diff --git a/.github/workflows/ci-additional.yaml b/.github/workflows/ci-additional.yaml
index 9fc245db0ba..567c830b8bd 100644
--- a/.github/workflows/ci-additional.yaml
+++ b/.github/workflows/ci-additional.yaml
@@ -48,7 +48,7 @@ jobs:
       run:
         shell: bash -l {0}
     env:
-      PIXI_ENV: test
+      PIXI_ENV: "test-py313"
     steps:
       - uses: actions/checkout@v6
         with:
@@ -75,7 +75,7 @@ jobs:
 
       - name: Version info
         run: |
-          pixi run -e ${{env.PIXI_ENV}} python xarray/util/print_versions.py
+          pixi run -e ${{env.PIXI_ENV}} -- python xarray/util/print_versions.py
       - name: Run doctests
         run: |
           # Raise an error if there are warnings in the doctests, with `-Werror`.
@@ -84,7 +84,7 @@ jobs:
           #
           # If dependencies emit warnings we can't do anything about, add ignores to
           # `xarray/tests/__init__.py`.
-          pixi run -e ${{env.PIXI_ENV}} python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
+          pixi run -e ${{env.PIXI_ENV}} -- python -m pytest --doctest-modules xarray --ignore xarray/tests -Werror
 
   mypy:
     name: Mypy
@@ -94,7 +94,7 @@ jobs:
       run:
         shell: bash -l {0}
     env:
-      PIXI_ENV: test-with-typing
+      PIXI_ENV: test-py313-with-typing
 
     steps:
       - uses: actions/checkout@v6
@@ -117,14 +117,14 @@ jobs:
       - name: set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e ${{env.PIXI_ENV}} python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run -e ${{env.PIXI_ENV}} -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
       - name: Version info
         run: |
-          pixi run -e ${{env.PIXI_ENV}} python xarray/util/print_versions.py
+          pixi run -e ${{env.PIXI_ENV}} -- python xarray/util/print_versions.py
 
       - name: Run mypy
         run: |
-          pixi run -e ${{env.PIXI_ENV}} python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          pixi run -e ${{env.PIXI_ENV}} -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.1
@@ -166,14 +166,14 @@ jobs:
       - name: set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e ${{env.PIXI_ENV}} python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run -e ${{env.PIXI_ENV}} -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
       - name: Version info
         run: |
-          pixi run -e ${{env.PIXI_ENV}} python xarray/util/print_versions.py
+          pixi run -e ${{env.PIXI_ENV}} -- python xarray/util/print_versions.py
 
       - name: Run mypy
         run: |
-          pixi run -e ${{env.PIXI_ENV}} python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          pixi run -e ${{env.PIXI_ENV}} -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
 
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.1
@@ -191,7 +191,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        pixi-env: ["test-with-typing", "test-py311-with-typing"]
+        pixi-env: ["test-py313-with-typing", "test-py311-with-typing"]
     if: |
       always()
       && (
@@ -223,14 +223,14 @@ jobs:
       - name: set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e ${{ matrix.pixi-env }} python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run -e ${{ matrix.pixi-env }} -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
       - name: Version info
         run: |
-          pixi run -e ${{ matrix.pixi-env }} python xarray/util/print_versions.py
+          pixi run -e ${{ matrix.pixi-env }} -- python xarray/util/print_versions.py
 
       - name: Run pyright
         run: |
-          pixi run -e ${{ matrix.pixi-env }} python -m pyright xarray/
+          pixi run -e ${{ matrix.pixi-env }} -- python -m pyright xarray/
 
