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[gnuastro-commits] master 521daec6: New installed scripts: man-pages add
From: |
Mohammad Akhlaghi |
Subject: |
[gnuastro-commits] master 521daec6: New installed scripts: man-pages added, lintian warnings addressed |
Date: |
Thu, 17 Mar 2022 19:15:59 -0400 (EDT) |
branch: master
commit 521daec6857305c68434fe6a7d4147a14bf21556
Author: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Commit: Mohammad Akhlaghi <mohammad@akhlaghi.org>
New installed scripts: man-pages added, lintian warnings addressed
Until now, no man-page was constructed for the newly added installed
scripts since version 0.16! There were also a few other Bash-specific
features in some of the scripts (like using 'type' and the definition of a
function (where the parenthesis should touch). All of these were found
while test-packaging Gnuastro in Debian prior to the version 0.17 release:
Debian's Lintian found and reported these issues.
With this commit, all the issues have been addressed: the rules to create
man-pages for the new installed scripts have been added, and the non-POSIX
issues were also fixed in the scripts.
This commit includes the following two minor corrections also:
- I noticed a compiler warning for un-initialized variables in Table
during the build on Debian. So they are corrected.
- The new Lintian is warning long lines and in particular three very long
lines (sentences!) in the book (which included a multi-line
footnote). Those long lines have therefore been broken into smaller
sentances. This helps remove this warning, and also makes the text
easier to read.
- The word 'function' in the error message of a shell function caused a
false warning by Lintian, so they have been removed.
---
bin/script/fits-view.in | 2 +-
bin/script/psf-scale-factor.in | 6 ++++--
bin/script/psf-stamp.in | 7 ++++---
bin/table/arithmetic.c | 2 +-
doc/Makefile.am | 35 ++++++++++++++++++++++++++++++++++-
doc/gnuastro.texi | 15 ++++++++++++---
6 files changed, 56 insertions(+), 11 deletions(-)
diff --git a/bin/script/fits-view.in b/bin/script/fits-view.in
index b7bc0e4e..43ca333e 100755
--- a/bin/script/fits-view.in
+++ b/bin/script/fits-view.in
@@ -280,7 +280,7 @@ fi
# won't set this option at all and let DS9 use its default size.
ds9geoopt=""
if [ x"$ds9geometry" = x ]; then
- if type xrandr > /dev/null 2>/dev/null; then
+ if command -v xrandr > /dev/null 2>/dev/null; then
# The line with a '*' is the resolution of the used screen. We will
# then extract the height (second value) and set DS9's geometry
diff --git a/bin/script/psf-scale-factor.in b/bin/script/psf-scale-factor.in
index fc730e62..ea41307f 100644
--- a/bin/script/psf-scale-factor.in
+++ b/bin/script/psf-scale-factor.in
@@ -438,7 +438,8 @@ astcrop $inputs --hdu=$hdu --mode=img \
#
# Given a certain extension ('CLUMPS' or 'OBJECTS'), find the respective
# label.
-find_central_label () {
+find_central_label() {
+
# Input arguments
hdu=$1
@@ -447,8 +448,9 @@ find_central_label () {
CLUMPS) labname=clump;;
OBJECTS) labname=object;;
*) cat <<EOF
-$scriptname: ERROR: a bug! Please contact us at bug-gnuastro@gnu.org to fix
the problem. The first argument to 'find_central_label' function is not
'CLUMPS' or 'OBJECTS'
+$scriptname: ERROR: a bug! Please contact us at bug-gnuastro@gnu.org to fix
the problem. The first argument to 'find_central_label' is not 'CLUMPS' or
'OBJECTS'
EOF
+ exit 1
;;
