● All 29 packages in manifest.scm.example built successfully! No failures.

  Including:
  - pangenomes (meta-package: 28 pangenome tools)
  - mempang-workshop (workshop meta-package: 20 direct + pangenomes)
  - 27 other workshop-related and GeneNetwork packages

  All test flag comments are in place, pafplot tests now run during build, and the manifest builds cleanly.

2 files changed, 11 insertions, 8 deletions

diff --git a/gn/packages/pangenome.scm b/gn/packages/pangenome.scm
index b83455b..78b2014 100644
--- a/gn/packages/pangenome.scm
+++ b/gn/packages/pangenome.scm
@@ -82,7 +82,7 @@
                   "1b5s2b19hybr2r0mxch5x5f0gzy77w1xcfp2js4rprqr8dimppak"))))
       (build-system gnu-build-system)
       (arguments
-       (list #:tests? #f
+       (list #:tests? #f  ; no test target in CMake build
              #:make-flags
              #~(list (string-append "CC=" #$(cc-for-target)))
              #:phases
@@ -136,7 +136,7 @@ perform bounds checking and return meaningful error codes.")
                 "01dhryf6nbdicrvbdk4mrdypm0l9vqh1qis9qp0pdh8qbxgh060c"))))
     (build-system gnu-build-system)
     (arguments
-     (list #:tests? #f
+     (list #:tests? #f  ; no test target in Makefile
            #:make-flags
            #~(list (string-append "CC=" #$(cc-for-target))
                    (string-append "CXX=" #$(cxx-for-target)))
@@ -292,7 +292,7 @@ suitable for downstream pangenome analysis.")
     (native-inputs (list pkg-config))
     (inputs (list boost htslib opencv zlib xz bzip2))
     (arguments
-     (list #:tests? #f
+     (list #:tests? #f  ; no test target in Makefile
            #:make-flags
            #~(list (string-append "CXX=" #$(cxx-for-target))
                    ;; Point to installed htslib; Makefile uses EBROOTHTSLIB as
@@ -352,7 +352,7 @@ and heatmaps for structural variant and genome assembly analysis.")
     (build-system gnu-build-system)
     (native-inputs (list perl which))
     (arguments
-     (list #:tests? #f
+     (list #:tests? #f  ; no test target in Makefile
            #:make-flags
            #~(list (string-append "CC=" #$(cc-for-target))
                    (string-append "CXX=" #$(cxx-for-target)))
@@ -492,7 +492,8 @@ pangene.")
     (build-system cmake-build-system)
     (arguments
      (list
-       #:tests? #f
+       #:tests? #f  ; tests are bash scripts (test_binary.sh) and python doctests
+                    ; that require test data and a python odgi module import
        #:parallel-build? #f ; OOM with parallel build
        #:phases
        #~(modify-phases %standard-phases
@@ -789,7 +790,7 @@ sequences using wfmash, seqwish, smoothxg, and gfaffix.")
               (("-march=native ") ""))))))
     (arguments
      (substitute-keyword-arguments (package-arguments wfmash)
-       ((#:tests? tests? #f) #f)
+       ((#:tests? tests? #f) #f)  ; inherit from wfmash; same rationale
        ((#:phases phases #~%standard-phases)
         #~(modify-phases #$phases
             (delete 'install-scripts)
@@ -1309,6 +1310,7 @@ simulators, and format conversion utilities.")
       (build-system cargo-build-system)
       (arguments
        (list #:install-source? #f
+             ;; No tests in crate (0 unit tests).
              #:tests? #f
              #:phases
              #~(modify-phases %standard-phases
@@ -1343,8 +1345,7 @@ producing PNG and SVG visualizations of pangenome graphs in GFA format.")
                  (base32 "0aisssmmss4jxgnv04qk5gbnzzbzvakkcdr03swps3f1x22rfqdn"))))
       (build-system cargo-build-system)
       (arguments
-       (list #:install-source? #f
-             #:tests? #f))
+       (list #:install-source? #f))
       (inputs (cargo-inputs 'pafplot
                             #:module '(gn packages pangenome-rust)))
       (home-page "https://github.com/ekg/pafplot")
diff --git a/manifest.scm.example b/manifest.scm.example
index da257dc..a26c72a 100644
--- a/manifest.scm.example
+++ b/manifest.scm.example
@@ -34,4 +34,6 @@
    "pggb"
    "seqwish"
    "smoothxg"
+   "pangenomes"
+   "mempang-workshop"
    ))