lib/sh/util.sh: stderr_matches(): echo_vars @PIPESTATUS_ to assist debugging

bugfix: lib/sh/util.sh: stderr2stdout(): use piped_cmd to ignore SIGPIPE since the output of this will piped to another command

lib/sh/util.sh: setup_log_fd(): $log_fd: use 3 (stdlog) since other scripts are likely to use this for logging as well

fix: lib/sh/util.sh: setup_log_fd(): fd_set_default(): use $log_fd instead of repeating the value of it

lib/sh/util.sh: die(): log at higher log_level, since this is logging code

lib/sh/util.sh: highlight_log_msg(): log at higher log_level, since this is logging code

bugfix: lib/runscripts/util.run: $subdirs: adjusted log_level now that echo_vars is one log_level lower

bugfix: lib/sh/util.sh: stderr_matches(): only set benign_error=1 if the matched error occurred

lib/sh/util.sh: ignore_e(): also set benign_error=1

fix: lib/sh/util.sh: prep_try alias: removed inaccurate comment

bugfix: lib/sh/util.sh: stdout2fd(): moved after redir() which it depends on

fix: lib/sh/util.sh: command(): moved `|| die_e` to command__exec so it would be properly indented under the echoed command

lib/sh/util.sh: verbosity_compat(): log at higher log_level because it's logging code

lib/sh/util.sh: $benign_error: log at higher log_level because it's logging code

lib/runscripts/util.run: $wrap_fn: log at higher log_level because it's startup code

lib/sh/util.sh: $top_* vars, $is_outermost: log at higher log_level because it's startup code

lib/sh/util.sh: $top_script: echo_vars this like the other $top_* vars

lib/sh/util.sh: .(): log at higher log_level because it's startup code

lib/sh/util.sh: is_dot_script(): run with higher log_level since this is run at the beginning of the script

lib/sh/util.sh, runscripts/util.run: set_paths(): run with higher log_level to hide all the paths that are set at the beginning of the script

lib/sh/util.sh: added log++ stub

lib/sh/util.sh: added log_local stub

lib/sh/util.sh: added log() stub so internal commands can use it

fix: lib/sh/util.sh: echo_vars(): log at same log_level as echo_func so kw_params are displayed along with positional params

fix: lib/sh/util.sh: rel_path(): log this internal command at a higher log_level so it's normally hidden

fix: lib/sh/util.sh: log_msg!(): log split_lines at a higher log_level so it's normally hidden

bugfix: lib/sh/util.sh: stderr_matches(): `log_local; log++` should apply to just stdout_contains() and part of stderr2stdout() rather than all of stderr_matches()

lib/sh/util.sh: stderr_matches(): run at higher log_level because error-handling internals should not be logged by default

bugfix: lib/sh/db.sh: mysql_ctl(): need to ignore errors if not running

bugfix: lib/sh/util.sh: stderr_matches(): handle any error: only ignore_e if the error exit status was associated with the matched error message

bugfix: lib/sh/util.sh: stderr_matches(): handle any error: need force-exit with rethrow_exit() because caller's test of return status disables errexit

lib/sh/util.sh: added rethrow_exit(), which exits even where errexit is disabled

bugfix: lib/sh/db.sh: mysql_snapshot(): need to run `mysql_ctl start` even if there is an error

lib/sh/db.sh: mysql_snapshot(): $to: default to $from.bak

lib/sh/db.sh: added mysql_snapshot()

lib/sh/db.sh: added mysql_ctl()

lib/sh/db.sh: pg_cmd(): updated to use new sudo()

lib/runscripts/util.run: added sudo() override that uses $wrap_fn to support shell functions

fix: lib/runscripts/util.run: $wrap_fn: make it usable even if $top_script isn't world-executable

lib/sh/util.sh: sudo alias: use function instead so this can be overridden

lib/sh/util.sh: added is_intern()

lib/sh/util.sh: is_callable(): use just $1 because multiple args are not applicable

lib/sh/util.sh: added is_world_executable()

lib/sh/util.sh: added has_perms()

lib/sh/util.sh: esc_args(): renamed to just esc() because this can also be used on a single value

lib/sh/util.sh: added is_extern()

lib/sh/util.sh: added sudo alias to alias-expand command

lib/sh/db.sh: pg_cmd(): $as_root: use $sudo

lib/sh/util.sh: added $sudo

lib/sh/util.sh: added cp alias

lib/sh/db.sh: removed no longer used pg_as_root(), which was buggy anyway. use `as_root=1 ...` instead.

