Pipeline now downloads and uses an input dataset

In most analysis situations (except for simulations), an input dataset is
necessary, but that part of the pipeline was just left out and a general
`SURVEY' variable was set and never used. So with this commit, we actually
use a sample FITS file from the FITS standard webpage, show it (as well as
its histogram) and do some basic calculations on it.

This preparation of the input datasets is done in a generic way to enable
easy addition of more datasets if necessary.

7 files changed, 81 insertions, 6 deletions

diff --git a/reproduce/config/gnuastro/astconvertt.conf b/reproduce/config/gnuastro/astconvertt.conf
new file mode 100644
index 0000000..fc3ba04
--- /dev/null
+++ b/reproduce/config/gnuastro/astconvertt.conf
@@ -0,0 +1,31 @@
+# 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.
+#
+# 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/config/gnuastro/aststatistics.conf b/reproduce/config/gnuastro/aststatistics.conf
new file mode 100644
index 0000000..0bf3b83
--- /dev/null
+++ b/reproduce/config/gnuastro/aststatistics.conf
@@ -0,0 +1,34 @@
+# 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.
+#
+# 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/config/pipeline/INPUTS.mk b/reproduce/config/pipeline/INPUTS.mk
new file mode 100644
index 0000000..3522ecc
--- /dev/null
+++ b/reproduce/config/pipeline/INPUTS.mk
@@ -0,0 +1,9 @@
+# Input files necessary for this pipeline.
+#
+# This file is read by the configure script and running Makefiles.
+
+
+WFPC2IMAGE = WFPC2ASSNu5780205bx.fits
+WFPC2MD5   = a4791e42cd1045892f9c41f11b50bad8
+WFPC2SIZE  = 62kb
+WFPC2URL   = https://fits.gsfc.nasa.gov/samples
diff --git a/reproduce/config/pipeline/LOCAL.mk.in b/reproduce/config/pipeline/LOCAL.mk.in
index d6bf2c0..89e3e23 100644
--- a/reproduce/config/pipeline/LOCAL.mk.in
+++ b/reproduce/config/pipeline/LOCAL.mk.in
@@ -1,4 +1,8 @@
 # Local pipeline configuration.
+#
+# This is just a template for the `./configure' script to fill in. Please
+# don't make any change to this file.
 BDIR             = @bdir@
+INDIR            = @indir@
 DEPENDENCIES-DIR = @ddir@
 DOWNLOADER       = @downloader@
diff --git a/reproduce/config/pipeline/delete-me-wfpc2-quant.mk b/reproduce/config/pipeline/delete-me-wfpc2-quant.mk
new file mode 100644
index 0000000..2ff7456
--- /dev/null
+++ b/reproduce/config/pipeline/delete-me-wfpc2-quant.mk
@@ -0,0 +1,2 @@
+# Number of samples to create
+delete-me-wfpc2-quantile = 0.65
diff --git a/reproduce/config/pipeline/dependency-versions.mk b/reproduce/config/pipeline/dependency-versions.mk
index f85cdbf..dc45b81 100644
--- a/reproduce/config/pipeline/dependency-versions.mk
+++ b/reproduce/config/pipeline/dependency-versions.mk
@@ -5,6 +5,7 @@ bash-version        = 4.4.18
 bzip2-version       = 1.0.6
 cmake-version       = 3.12.4
 coreutils-version   = 8.30
+flock-version       = 0.2.3
 gawk-version        = 4.2.1
 ghostscript-version = 9.26
 git-version         = 2.19.1
diff --git a/reproduce/config/pipeline/web.mk b/reproduce/config/pipeline/web.mk
deleted file mode 100644
index 5af11a7..0000000
--- a/reproduce/config/pipeline/web.mk
+++ /dev/null
@@ -1,6 +0,0 @@
-# Web server(s) hosting the input data for this pipeline.
-#
-# This is the web page containing the files that must be located in the
-# `SURVEY' directory of `reproduce/config/pipeline/LOCAL.mk' on the local
-# system.
-web-survey = https://some.webpage.com/example/server