fix: use thyme everywhere

c-dilks · c-dilks · commit a3123f33e012 · 2025-04-17T18:57:42.000-04:00
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -99,7 +99,7 @@ jobs:
         run: ls *.tar.zst | xargs -I{} tar xavf {}
       - run: tree
       - name: run monitoring
-        run: bin/run-monitoring.sh -d ${{env.dataset}} --findhipo --series --focus-${{matrix.type}} validation_files
+        run: thyme histogram -d ${{env.dataset}} --findhipo --series --focus-${{matrix.type}} validation_files
       - run: tree slurm
       - run: tree outfiles
       - uses: actions/upload-artifact@v4
@@ -160,8 +160,8 @@ jobs:
       fail-fast: false
       matrix:
         include:
-          - { type: detectors,  args: '-n 4 --skip-mya' }
-          - { type: physics,    args: '' }
+          - { type: detectors, run_script: 'bin/thyme analysis',           args: '-n 4 --skip-mya' }
+          - { type: physics,   run_script: 'bin/run-physics-timelines.sh', args: '' }
     steps:
       - uses: actions/checkout@v4
       - name: download outfiles
@@ -178,7 +178,7 @@ jobs:
         run: ls *.tar.zst | xargs -I{} tar xavf {}
       - run: tree
       - name: run timelines
-        run: bin/run-${{matrix.type}}-timelines.sh -d ${{env.dataset}} ${{matrix.args}}
+        run: ${{matrix.run_script}} -d ${{env.dataset}} ${{matrix.args}}
       - run: tree outfiles
       - uses: actions/upload-artifact@v4
         with:
@@ -219,7 +219,7 @@ jobs:
           tree outfiles | xargs -0 -I{} echo {} >> $GITHUB_STEP_SUMMARY
           echo '```' >> $GITHUB_STEP_SUMMARY
       - name: deploy
-        run: bin/deploy-timelines.sh -d ${{env.dataset}} -c -t web
+        run: thyme deploy -d ${{env.dataset}} -c -t web
       - uses: actions/upload-artifact@v4
         with:
           name: web
diff --git a/data/metadata/README.md b/data/metadata/README.md
@@ -1,3 +1,3 @@
 # Metadata JSON files
 
-These files are used by `deploy-timelines.sh` to provide run filter controls on the front-end webpage.
+These files are used by `thyme deploy` to provide run filter controls on the front-end webpage.
diff --git a/doc/chef_guide.md b/doc/chef_guide.md
@@ -17,7 +17,7 @@ Output files will appear in your chosen output directory, within `hist/detectors
 ## :green_circle: Step 2: Make the timelines
 
 ```bash
-run-detectors-timelines.sh -d $dataset -i $out_dir/hist/detectors
+thyme analysis -d $dataset -i $out_dir/hist/detectors
 ```
 where `$out_dir` is your output directory from **Step 1** and `$dataset` is a unique name for this cook, _e.g._, `rga_v1.23`.
 
