[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -87,7 +87,7 @@ repos:
 ########################################################################
 
   - repo: "https://github.com/python-jsonschema/check-jsonschema"
-    rev: "0.14.3"
+    rev: "0.15.0"
     hooks:
       # Validate GitHub Actions against the schema provided by
       # SchemaStore.

analysis/lintf2_ether/gmx/gmx_Mdens-z_lintf2_ether.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     num_bins=$(printf "%.0f" "$(echo "scale=5; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
     if [ -z ${num_bins} ]; then
@@ -134,7 +134,7 @@ if [ -z ${num_bins} ]; then
         echo "${settings}_out_${system}.gro"
         echo "The file does not exist!"
         echo "Going to set num_bins to 2000"
-        echo "num_bins = ${num_bins}" 
+        echo "num_bins = ${num_bins}"
     fi
 fi
 

analysis/lintf2_ether/gmx/gmx_Ndens-z_lintf2_ether.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     num_bins=$(printf "%.0f" "$(echo "scale=5; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
     if [ -z ${num_bins} ]; then
@@ -134,7 +134,7 @@ if [ -z ${num_bins} ]; then
         echo "${settings}_out_${system}.gro"
         echo "The file does not exist!"
         echo "Going to set num_bins to 2000"
-        echo "num_bins = ${num_bins}" 
+        echo "num_bins = ${num_bins}"
     fi
 fi
 

analysis/lintf2_ether/gmx/gmx_Qdens-z_lintf2_ether.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     num_bins=$(printf "%.0f" "$(echo "scale=5; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
     if [ -z ${num_bins} ]; then
@@ -134,7 +134,7 @@ if [ -z ${num_bins} ]; then
         echo "${settings}_out_${system}.gro"
         echo "The file does not exist!"
         echo "Going to set num_bins to 2000"
-        echo "num_bins = ${num_bins}" 
+        echo "num_bins = ${num_bins}"
     fi
 fi
 

analysis/lintf2_ether/gmx/gmx_msd_electrodes_lintf2_ether.sh

@@ -152,7 +152,7 @@ if [[ ${system} == *gra* ]]; then
                   -endfit ${end_fit}\
         || exit
     echo "=================================================================="
-    
+
     echo -e "\n\n\n"
     echo "=================================================================="
     echo "15 16 17 21"\  # B3 B2 B1 graB
@@ -169,7 +169,7 @@ if [[ ${system} == *gra* ]]; then
                   -endfit ${end_fit}\
         || exit
     echo "=================================================================="
-    
+
     echo -e "\n\n\n"
     echo "=================================================================="
     echo "18 19 20 22"\  # T1 T2 T3 graT
@@ -186,7 +186,7 @@ if [[ ${system} == *gra* ]]; then
                   -endfit ${end_fit}\
         || exit
     echo "=================================================================="
-    
+
 else
     echo
     echo "Error: System contains no electrodes."

analysis/lintf2_ether/gmx/gmx_potential-z_lintf2_ether.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     num_bins=$(printf "%.0f" "$(echo "scale=5; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
     if [ -z ${num_bins} ]; then
@@ -134,7 +134,7 @@ if [ -z ${num_bins} ]; then
         echo "${settings}_out_${system}.gro"
         echo "The file does not exist!"
         echo "Going to set num_bins to 2000"
-        echo "num_bins = ${num_bins}" 
+        echo "num_bins = ${num_bins}"
     fi
 fi
 

analysis/lintf2_ether/gmx/submit_gmx_analyses_lintf2_ether.sh

@@ -174,7 +174,7 @@ get_num_bins () {
     # echo
     # echo "Going to determine the number of bins for the given bin width"
     # echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     num_bins=$(printf "%.0f" "$(echo "scale=5; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
     if [ -z ${num_bins} ]; then
@@ -226,29 +226,29 @@ while getopts s:e:ha:b:f:d:m:M:r:w:z:Z:W:lk option; do
         # Required arguments
         s  ) sflag=true; system=${OPTARG};;
         e  ) eflag=true; settings=${OPTARG};;
-        
+
         # Optional arguments
         h  ) information; usage; exit 0;;
-        
+
         a  ) aflag=true; analysis_type=${OPTARG};;
         l  ) lflag=true;;
-        
+
         b  ) bflag=true; begin=${OPTARG};;
         f  ) fflag=true; end=${OPTARG};;
         d  ) dflag=true; dt=${OPTARG};;
-        
+
         m  ) mflag=true; beginMSDfit=${OPTARG};;
         M  ) Mflag=true; endMSDfit=${OPTARG};;
         r  ) rflag=true; trestart=${OPTARG};;
-        
+
         w  ) wflag=true; bin_width=${OPTARG};;
-        
+
         z  ) zflag=true; zmin=${OPTARG};;
         Z  ) Zflag=true; zmax=${OPTARG};;
         W  ) Wflag=true; slab_width=${OPTARG};;
         l  ) lflag=true;;
         k  ) kflag=true;;
-        
+
         # Error management
         \? ) echo "Error: Unknown option: -${OPTARG}" >&2; usage; exit 1;;
         :  ) echo "Error: Missing option argument for -${OPTARG}" >&2; usage; exit 1;;

