chore(pixi): update pixi, tidy pixi.toml, update/apply ruff (#2139)

* update pixi version in ci workflows
* avoid some warnings in the pixi.toml file
* update ruff version in the pixi environment and apply ruff reformatting

Author: wpbonelli

.github/workflows/ci.yml

@@ -51,7 +51,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Check Fortran source formatting
         run: pixi run check-format
@@ -87,7 +87,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Setup MF6
         run: pixi run setup -Dwerror=true builddir
@@ -132,7 +132,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -249,7 +249,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -412,7 +412,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -515,7 +515,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install

.github/workflows/compilers.yml

@@ -99,7 +99,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install

.github/workflows/docs.yml

@@ -28,7 +28,7 @@ jobs:
 
       - uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Check spelling
         run: pixi run check-spelling
@@ -65,7 +65,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install
@@ -237,7 +237,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
 
       - name: Custom pixi install
         run: pixi run install

.github/workflows/large.yml

@@ -69,7 +69,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install

.github/workflows/pixi_auto_update.yml

@@ -14,7 +14,7 @@ jobs:
       - uses: actions/checkout@v4
       - uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           cache: false
 
       - name: Update pixi lock file

.github/workflows/release.yml

@@ -110,7 +110,7 @@ jobs:
       - name: Setup pixi
         uses: prefix-dev/[email protected]
         with:
-          pixi-version: v0.24.2
+          pixi-version: v0.40.1
           manifest-path: "modflow6/pixi.toml"
 
       - name: Custom pixi install

autotest/framework.py

@@ -518,15 +518,15 @@ def _compare_output(self, compare):
         rclose = get_rclose(self.workspace)
         cmp_path = self.workspace / compare
         if "mf6_regression" in compare:
-            assert self._compare_heads(
-                extensions=HDS_EXT, htol=htol
-            ), "head comparison failed"
-            assert self._compare_budgets(
-                extensions=CBC_EXT, rclose=rclose
-            ), "budget comparison failed"
-            assert self._compare_concentrations(
-                htol=htol
-            ), "concentration comparison failed"
+            assert self._compare_heads(extensions=HDS_EXT, htol=htol), (
+                "head comparison failed"
+            )
+            assert self._compare_budgets(extensions=CBC_EXT, rclose=rclose), (
+                "budget comparison failed"
+            )
+            assert self._compare_concentrations(htol=htol), (
+                "concentration comparison failed"
+            )
         else:
             assert self._compare_heads(
                 cpth=cmp_path,
@@ -562,9 +562,9 @@ def _run_sim_or_model(
         # make sure executable exists and framework knows about it
         tgt = Path(shutil.which(target))
         assert tgt.is_file(), f"Target executable not found: {target}"
-        assert (
-            tgt in self.targets.values()
-        ), "Targets must be explicitly registered with the test framework"
+        assert tgt in self.targets.values(), (
+            "Targets must be explicitly registered with the test framework"
+        )
 
         if self.verbose:
             print(f"Running {target} in {workspace}")

autotest/test_chf_dfw_loop.py

@@ -488,9 +488,9 @@ def check_output(idx, test):
     diff = obsvals["REACH14"] - answer["STAGE0000000014"]
     print(diff)
     print(diff.max(), diff.min())
-    assert np.allclose(
-        diff, 0.0, atol=0.06
-    ), f"Max diff with swr is {diff.min(), diff.max()}"
+    assert np.allclose(diff, 0.0, atol=0.06), (
+        f"Max diff with swr is {diff.min(), diff.max()}"
+    )
 
     # read the binary grid file
     fpth = test.workspace / f"{name}.disv1d.grb"
@@ -524,9 +524,9 @@ def check_output(idx, test):
                 f"residual for cell {n + 1} is {qresidual[n]} "
                 f"in position {ia[n] + 1} {passfail}"
             )
-        assert np.allclose(
-            qresidual, 0.0, atol=atol
-        ), "residual in flowja diagonal is not zero"
+        assert np.allclose(qresidual, 0.0, atol=atol), (
+            "residual in flowja diagonal is not zero"
+        )
 