@@ -26,7 +26,7 @@ Output will appear in `./outfiles/$dataset/`.
 ## :green_circle: Step 3: Deploy the timelines
 
 ```bash
-deploy-timelines.sh -d $dataset -t $target_dir -D
+thyme deploy -d $dataset -t $target_dir -D
 ```
 where `$target_dir` is a subdirectory of `/group/clas/www/clas12mon/html/hipo`, for example,
 ```bash
diff --git a/doc/dev_notes.md b/doc/dev_notes.md
@@ -12,7 +12,7 @@ flowchart TB
     dst[(Input HIPO Files)]:::data
 
     subgraph Data Monitoring
-        subgraph "<strong>bin/run-monitoring.sh</strong>"
+        subgraph "<strong>bin/thyme histogram</strong>"
             monitorDetectors["<strong>Make detector histograms</strong><br/>org.jlab.clas.timeline.histograms.run_histograms"]:::proc
             monitorPhysics["<strong>Make physics QA histograms</strong><br/>qa-physics/: monitorRead.groovy"]:::proc
         end
@@ -27,7 +27,7 @@ flowchart TB
     monitorPhysics   --> outmon
 
     subgraph Timeline Production
-        subgraph "<strong>bin/run-detectors-timelines.sh</strong>"
+        subgraph "<strong>bin/thyme analysis</strong>"
             timelineDetectorsPreQA["<strong>Make detector timelines</strong><br/>org.jlab.clas.timeline.analysis.run_analysis"]:::proc
             outTimelineDetectorsPreQA{{outfiles/$dataset/timeline_web_preQA/$detector/*.hipo}}:::timeline
             timelineDetectors["<strong>Draw QA lines</strong><br/>qa-detectors/: applyBounds.groovy"]:::proc
@@ -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/>bin/deploy-timelines.sh"]:::proc
+        deploy["<strong>Deployment</strong><br/>thyme deploy"]:::proc
         timelineDir{{timelines on web server}}:::timeline
     end
     outplots --> timelineDetectorsPreQA --> outTimelineDetectorsPreQA --> timelineDetectors --> outTimelineDetectors
@@ -69,7 +69,7 @@ Temporary files are additionally stored in `tmp/`, including backups (for the ca
 outfiles
 └── $dataset
     │
-    ├── timeline_detectors            # histograms, etc. for detector timelines, from `bin/run-monitoring.sh`
+    ├── timeline_detectors            # histograms, etc. for detector timelines, from `bin/thyme histogram`
     │   │
     │   ├── 5000                      # for run number 5000
     │   │   ├── out_HTCC_5000.hipo
@@ -79,7 +79,7 @@ outfiles
     │   ├── 5001                      # for run number 5001
     │   └── ...
     │
-    ├── timeline_physics              # histograms, etc. for physics timelines, from `bin/run-monitoring.sh`
+    ├── timeline_physics              # histograms, etc. for physics timelines, from `bin/thyme histogram`
     │   │
     │   ├── 5000                      # for run number 5000
     │   │   ├── data_table_5000.dat
@@ -105,25 +105,25 @@ outfiles
     │
     ├── timeline_web                  # final output timeline files, for deployment to web server
     │   │
-    │   ├── htcc                      # detector timelines, with QA, from `bin/run-detectors-timelines.sh`
+    │   ├── htcc                      # detector timelines, with QA, from `bin/thyme analysis`
     │   ├── ltcc
     │   ├── ...
     │   │
     │   ├── phys_qa                   # physics timelines, with QA, from `bin/run-physics-timelines.sh`
     │   ├── phys_qa_extra             # extra physics QA timelines, for experts
     │   └── qadb                      # QADB results timeline
     │
-    └── log                           # log files from `bin/run-*-timelines.sh` (not slurm logs (/farm_out/$LOGNAME/))
+    └── log                           # log files from `bin/thyme analysis` (not slurm logs (/farm_out/$LOGNAME/))
         ├── $timeline.out
         └── $timeline.err
 ```
 
