From 40da7c8cc19098f21d93e8f1720071a64759f9ee Mon Sep 17 00:00:00 2001 From: Pedram Ashofteh Ardakani Date: Sun, 3 May 2020 14:16:41 +0430 Subject: Remove extra spacing before and after code blocks Until now, the extra space made the padding look too big. * Changed this HTML code convention: ```html 

some code
``` * to this: ```html 
some code
``` And the extra space is gone. --- about.html | 112 +++++++++++++++++++------------------------------------------ 1 file changed, 35 insertions(+), 77 deletions(-) (limited to 'about.html') diff --git a/about.html b/about.html index cc233f1..248142a 100644 --- a/about.html +++ b/about.html @@ -212,9 +212,7 @@ command-line with the following command (you can come out of the "Info" environment by pressing q).

- 

-info make
-
+ 
info make

If you aren't familiar with the Info documentation format, we strongly recommend running $ info info and reading along. In less than an hour, @@ -549,14 +547,12 @@ info make create and go into the conventional master branch to start committing in your project later.

- 

-git clone https://git.maneage.org/project.git    # Clone/copy the project and its history.
+                        
git clone https://git.maneage.org/project.git    # Clone/copy the project and its history.
 mv project my-project                            # Change the name to your project's name.
 cd my-project                                    # Go into the cloned directory.
 git remote rename origin origin-maneage          # Rename current/only remote to "origin-maneage".
 git checkout -b master                           # Create and enter your own "master" branch.
-pwd                                              # Just to confirm where you are.
-                    

+pwd                                              # Just to confirm where you are.

  • Prepare to build project: The ./project configure command of the next step will build the different software packages within the "build" directory (that you will specify). Nothing else on your system @@ -572,10 +568,8 @@ pwd # Just to installed in the project build directory it will be removed. Again, don't worry, nothing will be installed outside the build directory.

    - 
    
-# On another terminal (go to top project source directory, last command above)
-./project --check-config
-
    • + 
    # On another terminal (go to top project source directory, last command above)
+./project --check-config

  • Test Maneage: Before making any changes, it is important to test it and see if everything works properly with the commands below. If there is any problem in the ./project configure or ./project make steps, @@ -587,11 +581,9 @@ pwd # Just to Maneage for your project. But before that, clean all the extra Maneage outputs with make clean as shown below.

    - 
    
-./project configure     # Build the project's software environment (can take an hour or so).
+                        
    ./project configure     # Build the project's software environment (can take an hour or so).
 ./project make          # Do the processing and build paper (just a simple demo).
-# Open 'paper.pdf' and see if everything is ok.
-
    • +# Open 'paper.pdf' and see if everything is ok.

  • Setup the remote: You can use any hosting facility that supports Git to keep an online copy of your project's version @@ -614,11 +606,9 @@ pwd # Just to command, you can actually check this (which local and remote branches are tracking each other).

    - 
    
-git remote add origin XXXXXXXXXX        # Newly created repo is now called 'origin'.
+                        
    git remote add origin XXXXXXXXXX        # Newly created repo is now called 'origin'.
 git push --set-upstream origin master   # Push 'master' branch to 'origin' (with tracking).
-git push origin maneage                 # Push 'maneage' branch to 'origin' (no tracking).
-
    • +git push origin maneage # Push 'maneage' branch to 'origin' (no tracking).

  • Title, short description and author: The title and basic information of your project's output PDF paper should be added in paper.tex. You should see the relevant place in the preamble (prior @@ -657,11 +647,9 @@ git push origin maneage # Push 'maneage' b download to XXXXX (any temporary string, you'll fix it in the end of your project, when its complete).

  • Delete all delete-me* files in the following directories:

    - 
    
-rm tex/src/delete-me*
+                                
    rm tex/src/delete-me*
 rm reproduce/analysis/make/delete-me*
-rm reproduce/analysis/config/delete-me*
-
    • +rm reproduce/analysis/config/delete-me*

  • Disable verification of outputs by removing the yes from reproduce/analysis/config/verify-outputs.conf. Later, when you are ready to submit your paper, or publish the dataset, activate @@ -672,10 +660,8 @@ rm reproduce/analysis/config/delete-me*

  • Re-make the project (after a cleaning) to see if you haven't introduced any errors.

