables():

virtual_ecosystem/core/config.py

@@ -8,7 +8,7 @@
 module for details.
 """  # noqa: D205
 
-import sys
+import tomllib
 from collections.abc import Sequence
 from copy import deepcopy
 from pathlib import Path
@@ -22,11 +22,6 @@
 from virtual_ecosystem.core.registry import MODULE_REGISTRY, register_module
 from virtual_ecosystem.core.schema import ValidatorWithDefaults, merge_schemas
 
-if sys.version_info[:2] >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib
-
 
 def config_merge(
     dest: dict, source: dict, conflicts: tuple = (), path: str = ""

virtual_ecosystem/core/variables.py

@@ -29,7 +29,7 @@
 
 import json
 import pkgutil
-import sys
+import tomllib
 from collections.abc import Hashable
 from dataclasses import asdict, dataclass, field
 from graphlib import CycleError, TopologicalSorter
@@ -46,11 +46,6 @@
 from virtual_ecosystem.core.logger import LOGGER
 from virtual_ecosystem.core.schema import ValidatorWithDefaults
 
-if sys.version_info[:2] >= (3, 11):
-    import tomllib
-else:
-    import tomli as tomllib
-
 
 def to_camel_case(snake_str: str) -> str:
     """Convert a snake_case string to CamelCase.

virtual_ecosystem/entry_points.py

@@ -7,9 +7,11 @@
 import argparse
 import sys
 import textwrap
+import tomllib
 from collections.abc import Sequence
 from pathlib import Path
 from shutil import copytree, ignore_patterns
+from tomllib import TOMLDecodeError
 from typing import Any
 
 import virtual_ecosystem as ve
@@ -19,13 +21,6 @@
 from virtual_ecosystem.core.logger import LOGGER
 from virtual_ecosystem.main import Progress, ve_run
 
-if sys.version_info[:2] >= (3, 11):
-    import tomllib
-    from tomllib import TOMLDecodeError
-else:
-    import tomli as tomllib
-    from tomli import TOMLDecodeError
-
 
 def _parse_param_str(s: str) -> dict[str, Any]:
     """Parse a single parameter string into a dict.

virtual_ecosystem/models/hydrology/above_ground.py

@@ -307,7 +307,7 @@ def calculate_soil_evaporation(
     saturation_vapour_pressure = calc_vp_sat(
         ta=temperature,
         core_const=pyrealm_const(),
-    ).astype(np.floating)  # pyrealm returning np.float64
+    )
 
     saturated_specific_humidity = (
         gas_constant_water_vapour * saturation_vapour_pressure

virtual_ecosystem/models/plants/plants_model.py

@@ -1278,7 +1278,7 @@ def partition_reproductive_tissue(
 
         non_propagule_mass = reproductive_tissue_mass - (
             n_propagules * self.model_constants.carbon_mass_per_propagule
-        ).astype(np.integer)
+        )
 
         return n_propagules, non_propagule_mass