Installing LiCSBAS

[RoySreeta]

Hello Dr. Yumorishita,
I have tried installing the LiCSBAS on Ubuntu using Anaconda and also not as root but the installation keeps showing one error " PYTHONPATH not set to LiCSBAS". Can you help me clarify this?

[yumorishita]

You need to execute source <your_LiCSBAS_path>/LiCSBAS/bashrc_LiCSBAS.sh to set the PYTHONPATH.
https://github.com/yumorishita/LiCSBAS/wiki/1_Installation#12-licsbas-module

[RoySreeta]

Hello Dr. Yumorishita,
I executed that line as mentioned by you and also in the manual, but it still shows the same thing as follows:

sreetama@sreetama:/roy$ source /home/sreetama/roy/LiCSBAS/bashrc_LiCSBAS.sh
sreetama@sreetama:/roy$ LiCSBAS_check_install.py

Python version: 3.11.5
OK

Check required modues and versions
astropy(5.1) OK
bs4(4.12.2) OK
h5py(3.9.0) OK
matplotlib(3.7.2) OK
numpy(1.25.2) OK
psutil(5.9.0) OK
requests(2.31.0) OK
statsmodels(0.14.0) OK
ERROR: No module named '_gdal'

Check LiCSBAS commands
OK

Check LiCSBAS library
ERROR: PYTHONPATH is not set to LiCSBAS library

[yumorishita]

What is the return of echo $PYTHONPATH?

[RoySreeta]

Hello Dr. Yumorishita
This is the return as you asked:
sreetama@sreetama:~/Desktop$ echo $PYTHONPATH
/home/sreetama/licsbas/LiCSBAS/LiCSBAS_lib:

[yumorishita]

It is strange. The PYTHONPATH should be /home/sreetama/roy/LiCSBAS/LiCSBAS_lib if you run source /home/sreetama/roy/LiCSBAS/bashrc_LiCSBAS.sh.
What is the return of ls /home/sreetama/licsbas/LiCSBAS/LiCSBAS_lib and ls /home/sreetama/roy/LiCSBAS/LiCSBAS_lib?

[RoySreeta]

Hello Dr. Yumorishita,
I had two folders previously, so I deleted one and kept only roy.
Now the PYTHONPATH is as follows as you have mentioned:
sreetama@sreetama:/roy$ source /home/sreetama/roy/LiCSBAS/bashrc_LiCSBAS.sh
sreetama@sreetama:/roy$ echo $PYTHONPATH
/home/sreetama/roy/LiCSBAS/LiCSBAS_lib:
Then its hows the following:
sreetama@sreetama:~/roy$ ls /home/sreetama/roy/LiCSBAS/LiCSBAS_lib:
ls: cannot access '/home/sreetama/roy/LiCSBAS/LiCSBAS_lib:': No such file or directory

[yumorishita]

/home/sreetama/roy/LiCSBAS/LiCSBAS_lib should exist. How did you get the LiCSBAS package?

[RoySreeta]

Hello Dr. Yumorishita,
I installed the versions of Python and Anaconda first. Then after creating this environment for the LiCSBAS, I got the LiCSBAS package by cloning into your LiCSBAS github by executing this lien as mentioned in the wiki:
git clone https://github.com/yumorishita/LiCSBAS.git

But despite running these steps I do not know why it is displaying that there is no such file or directory.
What do you suggest I do now?

[yumorishita]

In which directory did you run git clone?
I recommend removing the LiCSBAS directory once and executing git clone and following commands again. Please show all the commands, logs (stdout), and working directory.

[RoySreeta]

Hello Dr. Yumorishita,
I removed the LiCSBAS directory and executed as you suggested. Please take a look:
sreetama@sreetama:~$ conda install gdal shapely
Collecting package metadata (current_repodata.json): done
Solving environment: done

All requested packages already installed.

sreetama@sreetama:$ git clone https://github.com/yumorishita/LiCSBAS.git
Cloning into 'LiCSBAS'...
remote: Enumerating objects: 1316, done.
remote: Counting objects: 100% (439/439), done.
remote: Compressing objects: 100% (47/47), done.
remote: Total 1316 (delta 407), reused 392 (delta 392), pack-reused 877
Receiving objects: 100% (1316/1316), 5.79 MiB | 29.49 MiB/s, done.
Resolving deltas: 100% (759/759), done.
sreetama@sreetama:$ source ./LiCSBAS/bashrc_LiCSBAS.sh
sreetama@sreetama:~$ LiCSBAS_check_install.py

Python version: 3.11.5
OK

Check required modues and versions
astropy(5.1) OK
bs4(4.12.2) OK
h5py(3.9.0) OK
matplotlib(3.7.2) OK
numpy(1.25.2) OK
psutil(5.9.0) OK
requests(2.31.0) OK
statsmodels(0.14.0) OK
ERROR: No module named '_gdal'

Check LiCSBAS commands
OK

Check LiCSBAS library
ERROR: PYTHONPATH is not set to LiCSBAS library

ERROR: LiCSBAS install is NOT OK

sreetama@sreetama:$ ls
anaconda3 Desktop Documents Downloads LiCSBAS Music Pictures Public snap Templates Videos
sreetama@sreetama:$ ls LiCSBAS/
bashrc_LiCSBAS.sh batch_LiCSBAS.sh bin LICENSE LiCSBAS_lib LiCSBAS_requirements.txt LiCSBAS.yml README.md
sreetama@sreetama:~$

[yumorishita]

What is the return of ls LiCSBAS/LiCSBAS_lib?
I have no idea about the gdal error. I suggest trying downgrading Python from 3.11 to 3.8.

