Multiple approaches to solve question at https://lists.osgeo.org/pipermail/gdal-dev/2022-June/055949.html

gdal_csv_to_geopackage.py

import os
from osgeo import gdal

# gdal.UseExceptions()
# gdal.SetConfigOption('CPL_DEBUG', 'ON')

# Create a test CSV
file = "test.csv"
with open("test.csv", "w") as csv:
    csv.write("latitude,longitude\n")
    csv.write("61,-150")

# GDAL approach using gdal.VectorTranslate
ds = gdal.OpenEx(
    file, open_options=["X_POSSIBLE_NAMES=longitude", "Y_POSSIBLE_NAMES=latitude"]
)

gdal.VectorTranslate(
    "out.gpkg", ds, options='-f GPKG -a_srs "EPSG:4326" -nln layernameout'
)

# Geopandas approach
import geopandas

gdf = geopandas.read_file(file, x_possible_names="longitude", y_possible_names="latitude")
gdf.to_file("dataframe1.gpkg", driver="GPKG", crs='epsg:4326')

# Fiona approach
import fiona

cols_lon_lat = ["longitude", "latitude"]

with fiona.open(file) as infile:
    properties = dict(
        [[i, "str"] for i in infile.schema.get("properties") if i not in cols_lon_lat]
    )
    schema = {"geometry": "Point", "properties": properties}
    with fiona.open(
        "test_geopackage.gpkg",
        "w",
        driver="GPKG",
        crs="EPSG:4326",
        schema=schema,
        layer="layername",
    ) as gpkg:
        for _, row in infile.items():
            gpkg.write(
                {
                    "properties": {
                        k: v
                        for k, v in row.get("properties").items()
                        if k not in cols_lon_lat
                    },
                    "geometry": {
                        "type": "Point",
                        "coordinates": [
                            float(row.get("properties").get(col))
                            for col in cols_lon_lat
                        ],
                    },
                }
            )

Thanks for the examples, they are a good reference. I believe this should work too:

gdf = geopandas.read_file(file, x_possible_names="longitude", y_possible_names="latitude")
gdf.to_file("dataframe.gpkg", driver="GPKG")

See: geopandas/geopandas#2221

Thanks. Updated the gist. Do not forget the crs e.g

gdf.to_file("dataframe1.gpkg", driver="GPKG", crs='epsg:4326')

otherwise ogrinfo -so -al dataframe.gpkg output the following

INFO: Open of `dataframe.gpkg'
      using driver `GPKG' successful.

Layer name: dataframe
Geometry: Point
Feature Count: 1
Extent: (-150.000000, 61.000000) - (-150.000000, 61.000000)
Layer SRS WKT:
(unknown)
FID Column = fid
Geometry Column = geom
latitude: Real (0.0)
longitude: Real (0.0)

instead of

INFO: Open of `dataframe.gpkg'
      using driver `GPKG' successful.

Layer name: dataframe
Geometry: Point
Feature Count: 1
Extent: (-150.000000, 61.000000) - (-150.000000, 61.000000)
Layer SRS WKT:
GEOGCS["WGS 84",
    DATUM["WGS_1984",
        SPHEROID["WGS 84",6378137,298.257223563,
            AUTHORITY["EPSG","7030"]],
        AUTHORITY["EPSG","6326"]],
    PRIMEM["Greenwich",0,
        AUTHORITY["EPSG","8901"]],
    UNIT["degree",0.0174532925199433,
        AUTHORITY["EPSG","9122"]],
    AUTHORITY["EPSG","4326"]]
FID Column = fid
Geometry Column = geom
latitude: Real (0.0)
longitude: Real (0.0)