extract message out of all touched errors

src/scanpy/_utils/__init__.py

@@ -195,7 +195,8 @@ def _import_name(name: str) -> Any:
         try:
             obj = getattr(obj, name)
         except AttributeError:
-            raise RuntimeError(f"{parts[:i]}, {parts[i + 1 :]}, {obj} {name}")
+            msg = f"{parts[:i]}, {parts[i + 1 :]}, {obj} {name}"
+            raise RuntimeError(msg)
     return obj
 
 
@@ -1130,18 +1131,18 @@ def __contains__(self, key: str) -> bool:
 def _choose_graph(adata, obsp, neighbors_key):
     """Choose connectivities from neighbbors or another obsp column"""
     if obsp is not None and neighbors_key is not None:
-        raise ValueError(
-            "You can't specify both obsp, neighbors_key. Please select only one."
-        )
+        msg = "You can't specify both obsp, neighbors_key. Please select only one."
+        raise ValueError(msg)
 
     if obsp is not None:
         return adata.obsp[obsp]
     else:
         neighbors = NeighborsView(adata, neighbors_key)
         if "connectivities" not in neighbors:
-            raise ValueError(
+            msg = (
                 "You need to run `pp.neighbors` first to compute a neighborhood graph."
             )
+            raise ValueError(msg)
         return neighbors["connectivities"]
 
 

src/scanpy/neighbors/__init__.py

@@ -823,10 +823,11 @@ def _init_iroot(self):
         # set iroot directly
         if "iroot" in self._adata.uns:
             if self._adata.uns["iroot"] >= self._adata.n_obs:
-                logg.warning(
+                msg = (
                     f"Root cell index {self._adata.uns['iroot']} does not "
                     f"exist for {self._adata.n_obs} samples. It’s ignored."
                 )
+                logg.warning(msg)
             else:
                 self.iroot = self._adata.uns["iroot"]
             return
@@ -888,9 +889,8 @@ def _set_iroot_via_xroot(self, xroot: np.ndarray):
             condition, only relevant for computing pseudotime.
         """
         if self._adata.shape[1] != xroot.size:
-            raise ValueError(
-                "The root vector you provided does not have the correct dimension."
-            )
+            msg = "The root vector you provided does not have the correct dimension."
+            raise ValueError(msg)
         # this is the squared distance
         dsqroot = 1e10
         iroot = 0

src/scanpy/plotting/_anndata.py

@@ -848,9 +848,8 @@ def violin(
                 f"Expected number of y-labels to be `1`, found `{len(ylabel)}`."
             )
     elif len(ylabel) != len(keys):
-        raise ValueError(
-            f"Expected number of y-labels to be `{len(keys)}`, found `{len(ylabel)}`."
-        )
+        msg = f"Expected number of y-labels to be `{len(keys)}`, found `{len(ylabel)}`."
+        raise ValueError(msg)
 
     if groupby is not None:
         obs_df = get.obs_df(adata, keys=[groupby] + keys, layer=layer, use_raw=use_raw)

src/scanpy/plotting/_tools/paga.py

@@ -547,9 +547,8 @@ def is_flat(x):
 
     if isinstance(root, str):
         if root not in labels:
-            raise ValueError(
-                f"If `root` is a string, it needs to be one of {labels} not {root!r}."
-            )
+            msg = f"If `root` is a string, it needs to be one of {labels} not {root!r}."
+            raise ValueError(msg)
         root = list(labels).index(root)
     if isinstance(root, Sequence) and root[0] in labels:
         root = [list(labels).index(r) for r in root]

src/scanpy/readwrite.py

@@ -219,10 +219,11 @@ def read_10x_h5(
         adata = _read_v3_10x_h5(filename, start=start)
         if genome:
             if genome not in adata.var["genome"].values:
-                raise ValueError(
+                msg = (
                     f"Could not find data corresponding to genome '{genome}' in '{filename}'. "
                     f"Available genomes are: {list(adata.var['genome'].unique())}."
                 )
+                raise ValueError(msg)
             adata = adata[:, adata.var["genome"] == genome]
         if gex_only:
             adata = adata[:, adata.var["feature_types"] == "Gene Expression"]
@@ -766,9 +767,8 @@ def _read(
     **kwargs,
 ):
     if ext is not None and ext not in avail_exts:
-        raise ValueError(
-            f"Please provide one of the available extensions.\n{avail_exts}"
-        )
+        msg = f"Please provide one of the available extensions.\n{avail_exts}"
+        raise ValueError(msg)
     else:
         ext = is_valid_filename(filename, return_ext=True)
     is_present = _check_datafile_present_and_download(filename, backup_url=backup_url)
@@ -816,7 +816,7 @@ def _read(
     elif ext in {"txt", "tab", "data", "tsv"}:
         if ext == "data":
             logg.hint(
-                "... assuming '.data' means tab or white-space separated text file",
+                "... assuming '.data' means tab or white-space separated text file"
             )
             logg.hint("change this by passing `ext` to sc.read")
         adata = read_text(filename, delimiter, first_column_names)

src/scanpy/tools/_louvain.py

@@ -143,9 +143,8 @@ def louvain(
     partition_kwargs = dict(partition_kwargs)
     start = logg.info("running Louvain clustering")
     if (flavor != "vtraag") and (partition_type is not None):
-        raise ValueError(
-            '`partition_type` is only a valid argument when `flavour` is "vtraag"'
-        )
+        msg = '`partition_type` is only a valid argument when `flavour` is "vtraag"'
+        raise ValueError(msg)
     adata = adata.copy() if copy else adata
     if adjacency is None:
         adjacency = _choose_graph(adata, obsp, neighbors_key)

src/scanpy/tools/_sim.py

@@ -854,9 +854,8 @@ def build_boolCoeff(self):
                         raise ValueError(f"specify coupling value for {key} <- {g}")
                 else:
                     if np.abs(self.Coupl[self.varNames[key], g]) > 1e-10:
-                        raise ValueError(
-                            f"there should be no coupling value for {key} <- {g}"
-                        )
+                        msg = f"there should be no coupling value for {key} <- {g}"
+                        raise ValueError(msg)
             if self.verbosity > 1:
                 settings.m(0, "..." + key)
                 settings.m(0, rule)
@@ -1045,7 +1044,8 @@ def sample_coupling_matrix(
             check = True
             break
     if not check:
-        raise ValueError(f"did not find graph without cycles after{max_trial} trials")
+        msg = f"did not find graph without cycles after {max_trial} trials"
+        raise ValueError(msg)
     return Coupl, Adj, Adj_signed, n_edges
 
 

src/scanpy/tools/_utils.py

@@ -128,5 +128,6 @@ def get_init_pos_from_paga(
             else:
                 init_pos[subset] = group_pos
     else:
-        raise ValueError("Plot PAGA first, so that adata.uns['paga']with key 'pos'.")
+        msg = "Plot PAGA first, so that adata.uns['paga'] with key 'pos'."
+        raise ValueError(msg)
     return init_pos