Repository: geopandas/geopandas

Issue:
BUG: Unwarranted warning when reading a file with multiple layers and using a GeoDataFrame, GeoSeries as mask or bbox option
- [x] I have checked that this issue has not already been reported.

- [x] I have confirmed this bug exists on the latest version of geopandas.

- [x] (optional) I have confirmed this bug exists on the main branch of geopandas.

---

#### Code Sample, a copy-pastable example

```python
import os
import tempfile

import geopandas as gpd
from shapely.geometry import Point

data1 = {"geometry": [Point(1, 2), Point(2, 1)]}
gdf = gpd.GeoDataFrame(data1, crs="EPSG:4326")

tmpfile_path = tempfile.mktemp(suffix=".gpkg")
gdf.to_file(tmpfile_path, layer="layer1", driver="GPKG")
gdf.to_file(tmpfile_path, layer="layer2", driver="GPKG")

# This will raise an unwarranted warning:
result = gpd.read_file(tmpfile_path, bbox=gdf, layer="layer1")

if os.path.exists(tmpfile_path):
    os.remove(tmpfile_path)

```

#### Problem description

When reading a file with multiple layers, while providing the layer parameter, a warning saying "Specify the layer parameter" will still be issued if a GeoDataFrame or GeoSeries is provided as the bbox or the mask argument.

#### Expected Output
No warning should be shown if the layer is passed as an argument.

#### Output of ``geopandas.show_versions()``

<details>

SYSTEM INFO
-----------
python     : 3.11.4 (tags/v3.11.4:d2340ef, Jun  7 2023, 05:45:37) [MSC v.1934 64 bit (AMD64)]
machine    : Windows-10-10.0.22635-SP0

GEOS, GDAL, PROJ INFO
---------------------
GEOS       : 3.11.3
GEOS lib   : None
GDAL       : 3.8.5
PROJ       : 9.3.0

PYTHON DEPENDENCIES
-------------------
geopandas  : 1.0.1
numpy      : 1.26.4
pandas     : 2.2.2
pyproj     : 3.6.1
shapely    : 2.0.4
pyogrio    : 0.8.0
geoalchemy2: 0.14.7
geopy      : None
matplotlib : None
mapclassify: None
fiona      : 1.9.6
psycopg    : None
psycopg2   : 2.9.9 (dt dec pq3 ext lo64)
pyarrow    : 15.0.2

</details>



Discussion:

Patch:
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 5121798025..af80366958 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -4,6 +4,8 @@
 
 Bug fixes:
 
+- Fix unspecified layer warning being emitted while reading multilayer datasets, even
+  when layer is specified when using the mask or bbox keywords (#3378).
 - Properly support named aggregations over a geometry column in `GroupBy.agg` (#3368).
 
 ## Version 1.0.1 (July 2, 2024)
diff --git a/geopandas/io/file.py b/geopandas/io/file.py
index 37aa3038c0..af6f3bcea7 100644
--- a/geopandas/io/file.py
+++ b/geopandas/io/file.py
@@ -228,9 +228,9 @@ def _read_file(
         Keyword args to be passed to the engine, and can be used to write
         to multi-layer data, store data within archives (zip files), etc.
         In case of the "pyogrio" engine, the keyword arguments are passed to
-        `pyogrio.write_dataframe`. In case of the "fiona" engine, the keyword
+        `pyogrio.read_dataframe`. In case of the "fiona" engine, the keyword
         arguments are passed to fiona.open`. For more information on possible
-        keywords, type: ``import pyogrio; help(pyogrio.write_dataframe)``.
+        keywords, type: ``import pyogrio; help(pyogrio.read_dataframe)``.
 
 
     Examples
@@ -481,7 +481,7 @@ def _read_file_pyogrio(path_or_bytes, bbox=None, mask=None, rows=None, **kwargs)
 
     if bbox is not None:
         if isinstance(bbox, (GeoDataFrame, GeoSeries)):
-            crs = pyogrio.read_info(path_or_bytes).get("crs")
+            crs = pyogrio.read_info(path_or_bytes, layer=kwargs.get("layer")).get("crs")
             if isinstance(path_or_bytes, IOBase):
                 path_or_bytes.seek(0)
 
@@ -494,7 +494,7 @@ def _read_file_pyogrio(path_or_bytes, bbox=None, mask=None, rows=None, **kwargs)
     if mask is not None:
         # NOTE: mask cannot be used at same time as bbox keyword
         if isinstance(mask, (GeoDataFrame, GeoSeries)):
-            crs = pyogrio.read_info(path_or_bytes).get("crs")
+            crs = pyogrio.read_info(path_or_bytes, layer=kwargs.get("layer")).get("crs")
             if isinstance(path_or_bytes, IOBase):
                 path_or_bytes.seek(0)
 
@@ -526,7 +526,7 @@ def _read_file_pyogrio(path_or_bytes, bbox=None, mask=None, rows=None, **kwargs)
             stacklevel=3,
         )
         ignore_fields = kwargs.pop("ignore_fields")
-        fields = pyogrio.read_info(path_or_bytes)["fields"]
+        fields = pyogrio.read_info(path_or_bytes, layer=kwargs.get("layer"))["fields"]
         include_fields = [col for col in fields if col not in ignore_fields]
         kwargs["columns"] = include_fields
     elif "include_fields" in kwargs:


Test patch:
diff --git a/geopandas/io/tests/test_file.py b/geopandas/io/tests/test_file.py
index 014b1f3c92..b710f1f4fe 100644
--- a/geopandas/io/tests/test_file.py
+++ b/geopandas/io/tests/test_file.py
@@ -5,6 +5,7 @@
 import pathlib
 import shutil
 import tempfile
+import warnings
 from collections import OrderedDict
 from packaging.version import Version
 
@@ -1075,6 +1076,31 @@ def test_read_file_mask_gdf_mismatched_crs(df_nybb, engine, nybb_filename):
     assert filtered_df_shape == (2, 5)
 
 
+@pytest.mark.skipif(not HAS_PYPROJ, reason="pyproj not installed")
+def test_read_file_multi_layer_with_layer_arg_no_warning(tmp_path, engine):
+    # While reading a file with multiple layers, if the layer is properly
+    # specified, a "Specify layer" warning should not be emitted
+    data1 = {"geometry": [Point(1, 2), Point(2, 1)]}
+    gdf = geopandas.GeoDataFrame(data1, crs="EPSG:4326")
+    file_path = tmp_path / "out.gpkg"
+    gdf.to_file(file_path, layer="layer1", engine=engine)
+    gdf.to_file(file_path, layer="layer2", engine=engine)
+
+    with warnings.catch_warnings(record=True) as captured:
+        warnings.simplefilter("always")
+        read_file(file_path, bbox=gdf, layer="layer1", engine=engine)
+        read_file(file_path, mask=gdf, layer="layer1", engine=engine)
+        specify_layer_warnings = [
+            warning
+            for warning in captured
+            if warning.category == UserWarning
+            and "specify layer parameter" in str(warning.message).lower()
+        ]
+        assert (
+            len(specify_layer_warnings) == 0
+        ), "'Specify layer parameter' warning was raised, but the layer was specified."
+
+
 def test_read_file_bbox_mask_not_allowed(engine, nybb_filename):
     bbox = (
         1031051.7879884212,