1.0.3 install errors

[davidhoover]

I followed the directions for installing v1.0.3, but got these errors:

Using /lscratch/9076720/mamba/envs/model_angelo/lib/python3.10/site-packages/six-1.16.0-py3.10.egg
Finished processing dependencies for model-angelo==1.0.3
Writing weights to /lscratch/9076720/model_angelo_weights
Traceback (most recent call last):
  File "/lscratch/9076720/mamba/envs/model_angelo/bin/model_angelo", line 33, in <module>
    sys.exit(load_entry_point('model-angelo==1.0.3', 'console_scripts', 'model_angelo')())
  File "/lscratch/9076720/mamba/envs/model_angelo/lib/python3.10/site-packages/model_angelo-1.0.3-py3.10.egg/model_angelo/__main__.py", line 22, in main
  File "/lscratch/9076720/mamba/envs/model_angelo/lib/python3.10/site-packages/model_angelo-1.0.3-py3.10.egg/model_angelo/apps/build.py", line 25, in <module>
ModuleNotFoundError: No module named 'model_angelo.c_alpha'
Traceback (most recent call last):
  File "/lscratch/9076720/mamba/envs/model_angelo/bin/model_angelo", line 33, in <module>
    sys.exit(load_entry_point('model-angelo==1.0.3', 'console_scripts', 'model_angelo')())
  File "/lscratch/9076720/mamba/envs/model_angelo/lib/python3.10/site-packages/model_angelo-1.0.3-py3.10.egg/model_angelo/__main__.py", line 22, in main
  File "/lscratch/9076720/mamba/envs/model_angelo/lib/python3.10/site-packages/model_angelo-1.0.3-py3.10.egg/model_angelo/apps/build.py", line 25, in <module>
ModuleNotFoundError: No module named 'model_angelo.c_alpha'

It also complained bitterly about using python setup.py install, but I believe these are just warnings.

[jamaliki]

Hi!

So sorry about this, we've been playing around a bit with the install script. Could you try running the following command, while the model_angelo conda environment is activated?

pip install -e --force-reinstall git+https://github.com/3dem/model-angelo.git

[davidhoover]

Sorry, that didn't help. I still get errors.

[jamaliki]

What are the errors? Does it fix it if you do

pip install -e --force-reinstall git+https://github.com/3dem/model-angelo.git#egg=model-angelo

instead?

[davidhoover]

I just reran the installation, and it seems like the latest git repository has changed. I'm seeing a different error:

Successfully installed biopython-1.81 contourpy-1.1.1 cycler-0.11.0 einops-0.6.1 fair-esm-2.0.0 fonttools-4.42.1 kiwisolver-1.4.5 loguru-0.7.2 matplotlib-3.8.0 model-angelo-1.0.3 mrcfile-1.4.3 numpy-1.26.0 packaging-23.1 pandas-2.1.1 pillow-10.0.1 psutil-5.9.5 pyhmmer-0.10.2 pyparsing-3.1.1 python-dateutil-2.8.2 pytz-2023.3.post1 scipy-1.11.2 six-1.16.0 tqdm-4.66.1 tzdata-2023.3
Writing weights to /lscratch/9144866/model_angelo_weights
Traceback (most recent call last):
  File "/lscratch/9144866/mamba/envs/model_angelo/bin/model_angelo", line 33, in <module>
    sys.exit(load_entry_point('model-angelo', 'console_scripts', 'model_angelo')())
  File "/lscratch/9144866/git/model-angelo/model_angelo/__main__.py", line 22, in main
    import model_angelo.apps.build
  File "/lscratch/9144866/git/model-angelo/model_angelo/apps/build.py", line 23, in <module>
    import torch
ModuleNotFoundError: No module named 'torch'
Traceback (most recent call last):
  File "/lscratch/9144866/mamba/envs/model_angelo/bin/model_angelo", line 33, in <module>
    sys.exit(load_entry_point('model-angelo', 'console_scripts', 'model_angelo')())
  File "/lscratch/9144866/git/model-angelo/model_angelo/__main__.py", line 22, in main
    import model_angelo.apps.build
  File "/lscratch/9144866/git/model-angelo/model_angelo/apps/build.py", line 23, in <module>
    import torch
ModuleNotFoundError: No module named 'torch'

Trying your suggestion, I get this error:

$ pip install -e --force-reinstall git+https://github.com/3dem/model-angelo.git#egg=model-angelo
ERROR: --force-reinstall is not a valid editable requirement. It should either be a path to a local project or a VCS URL (beginning with bzr+http, bzr+https, bzr+ssh, bzr+sftp, bzr+ftp, bzr+lp, bzr+file, git+http, git+https, git+ssh, git+git, git+file, hg+file, hg+http, hg+https, hg+ssh, hg+static-http, svn+ssh, svn+http, svn+https, svn+svn, svn+file).