 # Notes on SWIF Workflows
 
-For [CLAS12 `swif` workflow](https://github.com/baltzell/clas12-workflow) integration, the `bin/run-monitoring.sh` script (which normally generates `slurm` jobs) has a specific mode `--swifjob`:
+For [CLAS12 `swif` workflow](https://github.com/baltzell/clas12-workflow) integration, the `bin/thyme histogram` command (which normally generates `slurm` jobs) has a specific mode `--swifjob`:
 ```bash
-bin/run-monitoring.sh --swifjob --focus-detectors   # generate files for detector timelines
-bin/run-monitoring.sh --swifjob --focus-physics     # generate files for physics QA timelines
+thyme histogram --swifjob --focus-detectors   # generate files for detector timelines
+thyme histogram --swifjob --focus-physics     # generate files for physics QA timelines
 ```
 Either or both of these commands is _all_ that needs to be executed on a runner node, within [`clas12-workflow`](https://github.com/baltzell/clas12-workflow); calling one of these will automatically run the wrapped code, with the following assumptions and conventions:
 - input HIPO files are at `./` and only a single run will be processed
@@ -149,7 +149,7 @@ top_level_target_directory
   │
   └── ...
 ```
-For compatibility with the file tree expected by downstream `bin/run-*-timelines.sh` scripts (see above), symbolic links may be made to these `timeline_{detectors,physics}` directories, but this is not required since these scripts also allow for the specification of an input directory.
+For compatibility with the file tree expected by downstream `thyme analysis` (see above), symbolic links may be made to these `timeline_{detectors,physics}` directories, but this is not required since these scripts also allow for the specification of an input directory.
 
 Separate `--focus-detectors` and `--focus-physics` options are preferred, since:
 - offers better organization of the contract data between `swif` jobs and downstream scripts
diff --git a/doc/procedure.md b/doc/procedure.md
@@ -15,17 +15,17 @@ This step reads input HIPO files (_e.g._, DST or `mon` files) and produces histo
 
 This step can either be run during the usual data cooking procedure, using [`clas12-workflow`](https://github.com/baltzell/clas12-workflow) (see its usage guide), or it may be run separately on already-cooked data using:
 ```bash
-bin/run-monitoring.sh
+thyme histogram
 ```
 Running it with no arguments will print the usage guide; use the `--help` option for more detailed guidance.
 
 > [!NOTE]
-> If you are performing physics QA for QADB, consider using [**prescaled trains**](/qa-physics/prescaler) (and `run-monitoring.sh` will need the `--flatdir` argument)
+> If you are performing physics QA for QADB, consider using [**prescaled trains**](/qa-physics/prescaler) (and `thyme histogram` will need the `--flatdir` argument)
 
 ### Example
-If using `clas12-workflow`, see it's documentation; otherwise if using `run-monitoring.sh`:
+If using `clas12-workflow`, see it's documentation; otherwise if using `thyme histogram`:
 ```bash
-bin/run-monitoring.sh -d rga_sp19_v5 /volatile/clas12/rg-a/production/pass0/sp19/v5/mon
+thyme histogram -d rga_sp19_v5 /volatile/clas12/rg-a/production/pass0/sp19/v5/mon
 ```
 - sets the `dataset` name to `"rga_sp19_v5"`, which will be referenced in subsequent steps
 - assumes the input data are found in `/volatile/clas12/rg-a/production/pass0/sp19/v5/mon`
@@ -36,7 +36,7 @@ sbatch ./slurm/job.rga_sp19_v5.detectors.slurm   # for detector timelines (need
 sbatch ./slurm/job.rga_sp19_v5.physics.slurm     # for physics timelines
 ```
 - monitor progress with Slurm tools (e.g., `squeue -u $LOGNAME`)
-- monitor output logs in `/farm_out/$LOGNAME/` or use `bin/error-print.sh`
+- monitor output logs in `/farm_out/$LOGNAME/` or use `thyme error`
 
 > [!NOTE]
 > - data monitoring for detector timelines is handled by the [`org.jlab.clas.timeline.histograms` package](/src/main/java/org/jlab/clas/timeline/histograms)
@@ -48,8 +48,8 @@ sbatch ./slurm/job.rga_sp19_v5.physics.slurm     # for physics timelines
 After Step 1 is complete, run the following Step 2 scripts to produce the timeline HIPO files and to run the automatic QA procedures. There is one script for each timeline type: run them with no arguments to print the usage guides:
 
 ```bash
-bin/run-detectors-timelines.sh
-bin/run-physics-timelines.sh
+thyme analysis             # for detector timelines
+run-physics-timelines.sh   # for physics timelines (will eventually be combined with 'thyme analysis')
 ```
 
 > [!IMPORTANT]
@@ -58,18 +58,16 @@ bin/run-physics-timelines.sh
 > - use the scripts' `-o` option to set the output locations
 
 ### Example
-**If** you used `clas12-workflow` for Step 1:
+**If** you used `clas12-workflow` for Step 1, the script arguments should be
 ```bash
-bin/run-detectors-timelines.sh -d rga_sp19_v5 -i /path/to/output/files   # for detector timelines
-bin/run-physics-timelines.sh   -d rga_sp19_v5 -i /path/to/output/files   # for physics timelines
+-d rga_sp19_v5 -i /path/to/output/files
 ```
 - 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
 
 **Otherwise**, you may omit the `-i /path/to/output/files` option (unless you customized it from Step 1):
 ```bash
-bin/run-detectors-timelines.sh -d rga_sp19_v5   # for detector timelines
-bin/run-physics-timelines.sh   -d rga_sp19_v5   # for physics timelines
+-d rga_sp19_v5
 ```
 - the dataset name must match that of Step 1, otherwise you need to specify the path to the input files with `-i`
 
