Merge pull request #117 from KumarLabJax/task/update-jabs-postprocess-version

Task/update jabs postprocess version

Author: bergsalex

nextflow.config

@@ -6,7 +6,7 @@ manifest {
     mainScript = "main.nf"
     defaultBranch = 'main'
     nextflowVersion = "!>=22.04.3"
-    version = "0.2.3"
+    version = "0.2.4"
     contributors = [
         [name: 'Brian Geuther'],
         [name: 'Alexander Berger-Liedtka']
@@ -25,7 +25,6 @@ params {
      * - path_depth: depth of the path to preserve in the output
      * - pubdir: directory to publish the results (defaults in profiles)
      */
-    version = '0.2.3'
     input_batch = null
     ignore_invalid_inputs = false
     profile = 'sumner2'
@@ -35,6 +34,11 @@ params {
     location = 'local'
     path_depth = 2
 
+    /* Image Versions */
+    image_version = '0.2.4'
+    jabs_postprocess_version = '0.5.2'
+    jabs_behavior_version = '0.36.1'
+
     /*
      * Parameters for the single mouse pipeline
      * - align_videos: align videos to a common start time

nextflow/configs/profiles/sumner2.config

@@ -195,16 +195,16 @@ process {
      * Runtime options
      */
     withLabel: "tracking" {
-        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/runtime/v${params.version}/latest.sif"
+        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/runtime/v${params.image_version}/latest.sif"
     }
     withLabel: "jabs_classify" {
-        container = "/projects/kumar-lab/meta/images/JABS-behavior-classifier/headless/v0.36.1/latest.sif"
+        container = "/projects/kumar-lab/meta/images/JABS-behavior-classifier/headless/v${params.jabs_behavior_version}/latest.sif"
     }
     withLabel: "jabs_postprocess" {
-        container = "/projects/kumar-lab/meta/images/JABS-postprocess/jabs-postprocess/v0.5.1/latest.sif"
+        container = "/projects/kumar-lab/meta/images/JABS-postprocess/jabs-postprocess/v${params.jabs_postprocess_version}/latest.sif"
     }
     withLabel: "jabs_table_convert" {
-        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/RBase/v${params.version}/latest.sif"
+        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/RBase/v${params.image_version}/latest.sif"
     }
     withLabel: "gait" {
         container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/gait-pipeline-2025-03-27.sif"
@@ -213,14 +213,14 @@ process {
         container = "/projects/kumar-lab/multimouse-pipeline/nextflow-containers/vfi-2025-03-27.sif"
     }
     withLabel: "sleap" {
-        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/sleap-1.4.1/v${params.version}/latest.sif"
+        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/sleap-1.4.1/v${params.image_version}/latest.sif"
     }
     withLabel: "sleap_io" {
-        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/sleap-io-0.2.0/v${params.version}/latest.sif"
+        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/sleap-io-0.2.0/v${params.image_version}/latest.sif"
     }
     withLabel: "rclone" {
         // executor.queueSize = 1
-        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/rclone/v${params.version}/latest.sif"
+        container = "/projects/kumar-lab/meta/images/mouse-tracking-runtime/rclone/v${params.image_version}/latest.sif"
         cpus = 1
         time = '48h'
         memory = '12GB'

pyproject.toml

@@ -1,6 +1,6 @@
 [project]
 name = "mouse-tracking"
-version = "0.2.3"
+version = "0.2.4"
 description = "Runtime environment for mouse tracking experiments"
 requires-python = ">=3.10,<3.11"
 packages = ["src/mouse_tracking"]
@@ -128,3 +128,9 @@ test = [
 lint = [
     "ruff>=0.11.2",
 ]
+docs = [
+    "mike>=2.1.3",
+    "mkdocs-autorefs>=1.4.3",
+    "mkdocs-jupyter>=0.25.1",
+    "mkdocs-material>=9.6.22",
+]