       - name: Upload pyright coverage to Codecov
         uses: codecov/codecov-action@v5.5.1
diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml
index 00a7ef4f7ca..456c4034a59 100644
--- a/.github/workflows/ci.yaml
+++ b/.github/workflows/ci.yaml
@@ -52,22 +52,22 @@ jobs:
       matrix:
         os: ["ubuntu-latest", "macos-latest", "windows-latest"]
         # Bookend python versions
-        pixi-env: ["test-py311", "test"]
+        pixi-env: ["test-py311", "test-py313"]
         pytest-addopts: [""]
         include:
           # Minimum python version:
-          - pixi-env: "test-bare-minimum"
+          - pixi-env: "test-py311-bare-minimum"
             os: ubuntu-latest
-          - pixi-env: "test-bare-min-and-scipy"
+          - pixi-env: "test-py311-bare-min-and-scipy"
             os: ubuntu-latest
-          - pixi-env: "test-min-versions"
+          - pixi-env: "test-py311-min-versions"
             os: ubuntu-latest
           # Latest python version:
-          - pixi-env: "test-no-numba"
+          - pixi-env: "test-py313-no-numba"
             os: ubuntu-latest
-          - pixi-env: "test-no-dask"
+          - pixi-env: "test-py313-no-dask"
             os: ubuntu-latest
-          - pixi-env: "test"
+          - pixi-env: "test-py313"
             pytest-addopts: "flaky"
             os: ubuntu-latest
           # The mypy tests must be executed using only 1 process in order to guarantee
@@ -76,7 +76,7 @@ jobs:
             pytest-addopts: "mypy"
             numprocesses: 1
             os: ubuntu-latest
-          - pixi-env: "test-with-typing"
+          - pixi-env: "test-py313-with-typing"
             numprocesses: 1
             os: ubuntu-latest
     steps:
@@ -101,7 +101,7 @@ jobs:
       - name: Set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e ${{env.PIXI_ENV}} python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run -e ${{ matrix.pixi-env }} -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
 
           if [[ "${{ matrix.pytest-addopts }}" != "" ]] ;
           then
@@ -128,11 +128,11 @@ jobs:
 
       - name: Version info
         run: |
-          pixi run -e ${{ matrix.pixi-env }} python xarray/util/print_versions.py
+          pixi run -e ${{ matrix.pixi-env }} -- python xarray/util/print_versions.py
 
       - name: Import xarray
         run: |
-          pixi run -e ${{ matrix.pixi-env }} python -c "import xarray"
+          pixi run -e ${{ matrix.pixi-env }} -- python -c "import xarray"
 
       - name: Restore cached hypothesis directory
         uses: actions/cache@v4
@@ -143,12 +143,12 @@ jobs:
           save-always: true
 
       - name: Run tests
-        run:
-          pixi run -e ${{ matrix.pixi-env }} python -m pytest -n ${{ matrix.numprocesses || 4 }}
-          --timeout 180
-          --cov=xarray
-          --cov-report=xml
-          --junitxml=pytest.xml
+        run: |
+          pixi run -e ${{ matrix.pixi-env }} -- python -m pytest -n ${{ matrix.numprocesses || 4 }} \
+            --timeout 180 \
+            --cov=xarray \
+            --cov-report=xml \
+            --junitxml=pytest.xml
 
       - name: Upload test results
         if: always()
diff --git a/.github/workflows/hypothesis.yaml b/.github/workflows/hypothesis.yaml
index 5ccf9c5be9e..3787077f0da 100644
--- a/.github/workflows/hypothesis.yaml
+++ b/.github/workflows/hypothesis.yaml
@@ -55,7 +55,7 @@ jobs:
         shell: bash -l {0}
 
     env:
-      PIXI_ENV: test
+      PIXI_ENV: "test-py313"
 