[davidhoover]

Rearranging the command, it seemed to work:

pip install --force-reinstall -e git+https://github.com/3dem/model-angelo.git#egg=model-angelo

But it didn't seem to download the weights files.

[jamaliki]

Ok, thank you so much for your patience. If you pull the latest code from the repository, and re-run the install script, all things including the weight download should work.

Please let me know if there are issues

[jowodo]

The installation run successfully for version 1.0.4 but not 1.0.3. This are the installation commands, which I used:

VERSION=1.0.4
URL='https://github.com/3dem/model-angelo'
TMPDIR=$(mktemp -d)
pushd $TMPDIR
git clone --depth 1 --branch v$VERSION -q $URL model-angelo
pushd model-angelo
TORCH_HOME=/scratch/mirror/modelangelo/$VERSION
mkdir -p $TORCH_HOME
sed -i "s/ -n model_angelo/ -n modelangelo-$VERSION/" install_script.sh
sed -i "s/model_angelo$/modelangelo-$VERSION/" install_script.sh
sed -i "s/model_angelo\"/modelangelo-$VERSION\"/" install_script.sh
source install_script.sh --download-weights
popd

It would be nice to be able to chose a name for the conda environment via a flag: e.g. -n or --name Unfortunately, the installation does not work for a central installation on a shared computational resource. When I try to activate the environment as a regular user, this is what I get:

[jowodo@login02 ~]$ conda activate modelangelo-1.0.4
[jowodo@login02 ~]$ echo $CONDA_DEFAULT_ENV
modelangelo-1.0.4
[jowodo@login02 ~]$ model_angelo -h
  File "/home/apps/conda/miniconda3/envs/modelangelo-1.0.4/bin/model_angelo", line 33, in <module>
    sys.exit(load_entry_point('model-angelo', 'console_scripts', 'model_angelo')())
  File "/home/apps/conda/miniconda3/envs/modelangelo-1.0.4/bin/model_angelo", line 22, in importlib_load_entry_point
    for entry_point in distribution(dist_name).entry_points
  File "/home/apps/conda/miniconda3/envs/modelangelo-1.0.4/lib/python3.10/importlib/metadata/__init__.py", line 969, in distribution
    return Distribution.from_name(distribution_name)
  File "/home/apps/conda/miniconda3/envs/modelangelo-1.0.4/lib/python3.10/importlib/metadata/__init__.py", line 548, in from_name
    raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: No package metadata was found for model-angelo
[jowodo@login02 ~]$  ls -l $CONDA_PREFIX/lib/python3.10/site-packages/model*
-rw-r--r-- 1 appadmin admin 34 Sep 29 12:31 /home/apps/conda/miniconda3/envs/modelangelo-1.0.4/lib/python3.10/site-packages/model-angelo.egg-link

Additionally, the models are not stored in $TORCH_HOME:

[appadmin@login02 ~]$ ls $TORCH_HOME -la
total 1
drwxr-sr-x 2 appadmin  appadmin 0 Sep 29 12:29 .
drwxrwsr-x 3 dataadmin appadmin 1 Sep 29 12:29 ..
[appadmin@login02 ~]$ ls ~/.cache/torch/hub/checkpoints/model_angelo_v1.0/
nucleotides  nucleotides_no_seq
[appadmin@login02 ~]$

[jamaliki]

Hi @jowodo ,

Yes, ModelAngelo-1.0.3 had installation issues. You're able to get 1.0.4 to install? Do you also have issues with the weights in 1.0.4, or is that just for 1.0.3?

[davidhoover]

Just to finish this, version 1.0.5 installed without errors. Nice!