scenicplus installation

[ktroule]

Describe the bug Hi! Thanks for providing this package and all the documentation. I'm not sure if this falls within the bug category.

I'm trying to install scenicplus on a linux based shared server as follows:

conda create --name scenicplus python=3.11
conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus

module load Rust/1.75.0-GCCcore-10.3.0
git checkout development
pip install .

Error output Just showing the last bits of the message.

Collecting pybigtools (from scenicplus==1.0a1)
  Using cached pybigtools-0.1.3.tar.gz (140 kB)
  Installing build dependencies ... done
  Getting requirements to build wheel ... done
  Preparing metadata (pyproject.toml) ... error
  error: subprocess-exited-with-error

  × Preparing metadata (pyproject.toml) did not run successfully.
  │ exit code: 1
  ╰─> [23 lines of output]
          Updating crates.io index
      warning: spurious network error (3 tries remaining): [28] Timeout was reached (Failed to connect to index.crates.io port 443 after 30019 ms: Timeout was reached)
      warning: spurious network error (2 tries remaining): [28] Timeout was reached (Failed to connect to index.crates.io port 443 after 30010 ms: Timeout was reached)
      warning: spurious network error (1 tries remaining): [28] Timeout was reached (Failed to connect to index.crates.io port 443 after 30020 ms: Timeout was reached)
      error: failed to get `bigtools` as a dependency of package `pybigtools v0.1.3 (/wscratch/pip-install-2vg0wj7y/pybigtools_4f5299bb443945cbaa092ce148fa5438/pybigtools)`

      Caused by:
        failed to query replaced source registry `crates-io`

      Caused by:
        download of config.json failed

      Caused by:
        failed to download from `https://index.crates.io/config.json`

      Caused by:
        [28] Timeout was reached (Failed to connect to index.crates.io port 443 after 30020 ms: Timeout was reached)
      💥 maturin failed
        Caused by: Cargo metadata failed. Does your crate compile with `cargo build`?
        Caused by: `cargo metadata` exited with an error:
      Error running maturin: Command '['maturin', 'pep517', 'write-dist-info', '--metadata-directory', '/wscratch/pip-modern-metadata-2l9fzta5', '--interpreter', '/projects/ngs_eco/users/conda_envs/scenicplus/bin/python3.11']' returned non-zero exit status 1.
      Checking for Rust toolchain....
      Running `maturin pep517 write-dist-info --metadata-directory /wscratch/pip-modern-metadata-2l9fzta5 --interpreter /projects/ngs_eco/users/conda_envs/scenicplus/bin/python3.11`
      [end of output]

  note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

To me it seems related to big tools/pybigtools installation. I've tried to install these packages independently and a similar error pops. Do you have any hint to solve this?

If I do cargo 1.75.0-nightly I get cargo 1.75.0-nightly Thanks for your time and help.

[ktroule]

I also find many packages for which I have to remove the version on requirements.txt I'm removing the version of each of failing packages to see if I can install it. Example:

ERROR: Could not find a version that satisfies the requirement scikit-image==0.22.0 (from scenicplus) (from versions: 0.7.2, 0.8.0, 0.8.1, 0.8.2, 0.9.0, 0.9.1, 0.9.3, 0.10.0, 0.10.1, 0.11.2, 0.11.3, 0.12.0, 0.12.1, 0.12.2, 0.12.3, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.14.2, 0.14.3, 0.14.5, 0.15.0, 0.16.2, 0.17.1, 0.17.2, 0.18.0, 0.18.1, 0.18.2, 0.18.3, 0.19.0rc0, 0.19.0, 0.19.1, 0.19.2, 0.19.3, 0.20.0.dev0, 0.20.0rc2, 0.20.0rc3, 0.20.0rc4, 0.20.0rc5, 0.20.0rc6, 0.20.0rc7, 0.20.0rc8, 0.20.0, 0.21.0rc0, 0.21.0rc1, 0.21.0)
ERROR: No matching distribution found for scikit-image==0.22.0

[SeppeDeWinter]

Hi @ktroule

Unfortunately I was not able to replicate your issue. I'm using a different Rust version though.

mamba create scenicplus_test python=3.11
mamba activate scenicplus_test

git clone https://github.com/aertslab/scenicplus
cd scenicplus
git checkout development

module load Rust/1.73.0-GCCcore-12.2.0

pip install . --no-cache-dir

Installs everything fine for me.

All the best,

Seppe

[irepansalvador]

Hi @SeppeDeWinter and @ktroule,

I found the exact same error as ktroule when trying to install scenicplus in a cluster. In my case with the rust version: Rust/1.65.0-GCCcore-12.2.0

conda create --name scenicplus python=3.11
conda activate scenicplus
git clone https://github.com/aertslab/scenicplus
cd scenicplus

module load Rust/1.65.0-GCCcore-12.2.0
git checkout development
pip install .

@SeppeDeWinter I suppose this is then related to the specific version of Rust used? I will try to use the same as you show.

best, Irepan

[irepansalvador]

Hi again,

I have managed to install scenicplus. First I installed the same rust version as mentioned by @SeppeDeWinter

curl --proto '=https' --tlsv1.2 -sSf https://sh.rustup.rs/ | sh -s -- --default-toolchain=1.73.0

But I ran into another error that seemed to be related with the GCC version used by default ERROR: Could not build wheels for annoy

So I loaded a newer version of GCC available and tried to install again, and this time it finished without error.

module load GCC/12.2.0
pip install . --no-cache-dir

This last part is also mentioned in here:

best, Irepan

[ktroule]

Hi.

Somehow I also managed to install it, not really sure how.

Kind regards.