doc: cleanup

Author: c-dilks

bin/deploy-timelines.sh

@@ -13,10 +13,9 @@ usage() {
   Run clas12-timeline commands.
 
   COMMAND: the command to run, one of:
-      histogram     Run the timeline histogramming jobs
-      analysis      Analyze the histograms and generate timelines
-      deploy        Deploy the timelines to the web server
-      error         Scan for errors in Slurm logs
+      histogram     Run the timeline histogramming jobs (Step 1)
+      analysis      Analyze the histograms and generate timelines (Step 2)
+      error         Scan for errors in Slurm logs (for Step 1)
 
   OPTIONS: Each command has its own set of options; run a command with no
            additional options to see usage for that command.
@@ -37,7 +36,6 @@ shift
 case $cmd in
   hi*) exec $TIMELINESRC/bin/thyme-histogram "$@" ;;
   an*) exec $TIMELINESRC/bin/thyme-analysis "$@" ;;
-  de*) exec $TIMELINESRC/bin/thyme-deploy "$@" ;;
   er*) exec $TIMELINESRC/bin/thyme-error "$@" ;;
   -v|--version)
     echo $(mvn -q -Dexec.executable=echo -Dexec.args='${project.version}' --non-recursive exec:exec -f $TIMELINESRC/pom.xml || echo "UNKNOWN")

bin/thyme

@@ -27,12 +27,12 @@ done
 
 # usage
 sep="================================================================"
-usage() {
+usageTerse() {
   echo """
   $sep
   USAGE: thyme analysis [OPTIONS]...
   $sep
-  Analyzes histograms and produces timeline HIPO files
+  Analyzes histograms and produces timelines.
 
   CHEF OPTIONS: most of these are required for chef's production
 
@@ -59,8 +59,10 @@ $(find $TIMELINESRC/data/metadata -name "*.json" -exec basename {} .json \; | se
     -n [NOTE]           additional note that will be shown on the clas12mon webpage
                         (i.e., the README file); surround your note in quotes
                         - default: ''
-
-  ADDITIONAL OPTIONS:
+  """>&2
+}
+usageVerbose() {
+  echo """  ADDITIONAL OPTIONS:
 
     -o [OUTPUT_DIR]     output directory for the analyzed timelines
                         default = ./outfiles/[DATASET_NAME]
@@ -90,7 +92,8 @@ $(find $TIMELINESRC/data/metadata -name "*.json" -exec basename {} .json \; | se
   """ >&2
 }
 if [ $# -eq 0 ]; then
-  usage
+  usageTerse
+  echo "  For more options, run with '--help'" >&2
   exit 101
 fi
 
@@ -123,7 +126,8 @@ while getopts "d:i:p:f:n:o:j:t:m:h-:" opt; do
   esac
 done
 if ${modes['help']}; then
-  usage
+  usageTerse
+  usageVerbose
   exit 101
 fi
 

bin/thyme-analysis

@@ -26,7 +26,9 @@ outputDir=""
 sep="================================================================"
 usageTerse() {
   echo """
-  Run the timeline histogramming jobs
+  Run the timeline histogramming jobs.
+  NOTE: This is not for chefs; instead, use the chef's workflow.
+
   $sep
   USAGE: thyme histogram -d [DATASET_NAME] [RUN_DIRECTORY]
   $sep
@@ -40,14 +42,13 @@ usageTerse() {
   one is for detector QA timelines and the other is for physics QA timelines.
   Output files will appear in ./outfiles/[DATASET_NAME]
 
-  For more options, run:
-    $0 --help
+  For more options, run with '--help'
   """ >&2
 }
 usageVerbose() {
   echo """
   $sep
-  USAGE: $0  [OPTIONS]...  [RUN_DIRECTORY]...
+  USAGE: thyme histogram  [OPTIONS]...  [RUN_DIRECTORY]...
   $sep
 
   REQUIRED ARGUMENTS: