Error setting up environment following the Install from conda-forge instructions

[jeremyg19]

I ran the following

conda create -n geo python=3.11
conda activate geo
conda install -c conda-forge mamba
mamba install -c conda-forge lidar

After

python
from lidar import *

I get the following

Traceback (most recent call last):
File "", line 1, in
File "/home/jagraham/mambaforge/envs/geo/lib/python3.11/site-packages/lidar/init.py", line 9, in
from .filling import (
File "/home/jagraham/mambaforge/envs/geo/lib/python3.11/site-packages/lidar/filling.py", line 11, in
from osgeo import gdal, ogr, osr
File "/home/jagraham/mambaforge/envs/geo/lib/python3.11/site-packages/osgeo/gdal.py", line 82, in
from osgeo.gdalconst import *
File "/home/jagraham/mambaforge/envs/geo/lib/python3.11/site-packages/osgeo/gdalconst.py", line 309, in
GAAT_BOOLEAN = _gdalconst.GAAT_BOOLEAN
^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'osgeo._gdalconst' has no attribute 'GAAT_BOOLEAN'

I thought that the mamba solver finds the right GDAL version to install to build the environment. Is it still required to do the

sudo add-apt-repository ppa:ubuntugis/ppa
sudo apt-get update
sudo apt-get install gdal-bin libgdal-dev

And if so does that make system-wide changes or just in the created conda environment?

Here below is the callback from mamba install -c conda-forge lidar

(geo) jagraham@precision7770a:~/Documents/git/geo_stac$ mamba install -c conda-forge lidar

              __    __    __    __                                                                                     
             /  \  /  \  /  \  /  \                                                                                    
            /    \/    \/    \/    \                                                                                   

███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ ____
/ / _/ _/ _/ \ o _,
/ / ___/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝

    mamba (1.4.2) supported by @QuantStack

    GitHub:  https://github.com/mamba-org/mamba
    Twitter: https://twitter.com/QuantStack

█████████████████████████████████████████████████████████████

Looking for: ['lidar']

warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/497deca9.json" was modified by another program
warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/09cdf8bf.json" was modified by another program
warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/47929eba.json" was modified by another program
warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/3e39a7aa.json" was modified by another program
warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/2ce54b42.json" was modified by another program
warning libmamba Cache file "/home/jagraham/mambaforge/pkgs/cache/4ea078d6.json" was modified by another program
pkgs/main/noarch 904.8kB @ 1.5MB/s 0.6s
pkgs/r/linux-64 1.9MB @ 2.7MB/s 0.7s
pkgs/r/noarch 2.3MB @ 1.9MB/s 0.7s
pkgs/main/linux-64 8.2MB @ 3.2MB/s 2.6s
conda-forge/noarch 22.3MB @ 6.7MB/s 3.5s
conda-forge/linux-64 49.6MB @ 6.0MB/s 8.7s

Pinned packages:

• python 3.11.*

Transaction

Prefix: /home/jagraham/mambaforge/envs/geo

Updating specs:

• lidar
• ca-certificates
• openssl

Package Version Build Channel Size
───────────────────────────────────────────────────────────────────────────────────────────────────
Install:
───────────────────────────────────────────────────────────────────────────────────────────────────

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• libtiff 4.7.0 hd9ff511_3 conda-forge/linux-64 Cached
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• lidar 0.8.4 pyhd8ed1ab_0 conda-forge/noarch Cached
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• xerces-c 3.2.5 h988505b_2 conda-forge/linux-64 Cached
• xorg-libice 1.1.2 hb9d3cd8_0 conda-forge/linux-64 Cached
• xorg-libsm 1.2.5 he73a12e_0 conda-forge/linux-64 Cached
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• xorg-libxdmcp 1.1.5 hb9d3cd8_0 conda-forge/linux-64 Cached
• xorg-libxext 1.3.6 hb9d3cd8_0 conda-forge/linux-64 Cached
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• xyzservices 2025.1.0 pyhd8ed1ab_0 conda-forge/noarch Cached
• zfp 1.0.1 h5888daf_2 conda-forge/linux-64 Cached
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• zlib-ng 2.2.4 h7955e40_0 conda-forge/linux-64 Cached
• zstandard 0.19.0 py311hd4cff14_0 conda-forge/linux-64 Cached

Change:
───────────────────────────────────────────────────────────────────────────────────────────────────

• libxml2 2.13.6 h0d44e9d_0 conda-forge

• libxml2 2.13.6 h8d12d68_0 conda-forge/linux-64 Cached

Summary:

Install: 210 packages
Change: 1 packages

Total download: 0 B

───────────────────────────────────────────────────────────────────────────────────────────────────

Confirm changes: [Y/n] y

Downloading and Extracting Packages

Preparing transaction: done
Verifying transaction: done
Executing transaction: done

[jeremyg19]

I was able to get around the error by first creating a mamba environment with gdal geopandas richdem etc then pip install lidar

[giswqs]

This is a common gdal installation issue. What I would recommend is to install gdal first and make sure it is working properly before installing lidar.

First, remove the existing conda env: conda remove -n geo --all

Then, create a new conda env

conda create -n geo python=3.11
conda activate geo
conda install -c conda-forge mamba
mamba install gdal

Then test if gdal workshop properly

python
from osgeo import gdal

If not, try installing gdal from conda-forge, or try a different gdal version.

If yes,

mamba install -c conda-forge lidar

[jeremyg19]

Thanks for the super quick response. I removed and recreated the environment. Then -

from osgeo import gdal worked fine

but then

exit()
mamba install -c conda-forge lidar
python 
from osgeo import gdal

results in

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/jagraham/mambaforge/envs/vernal_pool/lib/python3.11/site-packages/osgeo/gdal.py", line 82, in <module>
    from osgeo.gdalconst import *
  File "/home/jagraham/mambaforge/envs/vernal_pool/lib/python3.11/site-packages/osgeo/gdalconst.py", line 309, in <module>
    GAAT_BOOLEAN = _gdalconst.GAAT_BOOLEAN
                   ^^^^^^^^^^^^^^^^^^^^^^^
AttributeError: module 'osgeo._gdalconst' has no attribute 'GAAT_BOOLEAN'

I do have the pip installed version working fine though

[giswqs]

What is the gdal versions before and after installing lidar?

[jeremyg19]

on the install I get
+ gdal 3.10.2

and

mamba install -c conda-forge lidar

doesn't show any changes to gdal