fix: remove final traces of deploy scripts

Author: c-dilks

README.md

@@ -1,6 +1,6 @@
 # clas12-timeline
 
-Timeline production for CLAS12. Timelines are deployed to [`clas12mon`](https://clas12mon.jlab.org).
+Timeline production for CLAS12. Timelines are published to [`clas12mon`](https://clas12mon.jlab.org).
 
 | Table of Contents                                            |                                                      |
 | ---                                                          | ---                                                  |

bin/qtl-analysis

@@ -426,7 +426,7 @@ if [ ${#failedJobs[@]} -gt 0 ]; then
     printError "job '$failedJob' returned non-zero exit code; error log dump:"
     cat $logDir/$failedJob.err
     if [ "$failedJob" = "hipo-check" ]; then
-      printWarning "These HIPO files are TIMELINE files; if this '$failedJob' job is the ONLY failed job, you may proceed with timeline deployment, but these failed timelines will not be deployed."
+      printWarning "These HIPO files are TIMELINE files; they will NOT be published"
     fi
   done
   somethingFailed=true

bin/qtl-physics

@@ -8,6 +8,7 @@ source $(dirname $0)/../libexec/environ.sh
 inputDir=""
 dataset=""
 outputDir=""
+publishDir=""
 
 # usage
 sep="================================================================"
@@ -25,6 +26,8 @@ usage() {
     -i [INPUT_DIR]      input directory
                         default = ./outfiles/[DATASET_NAME]
 
+    -p [PUBLISH_DIR]    publish timeline results (see 'qtl analysis')
+
   OPTIONAL OPTIONS:
 
     -o [OUTPUT_DIR]     output directory
@@ -40,14 +43,15 @@ fi
 
 # parse options
 helpMode=false
-while getopts "d:i:o:h-:" opt; do
+while getopts "d:i:p:o:h-:" opt; do
   case $opt in
     d)
       echo $OPTARG | grep -q "/" && printError "dataset name must not contain '/' " && exit 100
       dataset=$OPTARG
       ;;
     i) inputDir=$OPTARG ;;
     o) outputDir=$OPTARG ;;
+    p) publishDir=$OPTARG ;;
     h) helpMode=true ;;
     -)
       [ "$OPTARG" != "help" ] && printError "unknown option --$OPTARG"
@@ -65,6 +69,7 @@ fi
 [ -z "$inputDir" ] && inputDir=$(pwd -P)/outfiles/$dataset/timeline_physics
 [ ! -d $inputDir ] && printError "input directory $inputDir does not exist" && exit 100
 [ -z "$outputDir" ] && outputDir=$(realpath $(pwd -P)/outfiles/$dataset) || outputDir=$(realpath $outputDir)
+[ -z "$publishDir" ] && printError "need publishing directory, option '-p'" && exit 100
 
 # set subdirectories
 qaDir=$outputDir/timeline_physics_qa

doc/dev_notes.md

@@ -39,7 +39,7 @@ flowchart TB
     subgraph Final Timelines
         outTimelinePhysics{{outfiles/$dataset/timeline_web/phys_*/*}}:::timeline
         outTimelineDetectors{{outfiles/$dataset/timeline_web/$detector/*.hipo}}:::timeline
-        deploy["<strong>Deployment</strong><br/>qtl deploy"]:::proc
+        deploy["<strong>Publishing</strong><br/>handled by qtl analysis"]:::proc
         timelineDir{{timelines on web server}}:::timeline
     end
     outplots --> timelineDetectorsPreQA --> outTimelineDetectorsPreQA --> timelineDetectors --> outTimelineDetectors

