IMPORTANT: software config directly under reproduce/software/config

Until now the software configuration parameters were defined under the
`reproduce/software/config/installation/' directory. This was because the
configuration parameters of analysis software (for example Gnuastro's
configurations) were placed under there too. But this was terribly
confusing, because the run-time options of programs falls under the
"analysis" phase of the project.

With this commit, the Gnuastro configuration files have been moved under
the new `reproduce/analysis/config/gnuastro' directory and the software
configuration files are directly under `reproduce/software/config'. A clean
build was done with this change and it didn't crash, but it may cause
crashes in derived projects, so after merging with Maneage, please
re-configure your project to see if anything has been missed. Please let us
know if there is a problem.

11 files changed, 5 insertions, 133 deletions

diff --git a/reproduce/software/config/installation/LOCAL.conf.in b/reproduce/software/config/LOCAL.conf.in
index 0579218..0579218 100644
--- a/reproduce/software/config/installation/LOCAL.conf.in
+++ b/reproduce/software/config/LOCAL.conf.in
diff --git a/reproduce/software/config/installation/TARGETS.conf b/reproduce/software/config/TARGETS.conf
index d2d5e2c..84962f7 100644
--- a/reproduce/software/config/installation/TARGETS.conf
+++ b/reproduce/software/config/TARGETS.conf
@@ -18,7 +18,7 @@
 # All software that are currently available for installation can be seen in
 # the following file.
 #
-#     reproduce/software/config/installation/versions.conf
+#     reproduce/software/config/versions.conf
 #
 # Please add any software that you need for your project in the respective
 # part below (using its name in `versions.conf', but without the `-version'
diff --git a/reproduce/software/config/installation/checksums.conf b/reproduce/software/config/checksums.conf
index 7531749..37fe64d 100644
--- a/reproduce/software/config/installation/checksums.conf
+++ b/reproduce/software/config/checksums.conf
@@ -71,9 +71,9 @@ zlib-checksum = 73fd3fff4adeccd4894084c15ddac89890cd10ef105dd5e1835e1e9bbb6a49ff
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.conf' will be built as
-# part of a project. To specify a software there, just remove the
-# `-checksum' suffix from the list below.
+# `reproduce/software/config/TARGETS.conf' will be built as part of a
+# project. To specify a software there, just remove the `-checksum' suffix
+# from the list below.
 apachelog4cxx-checksum = aa59ce549c2c5cbeec031361dfce09cdfc3e62ee3bc9ecbc809507b7ec878c14409b98536b7d13c27690809c8e9d5ebafc3589c9fb5e4aecd5cc064943ae7d6b
 apr-checksum = daa140c83c7e2c45c3980d9dc81d34fa662bebd050653562c39572d0ddf2eaedb71767c518a59d77f59db9b32e00221ef48b9f72ec3666c4521dd511969f3706
 apr-util-checksum = 84da76e9b64da2de0996d4d6f3ab3f23db3724eb6352d218e0e8196bcc0b0a5d4fe791f41b4cc350ce3d04cce3bb3cf8bfb513d777d0cd030928368e6b55a536
diff --git a/reproduce/software/config/gnuastro/astbuildprog.conf b/reproduce/software/config/gnuastro/astbuildprog.conf
deleted file mode 100644
index 7adb4d1..0000000
--- a/reproduce/software/config/gnuastro/astbuildprog.conf
+++ /dev/null
@@ -1,16 +0,0 @@
-# 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/software/config/gnuastro/astconvertt.conf b/reproduce/software/config/gnuastro/astconvertt.conf
deleted file mode 100644
index 770ac39..0000000
--- a/reproduce/software/config/gnuastro/astconvertt.conf
+++ /dev/null
@@ -1,33 +0,0 @@
-# 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/software/config/gnuastro/aststatistics.conf b/reproduce/software/config/gnuastro/aststatistics.conf
deleted file mode 100644
index 90f985d..0000000
--- a/reproduce/software/config/gnuastro/aststatistics.conf
+++ /dev/null
@@ -1,36 +0,0 @@
-# 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/software/config/gnuastro/gnuastro.conf b/reproduce/software/config/gnuastro/gnuastro.conf
deleted file mode 100644
index 82cb100..0000000
--- a/reproduce/software/config/gnuastro/gnuastro.conf
+++ /dev/null
@@ -1,43 +0,0 @@
-# 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/software/config/installation/numpy-scipy.cfg b/reproduce/software/config/numpy-scipy.cfg
index 82cc1e1..82cc1e1 100644
--- a/reproduce/software/config/installation/numpy-scipy.cfg
+++ b/reproduce/software/config/numpy-scipy.cfg
diff --git a/reproduce/software/config/installation/texlive-packages.conf b/reproduce/software/config/texlive-packages.conf
index c53e170..c53e170 100644
--- a/reproduce/software/config/installation/texlive-packages.conf
+++ b/reproduce/software/config/texlive-packages.conf
diff --git a/reproduce/software/config/installation/texlive.conf b/reproduce/software/config/texlive.conf
index b5075c6..b5075c6 100644
--- a/reproduce/software/config/installation/texlive.conf
+++ b/reproduce/software/config/texlive.conf
diff --git a/reproduce/software/config/installation/versions.conf b/reproduce/software/config/versions.conf
index 39642d4..0c2cd0b 100644
--- a/reproduce/software/config/installation/versions.conf
+++ b/reproduce/software/config/versions.conf
@@ -69,7 +69,7 @@ zlib-version = 1.2.11
 # ------------------------------------------
 #
 # These are programs and libraries that are optional, The ones in
-# `reproduce/software/config/installation/TARGETS.conf' will be built as
+# `reproduce/software/config/TARGETS.conf' will be built as
 # part of a project. To specify a software there, just remove the
 # `-version' suffix from the list below.
 apachelog4cxx-version = 0.10.0-603-014954db