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authorMohammad Akhlaghi <mohammad@akhlaghi.org>2018-11-19 13:50:44 +0000
committerMohammad Akhlaghi <mohammad@akhlaghi.org>2018-11-19 13:50:44 +0000
commit9bf8de7155e2a7917c7c972ab332da0c758a0d6d (patch)
treefc313027aaaadd0b576366b550e5a64d0f899dda
parent5ae1fdc475d4476c6371fc5b27880634782549d9 (diff)
Minor corrections for easy applying of checklist
After going through the checklist for starting a new project based on the pipeline, I noticed some parts that could be modified to be more clear. They are now applied.
-rw-r--r--README.md56
-rw-r--r--reproduce/src/make/initialize.mk12
2 files changed, 38 insertions, 30 deletions
diff --git a/README.md b/README.md
index 985ad3b..3483fb9 100644
--- a/README.md
+++ b/README.md
@@ -448,18 +448,20 @@ advanced in later stages of your work.
- **Test the pipeline**: Before making any changes, it is important to
test the pipeline and see if everything works properly with the
commands below. If there is any problem in the `./configure` or `make`
- steps, please contact us to fix the problem before continuing. After
- `make` is finished, open `paper.pdf` and if it looks fine, you are
- ready to start customizing the pipeline for your project. But before
- that, clean all the extra pipeline outputs with `make clean` as shown
- below.
+ steps, please contact us to fix the problem before continuing. Since
+ the building of dependencies in `./configure` can take long, you can
+ take the next few steps (editing the files) while its working (they
+ don't affect the configuration). After `make` is finished, open
+ `paper.pdf` and if it looks fine, you are ready to start customizing
+ the pipeline for your project. But before that, clean all the extra
+ pipeline outputs with `make clean` as shown below.
```shell
$ ./configure # Set top directories and build dependencies.
$ make # Run the pipeline.
# Open 'paper.pdf' and see if everything is ok.
- $ make distclean # Remove all pipeline outputs.
+ $ make clean # Delete high-level outputs.
```
- **Copyright**, **name** and **date**: Go over the existing scripting
@@ -478,12 +480,12 @@ advanced in later stages of your work.
- **Title**, **short description** and **author** in source files: In this
raw skeleton, the title or short description of your project should be
- added in the following two files: `Makefile` (the first line), and
- `tex/preamble-header.tex` (the last two groups of lines, along with
- the names of you and your colleagues). In both cases, the texts you
- should replace are all in capital letters to make them easier to
- identify. Of course, if you use a different LaTeX method of managing
- the title and authors, please feel free to use your own methods.
+ added in the following two files: `reproduce/src/make/Top-Makefile`
+ (the first line), and `tex/preamble-header.tex`. In both cases, the
+ texts you should replace are all in capital letters to make them
+ easier to identify. Of course, if you use a different LaTeX method of
+ managing the title and authors, please feel free to use your own
+ methods after finishing this checklist and doing your first commit.
- **Gnuastro**: GNU Astronomy Utilities (Gnuastro) is currently a
dependency of the pipeline which will be built and used. The main
@@ -493,6 +495,7 @@ advanced in later stages of your work.
below to make them more readable.
- Delete marked part(s) in `configure`.
+ - Delete `astnoisechisel` from the value of `top-level-programs` in `reproduce/src/make/dependencies.mk`. You can keep the rule to build `astnoisechisel`, since its not in the `top-level-programs` list, it (and all its dependencies) will be ignored.
- Delete marked parts in `reproduce/src/make/initialize.mk`.
- Delete `and Gnuastro \gnuastroversion` from `tex/preamble-style.tex`.
@@ -509,8 +512,8 @@ advanced in later stages of your work.
work. Therefore, also check and update `README` one last time when you
are ready to publish your work (and its reproduction pipeline).
