Generate html manuals with OUTGOING, copy html manuals for 3.21

Author: jwokaty

BBS-make-OUTGOING.py

@@ -11,6 +11,7 @@
 import os
 import time
 import shutil
+import subprocess
 
 import bbs.fileutils
 import bbs.parse
@@ -119,6 +120,7 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
         if BBSvars.buildtype in ['workflows', 'books', 'bioc-mac-arm64']:
             pass
         elif source_node:
+            # pdf manuals
             pdf_file = os.path.join(BBSvars.products_in_rdir.path,
                                     BBSutils.getSourceNode(),
                                     'checksrc',
@@ -131,6 +133,20 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
                 os.link(pdf_file, dst) # create hard link to avoid making a copy
             else:
                 print("BBS> [stage6b]     SKIPPED (file %s doesn't exist)" % pdf_file)
+            # html manuals
+            rel_link = "../../%s/man/%s.html"
+            hooks = f"hooks <- list(pkg_href = function(pkg) sprintf('{rel_link}', pkg, pkg));"
+            html_file = os.path.join(BBSvars.Central_rdir.path,
+                                     "OUTGOING/manuals",
+                                    '%s.html' % pkg)
+            Rexpr = hooks + f"tools::pkg2HTML('{pkg_path}',out='{html_file}',hooks=hooks)"
+            cmd = BBSbase.Rexpr2syscmd(Rexpr)
+            try:
+                print(Rexpr)
+                subprocess.run(cmd, stdout=None, stderr=subprocess.STDOUT,
+                              shell=True, check=True)
+            except subprocess.CalledProcessError as e:
+                print("BBS> [stage6b]     SKIPPED (could not generate %s)" % html_file)
     print('BBS> [stage6b] END copying outgoing packages from %s.' % srcdir)
     return
 

propagation/3.21/updateReposPkgs-bioc.sh

@@ -67,10 +67,13 @@ echo ""
 MANUALS_DEST="$REPOS_ROOT/manuals"
 MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
 echo "Updating $BIOC_VERSION/bioc repo with reference manuals..."
-for i in `ls $MANUALS_SRC`; do
+for i in `ls $MANUALS_SRC/*.pdf`; do
 	pkg=`echo $i| awk '{split($0,a,".pdf"); print(a[1])}'`
 	mkdir -p $MANUALS_DEST/$pkg/man
-	cp --update --verbose $MANUALS_SRC/$i $MANUALS_DEST/$pkg/man
+	cp --update --verbose $MANUALS_SRC/$i.pdf $MANUALS_DEST/$pkg/man
+        if [ -f $i.html ]; then
+		cp --update --verbose $MANUALS_SRC/$i.html $MANUALS_DEST/$pkg/man
+	fi
 done
 
 echo "DONE."