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Until now, the main download script could only check one server for the
given URL. However, ultimately the actual server that a file is downloaded
from is irrelevant for this project: we actually check its
checksum. Especially in the case of software (which are distributed over
many servers), this can usually be very annoying: the servers may not
properly communicate with the running system and even the 10 trials won't
be enough.
With this commit, the download script
`reproduce/analysis/bash/download-multi-try' can take a new optional
argument (a 5th argument). It assumes this argument is a space-separated
list of server(s) to use as backup for the original URL. When downloading
from the original URL fails, it will look into this list and try
downloading the same file from each given server.
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Now that its 2020, its necessary to include this year in the copyright
statements.
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Until now, this script would always only work with a file-lock. But in some
scenarios, we might want to download in parallel. For example when the
system has multiple ports to the internet.
With this commit, we have added this feature: when the lockfile name is
`nolock', it won't lock and will download in parallel.
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Until now, the `download-multi-try' script assumed GNU Bash features (when
comparing the number of attempts at downloading), but it didn't explicitly
ask the operating system to be run with Bash. As a result, when weaker
shells were used (like the default Debian minimalist `dash' shell), the `>'
("larger than" operator in a math context) is interpreted a redirection and
two extra files are created: `1' and `maxcount'!
With this commit, we now start this script with `/bin/bash'. Ofcourse, this
will assume that the host has GNU Bash installed, but we are also making
this assumption in the configure script. So atleast for now, Bash (any
version) is a critical dependency of this template anyway.
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Until now, the software building and analysis steps of the pipeline were
intertwined. However, these steps (of how to build a software, and how to
use it) are logically completely independent.
Therefore with this commit, the pipeline now has a new architecture
(particularly in the `reproduce' directory) to emphasize this distinction:
The `reproduce' directory now has the two `software' and `analysis'
subdirectories and the respective parts of the previous architecture have
been broken up between these two based on their function. There is also no
more `src' directory. The `config' directory for software and analysis is
now mixed with the language-specific directories.
Also, some of the software versions were also updated after some checks
with their webpages.
This new architecture will allow much more focused work on each part of the
pipeline (to install the software and to run them for an analysis).
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