style: unify import messages

src/scanpy/external/exporting.py

@@ -577,11 +577,8 @@ def cellbrowser(  # noqa: PLR0913
     """
     try:
         import cellbrowser.cellbrowser as cb
-    except ImportError:
-        logg.error(
-            "The package cellbrowser is not installed. "
-            "Install with 'pip install cellbrowser' and retry."
-        )
+    except ImportError as e:
+        e.add_note("Please install `cellbrowser` and try again.")
         raise
 
     data_dir = str(data_dir)

src/scanpy/external/pp/_bbknn.py

@@ -133,8 +133,8 @@ def bbknn(  # noqa: PLR0913
     try:
         from bbknn import bbknn
     except ImportError as e:
-        msg = "Please install bbknn: `pip install bbknn`."
-        raise ImportError(msg) from e
+        e.add_note("Please install `bbknn` and try again.")
+        raise
     return bbknn(
         adata=adata,
         batch_key=batch_key,

src/scanpy/external/pp/_dca.py

@@ -180,8 +180,8 @@ def dca(  # noqa: PLR0913
     try:
         from dca.api import dca
     except ImportError as e:
-        msg = "Please install dca package (>= 0.2.1) via `pip install dca`"
-        raise ImportError(msg) from e
+        e.add_note("Please install `dca` (≥ 0.2.1) and try again.")
+        raise e
 
     return dca(
         adata,

src/scanpy/external/pp/_harmony_integrate.py

@@ -90,8 +90,8 @@ def harmony_integrate(
     try:
         import harmonypy
     except ImportError as e:
-        msg = "\nplease install harmonypy:\n\n\tpip install harmonypy"
-        raise ImportError(msg) from e
+        e.add_note("Please install `harmonypy` and try again.")
+        raise
 
     x = adata.obsm[basis].astype(np.float64)
 

src/scanpy/external/pp/_magic.py

@@ -140,8 +140,8 @@ def magic(  # noqa: PLR0913
     try:
         from magic import MAGIC
     except ImportError as e:
-        msg = "Please install magic package via `pip install magic-impute`"
-        raise ImportError(msg) from e
+        e.add_note("Please install `magic-impute` and try again.")
+        raise
     else:
         if pkg_version("magic-impute") < Version(MIN_VERSION):
             msg = (

src/scanpy/external/pp/_mnn_correct.py

@@ -133,8 +133,8 @@ def mnn_correct(  # noqa: PLR0913
         import mnnpy
         from mnnpy import mnn_correct
     except ImportError as e:
-        msg = "Please install the package mnnpy (https://github.com/chriscainx/mnnpy). "
-        raise ImportError(msg) from e
+        e.add_note("Please install `mnnpy` and try again.")
+        raise
 
     n_jobs = settings.n_jobs if n_jobs is None else n_jobs
 

src/scanpy/external/pp/_scanorama_integrate.py

@@ -109,8 +109,8 @@ def scanorama_integrate(
     try:
         import scanorama
     except ImportError as e:
-        msg = "\nplease install Scanorama:\n\n\tpip install scanorama"
-        raise ImportError(msg) from e
+        e.add_note("Please install `scanorama` and try again.")
+        raise
 
     # Get batch indices in linear time.
     curr_batch = None

src/scanpy/external/tl/_harmony_timeseries.py

@@ -135,8 +135,8 @@ def harmony_timeseries(
     try:
         import harmony
     except ImportError as e:
-        msg = "\nplease install harmony:\n\n\tpip install harmonyTS"
-        raise ImportError(msg) from e
+        e.add_note("Please install `harmonyTS` and try again.")
+        raise
 
     adata = adata.copy() if copy else adata
     logg.info("Harmony augmented affinity matrix")

src/scanpy/external/tl/_palantir.py

@@ -333,9 +333,9 @@ def palantir_results(
     return pr_res
 
 
-def _check_import():
+def _check_import() -> None:
     try:
         import palantir  # noqa: F401
     except ImportError as e:
-        msg = "\nplease install palantir:\n\tpip install palantir"
-        raise ImportError(msg) from e
+        e.add_note("Please install `palantir` and try again.")
+        raise

src/scanpy/external/tl/_phate.py

@@ -152,11 +152,8 @@ def phate(  # noqa: PLR0913
     try:
         import phate
     except ImportError as e:
-        msg = (
-            "You need to install the package `phate`: please run `pip install "
-            "--user phate` in a terminal."
-        )
-        raise ImportError(msg) from e
+        e.add_note("Please install `phate` and try again.")
+        raise
     x_phate = phate.PHATE(
         n_components=n_components,
         k=k,

src/scanpy/external/tl/_sam.py

@@ -206,13 +206,8 @@ def sam(  # noqa: PLR0913
     try:
         from samalg import SAM
     except ImportError as e:
-        msg = (
-            "\nplease install sam-algorithm: \n\n"
-            "\tgit clone git://github.com/atarashansky/self-assembling-manifold.git\n"
-            "\tcd self-assembling-manifold\n"
-            "\tpip install ."
-        )
-        raise ImportError(msg) from e
+        e.add_note("Please install `sc-sam` and try again.")
+        raise
 
     logg.info("Self-assembling manifold")
 

src/scanpy/external/tl/_trimap.py

@@ -103,8 +103,8 @@ def trimap(  # noqa: PLR0913
     try:
         from trimap import TRIMAP
     except ImportError as e:
-        msg = "\nplease install trimap: \n\n\tsudo pip install trimap"
-        raise ImportError(msg) from e
+        e.add_note("Please install `trimap` and try again.")
+        raise
     adata = adata.copy() if copy else adata
     start = logg.info("computing TriMap")
     adata = adata.copy() if copy else adata

src/scanpy/external/tl/_wishbone.py

@@ -103,8 +103,8 @@ def wishbone(
     try:
         from wishbone.core import wishbone as c_wishbone
     except ImportError as e:
-        msg = "\nplease install wishbone:\n\n\thttps://github.com/dpeerlab/wishbone"
-        raise ImportError(msg) from e
+        e.add_note("Please install `wishbone` and try again.")
+        raise
 