     steps:
       - uses: actions/checkout@v6
diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
index a3052957b0b..75ffddfda0c 100644
--- a/.github/workflows/upstream-dev-ci.yaml
+++ b/.github/workflows/upstream-dev-ci.yaml
@@ -79,15 +79,15 @@ jobs:
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Version info
         run: |
-          pixi run -e ${{matrix.pixi-env}} python xarray/util/print_versions.py
+          pixi run -e ${{matrix.pixi-env}} -- python xarray/util/print_versions.py
       - name: Import xarray
         run: |
-          pixi run -e ${{matrix.pixi-env}} python -c 'import xarray'
+          pixi run -e ${{matrix.pixi-env}} -- python -c 'import xarray'
       - name: Run Tests
         if: success()
         id: status
         run: |
-          pixi run -e ${{matrix.pixi-env}} python -m pytest --timeout=60 -rf -nauto \
+          pixi run -e ${{matrix.pixi-env}} -- python -m pytest --timeout=60 -rf -nauto \
             --report-log output-${{ matrix.pixi-env }}-log.jsonl
       - name: Generate and publish the report
         if: |
@@ -138,13 +138,13 @@ jobs:
       - name: set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e ${{matrix.pixi-env}} python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run -e ${{matrix.pixi-env}} -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
       - name: Version info
         run: |
-          pixi run -e ${{matrix.pixi-env}} python xarray/util/print_versions.py
+          pixi run -e ${{matrix.pixi-env}} -- python xarray/util/print_versions.py
       - name: Run mypy
         run: |
-          pixi run -e ${{matrix.pixi-env}} python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          pixi run -e ${{matrix.pixi-env}} -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@v5.5.1
         with:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index b216fdf6775..a891a84a6a3 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -35,7 +35,7 @@ repos:
       - id: blackdoc
         exclude: "generate_aggregations.py"
         # make sure this is the most recent version of black
-        additional_dependencies: ["black==25.9.0"]
+        additional_dependencies: ["black==25.11.0"]
   - repo: https://github.com/rbubley/mirrors-prettier
     rev: v3.7.3
     hooks:
diff --git a/pixi.toml b/pixi.toml
index e77edb26c9f..531d829340b 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -3,104 +3,6 @@ preview = ["pixi-build"]
 channels = ["conda-forge", "nodefaults"]
 platforms = ["win-64", "linux-64", "osx-arm64"]
 
-[environments]
-# Testing
-# test-just-xarray = { features = ["test"] } # https://github.com/pydata/xarray/pull/10888/files#r2511336147
-test-no-numba = { features = [
-  "py313",
-  "test",
-  "backends",
-  "accel",
-  "dask",
-  "viz",
-  "extras",
-] }
-test-no-dask = { features = [
-  "py312",
-  "test",
-  "backends",
-  "accel",
-  "numba",
-  "viz",
-  "extras",
-] }
-test = { features = [
-  "py313",
-  "test",
-  "backends",
-  "accel",
-  "numba",
-  "dask",
-  "viz",
-  "extras",
-] }
-test-nightly = { features = [
-  "py313",
-  "nightly",
-  "test",
-  # "typing",
-], no-default-feature = true }
-
-
-test-py311 = { features = [
-  "py311",
-  "test",
-  "backends",
-  "accel",
-  "numba",
-  "dask",
-  "viz",
-  "extras",
-] }
-
-test-py311-with-typing = { features = [
-  "py311",
-  "test",
-  "backends",
-  "accel",
-  "numba",
-  "dask",
-  "viz",
-  "extras",
-  "typing",
-] }
-
-test-with-typing = { features = [
-  "py313",
-  "test",
-  "backends",
-  "accel",
-  "numba",
-  "dask",
-  "viz",
-  "extras",
-  "typing",
-] }
-
-test-bare-minimum = { features = ["test", "minimal"] }
-test-bare-min-and-scipy = { features = [
-  "test",
-  "minimal",
-  "minimum-scipy",
-] }
-test-min-versions = { features = [
-  "test",
-  "min-versions",
-] }
-
-
-# Extra
-typing = { features = ["typing"] }
-doc = { features = [
-  "doc",
-  "backends",
-  "test",
-  "accel",
-  "viz",
-  "extras",
-] }
-pre-commit = { features = ["pre-commit"], no-default-feature = true }
-
 [package]
 name = "xarray"
 version = "dynamic" # dynamic versioning needs better support in pixi https://github.com/prefix-dev/pixi/issues/2923#issuecomment-2598460666 . Putting `version = "dynamic"` here for now until pixi recommends something else.
@@ -126,15 +28,6 @@ xarray = { path = "." }
 [target.linux-64.dependencies]
 pydap-server = "*"
 
-[feature.minimal.dependencies]
-# minimal versions
-python = "3.11.*"
-numpy = "1.26.*"
-pandas = "2.2.*"
-
-[feature.minimum-scipy.dependencies]
-scipy = "1.13.*"
-
 [feature.py311.dependencies]
 python = "3.11.*"
 
