From 4722ea598edd6b630227404c48c1c09ac527e9b8 Mon Sep 17 00:00:00 2001
From: Mohammad Akhlaghi <mohammad@akhlaghi.org>
Date: Sun, 14 Apr 2019 17:48:40 +0100
Subject: Replaced all occurances of pipeline in text

All occurances of "pipeline" have been chanaged to "project" or "template"
withint the text (comments, READMEs, and comments) of the template. The
main template branch is now also named `template'.

This was all because `pipeline' is too generic and couldn't be
distinguished from the base, and customized project.
---
 paper.tex | 100 +++++++++++++++++++++++++++++++-------------------------------
 1 file changed, 50 insertions(+), 50 deletions(-)

(limited to 'paper.tex')

diff --git a/paper.tex b/paper.tex
index 306c81c..6939284 100644
--- a/paper.tex
+++ b/paper.tex
@@ -37,27 +37,28 @@
 %% Start writing.
 \begin{document}
 
-%% Abstract, keywords and reproduction pipeline notice.
+%% Project abstract and keywords.
 \includeabstract{
 
-  You have completed the reproduction pipeline and are ready to configure
-  and implement it for your own research. This template reproduction
-  pipeline and document contains almost all the elements that you will need
-  in a research project containing the downloading of raw data, processing
-  it, including them in plots and report, including this abstract, figures
-  and bibliography. If you use this pipeline in your work, don't forget to
-  add a notice to clearly let the readers know that your work is
-  reproducible. If this pipeline proves useful in your research, please
-  cite \citet{gnuastro}.
+  You have completed the reproducible paper template and are ready to
+  configure and implement it for your own research. This template contains
+  almost all the elements that you will need in a research project
+  containing the downloading of raw data and necessary software, building
+  the software, and processing the data with the software in a
+  highly-controlled environment. It then allows including the results in
+  plots and producing the final report, including this abstract, figures
+  and bibliography. If you design your project with this template's
+  infra-structure in your work, don't forget to add a notice and clearly
+  let the readers know that your work is reproducible. If this template
+  proves useful in your research, please cite \citet{gnuastro}.
 
   \vspace{0.25cm}
 
   \textsl{Keywords}: Add some keywords for your research here.
 
   \textsl{Reproducible paper}: All quantitave results (numbers and plots)
-  in this paper are exactly reproducible with reproduction pipeline
-  \pipelineversion{}
-  (\url{https://gitlab.com/makhlaghi/reproducible-paper}).}
+  in this paper are exactly reproducible (version \pipelineversion{},
+  \url{https://gitlab.com/makhlaghi/reproducible-paper}).}
 
 %% To add the first page's headers.
 \thispagestyle{firststyle}
@@ -68,19 +69,18 @@
 
 %% Start of the main body of text.
 \section{Congratulations!}
-Congratulations on running the reproduction pipeline! You can now follow
-the checklist in the \texttt{README.md} file to customize this pipeline to
-your exciting research project.
+Congratulations on running the raw template project! You can now follow the
+checklist in the \texttt{README.md} file to customize this template to your
+exciting research project.
 
 Just don't forget to \emph{never} use numbers or fixed strings (for example
 database urls like \url{\wfpctwourl}) directly within your \LaTeX{}
-source. Read them directly from your configuration files or outputs of the
-programs as part of the reproduction pipeline and import them into \LaTeX{}
-as macros through the \texttt{tex/pipeline/macros/pipeline.tex} file
-(created after running the pipeline). See the several examples within the
-pipeline for a demonstration. For some recent real-world examples, the
-reproduction pipelines for Sections 4 and 7.3 of \citet{bacon17} are
-available at
+source. Read them directly from your configuration files, or processing
+outputs, and import them into \LaTeX{} as macros through the
+\texttt{tex/pipeline/macros/pipeline.tex} file (created after running the
+project). See the several existing examples within the template for a
+demonstration. For some recent real-world examples, the reproducible
+project sources for Sections 4 and 7.3 of \citet{bacon17} are available at
 \href{https://doi.org/10.5281/zenodo.1164774}{zenodo.1164774}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-origin-only-hst-magnitudes}},
 or
 \href{https://doi.org/10.5281/zenodo.1163746}{zenodo.1163746}\footnote{\url{https://gitlab.com/makhlaghi/muse-udf-photometry-astrometry}}. Working
@@ -126,15 +126,15 @@ histogram and basic statstics were generated with Gnuastro's
 
