Merge branch 'dev' into paper_notebook_fixes

.github/workflows/ci.yml

@@ -74,5 +74,6 @@ jobs:
       - name: Run tests
         shell: bash -l {0}
         run: |
-          PYTEST_ARGS="--nbval-lax --nbval-current-env --nbval-cell-timeout=1800"
-          pytest $PYTEST_ARGS
+          PYTEST_ARGS="--nbval-lax --nbval-current-env --nbval-cell-timeout=7200"
+          PYTEST_IGNORE="--ignore=notebooks/custom_kinfraglib/2_3_custom_filters_paper.ipynb"
+          pytest $PYTEST_ARGS $PYTEST_IGNORE

README.md

@@ -1,6 +1,6 @@
 # KinFragLib: Kinase-focused fragment library
 
-[![GitHub Actions Build Status](https://github.com/volkamerlab/KinFragLib/workflows/CI/badge.svg)](https://github.com/volkamerlab/KinFragLib/actions?query=workflow%3ACI)
+[![GitHub Actions Build Status](https://github.com/volkamerlab/KinFragLib/actions/workflows/ci.yml/badge.svg)](https://github.com/volkamerlab/KinFragLib/actions?query=branch%3Amaster+workflow%3ACI)
 
 ![KinFragLib workflow](./docs/img/toc_github_kinfraglib.png)
 

kinfraglib/filters/retro.py

@@ -3,6 +3,7 @@
 """
 
 import multiprocessing as mp
+import os
 import pandas as pd
 import requests
 import redo
@@ -1387,6 +1388,13 @@ def save_fragment_library_to_sdfs(path_output, fragment_library_concat):
     path_output = Path(path_output)
     path_output.mkdir(parents=True, exist_ok=True)
 
+    subpockets = ["AP", "SE", "FP", "GA", "B1", "B2", "X"]
+    # remove all {subpocket}.sdf files before writing to avoid death files
+    for subpocket in subpockets:
+        # check if files {subpocket}.sdf exists
+        if (path_output / f"{subpocket}.sdf").exists():
+            os.remove(path_output / f"{subpocket}.sdf")
+
     for subpocket, fragments in fragment_library_concat.groupby("subpocket"):
         with Chem.SDWriter(str(path_output / f"{subpocket}.sdf")) as w:
             for mol in fragments.ROMol_original:

notebooks/custom_kinfraglib/1_4_custom_filters_pairwise_retrosynthesizability.ipynb

@@ -1245,8 +1245,8 @@
       "Checking if all fragment pairs were requested..\n",
       "All fragment pairs were requested.\n",
       "Done.\n",
-      "CPU times: user 9min 37s, sys: 4.41 s, total: 9min 41s\n",
-      "Wall time: 11min 50s\n"
+      "CPU times: user 12min 9s, sys: 6.03 s, total: 12min 15s\n",
+      "Wall time: 15min 43s\n"
      ]
     }
    ],
@@ -3289,7 +3289,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.19"
+   "version": "3.8.undefined"
   }
  },
  "nbformat": 4,