Add codespell support (config, workflow to detect/not fix) and make it fix few typos

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+skip = .git*,.codespellrc,testdata,config.json
+check-hidden = true
+# ignore-regex = 
+# ignore-words-list =

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

README.md

@@ -113,7 +113,7 @@ Start script can output startup log to stdout, or any error messages to stderr.
 
 This script will be executed by workflow manager periodically to query status of the application. You can simply check for the PID of the application to make sure that it's running, or for a batch system, you can use commands such as `qstat` or `condor_status` to query for your application.
 
-Please see [ABCD default hook scritps](https://github.com/brain-life/abcd-spec/tree/master/hooks) as an example.
+Please see [ABCD default hook scripts](https://github.com/brain-life/abcd-spec/tree/master/hooks) as an example.
 
 #### Exit Code
 
@@ -229,7 +229,7 @@ SERVICE_BRANCH: Name of the service branch (if specified by the user)
 
 ### Workflow directory
 
-ABCD workflow manager should git clones requested service on remote resource's scratch space as a new work directory for each task and set the current directory to that directory prior to executing ABCD hooks. Application can therefore expect to find all files that are distributed via the specifed github repository (with `--depth 1` to omit git history, however).
+ABCD workflow manager should git clones requested service on remote resource's scratch space as a new work directory for each task and set the current directory to that directory prior to executing ABCD hooks. Application can therefore expect to find all files that are distributed via the specified github repository (with `--depth 1` to omit git history, however).
 
 ### Input Parameters (config.json)
 

hooks/bl2bids.py

@@ -83,7 +83,7 @@
             name+="_task-id%d" %(id+1)
 
     #meta contains both acq and acquisition set to different value
-    #I am not sure why, but let's make acqusition take precedence
+    #I am not sure why, but let's make acquisition take precedence
     acq = None
     if "acquisition" in input["meta"]:
         acq = utils.clean(input["meta"]["acquisition"])
@@ -370,7 +370,7 @@
         utils.outputSidecar(dest+"_eeg.json", input)
 
     else:
-        #others are considered delivatives and the entire files/dirs will be copied over
+        #others are considered derivatives and the entire files/dirs will be copied over
         for key in input["keys"]:
             print("..", key)
             base = os.path.basename(config[key])

hooks/direct/status

@@ -20,7 +20,7 @@ function check_exit()
         #echo "finished with exit code $code"
         logfile=$(ls -rt *.log | tail -1)
 	tail -10 $logfile | grep -v -e '^$' | tail -1
-        exit 2 #faild!
+        exit 2 #failed!
     fi
 }
 check_exit

hooks/pbs/start

@@ -59,7 +59,7 @@ else
 	echo "./$main" >> _main
 fi
 echo "echo \$? > exit-code" >> _main
-chmod +x $main #in case user fogets it
+chmod +x $main #in case user forgets it
 
 echo "kill \$smonpid" >> _main
 

hooks/slurm/status

@@ -80,7 +80,7 @@ if [ $jobstate == "RUNNING" ]; then
 fi
 
 echo $jobstate
-if [ $jobstate == "COMPLETEING" ]; then
+if [ $jobstate == "COMPLETING" ]; then
     exit 0
 fi
 if [ $jobstate == "CONFIGURING" ]; then

hooks/smon

@@ -33,7 +33,7 @@ with open(name, "w") as outfile:
     if "PBS_NUM_PPN" in os.environ:
         max_ppn = int(os.environ["PBS_NUM_PPN"])
     #from https://slurm.schedmd.com/srun.html
-    if "SLURM_CPUS_ON_NODE" in os.environ: #incase SLURM_NTASKS is not set?
+    if "SLURM_CPUS_ON_NODE" in os.environ: #in case SLURM_NTASKS is not set?
         max_ppn = int(os.environ["SLURM_CPUS_ON_NODE"])
     if "SLURM_NTASKS" in os.environ:
         max_ppn = int(os.environ["SLURM_NTASKS"])
@@ -96,7 +96,7 @@ with open(name, "w") as outfile:
     #dump info that doesn't change on the first entry
     json.dump({
         "time": time.time(), 
-        "uname": os.uname(), #os/kernerl/hostname version
+        "uname": os.uname(), #os/kernel/hostname version
         "cpu_total": os.sysconf('SC_NPROCESSORS_CONF'),
         "cpu_requested": max_ppn,