diff options
| -rw-r--r-- | README.md | 56 | ||||
| -rw-r--r-- | reproduce/src/make/initialize.mk | 12 |
2 files changed, 38 insertions, 30 deletions
@@ -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}' \ |