Merge pull request #704 from MannLabs/fix_e2e_slurm

Fix e2e slurm

Author: mschwoer

README.md

@@ -176,6 +176,18 @@ In case of issues, check out the following:
 * [Issues](https://github.com/MannLabs/alphadia/issues): Try a few different search terms to find out if a similar problem has been encountered before
 * [Discussions](https://github.com/MannLabs/alphadia/discussions): Check if your problem or feature requests has been discussed before.
 
+### Problem: Error when downloading the peptdeep pretrained models
+If on startup you receive an error like
+`FileNotFoundError: [Errno 2] No such file or directory: '<some_directory>/peptdeep/pretrained_models'`,
+it could be due to missing write permissions on `<some_directory>`.
+
+#### Solution
+For now, you need to create this directory yourself and manually download the file
+```
+mkdir -p <some_directory>/peptdeep/pretrained_models && cd <some_directory>/peptdeep/pretrained_models
+wget https://github.com/MannLabs/alphapeptdeep/releases/download/pre-trained-models/pretrained_models.zip
+```
+
 ---
 ## Citations
 

tests/e2e_tests/calc_metrics.py

@@ -12,7 +12,10 @@
 import matplotlib.pyplot as plt
 import pandas as pd
 
-from tests.e2e_tests.prepare_test_data import OUTPUT_DIR_NAME, get_test_case
+try:
+    from tests.e2e_tests.prepare_test_data import OUTPUT_DIR_NAME, get_test_case
+except ModuleNotFoundError:
+    from prepare_test_data import OUTPUT_DIR_NAME, get_test_case
 
 try:
     import neptune