    - 
    
-./project make clean
-./project make
-
    • + 
    ./project make clean
+./project make

  • Don't merge some files in future updates: As described below, you can later update your infra-structure (for example to fix bugs) by @@ -694,15 +680,13 @@ rm reproduce/analysis/config/delete-me* other change in that file. Also, don't add core Maneage Makefiles, otherwise Maneage can break on the next run.

    - 
    
-echo "paper.tex merge=ours" > .gitattributes
+                            
    echo "paper.tex merge=ours" > .gitattributes
 echo "tex/src/delete-me.mk merge=ours" >> .gitattributes
 echo "tex/src/delete-me-demo.mk merge=ours" >> .gitattributes
 echo "reproduce/analysis/make/delete-me.mk merge=ours" >> .gitattributes
 echo "reproduce/software/config/TARGETS.conf merge=ours" >> .gitattributes
 echo "reproduce/analysis/config/delete-me-num.conf merge=ours" >> .gitattributes
-git add .gitattributes
-
    • +git add .gitattributes

  • Copyright and License notice: It is necessary that all the "copyright-able" files in your project (those larger than 10 lines) have a copyright and license notice. Please take a moment to look at @@ -720,10 +704,8 @@ git add .gitattributes tex/src/preamble-header.tex, reproduce/analysis/make/top-make.mk, and generally, all the files you modified in the previous step.

    - 
    
-Copyright (C) 2018-2020 Existing Name <existing@email.address>
-Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS>
-
    • + 
    Copyright (C) 2018-2020 Existing Name <existing@email.address>
+Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS>

  • Configure Git for fist time: If this is the first time you are running Git on this system, then you have to configure it with some basic information in order to have essential information in the commit @@ -732,11 +714,9 @@ Copyright (C) 2020 YOUR NAME <YOUR@EMAIL.ADDRESS> can also specify your favorite text editor for making the commit (emacs, vim, nano, and etc.).

    - 
    
-git config --global user.name "YourName YourSurname"
+                            
    git config --global user.name "YourName YourSurname"
 git config --global user.email your-email@example.com
-git config --global core.editor nano
-
    • +git config --global core.editor nano

  • Your first commit: You have already made some small and basic changes in the steps above and you are in your project's master branch. So, you can officially make your first commit in your @@ -745,16 +725,14 @@ git config --global core.editor nano always re-build the system before a commit to be sure it works as expected.

    - 
    
-git status                 # See which files you have changed.
+                            
    git status                 # See which files you have changed.
 git diff                   # Check the lines you have added/changed.
 ./project make             # Make sure everything builds successfully.
 git add -u                 # Put all tracked changes in staging area.
 git status                 # Make sure everything is fine.
 git diff --cached          # Confirm all the changes that will be committed.
 git commit                 # Your first commit: put a good description!
-git push                   # Push your commit to your remote.
-
    • +git push # Push your commit to your remote.

  • Start your exciting research: You are now ready to add flesh and blood to this raw skeleton by further modifying and adding your exciting research steps. You can use the "published works" section in @@ -798,9 +776,7 @@ git push # Push your commit to your remo dataset with the command below and replace it with your input's dataset.

    - 
    
-grep -ir wfpc2 ./*
-
    • + 
    grep -ir wfpc2 ./*

  • README.md: Correct all the XXXXX place holders (name of your project, your own name, address of your project's online/remote repository, link to download dependencies and etc). Generally, read @@ -861,9 +837,7 @@ grep -ir wfpc2 ./* attempt, the ./project make script should be run with the --prepare-redo option, or you can delete the special file above.