[LMurrayBergquist]

I had exactly the same problem, and same output as RoySreeta, I tried downgrading from python 3.11 to 3.8 and using gdal=2.4, but now the error is just slightly different, it can't find osgeo instead of "_gdal":

(base) [louisa@localhost ~]$ LiCSBAS_check_install.py

Python version: 3.8.5
OK

Check required modues and versions
astropy(4.0.2) OK
bs4(4.9.3) OK
h5py(2.10.0) OK
matplotlib(3.3.2) OK
numpy(1.19.2) OK
psutil(5.7.2) OK
requests(2.24.0) OK
statsmodels(0.12.0) OK
ERROR: No module named 'osgeo'

Check LiCSBAS commands
OK

Check LiCSBAS library
ERROR: PYTHONPATH is not set to LiCSBAS library

ERROR: LiCSBAS install is NOT OK

(base) [louisa@localhost ~]$ echo $PYTHONPATH
/home/louisa/Software/LiCSBAS2/LiCSBAS_lib

[yumorishita]

I cannot reproduce the error... What OS do you use?

[LMurrayBergquist]

I am running it in a VirtualBox with Fedora 32, and I am using bash for the shell.

[yumorishita]

@LMurrayBergquist How did you get the LiCSBAS package? What is the return of ls /home/louisa/Software/LiCSBAS2/LiCSBAS_lib and conda list?

[RoySreeta]

Hello Dr. Yumorishita,
I downgraded to Python Version 3.8 and i ran the command as you asked. This is what it shows:
licsbas) sreetama@sreetama:/LiCSBAS$ echo $PYTHONPATH
/home/sreetama/LiCSBAS/LiCSBAS_lib:
(licsbas) sreetama@sreetama:/LiCSBAS$ cd LiCSBAS_lib/
(licsbas) sreetama@sreetama:/LiCSBAS/LiCSBAS_lib$ ls
cmocean GMT LiCSBAS_plot_lib.py
colorcet LiCSBAS_inv_lib.py LiCSBAS_tools_lib.py
extract_cmaps_GMT.sh LiCSBAS_io_lib.py SCM
extract_cmaps_SCM.sh LiCSBAS_loop_lib.py
(licsbas) sreetama@sreetama:/LiCSBAS/LiCSBAS_lib$

[LMurrayBergquist]

Hello,
I got LiCSBAS from the Wiki instructions: https://github.com/yumorishita/LiCSBAS/wiki/1_Installation
But in step 1.2 I did: "git clone https://github.com/yumorishita/LiCSBAS2.git" instead of "/LiCSBAS.git"

This is the ls output:
(licsbas) [louisa@localhost ~]$ ls Software/LiCSBAS2/LiCSBAS_lib/
cm_insar_qgis.xml colorcet extract_cmaps_SCM.sh LiCSBAS_inv_lib.py LiCSBAS_loop_lib.py LiCSBAS_tools_lib.py SCM
cmocean extract_cmaps_GMT.sh GMT LiCSBAS_io_lib.py LiCSBAS_plot_lib.py pycache

The "conda list" output is quite long, do you want to see all of it or just gdal?
(licsbas) [louisa@localhost ~]$ conda list | grep "gdal"
gdal 3.4.1 py39h2c27f0e_0
libgdal 3.4.1 hdd9df00_0

[yumorishita]

@RoySreeta There should be no problem. Do you still get an error in LiCSBAS_check_install.py? What is your OS?

@LMurrayBergquist Everything looks fine. I have no idea about the error...

[RoySreeta]

Hello Dr. Yumorishita,
Yes, unfortunately despite everything being alright I'm still getting the same error. I'm using Linux.

[yumorishita]

Below is my example. Can you try the same commands and tell me the return?

$ echo $PYTHONPATH
/home/morishita/software/LiCSBAS2/LiCSBAS_lib:
$ ls ${PYTHONPATH%:}
GMT                  LiCSBAS_plot_lib.py   cm_insar_qgis.xml     extract_cmaps_SCM.sh
LiCSBAS_inv_lib.py   LiCSBAS_tools_lib.py  cmocean
LiCSBAS_io_lib.py    SCM                   colorcet
LiCSBAS_loop_lib.py  __pycache__           extract_cmaps_GMT.sh
$ python3
Python 3.11.3 (main, Apr 19 2023, 23:54:32) [GCC 11.2.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import LiCSBAS_io_lib
>>> 

[LMurrayBergquist]

Hello, this is what mine returned:

[yumorishita]

Please try:
https://stackoverflow.com/questions/71904252/gdalinfo-error-while-loading-shared-libraries-libtiledb-so-2-2-cannot-open-sh

[RoySreeta]

Hello Dr. Yumorishita,
I installed the gdal poppler and my LiCSBAS installation is finally OK. Thanks for your help!