@@ -86,16 +84,16 @@ bin/run-physics-timelines.sh   -d rga_sp19_v5   # for physics timelines
 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
-bin/deploy-timelines.sh
+thyme deploy
 ```
 
 If all went well, a URL for the new timelines will be printed; open it in a browser to view them.
 
 ### Example
 ```bash
-bin/deploy-timelines.sh -d rga_sp19_v5 -t rga/sp19/pass0/v5 -D   # deploy to a run-group web directory (for chefs)
+thyme deploy -d rga_sp19_v5 -t rga/sp19/pass0/v5 -D   # deploy to a run-group web directory (for chefs)
 ### or ###
-bin/deploy-timelines.sh -d rga_sp19_v5 -t $LOGNAME/my_test -D    # deploy to a personal web directory (for testing)
+thyme 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
diff --git a/qa-detectors/README.md b/qa-detectors/README.md
@@ -22,9 +22,9 @@ The specifications are specified by text files in [the `cuts` directory](cuts).
 ## Procedure
 - Run one of:
   ```bash
-  ../bin/run-detectors-timelines.sh               # print usage guide
-  ../bin/run-detectors-timelines.sh  --focus-qa   # run detector QA only (for debugging this QA code; you may need to set other options)
+  thyme analysis               # print usage guide
+  thyme analysis  --focus-qa   # run detector QA only (for debugging this QA code; you may need to set other options)
   ```
 - see [main documentation](../README.md) for more details
 - note to developers: if you want to run local scripts, call `source ../libexec/environ.sh` (this is
-  automatically done when running the wrapper `../bin/run-detectors-timelines.sh`)
+  automatically done when running the wrapper `thyme analysis`)
diff --git a/qa-physics/README.md b/qa-physics/README.md
@@ -43,13 +43,13 @@ For run-group specific notes, including the commands used to perform the QA, see
     * if you find that the DAQ-gated FC charge is larger than the ungated
       charge, you may have assumed here that the recharge option was ON, when
       actually it was OFF and needs to be ON
-* `../bin/run-monitoring.sh`: runs `monitorRead.groovy` on DSTs using `slurm`
+* `thyme histogram`: runs `monitorRead.groovy` on DSTs using `slurm`
   * **IMPORTANT**: call this first with the `--check-cache` option to make sure that ALL required DST files are cached; if all files are on `/cache`, you may proceed, removing the `--check-cache` option
   * **IMPORTANT**: if you do **NOT** want to analyze full DSTs, and prefer to analyze trains:
     * use the option `--flatdir`, since likely all the HIPO files are in a single directory
     * use the scripts in the [`prescaler/` directory](prescaler) if you want to create a random "prescale" train
   * wait for `slurm` jobs to finish
-  * inspect error logs (_e.g._, `../bin/error-print.sh`) to make sure all jobs ran successfully
+  * inspect error logs (_e.g._, `thyme error`) to make sure all jobs ran successfully
 * `../bin/run-physics-timelines.sh $dataset`, which does the following:
   * runs `datasetOrganize.sh`
   * runs `qaPlot.groovy` (on FD and FT)
diff --git a/qa-physics/docs/docDiagram.md b/qa-physics/docs/docDiagram.md
@@ -30,7 +30,7 @@ Note: output directories `$output_dir` and `$qa_dir` are typically set by wrappe
 ```mermaid
 flowchart TB
 
-    subgraph "Automated by ../bin/run-monitoring.sh"
+    subgraph "Automated by thyme histogram"
       dst{{DSTs}}:::data
       monitorRead[monitorRead.groovy]:::auto
       monitorReadOut{{$output_dir/data_table_$run.dat<br>$output_dir/monitor_$run.hipo}}:::data
diff --git a/qa-physics/notes/rga_fa18.md b/qa-physics/notes/rga_fa18.md
@@ -9,13 +9,13 @@ We will use the `nSidis` train.
 
 First make sure all skim files are cached:
 ```bash
-bin/run-monitoring.sh -d rga_fa18_inbending_nSidis  --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus-1/pass2/main/train/nSidis
-bin/run-monitoring.sh -d rga_fa18_outbending_nSidis --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus+1/pass2/train/nSidis
+thyme histogram -d rga_fa18_inbending_nSidis  --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus-1/pass2/main/train/nSidis
+thyme histogram -d rga_fa18_outbending_nSidis --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus+1/pass2/train/nSidis
 ```
 then run monitoring
 ```bash
-bin/run-monitoring.sh -d rga_fa18_inbending_nSidis  --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus-1/pass2/main/train/nSidis
-bin/run-monitoring.sh -d rga_fa18_outbending_nSidis --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus+1/pass2/train/nSidis
+thyme histogram -d rga_fa18_inbending_nSidis  --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus-1/pass2/main/train/nSidis
+thyme histogram -d rga_fa18_outbending_nSidis --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/fall2018/torus+1/pass2/train/nSidis
 ```
 
 ## Double check that we have all the runs
@@ -35,10 +35,10 @@ bin/run-physics-timelines.sh -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
-bin/deploy-timelines.sh -d rga_fa18_inbending_nSidis  -t $LOGNAME -D
-bin/deploy-timelines.sh -d rga_fa18_outbending_nSidis -t $LOGNAME -D
+thyme deploy -d rga_fa18_inbending_nSidis  -t $LOGNAME -D
+thyme deploy -d rga_fa18_outbending_nSidis -t $LOGNAME -D
 
 # common area
-bin/deploy-timelines.sh -d rga_fa18_inbending_nSidis  -t rga/pass2/fa18/qa -D
-bin/deploy-timelines.sh -d rga_fa18_outbending_nSidis -t rga/pass2/fa18/qa -D
+thyme deploy -d rga_fa18_inbending_nSidis  -t rga/pass2/fa18/qa -D
+thyme deploy -d rga_fa18_outbending_nSidis -t rga/pass2/fa18/qa -D
 ```
diff --git a/qa-physics/notes/rga_sp19.md b/qa-physics/notes/rga_sp19.md
@@ -26,12 +26,12 @@ start-workflow.sh rga-a-sp19*.json  ## check that this is the correct JSON file
 
