Use extractManuals for bioc and experiment builds and generate html manuals for 3.21, 3.22

BBS-make-OUTGOING.py

@@ -85,14 +85,6 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
         errmsg = "Directory '%s' does not exist!\n\n" % srcdir + \
                  "  %s is late or stopped building?" % node_hostname
         raise FileExistsError(errmsg)
-    ## Workflow and book packages do not have manuals/ because we do not run
-    ## `R CMD check`.
-    manuals_dir = '../manuals'
-    if BBSvars.buildtype in ['workflows', 'books', 'bioc-mac-arm64']:
-        pass
-    elif source_node:
-        print('BBS> [stage6b] mkdir %s' % manuals_dir)
-        os.mkdir(manuals_dir)
     print('BBS> [stage6b] BEGIN copying outgoing packages from %s.' % srcdir)
     node_Arch = BBSutils.getNodeSpec(node_hostname, 'Arch')
     node_pkgType = BBSutils.getNodeSpec(node_hostname, 'pkgType')
@@ -116,22 +108,6 @@ def copy_outgoing_pkgs(products_in_subdir, source_node):
             os.link(pkg_path, pkg_file)  # create hard link to avoid making a copy
         else:
             print("BBS> [stage6b]     SKIPPED (file %s doesn't exist)" % pkg_path)
-        ## Get reference manual from pkg.Rcheck directory.
-        if BBSvars.buildtype in ['workflows', 'books', 'bioc-mac-arm64']:
-            pass
-        elif source_node:
-            pdf_file = os.path.join(BBSvars.products_in_rdir.path,
-                                    BBSutils.getSourceNode(),
-                                    'checksrc',
-                                    '%s.Rcheck' % pkg,
-                                    '%s-manual.pdf' % pkg)
-            print('BBS> [stage6b]   - copying %s to OUTGOING/manuals folder...' % pdf_file)
-            if os.path.exists(pdf_file):
-                dst = os.path.join(manuals_dir, '%s.pdf' % pkg)
-                #shutil.copy(pdf_file, dst)
-                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)
     print('BBS> [stage6b] END copying outgoing packages from %s.' % srcdir)
     return
 

propagation/3.21/prepareRepos-bioc.config

@@ -7,7 +7,7 @@ MEAT0_PATH="/home/biocbuild/bbs-3.21-bioc/MEAT0"
 # Manuals were already copied from
 # /home/biocbuild/public_html/BBS/3.21/bioc/OUTGOING/manuals
 # by updateReposPkgs-bioc.sh so don't need to be extracted.
-EXTRACT_MANUALS="FALSE"
+EXTRACT_MANUALS="TRUE"
 REPOS_ROOT="$VIEW_ROOT/bioc"
 REPOS_URL="$VIEW_URL/bioc"
 STATS_URL="https://bioconductor.org/packages/stats/bioc"

propagation/3.21/prepareRepos-data-experiment.config

@@ -7,7 +7,7 @@ MEAT0_PATH="/home/biocbuild/bbs-3.21-data-experiment/MEAT0"
 # Manuals were already copied from
 # /home/biocbuild/public_html/BBS/3.21/data-experiment/OUTGOING/manuals
 # by updateReposPkgs-data-experiment.sh so don't need to be extracted.
-EXTRACT_MANUALS="FALSE"
+EXTRACT_MANUALS="TRUE"
 REPOS_ROOT="$VIEW_ROOT/data/experiment"
 REPOS_URL="$VIEW_URL/data/experiment"
 STATS_URL=""

propagation/3.21/updateReposPkgs-bioc.sh

@@ -1,5 +1,4 @@
 #!/bin/bash
-
 set -e  # exit immediately if a simple command returns a non-zero status
 
 cd "$HOME/propagation/3.21"
@@ -58,20 +57,5 @@ update_repo "$MAC_BIG_SUR_arm64_CONTRIB" "mac.binary.big-sur-arm64" "tgz"
 
 echo ""
 
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-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
-	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
-done
-
 echo "DONE."
 exit 0

propagation/3.21/updateReposPkgs-data-annotation.sh

@@ -42,22 +42,5 @@ echo ""
 echo "Updating $BIOC_VERSION/data/annotation repo with source packages..."
 update_repo "$SRC_CONTRIB" "source" "tar.gz"
 
-echo ""
-
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-MANUALS_DEST="$REPOS_ROOT/manuals"
-MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
-echo "Updating $BIOC_VERSION/data/annotation repo with reference manuals..."
-for i in `ls $MANUALS_SRC`; 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
-done
-
 echo "DONE."
 exit 0

propagation/3.21/updateReposPkgs-data-experiment.sh

@@ -42,22 +42,5 @@ echo ""
 echo "Updating $BIOC_VERSION/data/experiment repo with source packages..."
 update_repo "$SRC_CONTRIB" "source" "tar.gz"
 
-echo ""
-
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-MANUALS_DEST="$REPOS_ROOT/manuals"
-MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
-echo "Updating $BIOC_VERSION/data/experiment repo with reference manuals..."
-for i in `ls $MANUALS_SRC`; 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
-done
-
 echo "DONE."
 exit 0

propagation/3.22/prepareRepos-bioc.config

@@ -7,7 +7,7 @@ MEAT0_PATH="/home/biocbuild/bbs-3.22-bioc/MEAT0"
 # Manuals were already copied from
 # /home/biocbuild/public_html/BBS/3.22/bioc/OUTGOING/manuals
 # by updateReposPkgs-bioc.sh so don't need to be extracted.
-EXTRACT_MANUALS="FALSE"
+EXTRACT_MANUALS="TRUE"
 REPOS_ROOT="$VIEW_ROOT/bioc"
 REPOS_URL="$VIEW_URL/bioc"
 STATS_URL="https://bioconductor.org/packages/stats/bioc"

propagation/3.22/prepareRepos-data-experiment.config

@@ -7,7 +7,7 @@ MEAT0_PATH="/home/biocbuild/bbs-3.22-data-experiment/MEAT0"
 # Manuals were already copied from
 # /home/biocbuild/public_html/BBS/3.22/data-experiment/OUTGOING/manuals
 # by updateReposPkgs-data-experiment.sh so don't need to be extracted.
-EXTRACT_MANUALS="FALSE"
+EXTRACT_MANUALS="TRUE"
 REPOS_ROOT="$VIEW_ROOT/data/experiment"
 REPOS_URL="$VIEW_URL/data/experiment"
 STATS_URL=""

propagation/3.22/updateReposPkgs-bioc.sh

@@ -58,20 +58,5 @@ update_repo "$MAC_BIG_SUR_arm64_CONTRIB" "mac.binary.big-sur-arm64" "tgz"
 
 echo ""
 
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-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
-	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
-done
-
 echo "DONE."
 exit 0

propagation/3.22/updateReposPkgs-data-annotation.sh

@@ -42,22 +42,5 @@ echo ""
 echo "Updating $BIOC_VERSION/data/annotation repo with source packages..."
 update_repo "$SRC_CONTRIB" "source" "tar.gz"
 
-echo ""
-
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-MANUALS_DEST="$REPOS_ROOT/manuals"
-MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
-echo "Updating $BIOC_VERSION/data/annotation repo with reference manuals..."
-for i in `ls $MANUALS_SRC`; 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
-done
-
 echo "DONE."
 exit 0

propagation/3.22/updateReposPkgs-data-experiment.sh

@@ -42,22 +42,5 @@ echo ""
 echo "Updating $BIOC_VERSION/data/experiment repo with source packages..."
 update_repo "$SRC_CONTRIB" "source" "tar.gz"
 
-echo ""
-
-## FIXME: Why aren't manuals propagated based on the same criteria as source
-## packages? Looks like the former are propagated based on their timestamps
-## only (see below) while for source packages we use the more refined
-## propagation criteria. This can easily lead to situations where the manual
-## available on a package landing page doesn't match the version of the
-## source package. Not good!
-MANUALS_DEST="$REPOS_ROOT/manuals"
-MANUALS_SRC="$BBS_OUTGOING_DIR/manuals"
-echo "Updating $BIOC_VERSION/data/experiment repo with reference manuals..."
-for i in `ls $MANUALS_SRC`; 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
-done
-
 echo "DONE."
 exit 0