- - **Input dataset**: The user manages the top-level directory of the input
- data through the variables set in
+ - **Input dataset (can be done later)**: The user manages the top-level
+ directory of the input data through the variables set in
`reproduce/config/pipeline/LOCAL.mk.in` (the user actually edits a
`LOCAL.mk` file that is created by `configure` from the `.mk.in` file,
but the `.mk` file is not under version control). Datasets are usually
@@ -538,13 +541,14 @@ advanced in later stages of your work.
$ grep -r survey ./
```
- - **Other input datasets**: Add any other input datasets that may be
- necessary for your research to the pipeline based on the example
- above.
+ - **Other input datasets (can be done later)**: Add any other input
+ datasets that may be necessary for your research to the pipeline based
+ on the example above.
- - **Delete dummy parts**: The template pipeline contains some parts that
- are only for the initial/test run, not for any real analysis. The
- respective files to remove and parts to fix are discussed here.
+ - **Delete dummy parts (can be done later)**: The template pipeline
+ contains some parts that are only for the initial/test run, not for
+ any real analysis. The respective files to remove and parts to fix are
+ discussed here.
- `paper.tex`: Delete the text of the abstract and the paper's main
body, *except* the "Acknowledgements" section. This reproduction
@@ -571,12 +575,12 @@ advanced in later stages of your work.
commit to be sure it works as expected).
```shell
- $ make clean # Delete outputs ('make distclean' for all outputs)
- $ make # Build the pipeline to ensure everything is fine.
- $ git add -u # Stage all the changes.
- $ git status # Make sure everything is fine.
- $ git commit # Your first commit, add a nice description.
- $ git tag -a v0 # Tag this as the zero-th version of your pipeline.
+ $ ./.local/bin/make clean # Delete outputs ('make distclean' for everything)
+ $ ./.local/bin/make # Build the pipeline to ensure everything is fine.
+ $ git add -u # Stage all the changes.
+ $ git status # Make sure everything is fine.
+ $ git commit # Your first commit, add a nice description.
+ $ git tag -a v0 # Tag this as the zero-th version of your pipeline.
```
- **Setup the remote**: You can use any [hosting
diff --git a/reproduce/src/make/initialize.mk b/reproduce/src/make/initialize.mk
index 9639c79..2cc393c 100644
--- a/reproduce/src/make/initialize.mk
+++ b/reproduce/src/make/initialize.mk
@@ -40,9 +40,10 @@ lockdir = $(BDIR)/locks
texbdir = $(texdir)/build
tikzdir = $(texbdir)/tikz
mtexdir = $(texdir)/macros
-gconfdir = reproduce/config/gnuastro
pconfdir = reproduce/config/pipeline
-
+# --------- Delete for no Gnuastro ---------
+gconfdir = reproduce/config/gnuastro
+# ------------------------------------------
@@ -199,8 +200,6 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
$(call pvcheck, gs, $(ghostscript-version), GPL Ghostscript, \
ghostscriptversion)
$(call pvcheck, git, $(git-version), Git, gitversion)
- $(call pvcheck, astnoisechisel, $(gnuastro-version), Gnuastro, \
- gnuastroversion)
$(call pvcheck, grep, $(grep-version), GNU Grep, grepversion)
$(call pvcheck, libtool, $(libtool-version), GNU Libtool, \
libtoolversion)
@@ -211,6 +210,11 @@ $(mtexdir)/initialize.tex: | $(mtexdir)
$(call pvcheck, which, $(which-version), GNU Which, whichversion)
$(call pvcheck, xz, $(xz-version), XZ Utils, xzversion)
+ # --------- Delete for no Gnuastro ---------
+ $(call pvcheck, astnoisechisel, $(gnuastro-version), Gnuastro, \
+ gnuastroversion)
+ # ------------------------------------------
+
# Bzip2 prints its version in standard error, not standard output!
echo "" | bzip2 --version &> $@_bzip2_ver;
v=$$(awk 'NR==1 && /'$(bzip2-version)'/{print "y"; exit 0}' \