analysis/lintf2_ether/mdt/submit_mdt_analyses_lintf2_ether.sh

@@ -193,29 +193,29 @@ while getopts s:e:ha:b:f:d:n:r:c:i:I:z:Z:W:lk option; do
         # Required arguments
         s  ) sflag=true; system=${OPTARG};;
         e  ) eflag=true; settings=${OPTARG};;
-        
+
         # Optional arguments
         h  ) information; usage; exit 0;;
-        
+
         a  ) aflag=true; analysis_type=${OPTARG};;
-        
+
         b  ) bflag=true; begin=${OPTARG};;
         f  ) fflag=true; end=${OPTARG};;
         d  ) dflag=true; every=${OPTARG};;
         n  ) nflag=true; nblocks=${OPTARG};;
         r  ) rflag=true; restart=${OPTARG};;
-        
+
         c  ) cflag=true; cutoff=${OPTARG};;
 #         w  ) wflag=true; bin_width=${OPTARG};;
         i  ) iflag=true; li_ix=${OPTARG};;
         I  ) Iflag=true; intermittency=${OPTARG};;
-        
+
         z  ) zflag=true; zmin=${OPTARG};;
         Z  ) Zflag=true; zmax=${OPTARG};;
         W  ) Wflag=true; slab_width=${OPTARG};;
         l  ) lflag=true;;
         k  ) kflag=true;;
-        
+
         # Error management
         \? ) echo "Error: Unknown option: -${OPTARG}" >&2; usage; exit 1;;
         :  ) echo "Error: Missing option argument for -${OPTARG}" >&2; usage; exit 1;;

analysis/lintf2_ether/pyemma/msm_cktest.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)

analysis/lintf2_ether/pyemma/msm_discrete.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)

analysis/lintf2_ether/pyemma/msm_discrete.sh.old_xtc

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)

analysis/lintf2_ether/pyemma/msm_its.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)

analysis/lintf2_ether/pyemma/msm_mm.sh

@@ -58,7 +58,7 @@ get_num_bins () {
     echo
     echo "Going to determine the number of bins for the given bin width"
     echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)

analysis/lintf2_ether/pyemma/submit_pyemma_analyses_lintf2_ether.sh

@@ -95,7 +95,7 @@ get_num_bins () {
     # echo
     # echo "Going to determine the number of bins for the given bin width"
     # echo "of ${bin_width}"
-    
+
     box_length_z=$(gmx_get_box_lengths.sh -f ${settings}_out_${system}.gro -z || exit)
     box_length_z=$(echo "scale=4; ${box_length_z} * 10" | bc || exit )  # nm -> Angstrom
     num_bins=$(printf "%.0f" "$(echo "scale=4; ${box_length_z}/${bin_width}" | bc || exit)" || exit)
@@ -154,24 +154,24 @@ while getopts s:e:ha:r:b:f:d:D:w:l:t:u option; do
         # Required arguments
         s  ) sflag=true; system=${OPTARG};;
         e  ) eflag=true; settings=${OPTARG};;
-        
+
         # Optional arguments
         h  ) information; usage; exit 0;;
-        
+
         a  ) aflag=true; analysis_type=${OPTARG};;
         r  ) rflag=true; residue=${OPTARG};;
-        
+
         b  ) bflag=true; begin=${OPTARG};;
         f  ) fflag=true; end=${OPTARG};;
         d  ) dflag=true; every=${OPTARG};;
-        
+
         D  ) Dflag=true; direction=${OPTARG};;
         w  ) wflag=true; bin_width=${OPTARG};;
-        
+
         l  ) lflag=true; lagtime=${OPTARG};;
         t  ) tflag=true; timestep="${OPTARG} ps";;
         u  ) uflag=true;;
-        
+
         # Error management
         \? ) echo "Error: Unknown option: -${OPTARG}" >&2; usage; exit 1;;
         :  ) echo "Error: Missing option argument for -${OPTARG}" >&2; usage; exit 1;;