lib/sh/db.sh: mysql_ANSI: fixed comment

lib/sh/db.sh: pg_dump(): support dumping entire cluster, and cluster users

lib/sh/db.sh: pg_cmd(): added $as_root switch

lib/sh/db.sh pg_dump(), bin/pg_dump_vegbien: --format=plain: removed comment that this is the plain format, because this is now self-documenting

lib/sh/db.sh pg_dump(), bin/pg_dump_vegbien: --format: use the long form of the formats to make the code self-documenting

fix: lib/PostgreSQL-MySQL.csv: preserve schema assignments by translating `SET search_path` to `USE`

bugfix: lib/runscripts/import.run: all(): also need to propagate $rm to import()

bugfix: lib/sh/util.sh: local_array/export_array: do need -a because that it's an array is apparently not autodetected by the () on Mac

lib/sql_gen.py: map_expr(): documented that unlike bin/repl SQL identifier handling, this does simplify the resulting expression

lib/sql_gen.py: map_expr(): documented that this is a special case of bin/repl SQL identifier handling which does not handle entire source files

bin/repl, lib/sql_gen.py Expression transforming: documented that this can also be done in Postgres with expression substitution (wiki.vegpath.org/Postgres_queries#expression-substitution)

bugfix: lib/runscripts/table.run: table_make_install(): need to ignore skip_table() errexit

lib/sh/util.sh: import_vars: documented that vars already set will not be overwritten

fix: lib/common.Makefile: $(nice): use an increment of +10 instead of +5 because +5 still leaves the shell sluggish

lib/common.Makefile: added $(nice) and use it everywhere its definition is used

fix: lib/sql_io.py: put_table(): don't warn if can't create pkey, because this just indicates that a set-returning function was used. this should get rid of the last of the confusing benign warnings in the test output.

fix: lib/sql.py: flatten(): don't warn if can't create pkey, because this just indicates that a set-returning function was used

lib/sql.py: run_query_into() added add_pkey_warn param to support turning off "could not create unique index" warnings, which are sometimes benign (eg. when using set-returning functions with column-based import)

lib/sh/util.sh: removed end_try_subshell, which now does the same thing as end_try

fix: lib/sh/archives.sh: unzip(): support -p option, which pipes extracted data to stdout

added lib/runscripts/extract_header.run

fix: lib/sh/make.sh: direct the user to use begin_target instead of set_make_vars (set_make_vars is now used by begin_target)

fix: lib/runscripts/util.run: to_top_file(): handle $_remake properly, without requiring deferred_check_target_exists to set to_file()'s flags

bugfix: lib/sh/util.sh: die(): usage: documented that if msg uses $(...), save_e is needed

bugfix: lib/sh/util.sh: already_exists_msg(): need to save_e, because new $(mk_hint) call resets $?

lib/sh/util.sh: die(): always errexit even if $e = 0, because die always indicates an error

lib/sh/util.sh: added rethrow!(), which always errexits, even if $e = 0

lib/sh/util.sh: rethrow(): also work in situations where $e is not set

lib/sh/util.sh: rethrow: made it a function since there is now no need for it to be an alias

lib/sh/util.sh: rethrow: removed `test "$e" != 0` since errexit only does anything if $e != 0

lib/sh/util.sh: removed separate rethrow_exit*, rethrow_subshell*, since they now do the same thing as rethrow*

lib/sh/util.sh: rethrow*!: use new errexit, which works in functions and subshells

lib/sh/util.sh: added errexit(), used in place of (exit "$1") because a bug in bash prevents subshells from triggering errexit

lib/sh/util.sh: added bool!()

fix: lib/sh/util.sh: redir(): need to indent before invoking an external command (not just in command__exec(), but for all redir() calls)

lib/sh/make.sh: with_rm(): documented that it only works inside a runscript target that starts w/ begin_target

*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)

lib/sh/make.sh: self_make(): renamed to with_rm() for clarity, since this is used only to progagate $rm, and does not also invoke a command with the same name as the current function, as the name might suggest

lib/runscripts/util.run: support conventional main() method as well as `all` target

bugfix: lib/sh/sync.sh: don't unintentionally rsync-ignore explicitly-specified files

lib/sh/util.sh: filesystem: added is_*(), could_be_*()

lib/sh/util.sh: added contains_match()

lib/sh/util.sh: added ends_with()

bugfix: lib/common.Makefile: $(add*): need to wrap w/ $(wildcard) to prevent "targets don't exist" error, because svn 1.7 does not suppress this error even with --force

bugfix: lib/runscripts/table.run: schema/make calls: need to use `make schema` instead because old-style datasources don't have a top-level runscript (the absence of this identifies them as old-style so inputs/input.Makefile works correctly)

bugfix: lib/sh/util.sh: DON'T do `shopt -s lastpipe` because this causes a segfault on Linux in stderr_matches(). (it also isn't supported on Mac.) use @PIPESTATUS instead. note that we do not currently need lastpipe, since we use @PIPESTATUS (which actually provides more functionality for our purposes).

fix: lib/sh/util.sh: echo_func(): file/line #: display with regular color because the lighter color actually draws attention to rather than away from the faded text

lib/sh/util.sh: added plain()

bugfix: lib/sql_io.py: put_table(): is_literals: `return sql.value(cur): need to use sql.value_or_none() instead to support multi-row functions, such as _split() used in specimens data`