doc/procedure.md

@@ -52,23 +52,21 @@ qtl analysis  # for detector timelines
 qtl physics   # for physics timelines (will eventually be combined with 'qtl analysis')
 ```
 
-> [!IMPORTANT]
+> [!TIP]
 > If you are processing a large data set on `ifarm`, direct your output files to a location within `/volatile`. Either:
 > - make a symbolic link in your working directory named `outfiles` pointing to a location within `/volatile`
 > - use the scripts' `-o` option to set the output locations
 
 ### Example
 **If** you used `clas12-workflow` for Step 1, the script arguments should be
 ```bash
--d rga_sp19_v5 -i /path/to/output/files
+-d rga_sp19_v5 -i /path/to/output/files -p some/publish/directory
 ```
 - the dataset is _given_ the name `"rga_sp19_v5"` (and does not have to be related to any name given from Step 1)
 - the output from `clas12-workflow` is `/path/to/output/files`; its subdirectories should be run numbers
+- the publish directory given by `-p` is a subdirectory of the web server; see `qtl analysis` usage guide
 
-**Otherwise**, you may omit the `-i /path/to/output/files` option (unless you customized it from Step 1):
-```bash
--d rga_sp19_v5
-```
+**Otherwise**, you may omit the `-i /path/to/output/files` option (unless you customized it from Step 1)
 - the dataset name must match that of Step 1, otherwise you need to specify the path to the input files with `-i`
 
 
@@ -78,28 +76,3 @@ qtl physics   # for physics timelines (will eventually be combined with 'qtl ana
 >   see [its documentation](/qa-detectors/README.md)
 > - physics timeline production and QA are handled by the [`qa-physics/` subdirectory](/qa-physics);
 >   see [their documentation](/qa-physics/README.md)
-
-<!-- FIXME
-we need to remove 'qtl deploy' stuff everywhere...
--->
-
-<!-- ## 🟢 Step 3: Deployment -->
-<!---->
-<!-- To view the timelines on the web, you must deploy them by copying the timeline HIPO files to a directory with a running web server. Note that you must have write-permission for that directory. To deploy, run (with no arguments, for the usage guide): -->
-<!---->
-<!-- ```bash -->
-<!-- qtl deploy -->
-<!-- ``` -->
-<!---->
-<!-- If all went well, a URL for the new timelines will be printed; open it in a browser to view them. -->
-<!---->
-<!-- ### Example -->
-<!-- ```bash -->
-<!-- qtl deploy -d rga_sp19_v5 -t rga/sp19/pass0/v5 -D   # deploy to a run-group web directory (for chefs) -->
-<!-- ### or ### -->
-<!-- qtl deploy -d rga_sp19_v5 -t $LOGNAME/my_test -D    # deploy to a personal web directory (for testing) -->
-<!-- ``` -->
-<!-- - this will _only_ print what will be done: deploy the timelines from dataset `"rga_sp19_v5"` (defined in previous step(s)) to the printed path -->
-<!--   - you must have write access to that path; contact the maintainers if you need help with this -->
-<!--   - if you are a chef, consider using the appropriate run group subdirectory, _e.g._, `rga/sp19/pass0/v5` -->
-<!-- - if it looks correct, remove the `-D` option to deploy for real and follow the printed URL -->

qa-physics/notes/rga_fa18.md

@@ -28,17 +28,6 @@ qtl histogram -d rga_fa18_outbending_nSidis --submit --flatdir --focus-physics /
 
 Make the timelines:
 ```bash
-bin/qtl physics -d rga_fa18_inbending_nSidis
-bin/qtl physics -d rga_fa18_outbending_nSidis
-```
-
-Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
-```bash
-# your area, for testing
-qtl deploy -d rga_fa18_inbending_nSidis  -t $LOGNAME -D
-qtl deploy -d rga_fa18_outbending_nSidis -t $LOGNAME -D
-
-# common area
-qtl deploy -d rga_fa18_inbending_nSidis  -t rga/pass2/fa18/qa -D
-qtl deploy -d rga_fa18_outbending_nSidis -t rga/pass2/fa18/qa -D
+bin/qtl physics -d rga_fa18_inbending_nSidis -p rga/pass2/fa18/qa
+bin/qtl physics -d rga_fa18_outbending_nSidis -p rga/pass2/fa18/qa
 ```

qa-physics/notes/rga_sp19.md

@@ -48,17 +48,6 @@ qtl histogram -d rga_sp19_nSidis --submit --flatdir --focus-physics /cache/clas1
 
 Make the timelines:
 ```bash
-bin/qtl physics -d rga_sp19_prescaled
-bin/qtl physics -d rga_sp19_nSidis
-```
-
-Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
-```bash
-# your area, for testing
-qtl deploy -d rga_sp19_prescaled -t $LOGNAME -D
-qtl deploy -d rga_sp19_nSidis -t $LOGNAME -D
-
-# common area
-qtl deploy -d rga_sp19_prescaled -t rga/pass2/sp19/qa -D
-qtl deploy -d rga_sp19_nSidis -t rga/pass2/sp19/qa -D
+bin/qtl physics -d rga_sp19_prescaled -p rga/pass2/sp19/qa
+bin/qtl physics -d rga_sp19_nSidis -p rga/pass2/sp19/qa
 ```

qa-physics/notes/rgb_fa19.md

@@ -31,14 +31,5 @@ qtl histogram -d rgb_fa19_sidisdvcs --submit --flatdir --focus-physics \
 
 Make the timelines:
 ```bash
-bin/qtl physics -d rgb_fa19_sidisdvcs
-```
-
-Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
-```bash
-# your area, for testing
-qtl deploy -d rgb_fa19_sidisdvcs  -t $LOGNAME -D
-
-# common area
-qtl deploy -d rgb_fa19_sidisdvcs  -t rgb/pass2/qa/fa19 -D
+bin/qtl physics -d rgb_fa19_sidisdvcs -p rgb/pass2/qa/fa19
 ```

qa-physics/notes/rgb_sp19.md

@@ -26,14 +26,5 @@ qtl histogram -d rgb_sp19_sidisdvcs --submit --flatdir --focus-physics /cache/cl
 
 Make the timelines:
 ```bash
-bin/qtl physics -d rgb_sp19_sidisdvcs
-```
-
-Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
-```bash
-# your area, for testing
-qtl deploy -d rgb_sp19_sidisdvcs  -t $LOGNAME -D
-
-# common area
-qtl deploy -d rgb_sp19_sidisdvcs  -t rgb/pass2/qa/sp19 -D
+bin/qtl physics -d rgb_sp19_sidisdvcs -p rgb/pass2/qa/sp19
 ```

qa-physics/notes/rgb_wi20.md

@@ -26,14 +26,5 @@ qtl histogram -d rgb_wi20_sidisdvcs --submit --flatdir --focus-physics /cache/cl
 
 Make the timelines:
 ```bash
-bin/qtl physics -d rgb_wi20_sidisdvcs
-```
-
-Deploy either to your area or the common area (remove the `-D` option once you confirm this is the correct directory):
-```bash
-# your area, for testing
-qtl deploy -d rgb_wi20_sidisdvcs  -t $LOGNAME -D
-
-# common area
-qtl deploy -d rgb_wi20_sidisdvcs  -t rgb/pass2/qa/wi20 -D
+bin/qtl physics -d rgb_wi20_sidisdvcs -p rgb/pass2/qa/wi20
 ```