diff --git a/BBS-make-OUTGOING.py b/BBS-make-OUTGOING.py index 8bad53a7..9e2028a5 100755 --- a/BBS-make-OUTGOING.py +++ b/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 diff --git a/propagation/3.21/prepareRepos-bioc.config b/propagation/3.21/prepareRepos-bioc.config index 790c2fca..c5be9a9a 100644 --- a/propagation/3.21/prepareRepos-bioc.config +++ b/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" diff --git a/propagation/3.21/prepareRepos-data-experiment.config b/propagation/3.21/prepareRepos-data-experiment.config index ce33caa8..52ad3b47 100644 --- a/propagation/3.21/prepareRepos-data-experiment.config +++ b/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="" diff --git a/propagation/3.21/updateReposPkgs-bioc.sh b/propagation/3.21/updateReposPkgs-bioc.sh index 63648e99..daee2e8f 100755 --- a/propagation/3.21/updateReposPkgs-bioc.sh +++ b/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 diff --git a/propagation/3.21/updateReposPkgs-data-annotation.sh b/propagation/3.21/updateReposPkgs-data-annotation.sh index 6a3fffdf..5c6d23f6 100755 --- a/propagation/3.21/updateReposPkgs-data-annotation.sh +++ b/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 diff --git a/propagation/3.21/updateReposPkgs-data-experiment.sh b/propagation/3.21/updateReposPkgs-data-experiment.sh index 8693ff9f..fe6aaf5a 100755 --- a/propagation/3.21/updateReposPkgs-data-experiment.sh +++ b/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 diff --git a/propagation/3.22/prepareRepos-bioc.config b/propagation/3.22/prepareRepos-bioc.config index 79c50c0b..389684db 100644 --- a/propagation/3.22/prepareRepos-bioc.config +++ b/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" diff --git a/propagation/3.22/prepareRepos-data-experiment.config b/propagation/3.22/prepareRepos-data-experiment.config index 55b17afe..f0b66899 100644 --- a/propagation/3.22/prepareRepos-data-experiment.config +++ b/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="" diff --git a/propagation/3.22/updateReposPkgs-bioc.sh b/propagation/3.22/updateReposPkgs-bioc.sh index ba4aeccd..fc36ff0a 100755 --- a/propagation/3.22/updateReposPkgs-bioc.sh +++ b/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 diff --git a/propagation/3.22/updateReposPkgs-data-annotation.sh b/propagation/3.22/updateReposPkgs-data-annotation.sh index da8d1316..96776e8a 100755 --- a/propagation/3.22/updateReposPkgs-data-annotation.sh +++ b/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 diff --git a/propagation/3.22/updateReposPkgs-data-experiment.sh b/propagation/3.22/updateReposPkgs-data-experiment.sh index ffaa53ab..54417fb9 100755 --- a/propagation/3.22/updateReposPkgs-data-experiment.sh +++ b/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