style: str.format to f-string

src/cooler/balance.py

@@ -173,9 +173,7 @@ def _balance_cisonly(
 
         else:
             warnings.warn(
-                "Iteration limit reached without convergence on {}.".format(
-                    chroms[cid]
-                ),
+                f"Iteration limit reached without convergence on {chroms[cid]}.",
                 ConvergenceWarning,
             )
 

src/cooler/cli/_util.py

@@ -128,7 +128,7 @@ def parse_bins(arg):
             )
         except pd.parser.CParserError as e:
             raise ValueError(
-                f'Failed to parse bins file "{arg}": {str(e)}'
+                f'Failed to parse bins file "{arg}": {e!s}'
             ) from e
 
         chromtable = (

src/cooler/create/_ingest.py

@@ -800,7 +800,7 @@ def __init__(
             if f.exists2(c1, c2) and f.exists2(c2, c1):
                 raise RuntimeError(
                     "Pairs are not triangular: found blocks "
-                    + "'{0}|{1}'' and '{1}|{0}'".format(c1, c2)
+                    + f"'{c1}|{c2}'' and '{c2}|{c1}'"
                 )
 
         # dumb heuristic to prevent excessively large chunks on one worker
@@ -816,8 +816,8 @@ def __init__(
             self.n_chunks = max(self.n_chunks, n_chunks)
             if self.n_chunks > old_n:
                 logger.info(
-                    "Pairs file has {} lines. "
-                    "Increasing max-split to {}.".format(n_lines, self.n_chunks)
+                    f"Pairs file has {n_lines} lines. "
+                    f"Increasing max-split to {self.n_chunks}."
                 )
 
         # all requested contigs will be placed in the output matrix

src/cooler/fileops.py

@@ -353,10 +353,10 @@ def tree_widget(group, expand, level):
         import ipytree
     except ImportError as error:
         raise ImportError(
-            "{}: Run `pip install ipytree` or `conda install ipytree`"
+            f"{error}: Run `pip install ipytree` or `conda install ipytree`"
             "to get the required ipytree dependency for displaying the tree "
             "widget. If using jupyterlab, you also need to run "
-            "`jupyter labextension install ipytree`".format(error)
+            "`jupyter labextension install ipytree`"
         ) from None
 
     result = ipytree.Tree()

src/cooler/reduce.py

@@ -234,8 +234,8 @@ def merge_coolers(
         for col in columns:
             if col not in pixel_dtypes:
                 raise ValueError(
-                    "Pixel value column '{}' not found in "
-                    "input '{}'.".format(col, clr.filename)
+                    f"Pixel value column '{col}' not found in "
+                    f"input '{clr.filename}'."
                 )
             else:
                 dtype_map[col].append(pixel_dtypes[col])
@@ -473,8 +473,8 @@ def get_multiplier_sequence(resolutions, bases=None):
     for i, p in enumerate(pred):
         if p == -1 and resn[i] not in bases:
             raise ValueError(
-                "Resolution {} cannot be derived from "
-                "the base resolutions: {}.".format(resn[i], bases)
+                f"Resolution {resn[i]} cannot be derived from "
+                f"the base resolutions: {bases}."
             )
 
     return resn, pred, mult
@@ -683,8 +683,8 @@ def coarsen_cooler(
     for col in columns:
         if col not in input_dtypes:
             raise ValueError(
-                "Pixel value column '{}' not found in "
-                "input '{}'.".format(col, clr.filename)
+                f"Pixel value column '{col}' not found in "
+                f"input '{clr.filename}'."
             )
         else:
             dtypes.setdefault(col, input_dtypes[col])
@@ -867,7 +867,7 @@ def legacy_zoomify(input_uri, outfile, nproc, chunksize, lock=None):
     logger.info(f"quad tile cover: {2 ** n_zooms}")
     logger.info(
         "Copying base matrix to level "
-        + "{0} and producing {0} new zoom levels ".format(n_zooms)
+        + f"{n_zooms} and producing {n_zooms} new zoom levels "
         + "counting down to 0..."
     )
 

src/cooler/util.py

@@ -256,9 +256,7 @@ def fetch_chromsizes(db, **kwargs):
 
     """
     return read_chromsizes(
-        "http://hgdownload.cse.ucsc.edu/goldenPath/{}/database/chromInfo.txt.gz".format(
-            db
-        ),
+        f"http://hgdownload.cse.ucsc.edu/goldenPath/{db}/database/chromInfo.txt.gz",
         **kwargs
     )
 
@@ -634,7 +632,7 @@ def _nonempty_scalar(x):
             return _scalar_from_dtype(dtype)
         else:
             raise TypeError(
-                "Can't handle meta of type " "'{}'".format(type(x).__name__)
+                "Can't handle meta of type " f"'{type(x).__name__}'"
             )
 
     def _empty_series(name, dtype, index=None):
@@ -661,7 +659,7 @@ def _empty_series(name, dtype, index=None):
     elif isinstance(x, (list, tuple)):
         if not all(isinstance(i, tuple) and len(i) == 2 for i in x):
             raise ValueError(
-                "Expected iterable of tuples of (name, dtype), " "got {}".format(x)
+                "Expected iterable of tuples of (name, dtype), " f"got {x}"
             )
         return pd.DataFrame(
             {c: _empty_series(c, d, index=index) for (c, d) in x},