add 'cid' to the targets2Bignored, insert dir/file test in run shell …

…script

dfpl/feedforwardNN.py

@@ -480,7 +480,7 @@ def train_nn_models(df: pd.DataFrame, opts: options.TrainOptions) -> None:
     """
 
     # find target columns
-    names_y = [c for c in df.columns if c not in ['id', 'smiles', 'fp', 'inchi', 'fpcompressed']]
+    names_y = [c for c in df.columns if c not in ['cid', 'id', 'smiles', 'fp', 'inchi', 'fpcompressed']]
 
     # For each individual target train a model
     for target in names_y:  # [:2]:

scripts/run-all-publication-cases.sh

@@ -4,28 +4,31 @@
 # Importantly, the conda environment needs to be set up and actived! For certain machines/HPC,
 # we have a batch-job that does exactly that and then calls this file
 
-python -m dfpl convert -f "data"
-python -m dfpl train -f "validation/case_00/train_AC_S.json"
-python -m dfpl train -f "validation/case_00/train_AC_D.json"
-
-python -m dfpl train -f "validation/case_01/train.json"
-python -m dfpl train -f "validation/case_01/train_0p5.json"
-python -m dfpl train -f "validation/case_01/train_0p6.json"
-python -m dfpl train -f "validation/case_01/train_0p7.json"
-python -m dfpl train -f "validation/case_01/train_0p8.json"
-python -m dfpl train -f "validation/case_01/train_0p9.json"
-python -m dfpl train -f "validation/case_01/train_1p0.json"
-
-python -m dfpl train -f "validation/case_02/train.json"
-python -m dfpl train -f "validation/case_02/train_0p5.json"
-python -m dfpl train -f "validation/case_02/train_0p6.json"
-python -m dfpl train -f "validation/case_02/train_0p7.json"
-python -m dfpl train -f "validation/case_02/train_0p8.json"
-python -m dfpl train -f "validation/case_02/train_0p9.json"
-python -m dfpl train -f "validation/case_02/train_1p0.json"
-
-python -m dfpl train -f "validation/case_03/train.json"
-
-python -m dfpl predict -f "validation/case_07/predict_bestER03.json"
-python -m dfpl predict -f "validation/case_07/predict_bestARext03.json"
-python -m dfpl predict -f "validation/case_07/predict_bestED03.json"
+D="data"; if [ -d $D ] python -m dfpl convert -f $D; fi
+
+F="validation/case_00/train_AC_S.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_00/train_AC_D.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+
+F="validation/case_01/train.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F= "validation/case_02/train.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+
+F="validation/case_03/train.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+
+F="validation/case_07/predict_bestER03.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_07/predict_bestARext03.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_07/predict_bestED03.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+
+F="validation/case_01/train_0p5.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_01/train_0p6.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_01/train_0p7.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_01/train_0p8.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_01/train_0p9.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_01/train_1p0.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+
+F="validation/case_02/train_0p5.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_02/train_0p6.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_02/train_0p7.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_02/train_0p8.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_02/train_0p9.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+F="validation/case_02/train_1p0.json"; if [ -f $F ]; then python -m dfpl train -f $F; fi
+