Aaron M. Ucko pushed to branch master at Debian Med / ncbi-entrez-direct
Commits: 94ca7b92 by Aaron M. Ucko at 2020-06-28T21:00:44-04:00 Start work on ncbi-entrez-direct 13.7.20200615+dfsg-2. - - - - - 146d078d by Aaron M. Ucko at 2020-06-28T21:08:52-04:00 Install ftp-cp, ftp-ls, nquire, and transmute as simple wrappers. debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple wrappers for edirect (with no .pl suffix) now that they're no longer independent Perl scripts (as of 12.3.20191024[+ds]), fixing a regression caught by autopkgtest. - - - - - a124a1f4 by Aaron M. Ucko at 2020-06-28T21:11:04-04:00 d/tests/run-unit-test: Correct invocation of filter-stop-words filter-stop-words ignores its arguments and reads from standard input. - - - - - 36914b99 by Aaron M. Ucko at 2020-06-28T21:11:51-04:00 Finalize ncbi-entrez-direct 13.7.20200615+dfsg-2 for unstable. - - - - - 3 changed files: - debian/changelog - debian/rules - debian/tests/run-unit-test Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,14 @@ +ncbi-entrez-direct (13.7.20200615+dfsg-2) unstable; urgency=medium + + * debian/rules: Install ftp-cp, ftp-ls, nquire, and transmute as simple + wrappers for edirect (with no .pl suffix) now that they're no longer + independent Perl scripts (as of 12.3.20191024[+ds]), fixing a + regression caught by autopkgtest. + * debian/tests/run-unit-test: Correct invocation of filter-stop-words + (which ignores its arguments and reads from standard input). + + -- Aaron M. Ucko <[email protected]> Sun, 28 Jun 2020 21:11:51 -0400 + ncbi-entrez-direct (13.7.20200615+dfsg-1) unstable; urgency=medium * New upstream release. ===================================== debian/rules ===================================== @@ -15,7 +15,8 @@ LIB_DIR = /usr/lib/$(PACKAGE) MODES = address blast citmatch contact filter link notify post proxy search \ spell STD_WRAPPERS = $(MODES:%=bin/e%) -WRAPPERS = $(STD_WRAPPERS) bin/esummary +OTHER_WRAPPERS = esummary ftp-cp ftp-ls nquire transmute +WRAPPERS = $(STD_WRAPPERS) $(OTHER_WRAPPERS:%=bin/%) AS_IS_SCRIPTS = amino-acid-composition archive-pubmed between-two-genes \ enquire entrez-phrase-search esample exclude-uid-lists \ expand-current fetch-extras fetch-pubmed filter-stop-words \ @@ -26,8 +27,7 @@ BASH_SCRIPTS = index-extras index-themes BIN_BASH_SCRIPTS = $(BASH_SCRIPTS:%=bin/%) DL_SCRIPTS = download-ncbi-data download-pubmed download-sequence BIN_DL_SCRIPTS = $(DL_SCRIPTS:%=bin/%) -PERL_SCRIPTS = edirutil ftp-cp ftp-ls gbf2xml nquire run-ncbi-converter \ - transmute +PERL_SCRIPTS = edirutil gbf2xml run-ncbi-converter BIN_PERL_SCRIPTS = $(PERL_SCRIPTS:%=bin/%) # Only bt-link and xplore need this treatment at present, # but list all bt-* scripts to be safe. @@ -82,6 +82,26 @@ bin/esummary: bin/edirect echo 'exec /usr/bin/edirect -fetch -format docsum "$$@"' >> $@ chmod +x $@ +bin/ftp-cp: bin/edirect + echo '#!/bin/sh' > $@ + echo 'exec /usr/bin/edirect -ftpcp "$$@"' >> $@ + chmod +x $@ + +bin/ftp-ls: bin/edirect + echo '#!/bin/sh' > $@ + echo 'exec /usr/bin/edirect -ftpls "$$@"' >> $@ + chmod +x $@ + +bin/nquire: bin/edirect + echo '#!/bin/sh' > $@ + echo 'exec /usr/bin/edirect -nquir "$$@"' >> $@ + chmod +x $@ + +bin/transmute: bin/edirect + echo '#!/bin/sh' > $@ + echo 'exec /usr/bin/edirect -tmute "$$@"' >> $@ + chmod +x $@ + $(BIN_BASH_SCRIPTS): bin/%: % mkdir -p bin sed -e '$(FIX_BASH_SHEBANG)' $< > $@ ===================================== debian/tests/run-unit-test ===================================== @@ -38,7 +38,7 @@ echo -e "\e[92m\e[1mPassed\e[0m" echo echo -e "\e[93m\e[1mTest 4: filter-stop-words\e[0m" -filter-stop-words stopwords +filter-stop-words < stopwords echo -e "\e[92m\e[1mPassed\e[0m" echo echo -e "\e[93m\e[1mTest 5: gbf2xml\e[0m" View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056 -- View it on GitLab: https://salsa.debian.org/med-team/ncbi-entrez-direct/-/compare/14173f9c25d4b41220fb0566b89266390037131c...36914b997fe7b6f71dbe208a0f2e29e2ca47f056 You're receiving this email because of your account on salsa.debian.org.
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