 For the prescaled train:
 ```bash
-bin/run-monitoring.sh -d rga_sp19_prescaled --submit --focus-physics PATH_TO_PRESCALED_TRAIN
+thyme histogram -d rga_sp19_prescaled --submit --focus-physics PATH_TO_PRESCALED_TRAIN
 ```
 
 For the SIDIS train, `nSidis`, first make sure all skim files are cached:
 ```bash
-bin/run-monitoring.sh -d rga_sp19_nSidis --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
+thyme histogram -d rga_sp19_nSidis --check-cache --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
 ```
 If they are not:
 ```bash
@@ -41,7 +41,7 @@ jcache get $(cat jlist.txt)
 ```
 then run monitoring
 ```bash
-bin/run-monitoring.sh -d rga_sp19_nSidis --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
+thyme histogram -d rga_sp19_nSidis --submit --flatdir --focus-physics /cache/clas12/rg-a/production/recon/spring2019/torus-1/pass2/dst/train/nSidis
 ```
 
 ## Make timelines
@@ -55,10 +55,10 @@ bin/run-physics-timelines.sh -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
-bin/deploy-timelines.sh -d rga_sp19_prescaled -t $LOGNAME -D
-bin/deploy-timelines.sh -d rga_sp19_nSidis -t $LOGNAME -D
+thyme deploy -d rga_sp19_prescaled -t $LOGNAME -D
+thyme deploy -d rga_sp19_nSidis -t $LOGNAME -D
 
 # common area
-bin/deploy-timelines.sh -d rga_sp19_prescaled -t rga/pass2/sp19/qa -D
-bin/deploy-timelines.sh -d rga_sp19_nSidis -t rga/pass2/sp19/qa -D
+thyme deploy -d rga_sp19_prescaled -t rga/pass2/sp19/qa -D
+thyme deploy -d rga_sp19_nSidis -t rga/pass2/sp19/qa -D
 ```
diff --git a/qa-physics/notes/rgb_fa19.md b/qa-physics/notes/rgb_fa19.md
diff --git a/qa-physics/notes/rgb_sp19.md b/qa-physics/notes/rgb_sp19.md
diff --git a/qa-physics/notes/rgb_wi20.md b/qa-physics/notes/rgb_wi20.md
diff --git a/qa-physics/notes/rgc_su22.md b/qa-physics/notes/rgc_su22.md
diff --git a/util/test-swifjob.sh b/util/test-swifjob.sh

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,3 @@`
`1`	`1`	`# Metadata JSON files`
`2`	`2`
`3`		-These files are used by `deploy-timelines.sh` to provide run filter controls on the front-end webpage.
	`3`	+These files are used by `thyme deploy` to provide run filter controls on the front-end webpage.