@@ -203,13 +96,21 @@ iris = "*"
 # array
 jax = "*" # no way to get cpu-only jaxlib from conda if gpu is present
 
+[feature.minimal.dependencies]
+# minimal versions
+python = "3.11.*"
+numpy = "1.26.*"
+pandas = "2.2.*"
+
+[feature.minimum-scipy.dependencies]
+scipy = "1.13.*"
+
 [feature.min-versions.dependencies]
 # minimal versions for all dependencies
 # Note that when you update min-supported versions, you should:
 # - Update the min version lower-bound in the corresponding feature(s) where applicable
 # - Update this section to pin to the min version
 
-python = "3.11.*"
 array-api-strict = "1.1.*" # dependency for testing the array api compat
 boto3 = "1.34.*"
 bottleneck = "1.4.*"
@@ -233,13 +134,10 @@ nc-time-axis = "1.4.*"
 netcdf4 = "1.6.*"
 numba = "0.60.*"
 numbagg = "0.8.*"
-numpy = "1.26.*"
 packaging = "24.1.*"
-pandas = "2.2.*"
 pint = "0.24.*"
 pydap = "3.5.*"
 rasterio = "1.3.*"
-scipy = "1.13.*"
 seaborn = "0.13.*"
 sparse = "0.15.*"
 toolz = "0.12.*"
@@ -320,11 +218,11 @@ test = { cmd = "pytest" }
 kerchunk = "*"
 ipykernel = "*"
 ipywidgets = "*"                   # silence nbsphinx warning
-ipython = '*'
-jupyter_client = '*'
-jupyter_sphinx = '*'
-nbsphinx = '*'
-ncdata = '*'
+ipython = "*"
+jupyter_client = "*"
+jupyter_sphinx = "*"
+nbsphinx = "*"
+ncdata = "*"
 pydata-sphinx-theme = "*"
 pyproj = "*"
 rich = "*"                         # for Zarr tree()
@@ -379,3 +277,103 @@ pre-commit = "*"
 
 [feature.pre-commit.tasks]
 pre-commit = { cmd = "pre-commit" }
+
+[environments]
+# Testing
+# test-just-xarray = { features = ["test"] } # https://github.com/pydata/xarray/pull/10888/files#r2511336147
+test-py313-no-numba = { features = [
+  "py313",
+  "test",
+  "backends",
+  "accel",
+  "dask",
+  "viz",
+  "extras",
+] }
+test-py313-no-dask = { features = [
+  "py312",
+  "test",
+  "backends",
+  "accel",
+  "numba",
+  "viz",
+  "extras",
+] }
+test-py313 = { features = [
+  "py313",
+  "test",
+  "backends",
+  "accel",
+  "numba",
+  "dask",
+  "viz",
+  "extras",
+] }
+test-nightly = { features = [
+  "py313",
+  "nightly",
+  "test",
+  # "typing",
+], no-default-feature = true }
+
+
+test-py311 = { features = [
+  "py311",
+  "test",
+  "backends",
+  "accel",
+  "numba",
+  "dask",
+  "viz",
+  "extras",
+] }
+
+test-py311-with-typing = { features = [
+  "py311",
+  "test",
+  "backends",
+  "accel",
+  "numba",
+  "dask",
+  "viz",
+  "extras",
+  "typing",
+] }
+
+test-py313-with-typing = { features = [
+  "py313",
+  "test",
+  "backends",
+  "accel",
+  "numba",
+  "dask",
+  "viz",
+  "extras",
+  "typing",
+] }
+
+test-py311-bare-minimum = { features = ["test", "minimal"] }
+test-py311-bare-min-and-scipy = { features = [
+  "test",
+  "minimal",
+  "minimum-scipy",
+] }
+test-py311-min-versions = { features = [
+  "test",
+  "minimal",
+  "minimum-scipy",
+  "min-versions",
+] }
+
+
+# Extra
+typing = { features = ["typing"] }
+doc = { features = [
+  "doc",
+  "backends",
+  "test",
+  "accel",
+  "viz",
+  "extras",
+] }
+pre-commit = { features = ["pre-commit"], no-default-feature = true }