Open ponomarevsy opened 1 year ago
Hi @ponomarevsy,
Thank you for your interest in using resmico and reporting issues!
(1) can you please give details on your machine, and how you created an environment and installed resmico? this error happens because cython extension was not compiled. Please have a look at the different installation options https://github.com/leylabmpi/resmico#installation
(2) this error is fixed in one of the latest commits exactly in the way you described https://github.com/leylabmpi/resmico/commit/46ca9846579468c9cf7e993be669b8c4e7a781ad
(3) is not critical, it doesn't affect model predictions and saving of the results
Hi Olga! Thanks for getting back to me. Actually, I used mamba to install resmico (since conda could NOT resolve all the dependencies well; I should have used pip instead):
Installed Resmico 1.2.2 with Mamba under resmico-1.2.2 environment name:
conda create -n resmico-1.2.2 python=3.8
source activate resmico-1.2.2
conda install mamba
mamba install resmico=1.2.2 (should I use 'pip install resmico==1.2.2' instead)
mamba install pytest pytest-console-scripts
Installed Samtools:
conda install samtools
(resmico-1.2.2) [appbuild@ai-submit2](master|…)» conda list resmico
# packages in environment at /sysapps/cluster/software/Anaconda3/2022.05/envs/resmico-1.2.2:
#
# Name Version Build Channel
resmico 1.2.2 py38h5cf8b27_1 bioconda
What would you suggest I do now, remove mamba installation and install via pip or start from scratch? Please let me know.
(1) ./resmico/tests/ from GitHub repo fail with "cannot import name 'reader' from 'resmico'":
(2) AttributeError: module 'numpy' has no attribute 'bool'.
Solution: Changed 3 lines with np.bool to just bool in file models_fl.py:
(3) Bad file descriptor error:
https://github.com/leylabmpi/resmico/issues/28
Solution: "this error should not affect the predictions" https://github.com/leylabmpi/resmico/issues/28
Please let me know if you have a solution for (1). How critical are (2) and (3)? Please let me know. Thank you!