esac
diff --git a/bin/script/psf-stamp.in b/bin/script/psf-stamp.in
index 55002d12..e0146e48 100644
--- a/bin/script/psf-stamp.in
+++ b/bin/script/psf-stamp.in
@@ -440,7 +440,8 @@ astcrop $inputs --hdu=$hdu --mode=img \
#
# Given a certain extension ('CLUMPS' or 'OBJECTS'), find the respective
# label.
-find_central_label () {
+find_central_label() {
+
# Input arguments
hdu=$1
@@ -449,9 +450,9 @@ find_central_label () {
CLUMPS) labname=clump;;
OBJECTS) labname=object;;
*) cat <<EOF
-$scriptname: ERROR: a bug! Please contact us at bug-gnuastro@gnu.org to fix
the problem. The first argument to 'find_central_label' function is not
'CLUMPS' or 'OBJECTS'
+$scriptname: ERROR: a bug! Please contact us at bug-gnuastro@gnu.org to fix
the problem. The first argument to 'find_central_label' is not 'CLUMPS' or
'OBJECTS'
EOF
- ;;
+ exit 1;;
esac
# Crop the labeled image.
diff --git a/bin/table/arithmetic.c b/bin/table/arithmetic.c
index f271c779..e2af7753 100644
--- a/bin/table/arithmetic.c
+++ b/bin/table/arithmetic.c
@@ -654,7 +654,7 @@ arithmetic_datetosec(struct tableparams *p, gal_data_t
**stack,
gal_data_t *out;
double subsec=NAN;
char *subsecstr=NULL;
- char *unit, *name, *comment;
+ char *unit=NULL, *name=NULL, *comment=NULL;
/* Input dataset. */
gal_data_t *in=arithmetic_stack_pop(stack, operator, NULL);
diff --git a/doc/Makefile.am b/doc/Makefile.am
index b73f0f41..9617f547 100644
--- a/doc/Makefile.am
+++ b/doc/Makefile.am
@@ -153,7 +153,10 @@ dist_man_MANS = $(MAYBE_ARITHMETIC_MAN)
$(MAYBE_BUILDPROG_MAN) \
$(MAYBE_MKCATALOG_MAN) $(MAYBE_MKNOISE_MAN) $(MAYBE_MKPROF_MAN) \
$(MAYBE_NOISECHISEL_MAN) $(MAYBE_QUERY_MAN) $(MAYBE_SEGMENT_MAN) \
$(MAYBE_STATISTICS_MAN) $(MAYBE_TABLE_MAN) $(MAYBE_WARP_MAN) \
- man/astscript-ds9-region.1 man/astscript-radial-profile.1 \
+ man/astscript-ds9-region.1 man/astscript-fits-view.1 \
+ man/astscript-psf-scale-factor.1 man/astscript-psf-select-stars.1 \
+ man/astscript-psf-stamp.1 man/astscript-psf-subtract.1 \
+ man/astscript-psf-unite.1 man/astscript-radial-profile.1 \
man/astscript-sort-by-night.1
@@ -255,6 +258,36 @@ man/astscript-ds9-region.1:
$(top_srcdir)/bin/script/ds9-region.in \
$(MAYBE_HELP2MAN) -n "Create an SAO DS9 region file from a table" \
--libtool $(toputildir)/script/astscript-ds9-region
+man/astscript-fits-view.1: $(top_srcdir)/bin/script/fits-view.in \
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "View FITS images in DS9 and tables in TOPCAT
based on contents" \
+ --libtool $(toputildir)/script/astscript-fits-view
+
+man/astscript-psf-scale-factor.1: $(top_srcdir)/bin/script/psf-scale-factor.in
\
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "Find factor to scale PSF to a given star in an
image" \
+ --libtool
$(toputildir)/script/astscript-psf-scale-factor
+
+man/astscript-psf-select-stars.1: $(top_srcdir)/bin/script/psf-select-stars.in
\
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "Select good stars for constructing the PSF" \
+ --libtool
$(toputildir)/script/astscript-psf-select-stars
+
+man/astscript-psf-stamp.1: $(top_srcdir)/bin/script/psf-stamp.in \
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "Make normalized stamp of star with background
objects masked" \
+ --libtool $(toputildir)/script/astscript-psf-stamp
+
+man/astscript-psf-subtract.1: $(top_srcdir)/bin/script/psf-subtract.in \
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "Subtract a given PSF model from the image of
star" \
+ --libtool $(toputildir)/script/astscript-psf-subtract
+
+man/astscript-psf-unite.1: $(top_srcdir)/bin/script/psf-unite.in \
+ $(ALLMANSDEP)
+ $(MAYBE_HELP2MAN) -n "Unite the outer and inner regions of the PSF into
one" \
+ --libtool $(toputildir)/script/astscript-psf-unite
+
man/astscript-radial-profile.1: $(top_srcdir)/bin/script/radial-profile.in \
$(ALLMANSDEP)
$(MAYBE_HELP2MAN) -n "Create a radial profile of an object in an image"
\
diff --git a/doc/gnuastro.texi b/doc/gnuastro.texi
index 08a6f580..f635572d 100644
--- a/doc/gnuastro.texi
+++ b/doc/gnuastro.texi
@@ -4680,7 +4680,9 @@ $ ds9 -mecube r_detected.fits -zscale -cmap sls -zoom to
fit
@end example
When looking at the raw input image (which is very ``shallow'': less than a
minute exposure!), you don't see anything so far out of the galaxy.
