Test against minimum dependencies, remove old deps (#2301)

Co-authored-by: Vecko <36369090+VeckoTheGecko@users.noreply.github.com>

Author: andrew-s28

.github/ci/recipe.yaml

@@ -29,23 +29,22 @@ requirements:
     - wheel
   run:
     - python >=3.11
-    - cftime
-    - dask
+    - cftime >=1.6.3
+    - dask >=2024.5.1
     - matplotlib-base >=2.0.2
-    - netcdf4 >=1.1.9
-    - numpy >=1.11
+    - netcdf4 >=1.7.2
+    - numpy >=2.1.0
     - platformdirs
     - pytest
-    - scipy >=0.16.0
     - trajan
-    - tqdm
-    - xarray >=0.10.8
-    - cf_xarray
-    - xgcm
-    - zarr >=2.11.0,!=2.18.0,<3
+    - tqdm >=4.50.0
+    - xarray >=2024.5.0
+    - cf_xarray >=0.8.6
+    - xgcm >=0.9.0
+    - zarr >=2.15.0,!=2.18.0,<3
     - uxarray>=2025.3.0
     - pyogrio # needed for geopandas (uxarray -> geoviews -> geopandas -> pyogrio, but for some reason conda doesn't pick it up automatically)
-    - pooch
+    - pooch >=1.8.0
 
 tests:
   - python:

.github/workflows/ci.yml

@@ -33,6 +33,8 @@ jobs:
         include:
           - os: ubuntu
             pixi-environment: "test-py311"
+          - os: ubuntu
+            pixi-environment: "test-minimum"
     steps:
       - uses: actions/checkout@v4
       - name: Restore cached pixi lockfile

.gitignore

@@ -29,5 +29,8 @@ src/parcels/_version_setup.py
 .pixi
 *.egg-info
 
-# Ignore pixi.lock file for now as Vecko is the only one using pixi for development. This should be checked into VCS if it becomes a more common tool.
+# Ignore pixi.lock file for this project. The con of 22k lines of noise it adds to diffs is not worth
+# the minor benefit of perfectly reproducible environments for all developers (and all the tooling that would
+# be required to support that - see https://github.com/pydata/xarray/issues/10732#issuecomment-3327780806
+# for more details)
 pixi.lock

pixi.toml

@@ -18,6 +18,7 @@ setuptools_scm = "*"
 
 [environments]
 test-latest = { features = ["test"], solve-group = "test" }
+test-minimum = { features = ["test", "minimum"], solve-group = "test" }
 test-py311 = { features = ["test", "py311"] }
 test-py312 = { features = ["test", "py312"] }
 test-notebooks = { features = ["test", "notebooks"], solve-group = "test" }
@@ -28,19 +29,31 @@ pre-commit = { features = ["pre-commit"], no-default-feature = true }
 [dependencies] # keep section in sync with pyproject.toml dependencies
 python = ">=3.11,<3.13"
 parcels = { path = "." }
-netcdf4 = ">=1.1.9"
-numpy = ">=1.9.1"
-tqdm = "*"
-xarray = ">=0.10.8"
+netcdf4 = ">=1.7.2"
+numpy = ">=2.1.0"
+tqdm = ">=4.50.0"
+xarray = ">=2024.5.0"
 uxarray = ">=2025.3.0"
-dask = ">=2.0"
-scikit-learn = "*"
-zarr = ">=2.11.0,!=2.18.0,<3"
+dask = ">=2024.5.1"
+zarr = ">=2.15.0,!=2.18.0,<3"
 xgcm = ">=0.9.0"
-cf_xarray = "*"
-cftime = ">=1.3.1"
-scipy = ">=0.16.0" #? Not sure if we rely on scipy internally anymore...
-pooch = "*"
+cf_xarray = ">=0.8.6"
+cftime = ">=1.6.3"
+pooch = ">=1.8.0"
+
+[feature.minimum.dependencies]
+python = "==3.11"
+netcdf4 = "==1.7.2"
+numpy = "==2.1.0"
+tqdm = "==4.50.0"
+xarray = "==2024.5.0"
+uxarray = "==2025.3.0"
+dask = "==2024.5.1"
+zarr = "==2.15.0"
+xgcm = "==0.9.0"
+cf_xarray = "==0.8.6"
+cftime = "==1.6.3"
+pooch = "==1.8.0"
 
 [feature.py311.dependencies]
 python = "3.11.*"

pyproject.toml

@@ -20,19 +20,18 @@ classifiers = [
   "Intended Audience :: Science/Research",
 ]
 dependencies = [
-  "cftime",
-  "numpy >=1.11",
-  "dask",
-  "netCDF4 >=1.1.9",
-  "zarr >=2.11.0,!=2.18.0,<3",
-  "tqdm",
+  "cftime >=1.6.3",
+  "numpy >=2.1.0",
+  "dask >=2024.5.1",
+  "netCDF4 >=1.7.2",
+  "zarr >=2.15.0,!=2.18.0,<3",
+  "tqdm >=4.50.0",
   "pytest",
-  "scipy >=0.16.0",
-  "xarray >=0.10.8",
-  "uxarray",
-  "pooch",
+  "xarray >=2024.5.0",
+  "uxarray >=2025.3.0",
+  "pooch >=1.8.0",
   "xgcm >=0.9.0",
-  "cf_xarray",
+  "cf_xarray >=0.8.6",
 ]
 
 [project.urls]