 {\small PGFP}lots\footnote{\url{https://ctan.org/pkg/pgfplots}} is a great
 tool to build the plots within \LaTeX{} and removes the necessity to add
-further dependencies (to create the plots) to your reproduction
-pipeline. There are high-level language libraries like Matplotlib which
-also generate plots. However, the problem is that they require many
-dependencies (Python, Numpy and etc). Installing these dependencies from
-source, is not easy and will harm the reproducibility of your paper. Note
-that after several years, the binary files of these high-level libraries,
-that you easily install today, will no longer be available in common
-repositories. Therefore building the libraries from source is the only
-option to reproduce your results.
+further dependencies (to create the plots) to your project. There are
+high-level language libraries like Matplotlib which also generate
+plots. However, the problem is that they require many dependencies (Python,
+Numpy and etc). Installing these dependencies from source, is not easy and
+will harm the reproducibility of your paper. Note that after several years,
+the binary files of these high-level libraries, that you easily install
+today, will no longer be available in common repositories. Therefore
+building the libraries from source is the only option to reproduce your
+results.
 
 Furthermore, since {\small PGFP}lots is built by \LaTeX{} it respects all
 the properties of your text (for example line width and fonts and
@@ -142,7 +142,7 @@ etc). Therefore the final plot blends in your paper much more nicely. It
 also has a wonderful
 manual\footnote{\url{http://mirrors.ctan.org/graphics/pgf/contrib/pgfplots/doc/pgfplots.pdf}}.
 
-This pipeline also defines two \LaTeX{} macros that allow you to mark text
+This template also defines two \LaTeX{} macros that allow you to mark text
 within your document as \emph{new} and \emph{notes}. For example, \new{this
   text has been marked as \texttt{new}.} \tonote{While this one is marked
   as \texttt{tonote}.} If you comment the line (by adding a `\texttt{\%}'
@@ -173,13 +173,12 @@ please add a notice close to the start of your paper or in the end of the
 abstract clearly mentioning that your work is fully reproducible.
 
 For the time being, we haven't written a specific paper only for this
-reproduction pipeline, so until then, we would be grateful if you could
-cite the first paper that used the first version of this pipeline:
-\citet{gnuastro}.
+template. Until then, we would be grateful if you could cite the first
+paper that used the early versions of this template: \citet{gnuastro}.
 
 After publication, don't forget to upload all the necessary data, software
-source code and the reproduction pipeline to a long-lasting host like
-Zenodo (\url{https://zenodo.org}).
+source code and the project's source to a long-lasting host like Zenodo
+(\url{https://zenodo.org}).
 
 
 
@@ -187,21 +186,22 @@ Zenodo (\url{https://zenodo.org}).
 
 \section{Acknowledgements}
 \new{Please include the following two paragraphs in the Acknowledgement
-  section of your paper. This reproduction pipeline was developed in
+  section of your paper. This reproducible paper template was developed in
   parallel with Gnuastro, so it benefited from the same grants. If you
-  don't use any of these packages in the final/customized pipeline, please
-  remove them. }
+  don't use Gnuastro in your final/customized project, please remove it
+  from the paragraph below, only mentioning the reproducible paper
+  template.}
 
 This research was partly done using GNU Astronomy Utilities (Gnuastro,
-ascl.net/1801.009), and reproduction pipeline \pipelineversion. Work on
-Gnuastro and the reproduction pipeline has been funded by the Japanese
-Ministry of Education, Culture, Sports, Science, and Technology (MEXT)
-scholarship and its Grant-in-Aid for Scientific Research (21244012,
-24253003), the European Research Council (ERC) advanced grant
-339659-MUSICOS, European Union’s Horizon 2020 research and innovation
-programme under Marie Sklodowska-Curie grant agreement No 721463 to the
-SUNDIAL ITN, and from the Spanish Ministry of Economy and Competitiveness
-(MINECO) under grant number AYA2016-76219-P.
+ascl.net/1801.009), and the reproducible paper template
+\pipelineversion. Work on Gnuastro and the reproducible paper template has
+been funded by the Japanese Ministry of Education, Culture, Sports,
+Science, and Technology (MEXT) scholarship and its Grant-in-Aid for
+Scientific Research (21244012, 24253003), the European Research Council
+(ERC) advanced grant 339659-MUSICOS, European Union’s Horizon 2020 research
+and innovation programme under Marie Sklodowska-Curie grant agreement No
+721463 to the SUNDIAL ITN, and from the Spanish Ministry of Economy and
+Competitiveness (MINECO) under grant number AYA2016-76219-P.
 
 \input{tex/pipeline/macros/dependencies.tex}
 
-- 
cgit v1.2.1