    - 
    
-./project make --prepare-redo
-
    • + 
    ./project make --prepare-redo

  • Pre-publication: add notice on reproducibility**: Add a notice somewhere prominent in the first page within your paper, informing the reader that your research is fully reproducible. For example in the @@ -981,9 +955,7 @@ grep -ir wfpc2 ./* here. If you use GNU Make, you can also see this page on your command-line:

    - 
    
-info make "automatic variables"
-
    • + 
    info make "automatic variables"

  • Debug: Since Make doesn't follow the common top-down paradigm, it can be a little hard to get accustomed to why you get an error or un-expected behavior. In such cases, run Make with the -d @@ -1004,15 +976,13 @@ info make "automatic variables" large2.fits and delete large1.fits in the same rule (when its no longer needed). We can later do the same with large2.fits when it is no longer needed and so on. - 

    
-large1.fits.txt: input.fits
+                                        
    large1.fits.txt: input.fits
 astarithmetic $< 2 + --output=$(subst .txt,,$@)
 echo "done" > $@
 large2.fits.txt: large1.fits.txt
 astarithmetic $(subst .txt,,$<) 2 - --output=$(subst .txt,,$@)
 rm $(subst .txt,,$<)
-echo "done" > $@
-                                        
    
+echo "done" > $@
    A more advanced Make programmer will use Make's call function to define a wrapper in reproduce/analysis/make/initialize.mk. This wrapper will replace $(subst .txt,,XXXXX). Therefore, it will be @@ -1031,8 +1001,7 @@ echo "done" > $@ deletion. For example, see the minimal working example Makefile below (which you can actually put in a Makefile and run if you have an input.fits in the same directory, and Gnuastro is installed). - 
    
-.ONESHELL:
+                                        
    .ONESHELL:
 .SHELLFLAGS = -ec
 all: mean-std.txt
 shm-maneage := /dev/shm/$(shell whoami)-maneage-XXXXXXXXXX
@@ -1049,8 +1018,7 @@ echo "$$out" > $@
 mean-std.txt: large2.txt
 input=$$(cat $<)
 aststatistics $$input.fits --mean --std > $@
-rm $$input.fits $$input
-                                        
    
+rm $$input.fits $$input
    The important point here is that the temporary name template (shm-maneage) has no suffix. So you can add the suffix corresponding to your desired format afterwards (for example @@ -1117,14 +1085,12 @@ rm $$input.fits $$input conflicts which might happen in the merge (updated settings that you have customized in Maneage).

    - 
    
-git checkout maneage
+                                                
    git checkout maneage
 git pull                            # Get recent work in Maneage
 git log XXXXXX..XXXXXX --reverse    # Inspect new work (replace XXXXXXs with hashs mentioned in output of previous command).
 git log --oneline --graph --decorate --all # General view of branches.
 git checkout master                 # Go to your top working branch.
-git merge maneage                   # Import all the work into master.
-
    • +git merge maneage # Import all the work into master.

  • Adding Maneage to a fork of your project: As you and your colleagues continue your project, it will be necessary to have separate forks/clones of it. But when you clone your own project on a @@ -1135,11 +1101,9 @@ git merge maneage # Import all the work below will setup the origin-maneage remote, and a local maneage branch to track it, on the new clone.

    - 
    
-git remote add origin-maneage https://git.maneage.org/project.git
+                                                
    git remote add origin-maneage https://git.maneage.org/project.git
 git fetch origin-maneage
-git checkout -b maneage --track origin-maneage/maneage
-
    • +git checkout -b maneage --track origin-maneage/maneage

  • Commit message: The commit message is a very important and useful aspect of version control. To make the commit message useful for others (or yourself, one year later), it is good to follow a @@ -1197,18 +1161,14 @@ git checkout -b maneage --track origin-maneage/maneage project):

    • - 
    
-git bundle create my-project-git.bundle --all
-
    + 
    git bundle create my-project-git.bundle --all
    - 

    
-git clone my-project-git.bundle
-
    + 

    git clone my-project-git.bundle

    @@ -1241,9 +1201,7 @@ git clone my-project-git.bundle architecture) and the standard program name. For example (from the Nix webpage):

    - 
    
-/nix/store/b6gvzjyb2pg0kjfwrjmg1vfhh54ad73z-firefox-33.1/
-
    + 
    /nix/store/b6gvzjyb2pg0kjfwrjmg1vfhh54ad73z-firefox-33.1/

    The important thing is that the "store" is not in the project's search path. After the complete installation of the software, symbolic links are -- cgit v1.2.1