Remove unused contrib/, libdivsufsort/, and .travis.yml

.gitignore

@@ -18,38 +18,14 @@ src/impl*/*_utest
 src/impl*/*_benchmark
 documentation/userguide/copyright.tex
 documentation/userguide/titlepage.tex
+documentation/userguide/titlepage_daemon.tex
 documentation/man/*.man
-libdivsufsort/divsufsort.h
-libdivsufsort/libdivsufsort.a
 src/libhmmer.a
 src/p7_config.h
-profmark/create-profmark
-profmark/rocplot
-src/alimask
-src/hmmalign
-src/hmmbuild
-src/hmmc2
-src/hmmconvert
-src/hmmemit
-src/hmmerfm-exactmatch
-src/hmmfetch
-src/hmmlogo
-src/hmmpgmd
-src/hmmpgmd_shard
-src/hmmpress
-src/hmmscan
-src/hmmsearch
-src/hmmsim
-src/hmmstat
 src/itest_brute
-src/jackhmmer
-src/makehmmerdb
-src/nhmmer
-src/nhmmscan
-src/phmmer
-src/frahmmbuild
-src/frahmmconvert
-src/frahmmemit
-src/frahmmer
-src/frahmmfetch
-src/frahmmstat
+src/bathalign
+src/bathbuild
+src/bathconvert
+src/bathfetch
+src/bathsearch
+src/bathstat

Makefile.in

@@ -26,8 +26,6 @@ SHELL          = /bin/sh
 # location of easel
 ESLDIR         = @HMMER_ESLDIR@
 
-# location of libdivsufsort for suffix array creation
-SADIR          = @HMMER_SADIR@
 
 
 # Package information
@@ -88,15 +86,13 @@ endif
 #
 all: 
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} all
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src           ${QUIET_SUBDIR1} all
 #	${QUIET_SUBDIR0}profmark      ${QUIET_SUBDIR1} all
 
 # dev: compile all executables, including drivers.
 #
 dev: 
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} dev
-	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} dev
 #	${QUIET_SUBDIR0}profmark   ${QUIET_SUBDIR1} dev
 
@@ -111,7 +107,6 @@ tests:
 check:
 	@command -v python3 >/dev/null 2>&1 || { echo >&2 "python3 is required for 'make check', but is not in your PATH. Aborting."; exit 1; }
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} tests
-	${QUIET_SUBDIR0}${SADIR}   ${QUIET_SUBDIR1} all	
 	${QUIET_SUBDIR0}src        ${QUIET_SUBDIR1} tests
 	${QUIET_SUBDIR0}${ESLDIR}  ${QUIET_SUBDIR1} check
 	${QUIET_SUBDIR0}testsuite  ${QUIET_SUBDIR1} check
@@ -157,7 +152,6 @@ clean:
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} clean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} clean
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} clean
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS TAGS.part gmon.out
 ifndef V
 	@echo '     ' CLEAN hmmer
@@ -171,7 +165,6 @@ distclean:
 	${QUIET_SUBDIR0}testsuite     ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}documentation ${QUIET_SUBDIR1} distclean
 	${QUIET_SUBDIR0}${ESLDIR}     ${QUIET_SUBDIR1} distclean
-	${QUIET_SUBDIR0}${SADIR}      ${QUIET_SUBDIR1} distclean
 	${QUIET}-rm -f config.log config.status
 	${QUIET}-rm -rf autom4te.cache
 	${QUIET}-rm -f *.o *~ Makefile.bak core TAGS TAGS.part gmon.out

configure.ac

@@ -120,7 +120,6 @@ BATH_VERSION="2.0"
 BATH_URL="https://github.com/TravisWheelerLab/BATH"
 
 HMMER_ESLDIR="easel"
-HMMER_SADIR="libdivsufsort"
 
 EASEL_DATE="Nov 2020"
 EASEL_COPYRIGHT="Copyright (C) 2020 Howard Hughes Medical Institute."
@@ -139,7 +138,6 @@ AC_SUBST(BATH_VERSION)
 AC_SUBST(BATH_URL)
 
 AC_SUBST(HMMER_ESLDIR)
-AC_SUBST(HMMER_SADIR)
 
 AC_SUBST(EASEL_DATE)
 AC_SUBST(EASEL_COPYRIGHT)
@@ -669,7 +667,6 @@ AC_CONFIG_FILES([ \
   documentation/man/Makefile                   \
   documentation/userguide/Makefile             \
   documentation/userguide/inclusions/Makefile  \
-  libdivsufsort/Makefile                       \
   ])
 
 # Easel Makefiles.
@@ -729,7 +726,6 @@ AC_CONFIG_FILES([ \
 AC_CONFIG_HEADERS([easel/decoy_config.h])   # Put this first to keep gnu 'autoheader' from overwriting a real config file.
 AC_CONFIG_HEADERS([src/p7_config.h])
 AC_CONFIG_HEADERS([easel/esl_config.h])
-AC_CONFIG_HEADERS([libdivsufsort/divsufsort.h])
 
 # the following incantation establishes a symlink of
 # src/impl_{whatever} to src/impl in the *build* directory.