     return
 

autotest/test_chf_dis.py

@@ -165,22 +165,22 @@ def check_grb_disv1d(fpth):
     assert grb.xorigin == xorigin, "xorigin in grb file is not correct"
     assert grb.yorigin == yorigin, "yorigin in grb file is not correct"
     assert grb.angrot == angrot, "angrot in grb file is not correct"
-    assert np.allclose(
-        grb.bot.reshape((nodes,)), np.zeros((nodes,))
-    ), "grb botm not correct"
+    assert np.allclose(grb.bot.reshape((nodes,)), np.zeros((nodes,))), (
+        "grb botm not correct"
+    )
     cellx = np.linspace(dx / 2, nreach * dx - dx / 2, nreach)
     celly = np.zeros(nreach)
     assert np.allclose(grb._datadict["CELLX"], cellx.flatten()), "cellx is not right"
     assert np.allclose(grb._datadict["CELLY"], celly.flatten()), "celly is not right"
     assert grb._datadict["IAVERT"].shape[0] == nodes + 1, "iavert size not right"
-    assert (
-        grb._datadict["IAVERT"][-1] - 1 == grb._datadict["JAVERT"].shape[0]
-    ), "javert size not right"
+    assert grb._datadict["IAVERT"][-1] - 1 == grb._datadict["JAVERT"].shape[0], (
+        "javert size not right"
+    )
     assert grb.ia.shape[0] == grb.ncells + 1, "ia in grb file is not correct size"
     assert grb.ja.shape[0] == grb.nja, "ja in grb file is not correct size"
-    assert np.allclose(
-        grb.idomain.reshape((nodes,)), idomain.reshape((nodes,))
-    ), "grb idomain not correct"
+    assert np.allclose(grb.idomain.reshape((nodes,)), idomain.reshape((nodes,))), (
+        "grb idomain not correct"
+    )
 
 
 def check_output(idx, test):
@@ -198,9 +198,9 @@ def check_output(idx, test):
     fpth = test.workspace / f"{modelname}.stage"
     sobj = flopy.utils.HeadFile(fpth, precision="double", text="STAGE")
     stage = sobj.get_data().reshape((nodes,))
-    assert np.allclose(
-        stage[idomain == 0], 3.0e30
-    ), "stage should have nodata values where idomain is zero"
+    assert np.allclose(stage[idomain == 0], 3.0e30), (
+        "stage should have nodata values where idomain is zero"
+    )
     assert stage[idomain == 1].max() == 1.0, "maximum stage should be 1.0"
     assert stage[idomain == 1].min() == 0.5, "minimum stage should be 0.5"
 

autotest/test_chf_dis_fdc.py

@@ -170,22 +170,22 @@ def check_grb_disv1d(fpth):
     assert grb.xorigin == xorigin, "xorigin in grb file is not correct"
     assert grb.yorigin == yorigin, "yorigin in grb file is not correct"
     assert grb.angrot == angrot, "angrot in grb file is not correct"
-    assert np.allclose(
-        grb.bot.reshape((nodes,)), np.zeros((nodes,))
-    ), "grb botm not correct"
+    assert np.allclose(grb.bot.reshape((nodes,)), np.zeros((nodes,))), (
+        "grb botm not correct"
+    )
     cellx = np.array([0.0, 2 * dx])  # node centers pushed all the way to left and right
     celly = np.zeros(nreach)
     assert np.allclose(grb._datadict["CELLX"], cellx.flatten()), "cellx is not right"
     assert np.allclose(grb._datadict["CELLY"], celly.flatten()), "celly is not right"
     assert grb._datadict["IAVERT"].shape[0] == nodes + 1, "iavert size not right"
-    assert (
-        grb._datadict["IAVERT"][-1] - 1 == grb._datadict["JAVERT"].shape[0]
-    ), "javert size not right"
+    assert grb._datadict["IAVERT"][-1] - 1 == grb._datadict["JAVERT"].shape[0], (
+        "javert size not right"
+    )
     assert grb.ia.shape[0] == grb.ncells + 1, "ia in grb file is not correct size"
     assert grb.ja.shape[0] == grb.nja, "ja in grb file is not correct size"
-    assert np.allclose(
-        grb.idomain.reshape((nodes,)), idomain.reshape((nodes,))
-    ), "grb idomain not correct"
+    assert np.allclose(grb.idomain.reshape((nodes,)), idomain.reshape((nodes,))), (
+        "grb idomain not correct"
+    )
 
 
 def check_output(idx, test):