Imported recent work in Maneage, minor conflicts fixed

A few minor conflicts came up that were easily fixed.

7 files changed, 132 insertions, 4 deletions

diff --git a/reproduce/analysis/config/gnuastro/astbuildprog.conf b/reproduce/analysis/config/gnuastro/astbuildprog.conf
new file mode 100644
index 0000000..7adb4d1
--- /dev/null
+++ b/reproduce/analysis/config/gnuastro/astbuildprog.conf
@@ -0,0 +1,16 @@
+# BuildProgram's configuration file depends on the build and is installed
+# along with the rest of Gnuastro. So we'll set any specific configuration
+# we want here, then import those.
+#
+# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice and
+# this notice are preserved.  This file is offered as-is, without any
+# warranty.
+
+# To keep the program's compiled excutable file, comment this line.
+deletecompiled 1
+
+# Import the built configuration file
+config .local/etc/astbuildprog.conf
\ No newline at end of file
diff --git a/reproduce/analysis/config/gnuastro/astconvertt.conf b/reproduce/analysis/config/gnuastro/astconvertt.conf
new file mode 100644
index 0000000..770ac39
--- /dev/null
+++ b/reproduce/analysis/config/gnuastro/astconvertt.conf
@@ -0,0 +1,33 @@
+# Default parameters (System) for ConvertType.
+# ConvertType is part of GNU Astronomy Utitlies.
+#
+# Use the long option name of each parameter followed by a value. The name
+# and value should be separated by atleast one white-space character (for
+# example ` '[space], or tab). Lines starting with `#' are ignored.
+#
+# For more information, please run these commands:
+#
+#  $ astconvertt --help                  # Full list of options, short doc.
+#  $ astconvertt -P                      # Print all options and used values.
+#  $ info astconvertt                    # All options and input/output.
+#  $ info gnuastro "Configuration files" # How to use configuration files.
+#
+# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice and
+# this notice are preserved.  This file is offered as-is, without any
+# warranty.
+
+# Input:
+
+# Output:
+ quality              100
+ widthincm            10.0
+ borderwidth          1
+ output               jpg
+
+# Flux:
+ invert               0
+
+# Common options
diff --git a/reproduce/analysis/config/gnuastro/aststatistics.conf b/reproduce/analysis/config/gnuastro/aststatistics.conf
new file mode 100644
index 0000000..90f985d
--- /dev/null
+++ b/reproduce/analysis/config/gnuastro/aststatistics.conf
@@ -0,0 +1,36 @@
+# Default parameters (System) for Statistics.
+# Statistics is part of GNU Astronomy Utitlies.
+#
+# Use the long option name of each parameter followed by a value. The name
+# and value should be separated by atleast one white-space character (for
+# example ` '[space], or tab). Lines starting with `#' are ignored.
+#
+# For more information, please run these commands:
+#
+#  $ aststatistics --help                # Full list of options, short doc.
+#  $ aststatistics -P                    # Print all options and used values.
+#  $ info aststatistics                  # All options and input/output.
+#  $ info gnuastro "Configuration files" # How to use configuration files.
+#
+# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice and
+# this notice are preserved.  This file is offered as-is, without any
+# warranty.
+
+# Input image:
+
+# Sky and its STD settings
+ khdu                 1
+ meanmedqdiff     0.005
+ outliersigma        10
+ outliersclip     3,0.2
+ smoothwidth          3
+ sclipparams      3,0.1
+
+# Histogram and CFP settings
+ numasciibins        70
+ asciiheight         10
+ numbins            100
+ mirrordist         1.5
diff --git a/reproduce/analysis/config/gnuastro/gnuastro.conf b/reproduce/analysis/config/gnuastro/gnuastro.conf
new file mode 100644
index 0000000..82cb100
--- /dev/null
+++ b/reproduce/analysis/config/gnuastro/gnuastro.conf
@@ -0,0 +1,43 @@
+# Default values for the common options to all the programs in GNU
+# Astronomy Utitlies.
+#
+# IMPORTANT NOTE: The `lastconfig' option is very important in a
+# reproducible environment. Because we don't want any of Gnuastro's
+# programs to go into an un-controlled environment (user or system wide
+# configuration files).
+#
+# The rest of this configuration file is taken from the default Gnuastro
+# configuration from its source (`bin/gnuastro.conf').
+#
+# Copyright (C) 2018-2020 Mohammad Akhlaghi <mohammad@akhlaghi.org>
+#
+# Copying and distribution of this file, with or without modification, are
+# permitted in any medium without royalty provided the copyright notice and
+# this notice are preserved.  This file is offered as-is, without any
+# warranty.
+
+# Local project settings (`config' has to be before `lastconfig').
+ config           .gnuastro/gnuastro-local.conf
+ lastconfig       1
+
+# Input:
+ hdu              1
+ ignorecase       1
+ searchin         name
+ stdintimeout     100000
+
+# Tessellation
+ tilesize         30,30
+ numchannels      1,1
+ remainderfrac    0.1
+ workoverch       0
+ interpmetric     radial
+ interpnumngb     9
+ interponlyblank  0
+
+# Output:
+ tableformat      fits-binary
+
+# Operating mode
+ quietmmap        0
+ minmapsize       2000000000
diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk
index 2736f2a..c804aaf 100644
--- a/reproduce/analysis/make/initialize.mk
+++ b/reproduce/analysis/make/initialize.mk
@@ -313,8 +313,8 @@ $(packagecontents): paper.pdf | $(texdir)
         # have this machine's local settings and are irrelevant for anyone
         # else.
 	rm -rf $$dir/tex/build/build*
-	rm $$dir/reproduce/software/config/installation/LOCAL.conf
-	rm $$dir/reproduce/software/config/gnuastro/gnuastro-local.conf
+	rm $$dir/reproduce/software/config/LOCAL.conf
+	rm $$dir/reproduce/analysis/config/gnuastro/gnuastro-local.conf
 
         # When submitting to places like arXiv, they will just run LaTeX
         # once and won't run `biber'. So we need to also keep the `.bbl'
diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk
index 30d537a..5461f71 100644
--- a/reproduce/analysis/make/top-make.mk
+++ b/reproduce/analysis/make/top-make.mk
@@ -21,7 +21,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/LOCAL.conf
 
 
 
diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk
index 1778c6b..be7482c 100644
--- a/reproduce/analysis/make/top-prepare.mk
+++ b/reproduce/analysis/make/top-prepare.mk
@@ -25,7 +25,7 @@
 
 # Load the local configuration (created after running
 # `./project configure').
-include reproduce/software/config/installation/LOCAL.conf
+include reproduce/software/config/LOCAL.conf