-You might just think to yourself that ``this is all noise, I have just dug too
deep and I'm following systematics''! If you feel like this, have a look at the
deep images of this system in @url{https://arxiv.org/abs/1501.04599, Watkins et
al. [2015]}, or a 12 hour deep image of this system (with a 12-inch telescope):
@url{https://i.redd.it/jfqgpqg0hfk11.jpg}@footnote{The image is taken from this
Reddit discussion:
@url{https://www.reddit.com/r/Astronomy/comments/9d6x0q/12_hours_of_exposu [...]
+You might just think to yourself that ``this is all noise, I have just dug too
deep and I'm following systematics''!
+If you feel like this, have a look at the deep images of this system in
@url{https://arxiv.org/abs/1501.04599, Watkins et al. [2015]}, or a 12 hour
deep image of this system (with a 12-inch telescope):
+@url{https://i.redd.it/jfqgpqg0hfk11.jpg}@footnote{The image is taken from
this Reddit discussion:
@url{https://www.reddit.com/r/Astronomy/comments/9d6x0q/12_hours_of_exposure_on_the_whirlpool_galaxy/}}.
In these deeper images you clearly see how the outer edges of the M51 group
follow this exact structure, below in @ref{Achieved surface brightness level},
we'll measure the exact level.
As the gradient in the @code{SKY} extension shows, and the deep images cited
above confirm, the galaxy's signal extends even beyond this.
@@ -7704,7 +7706,10 @@ $ ./configure LDFLAGS=-L/home/name/.local/lib
\
It can be annoying/buggy to do this when configuring every software that
depends on such libraries.
Hence, you can define these two variables in the most relevant startup file
(discussed above).
-The convention on using these variables doesn't include a colon to separate
values (as @command{PATH}-like variables do), they use white space characters
and each value is prefixed with a compiler option@footnote{These variables are
ultimately used as options while building the programs, so every value has be
an option name followed be a value as discussed in @ref{Options}.}: note the
@option{-L} and @option{-I} above (see @ref{Options}), for @option{-I} see
@ref{Headers}, and for @optio [...]
+The convention on using these variables doesn't include a colon to separate
values (as @command{PATH}-like variables do).
+They use white space characters and each value is prefixed with a compiler
option@footnote{These variables are ultimately used as options while building
the programs.
+Therefore every value has be an option name followed be a value as discussed
in @ref{Options}.}.
+Note the @option{-L} and @option{-I} above (see @ref{Options}), for
@option{-I} see @ref{Headers}, and for @option{-L}, see @ref{Linking}.
Therefore we have to keep the value in double quotation signs to keep the
white space characters and adding the following two lines to the startup file
of choice:
@example
@@ -7721,7 +7726,11 @@ To use programs that depend on these libraries, you need
to add @file{~/.local/l
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/name/.local/lib
@end example
-If you also want to access the Info (see @ref{Info}) and man pages (see
@ref{Man pages}) documentations add @file{~/.local/share/info} and
@file{~/.local/share/man} to your @command{INFOPATH}@footnote{Info has the
following convention: ``If the value of @command{INFOPATH} ends with a colon
[or it isn't defined] ..., the initial list of directories is constructed by
appending the build-time default to the value of @command{INFOPATH}.'' So when
installing in a non-standard directory and if [...]
+If you also want to access the Info (see @ref{Info}) and man pages (see
@ref{Man pages}) documentations add @file{~/.local/share/info} and
@file{~/.local/share/man} to your @command{INFOPATH}@footnote{Info has the
following convention: ``If the value of @command{INFOPATH} ends with a colon
[or it isn't defined] ..., the initial list of directories is constructed by
appending the build-time default to the value of @command{INFOPATH}.''
+So when installing in a non-standard directory and if @command{INFOPATH} was
not initially defined, add a colon to the end of @command{INFOPATH} as shown
below.
+Otherwise Info will not be able to find system-wide installed documentation:
+@*@command{echo 'export INFOPATH=$INFOPATH:/home/name/.local/share/info:' >>
~/.bashrc}@*
+Note that this is only an internal convention of Info: do not use it for other
@command{*PATH} variables.} and @command{MANPATH} environment variables
respectively.
@cindex Search directory order
@cindex Order in search directory
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