address comments from code review

src/xscen/io.py

@@ -1,6 +1,7 @@
 """Input/Output functions for xscen."""
 
 import datetime
+import json
 import logging
 import os
 import shutil as sh
@@ -252,7 +253,7 @@ def clean_incomplete(
         Name of variables that were completed. All other variables (except coordinates) will be removed.
         Use either `complete` or `incomplete`, not both.
     incomplete : sequence of strings, optional
-        Name of variables that should be removed.
+        Name of variables that should be removed. Coordinates and dimensions will never be removed through this function.
         Use either `complete` or `incomplete`, not both.
 
     Returns
@@ -261,6 +262,22 @@ def clean_incomplete(
     """
     path = Path(path)
 
+    def _del_var(pth):
+        msg = f"Removing {pth} from disk"
+        logger.warning(msg)
+        sh.rmtree(pth)
+
+        # Update the .zmetadata file
+        with (Path(path) / ".zmetadata").open("r") as f:
+            metadata = json.load(f)
+        [
+            metadata["metadata"].pop(k)
+            for k in list(metadata["metadata"].keys())
+            if k.startswith(f"{pth.name}/.")
+        ]
+        with (Path(path) / ".zmetadata").open("w") as f:
+            json.dump(metadata, f, indent=2)
+
     if complete is not None and incomplete is not None:
         raise ValueError("Use either `complete` or `incomplete`, not both.")
 
@@ -270,20 +287,17 @@ def clean_incomplete(
 
         for fold in filter(lambda p: p.is_dir(), path.iterdir()):
             if fold.name not in complete:
-                msg = f"Removing {fold} from disk"
-                logger.warning(msg)
-                sh.rmtree(fold)
+                _del_var(fold)
 
     elif incomplete is not None:
+        with xr.open_zarr(path) as ds:
+            incomplete = [
+                v for v in incomplete if (v not in ds.coords) and (v not in ds.dims)
+            ]
+
         for fold in filter(lambda p: p.is_dir(), path.iterdir()):
             if fold.name in incomplete:
-                msg = f"Removing {fold} from disk"
-                logger.warning(msg)
-                sh.rmtree(fold)
-
-    # Remove .zmetadata to avoid issues with zarr and xarray
-    if (path / ".zmetadata").exists():
-        Path.unlink(path / ".zmetadata")
+                _del_var(fold)
 
 
 def _coerce_attrs(attrs):

src/xscen/testing.py

@@ -1,5 +1,6 @@
 """Testing utilities for xscen."""
 
+import importlib.metadata
 import os
 import re
 from io import StringIO
@@ -357,77 +358,23 @@ def show_versions(
     -------
     str or None
     """
-    if deps is None:
-        deps = [
-            "xscen",
-            # Main packages
-            "cartopy",
-            "cftime",
-            "cf_xarray",
-            "clisops",
-            "dask",
-            "flox",
-            "fsspec",
-            "geopandas",
-            "h5netcdf",
-            "h5py",
-            "intake_esm",
-            "matplotlib",
-            "netCDF4",
-            "numcodecs",
-            "numpy",
-            "pandas",
-            "parse",
-            "pyyaml",
-            "rechunker",
-            "scipy",
-            "shapely",
-            "sparse",
-            "toolz",
-            "xarray",
-            "xclim",
-            "xesmf",
-            "zarr",
-            # Opt
-            "nc-time-axis",
-            "pyarrow",
-            # Dev
-            "babel",
-            "black",
-            "blackdoc",
-            "bump-my-version",
-            "coverage",
-            "coveralls",
-            "flake8",
-            "flake8-rst-docstrings",
-            "ipykernel",
-            "ipython",
-            "isort",
-            "jupyter_client",
-            "nbsphinx",
-            "nbval",
-            "pandoc",
-            "pooch",
-            "pre-commit",
-            "pytest",
-            "pytest-cov",
-            "ruff",
-            "setuptools",
-            "setuptools-scm",
-            "sphinx",
-            "sphinx-autoapi",
-            "sphinx-rtd-theme",
-            "sphinxcontrib-napoleon",
-            "sphinx-codeautolink",
-            "sphinx-copybutton",
-            "sphinx-mdinclude",
-            "watchdog",
-            "xdoctest",
-            "tox",
-            "build",
-            "wheel",
-            "pip",
-            "flake8-alphabetize",
+
+    def _get_xscen_dependencies():
+        xscen_metadata = importlib.metadata.metadata("xscen")
+        requires = xscen_metadata.get_all("Requires-Dist")
+        requires = [
+            req.split("[")[0]
+            .split(";")[0]
+            .split(">")[0]
+            .split("<")[0]
+            .split("=")[0]
+            .split("!")[0]
+            for req in requires
         ]
 
+        return ["xscen"] + requires
+
+    if deps is None:
+        deps = _get_xscen_dependencies()
+
     return _show_versions(file=file, deps=deps)

tests/test_ensembles.py

@@ -5,7 +5,6 @@
 import pytest
 import xarray as xr
 import xclim as xc
-from packaging.version import Version
 
 try:
     import xesmf as xe

tests/test_io.py

@@ -145,6 +145,7 @@ def test_complete(self, tmpdir, which):
             xs.io.clean_incomplete(Path(tmpdir) / "test.zarr", incomplete=["pr"])
         assert (Path(tmpdir) / "test.zarr/tas").exists()
         assert not (Path(tmpdir) / "test.zarr/pr").exists()
+        assert (Path(tmpdir) / "test.zarr/.zmetadata").exists()
 
         ds2 = xr.open_zarr(Path(tmpdir) / "test.zarr")
         assert "pr" not in ds2