Installing the latest development version issue

[LQC-wr]

Hi Nicheformer team,

I follow the README to install the latest development version and during the procedure of pip install -e, there is an error.

Is there a way to solve it? Thank you in advance!

[bjoaofelipe]

I am having the exact same issue

[cakirb]

Creating a conda environment with Python 3.11 (instead of 3.9) resolves the installation issue. This workaround was also reported here: #20.

In my case, this approach initially caused an error during package import due to an incompatible zarr-python version. I resolved it by upgrading the anndata package, but then had to downgrade pandas to 1.5.3. Although this created a version warning (anndata requires a higher pandas version), I haven’t encountered any problems running nicheformer with this setup so far.

This combination has been the most stable solution I could apply.

[cpu-yun]

Creating a conda environment with Python 3.11 (instead of 3.9) resolves the installation issue. This workaround was also reported here: #20.

In my case, this approach initially caused an error during package import due to an incompatible zarr-python version. I resolved it by upgrading the anndata package, but then had to downgrade pandas to 1.5.3. Although this created a version warning (anndata requires a higher pandas version), I haven’t encountered any problems running nicheformer with this setup so far.

This combination has been the most stable solution I could apply.

I follow your steps to install nicheformer successfully.But I encountered the following problem when running merfish_mouse_brain.ipynb.Did you also encounter it?
Thank you for reply.

[mattdlg]

Creating a conda environment with Python 3.11 (instead of 3.9) resolves the installation issue. This workaround was also reported here: #20.

In my case, this approach initially caused an error during package import due to an incompatible zarr-python version. I resolved it by upgrading the anndata package, but then had to downgrade pandas to 1.5.3. Although this created a version warning (anndata requires a higher pandas version), I haven’t encountered any problems running nicheformer with this setup so far.

This combination has been the most stable solution I could apply.

Hello. It is also the solution I tried but with Python 3.10 on my side instead of 3.11. But dowgrading pandas makes it impossible to use squidpy/anndata while upgrading it gives me conflict with merlin and dask.
Do you have the exact version of the packages you used, and do you know if 3.11 python would make a difference with 3.10 on that matter ?

My error was the following (with pandas 1.5.3):
anndata 0.11.4 depends on pandas!=2.1.0rc0, !=2.1.2 and >=1.4 squidpy 1.6.5 depends on pandas>=2.1.0 merlin-core 23.8.0 depends on pandas<1.6.0dev0 and >=1.2.0

[luobimuqinyan99]

Creating a conda environment with Python 3.11 (instead of 3.9) resolves the installation issue. This workaround was also reported here: #20.

In my case, this approach initially caused an error during package import due to an incompatible zarr-python version. I resolved it by upgrading the anndata package, but then had to downgrade pandas to 1.5.3. Although this created a version warning (anndata requires a higher pandas version), I haven’t encountered any problems running nicheformer with this setup so far.

This combination has been the most stable solution I could apply.

Hello, I solved the download issue using the method you provided, thank you very much. However, when running preprocess_Lu_2021.py, I encountered a package conflict error: ImportError: Dask requires version '2.0.0' or newer of 'pandas' (version '1.5.3' currently installed). I wanted to ask if you have encountered this issue as well, and if you could share the versions of the packages you're using. Thank you again!

[cakirb]

Hello,

Glad my suggestion worked well for you all.

@cpu-yun: I didn't encounter this issue, the error message seems kind of explanatory. Which step of the notebook did you get this error exactly?

@mattdlg, @luobimuqinyan99: These are the related package versions that I have in my conda environment, hope this helps:

anndata                  0.12.2
dask                     2024.1.1
dask-cuda                24.2.0
dask-image               2023.3.0
geopandas                1.0.1
merlin-core              23.8.0
merlin-dataloader        23.8.0
pandas                   1.5.3
rapids-dask-dependency   24.2.0
squidpy                  1.3.0

[luobimuqinyan99]

Hello, I followed your configuration to install the packages, but unfortunately, there are still conflicts. Could you please share how you installed them? Thank you very much.
ERROR: Cannot install anndata==0.12.2 and pandas==1.5.3 because these package versions have conflicting dependencies.

The conflict is caused by:
The user requested pandas==1.5.3
anndata 0.12.2 depends on pandas!=2.1.2 and >=2.1.0

[cakirb]

@luobimuqinyan99 As I mentioned in my first comment on this issue, I initially had to upgrade the anndata package. I believe I used --force-reinstall to ensure that everything required for that anndata version was installed cleanly. After that, I manually downgraded pandas. Although this anndata release technically requires a newer pandas version, I haven’t encountered any problems with this setup so far.

[luobimuqinyan99]

I've installed some packages using your version, but the zarr and numpy packages are still conflicting. I've tried many different zarr and numpy version combinations without success. Could you please send me a more complete list of all package versions? Thank you very much.