add 3.13, remove 3.10 (#142)

* add 3.13, remove 3.10, add numba coverage

* move to uv in ghactions

* add ruff to ci deps

* ruff and typo

* this is ttim ofc

* remove coveralls parallel
- seems overkill since all tests produce same coverage, no need to gather reports and merge after.

Author: dbrakenhoff

.github/workflows/ci.yml

@@ -17,48 +17,36 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: ["3.10", "3.11", "3.12"]
+        python-version: ["3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
 
-      - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+      - name: Install uv with Python ${{ matrix.python-version }}
+        uses: astral-sh/setup-uv@v6
         with:
+          enable-cache: true
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install -e .[ci]
+      - name: Install the project
+        run: uv sync --all-extras
 
       - name: ruff-lint
-        uses: chartboost/ruff-action@v1
+        run: uv run ruff check
 
       - name: ruff-format
-        uses: chartboost/ruff-action@v1
-        with:
-          args: "format --check"
+        run: uv run ruff format --check
 
       - name: Run tests
-        run: |
-          pytest ./tests
+        run: uv run pytest ./tests
 
       - name: Numba coverage
         run: |
-          NUMBA_DISABLE_JIT=1 pytest --cov-append ./tests/test_bessel.py 
+          NUMBA_DISABLE_JIT=1 uv run pytest --cov-append ./tests/test_bessel.py
 
 
       - name: Publish to coveralls.io
         uses: coverallsapp/github-action@v2
         with:
-          parallel: true
           github-token: ${{ secrets.GITHUB_TOKEN }}
-  
-  finish:
-    needs: test
-    runs-on: ubuntu-latest
-    steps:
-      - name: Close parallel build
-        uses: coverallsapp/github-action@v2
-        with:
-          parallel-finished: true
+  

pyproject.toml

@@ -14,7 +14,7 @@ maintainers = [
     { name = "Mark Bakker", email = "markbak@gmail.com" },
     { name = "Davíd Brakenhoff", email = "d.brakenhoff@artesia-water.nl" },
 ]
-requires-python = ">= 3.10"
+requires-python = ">= 3.11"
 dependencies = ["numpy", "scipy", "numba", "matplotlib", "lmfit", "pandas"]
 
 keywords = ["hydrology", "groundwater", "model", "analytic element method"]
@@ -29,9 +29,9 @@ classifiers = [
     "Operating System :: MacOS",
     "Programming Language :: Python",
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
+    "Programming Language :: Python :: 3.13",
     "Programming Language :: Python :: 3 :: Only",
     "Topic :: Scientific/Engineering :: Hydrology",
 ]
@@ -49,6 +49,7 @@ ci = [
     "jupyter",
     "shapely",
     "coveralls",
+    "ruff",
     "timml",
 ]
 docs = [

pytest.ini

@@ -1,4 +1,10 @@
 [pytest]
-addopts=--durations=0 -v --cov ttim --cov-config=.coveragerc
+addopts=    
+    --durations=0
+    -v
+    --cov=ttim
+    --cov-config=.coveragerc
+    --cov-report=lcov:./coverage/lcov.info
+    --cov-report=term
 markers =
     notebooks: run notebooks

ttim/aquifer.py

@@ -148,7 +148,7 @@ def compute_lab_eigvec(self, p, returnA=False, B=None):
         )
         d0 = p / self.D
         if B is not None:
-            d0 = d0 * B  # B is vector of load efficiency paramters
+            d0 = d0 * B  # B is vector of load efficiency parameters
         d0[:-1] += a[1:] / (self.c[1:] * self.T[:-1])
         d0[1:] += a[1:] / (self.c[1:] * self.T[1:])
         if self.topboundary[:3] == "lea":

ttim/src/test_bessel.py

@@ -1,6 +1,6 @@
 import numpy as np
-
 from ttim.bessel import bessel  # fortran compiled funcs
+
 from ttim.besselnumba import besselnumba  # numba funcs
 
 bessel.initialize()