Merge branch 'master' into devel

Author: ESCRI11

.github/workflows/docker-build.yml

@@ -24,18 +24,24 @@ on:
         required: true
         type: boolean
         default: true
-  workflow_run:
-    workflows: ["update OPG version"]
-    types:
-      - completed
+  push:
     branches:
       - master
+    paths:
+      - VERSION
+
+  pull_request:
+    branches:
+      - master
+    paths:
+      - VERSION
 
 jobs:
 
   build:
 
-    runs-on: ubuntu-latest
+    # runs-on: ubuntu-latest # free GH worker, not enough memory
+    runs-on: self-hosted # run on dev-bigomics-frankfurt self-hosted runner
 
     steps:
       -
@@ -67,10 +73,10 @@ jobs:
           push: true          
           no-cache: true
           build-args: |
-            BRANCH=${{ github.event.inputs.branch }}
-            update_playdata=${{ github.event.inputs.update_playdata }}
-            update_bigdash=${{ github.event.inputs.update_bigdash }}
-            update_playbase=${{ github.event.inputs.update_playbase }}
+            BRANCH=${{ github.event.inputs.branch || github.ref_name }}
+            update_playdata=${{ github.event.inputs.update_playdata || 'false' }}
+            update_bigdash=${{ github.event.inputs.update_bigdash || 'true' }}
+            update_playbase=${{ github.event.inputs.update_playbase || 'true' }}
           tags: |
-            ${{ github.event.inputs.branch == 'master' && format('{0}/omicsplayground:{1}', secrets.DOCKERHUB_USERNAME, steps.get_version.outputs.VERSION) || '' }}
-            ${{ github.event.inputs.branch != 'master' && format('{0}/omicsplayground:{1}', secrets.DOCKERHUB_USERNAME, github.event.inputs.branch) || '' }}
+            ${{ (github.event.inputs.branch || github.ref_name) == 'master' && format('{0}/omicsplayground:{1}, {0}/omicsplayground:latest', secrets.DOCKERHUB_USERNAME, steps.get_version.outputs.VERSION) || '' }}
+            ${{ (github.event.inputs.branch || github.ref_name) != 'master' && format('{0}/omicsplayground:{1}', secrets.DOCKERHUB_USERNAME, github.event.inputs.branch || github.ref_name) || '' }}

.github/workflows/update_version.yaml

@@ -37,11 +37,16 @@ jobs:
             # Set as environment variable for next steps
             echo "NEW_VERSION=$BUILD" >> $GITHUB_ENV
 
-      - name: Commit and push version changes
+      #- name: Update changelog
+      #  run: |
+      #      make changelog
+
+      - name: Commit and push version changes + changelog
         run: |
             git config --local user.name "$GITHUB_ACTOR"
             git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
             git add VERSION
+      # git add VERSION FEATURES.md CHANGELOG.md CHANGELOG-full.md CHANGELOG-pr.md 
             git commit -m "Update version to $NEW_VERSION"
             git pull --ff-only
             git push origin
@@ -52,3 +57,11 @@ jobs:
             git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com"
             git tag $NEW_VERSION
             git push origin $NEW_VERSION
+
+      - name: Create GitHub Release
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        run: |
+          gh release create "$NEW_VERSION" \
+            --title "Release $NEW_VERSION"
+    #        --notes-file FEATURES.md

CHANGELOG-full.md

@@ -1,14 +1,14 @@
-### v3.5.0 (2024-11-08)
+### v4.0.3+master250922 (2025-09-22)
 
 - Minor fixes and improvements in backend.
 
 
-### v3.4.3 (2024-07-22)
+### v4.0.2+master250917 (2025-09-17)
 
 - Minor fixes and improvements in backend.
 
 
-### v3.4.0 (2024-06-19)
+### v4.0.1+master250915 (2025-09-15)
 
 - Minor fixes and improvements in backend.
 

CHANGELOG-pr.md

@@ -1 +1 @@
-4.0.0+master250911
+v4.0.3+master250922

CHANGELOG.md

@@ -431,7 +431,8 @@ upload_module_normalization_server <- function(
               aa <- sort(unique(as.numeric(gsub(".*,|\\]", "", as.character(x.avg2)))))
               barplot(rbind(x.nar2, 1 - x.nar2),
                 beside = FALSE, names.arg = aa, las = 1,
-                xlab = "average intensity (log2)", ylab = "missing value ratio")
+                xlab = "average intensity (log2)", ylab = "missing value ratio"
+              )
               title("missingness vs. average intensity")
             } else {
               plot.new()
@@ -441,19 +442,22 @@ upload_module_normalization_server <- function(
 
           if (input$missing_plottype == "missingness per sample") {
             if (any(X2 > 0)) {
-              par(mfrow = c(1,1), mar = c(5, 5, 2, 2), mgp = c(2.5, 0.75, 0))
+              par(mfrow = c(1, 1), mar = c(5, 5, 2, 2), mgp = c(2.5, 0.75, 0))
               X3 <- imputedX()$X
-              pct.na <- colMeans(is.na(X3))*100
-              bp <- barplot(pct.na, col = "grey", xaxt = "n",
-                ylab = "Missing %", ylim = c(0, max(pct.na)+10),
-                cex.lab = 1.5, las = 2)
-              cex <- max(0.7, min(1.5, 5 / ncol(X3)))
-              text(x = bp, y = par("usr")[3] - 0.02 * diff(par("usr")[3:4]),
-                labels = names(pct.na), srt = 45, adj = 1, xpd = TRUE, cex = cex)
-              title("missingness per sample"); grid()
+              pct.na <- colMeans(is.na(X3)) * 100
+              bp <- barplot(pct.na,
+                col = "grey", xaxt = "n",
+                ylab = "Missing %", ylim = c(0, max(pct.na) + 10),
+                cex.lab = 1.5, las = 2
+              )
+              text(
+                x = bp, y = par("usr")[3] - 0.02 * diff(par("usr")[3:4]),
+                labels = names(pct.na), srt = 45, adj = 1, xpd = TRUE, cex = 1
+              )
+              title("missingness per sample")
+              grid()
               rm(X3)
-            }
-            else {
+            } else {
               plot.new()
               text(0.5, 0.5, "no missing values")
             }
@@ -833,8 +837,10 @@ upload_module_normalization_server <- function(
                         ## "multi-omics combat" = "combat"
                       )
                     } else {
-                      c("CPM", "CPM+quantile", "TMM", "quantile",
-                        "maxMedian", "maxSum", "reference")
+                      c(
+                        "CPM", "CPM+quantile", "TMM", "quantile",
+                        "maxMedian", "maxSum", "reference"
+                      )
                     },
                     selected = 1
                   ),

FEATURES.md

@@ -521,4 +521,4 @@ clean_custom_features <- function(features) {
   # Rejoin with commas
   features <- paste(feature_list, collapse = ", ")
   return(features)
-}
+}