Error (GDAL) while importing fiona in Python3 (Ubuntu 18.04)

I met the following error while importing Fiona in Python3 on Ubuntu 18.04 after having freshly upgraded GDAL to its version 3.1.0:

>>> import fiona
ERROR 4: Unable to open EPSG support file gcs.csv. 
         Try setting the GDAL_DATA environment variable to point 
         to the directory containing EPSG csv files.

Further details here:
https://github.com/OSGeo/gdal/issues/2500 https://github.com/geopandas/geopandas/issues/1408

It seems that both fiona and rasterio keep installing this gcs.csv file which is no more needed by GDAL apparently in /usr/local/lib/python3.6/dist-packages/fiona/gdal_data/ and /usr/local/lib/python3.6/dist-packages/rasterio/gdal_data/, both installed with sudo -H pip3 install -U <package-name>.

>>> import fiona
ERROR 4: Unable to open EPSG support file gcs.csv.  
         Try setting the GDAL_DATA environment variable to point 
         to the directory containing EPSG csv files.
>>> 

The same error is raised when calling the system tool fio in a bash terminal:

$ fio --help
ERROR 4: Unable to open EPSG support file gcs.csv.  
         Try setting the GDAL_DATA environment variable to point 
         to the directory containing EPSG csv files.
Usage: fio [OPTIONS] COMMAND [ARGS]...
(...)

But If I do import rasterio first, fiona stops complaining:

>>> import rasterio
>>> import fiona
>>> 

Environment

OS: Ubuntu 18.04.

Python3: Python 3.6.9 (default, Apr 18 2020, 01:56:04)

gdalinfo --version: GDAL 3.1.0, released 2020/05/03

fiona:

>>> import fiona
>>> fiona.__version__
'1.8.13.post1'
>>> fiona.__file__
'/usr/local/lib/python3.6/dist-packages/fiona/__init__.py'

EDIT

I first installed gdal from apt long time ago, prior to every other things, which for Ubuntu 18.04 is:

$ apt-cache policy gdal-bin
gdal-bin:
  Installed: 2.4.0+10-0bionic1
  Candidate: 2.4.0+10-0bionic1
  Version table:
 *** 2.4.0+10-0bionic1 100
        100 /var/lib/dpkg/status
     2.2.3+dfsg-2 500
        500 http://ch.archive.ubuntu.com/ubuntu bionic/universe amd64 Packages

I installed Fiona (and almost all my favorite geo spatial libraries) with pip (20.1), which is currently;
Fiona-1.8.13.post1-cp36-cp36m-manylinux1_x86_64.whl (14.7 MB)

and raterio:
rasterio-1.1.4-cp36-cp36m-manylinux1_x86_64.whl (18.2 MB)

I usually do it like:
sudo -H pip3 install -U <package-name> (-U for upgading to its latest available version).
That’s why the packages installed this way go to /usr/local instead of /usr directly. Which is fine.

Then, yesterday, I faced some issues while inserting data in a PostgreSQL v.12 database using ogr2ogr. I figured out it was fixed in a recent commit so I decided to upgrade GDAL itself, from source, because the version from apt was too old. Therefore, I downloaded version 3.1.0 from here; https://github.com/OSGeo/gdal/releases/tag/v3.1.0 , compiled it, and installed it using checkinstall tool.

Now gdal version is:

$ gdalinfo --version
GDAL 3.1.0, released 2020/05/03

Then I upgade the python gdal package also using pip. This was the shipped wheel:
GDAL-3.1.0-cp36-cp36m-linux_x86_64.whl =>

>>> from osgeo import gdal
>>> gdal.__version__
'3.1.0'
>>> gdal.__file__
'/usr/local/lib/python3.6/dist-packages/osgeo/gdal.py'
>>> 

I did not uninstall gdal 2.4 (the apt version) because many (many!) other softwares I also installed with apt, such as QGIS relies on it and would be dropped as well by apt!

After what I figured out the error message while loading geopandas, which brings me here aswell because loading fiona itself causes the same error. But strangely, if I load rasterio prior to fiona everything goes well. This is obscure to me.

Here is the last piece of information which was asked for:

>>> from fiona._env import get_gdal_release_name
>>> print(get_gdal_release_name())
2.4.4
>>> 

These are also the 3 places I can find the file causing troubles:

$ find /usr -iname gcs.csv
/usr/share/gdal/2.4/gcs.csv
/usr/local/lib/python3.6/dist-packages/rasterio/gdal_data/gcs.csv
/usr/local/lib/python3.6/dist-packages/fiona/gdal_data/gcs.csv

[rbuffat]

@demiurg @rdmurphy The fix is already merged in maint-1.8 branch but not yet released. Until a new release is out, you could either manually apply the fix from https://github.com/Toblerity/Fiona/issues/897#issuecomment-626223187 or use the maint-1.8 branch.

[jdmcbr]

Thanks @swiss-knight and @rbuffat. I did a fresh GDAL 3.1.2 install this weekend and started hitting this, and was confused given I knew the gcs.csv was no longer present in GDAL as of 3.0. Installing from maint-1.8 solved it!