Submodule path error for installing Task_1 code

[jingyunc]

I was try to install Task 1 code for the FeTS24 Challenge. I followed the Task 1 instructions until step 8 (pip install .), where I got following error:

  Preparing metadata (setup.py) ... done
Collecting openfl@ git+https://github.com/intel/openfl.git@f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f (from fets-challenge==2.0)
  Cloning https://github.com/intel/openfl.git (to revision f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f) to /tmp/pip-install-umyuqv17/openfl_6de81b4493e04a72a7842469596cdbd7
  Running command git clone --filter=blob:none --quiet https://github.com/intel/openfl.git /tmp/pip-install-umyuqv17/openfl_6de81b4493e04a72a7842469596cdbd7
  Running command git rev-parse -q --verify 'sha^f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f'
  Running command git fetch -q https://github.com/intel/openfl.git f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f
  Running command git checkout -q f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f
  Resolved https://github.com/intel/openfl.git to commit f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f
  Preparing metadata (setup.py) ... done
Collecting GANDLF@ git+https://github.com/CBICA/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278 (from fets-challenge==2.0)
  Cloning https://github.com/CBICA/GaNDLF.git (to revision e4d0d4bfdf4076130817001a98dfb90189956278) to /tmp/pip-install-umyuqv17/gandlf_7bee759db7a34001b96f1fd3e9852230
  Running command git clone --filter=blob:none --quiet https://github.com/CBICA/GaNDLF.git /tmp/pip-install-umyuqv17/gandlf_7bee759db7a34001b96f1fd3e9852230
  Running command git rev-parse -q --verify 'sha^e4d0d4bfdf4076130817001a98dfb90189956278'
  Running command git fetch -q https://github.com/CBICA/GaNDLF.git e4d0d4bfdf4076130817001a98dfb90189956278
  Running command git checkout -q e4d0d4bfdf4076130817001a98dfb90189956278
  Resolved https://github.com/CBICA/GaNDLF.git to commit e4d0d4bfdf4076130817001a98dfb90189956278
  Running command git submodule update --init --recursive -q
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Installing backend dependencies ... done
  Preparing metadata (pyproject.toml) ... done
Collecting fets@ git+https://github.com/FETS-AI/Algorithms.git@fets_challenge (from fets-challenge==2.0)
  Cloning https://github.com/FETS-AI/Algorithms.git (to revision fets_challenge) to /tmp/pip-install-umyuqv17/fets_df05ec67c4384f9e8c1a1a3531332640
  Running command git clone --filter=blob:none --quiet https://github.com/FETS-AI/Algorithms.git /tmp/pip-install-umyuqv17/fets_df05ec67c4384f9e8c1a1a3531332640
  Running command git checkout -b fets_challenge --track origin/fets_challenge
  Switched to a new branch 'fets_challenge'
  Branch 'fets_challenge' set up to track remote branch 'fets_challenge' from 'origin'.
  Resolved https://github.com/FETS-AI/Algorithms.git to commit 60e0b8761229edde18e3d707e3e3e5eb0c0fb80f
  Running command git submodule update --init --recursive -q
  **fatal: No url found for submodule path 'GANDLF' in .gitmodules**
  error: subprocess-exited-with-error
  
  × git submodule update --init --recursive -q did not run successfully.
  │ exit code: 128
  ╰─> See above for output.
  
  note: This error originates from a subprocess, and is likely not a problem with pip.
error: subprocess-exited-with-error

× git submodule update --init --recursive -q did not run successfully.
│ exit code: 128
╰─> See above for output.

Can anyone please suggest a fix? Thanks.

[sunyeongan]

Challenge/Task_1/setup.py

Line 32 in 524d6b9

'GANDLF @ git+https://github.com/CBICA/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278',

In my opinion, the problem appears to be caused by GANDALF's URL not existing. This needs to be fixed.

[jingyunc]

Thanks @sunyeongan for looking into this. Unfortunately, running pip install git+https://github.com/CBICA/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278 resulted in a series of package requirement conflicts.

Following Geeks-Sid's steps in #172, I was able to install gandlf. However, when I reran "pip install ." or just "pip install git+https://github.com/FETS-AI/Algorithms.git@fets_challenge", I got the same error as posted above. The error seemed from fets package.

[sunyeongan]

@jingyunc hello
I also experienced a similar issue.
The reason why the SimpleITK version does not match, the versions of various libraries do not match, so I forked two GaNDLF and FeTS-Algorithms repositories in my repository and modified the versions one by one, then changed line 32 of setup.py.

[sarthakpati]

@sunyeongan - could you provide the specifics of which repo/setup line you changed? Thanks!

[sunyeongan]

Hi @sarthakpati

At first, I modified the URL of install_requires in setup.py,

Challenge/Task_1/setup.py

Line 31 in 524d6b9

'openfl @ git+https://github.com/intel/openfl.git@f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f',

but an error occurred. So, I git cloned each library openfl, GaNDLF, and fets and installed them individually using pip. The process I did is below.

openfl
git clone https://github.com/intel/openfl.git
cd openfl
git checkout f4b28d710e2be31cdfa7487fdb4e8cb3a1387a5f
pip install .

GaNDLF
git clone https://github.com/CBICA/GaNDLF.git
cd GaNDLF
git checkout e4d0d4bfdf4076130817001a98dfb90189956278
pip install .

fets
git clone https://github.com/FETS-AI/Algorithms.git
cd Algorithms
git checkout 60e0b8761229edde18e3d707e3e3e5eb0c0fb80f
pip install .

A discussion related to this was carried out in the issue below.
#188 (comment)

I think

Challenge/Task_1/setup.py

Line 32 in 524d6b9

'GANDLF @ git+https://github.com/CBICA/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278',

should be changed to GANDLF @ git+https://github.com/mlcommons/GaNDLF.git@e4d0d4bfdf4076130817001a98dfb90189956278

[sunyeongan]

When checking each library with the pip show command, if the version is as shown in the picture below, the FeTS_Challenge.py code runs normally.

openfl

• version : 1.3

GaNDLF

• version : 0.0.14.dev0