     # Start cell index
     s = np.where(adata.obs_names == start_cell)[0]

src/scanpy/metrics/_metrics.py

@@ -205,8 +205,11 @@ def modularity_array(
     try:
         import igraph as ig
     except ImportError as e:  # pragma: no cover
-        msg = "igraph is require for computing modularity"
-        raise ImportError(msg) from e
+        e.add_note(
+            "`igraph` is required for computing modularity. "
+            "Please install `igraph` and try again."
+        )
+        raise
     igraph_mode: str = ig.ADJ_DIRECTED if is_directed else ig.ADJ_UNDIRECTED
     graph: ig.Graph = ig.Graph.Weighted_Adjacency(connectivities, mode=igraph_mode)
     return graph.modularity(_codes(labels))

src/scanpy/plotting/_utils.py

@@ -1132,12 +1132,12 @@ def _create_white_to_color_gradient(
     popt = np.get_printoptions()
     try:
         import colour
-    except ImportError:
-        msg = (
-            "Please install the `colour-science` package to use `group_colors`: "
-            "`pip install colour-science` or `pip install scanpy[plotting]`"
+    except ImportError as e:
+        e.add_note(
+            "`colour-science` is required for using `group_colors`. "
+            "Please install `scanpy[plotting]` (or `colour-science` directly) and try again."
         )
-        raise ImportError(msg) from None
+        raise
     finally:  # https://github.com/colour-science/colour/issues/1388
         np.set_printoptions(legacy=popt["legacy"])
 

src/scanpy/preprocessing/_highly_variable_genes.py

@@ -157,8 +157,8 @@ def _highly_variable_genes_seurat_v3(  # noqa: PLR0912, PLR0915
     try:
         from skmisc.loess import loess
     except ImportError as e:
-        msg = "Please install skmisc package via `pip install --user scikit-misc"
-        raise ImportError(msg) from e
+        e.add_note("Please install `scikit-misc` and try again.")
+        raise
     df = pd.DataFrame(index=adata.var_names)
     data = _get_obs_rep(adata, layer=layer)
     raise_if_dask_feature_axis_chunked(data)

src/scanpy/preprocessing/_scrublet/__init__.py

@@ -181,7 +181,10 @@ def scrublet(  # noqa: PLR0913
     if threshold is None and not find_spec("skimage"):  # pragma: no cover
         # Scrublet.call_doublets requires `skimage` with `threshold=None` but PCA
         # is called early, which is wasteful if there is not `skimage`
-        msg = "threshold is None and thus scrublet requires skimage, but skimage is not installed."
+        msg = (
+            "`threshold` is None and thus scrublet requires `scikit-image`. "
+            "Please install `scanpy[scrublet]` (or `scikit-image` directly) and try again."
+        )
         raise ValueError(msg)
 
     if copy:

src/scanpy/queries/_queries.py

@@ -67,8 +67,8 @@ def simple_query(
     try:
         from pybiomart import Server
     except ImportError as e:
-        msg = "This method requires the `pybiomart` module to be installed."
-        raise ImportError(msg) from e
+        e.add_note("Please install `pybiomart` and try again.")
+        raise
     server = Server(host, use_cache=use_cache)
     dataset = server.marts["ENSEMBL_MART_ENSEMBL"].datasets[f"{org}_gene_ensembl"]
     res = dataset.query(attributes=attrs, filters=filters, use_attr_names=True)
@@ -278,8 +278,8 @@ def enrich(
     try:
         from gprofiler import GProfiler
     except ImportError as e:
-        msg = "This method requires the `gprofiler-official` module to be installed."
-        raise ImportError(msg) from e
+        e.add_note("Please install `gprofiler-official` and try again.")
+        raise
     gprofiler = GProfiler(user_agent="scanpy", return_dataframe=True)
     gprofiler_kwargs = dict(gprofiler_kwargs)
     for k in ["organism"]:

src/scanpy/tools/_leiden.py

@@ -236,8 +236,10 @@ def _validate_flavor(
             try:
                 import leidenalg  # noqa: F401
             except ImportError as e:
-                msg = "Please install the leiden algorithm: `conda install -c conda-forge leidenalg` or `pip install leidenalg`."
-                raise ImportError(msg) from e
+                e.add_note(
+                    "Please install `scanpy[leiden]` (or `leidenalg` directly) and try again."
+                )
+                raise
             flavor = "leidenalg"
         case _:
             msg = f"flavor must be either 'igraph' or 'leidenalg', but {flavor!r} was passed"

tests/test_plotting.py

@@ -1916,7 +1916,7 @@ def test_dotplot_group_colors_raises_error_on_missing_dep(
     markers = ["CD79A"]
     group_colors = {"CD19+ B": "blue"}
 
-    with pytest.raises(ImportError, match="pip install colour-science"):
+    with pytest.raises(ImportError, match=r"colour-science.*required"):
         sc.pl.dotplot(
             adata,
             markers,