Using Git with GEOS-Chem: Difference between revisions

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This page describes how to use the [[Version control with Git|Git version control system]] to download and manage the GEOS-Chem source code package.
#REDIRECT [[Guide to using Git with GEOS-Chem]]
 
== Obtaining and installing Git ==
 
You will need to make sure that Git is installed on your system.  Please see [[Version_control_with_Git#Obtaining_and_installing_Git|this wiki post]] for more information.
 
== Downloading a new GEOS-Chem version ==
 
=== Initial download ===
 
==== Code directory ====
 
The GEOS-Chem source code repository has now been migrated from CVS to Git, and is now available for remote download.  We recommend that you download each new version of GEOS-Chem into a separate source code directory.
 
Users outside the Jacob group should use the following syntax:
 
git clone git://git.as.harvard.edu/bmy/GEOS-Chem/ LOCAL_DIR_NAME
 
Users at the Jacob group should instead use (on Rhea):
 
git clone /as/pub/git/bmy/GEOS-Chem LOCAL_DIR_NAME
 
where <tt>LOCAL-DIR-NAME</tt> is the name of the local directory on your disk into which the GEOS-Chem source code files will be placed.  It is up to you to pick <tt>LOCAL-DIR-NAME</tt>; some possible options are:
 
* <tt>Code.vXX-YY-ZZ
* GEOS-Chem.vXX-YY-ZZ
* G-C.vXX-YY-ZZ</tt>
 
Let's assume in the following examples that you want to download a copy of the GEOS-Chem repository for v8-03-01.  Typing this command:
 
git clone git://git.as.harvard.edu/bmy/GEOS-Chem/ Code.v8-03-01
 
will create a "clone" of the remote <tt>GEOS-Chem/</tt> repository into your local <tt>Code.v8-03-01</tt> directory.  The various system files are all stored in the <tt>Code.v8-03-01/.git</tt> subdirectory.  The files in <tt>Code.v8-03-01/</tt> are an exact copy of what was on the Git repository server at the time you downloaded it.
 
==== Run directories ====
 
Each of the GEOS-Chem run directories is saved as a separate Git repository,
rather than putting them into a single repository.  This is because some of
the files (i.e. restart files) can be very large.
 
The download options are:
 
  git clone git://git.as.harvard.edu/bmy/GEOS-Chem-rundirs/DIRECTORY-OPTION LOCAL_DIR_NAME
 
Users at the Jacob group should instead use (on Rhea):
 
git clone /as/pub/git/bmy/GEOS-Chem-rundirs/DIRECTORY-OPTION LOCAL_DIR_NAME
 
where DIRECTORY-OPTION may be one of the following:
{| border=1 cellspacing=0 cellpadding=5 width="70%"
|-align="left"
|width="25%" |2x2.5/geos4/SOA       
|width="75%" |2 x 2.5 G4 fullchem w/ SOA simulation
|-align="left"
|2x2.5/geos4/dicarbonyls 
|2 x 2.5 G4 fullchem w/ dicarbonyls option
|-align="left"
|2x2.5/geos4/isoprene     
|2 x 2.5 G4 fullchem w/ Caltech isoprene scheme
|-align="left"
|2x2.5/geos4/standard     
|2 x 2.5 G4 fullchem standard (43 tracers)
|}
 
 
{| border=1 cellspacing=0 cellpadding=5 width="70%"
|-align="left"
|width="25%" |2x2.5/geos5/SOA       
|width="75%" |2 x 2.5 G5 fullchem w/ SOA simulation
|-align="left"
|2x2.5/geos5/dicarbonyls 
|2 x 2.5 G5 fullchem w/ dicarbonyls option
|-align="left"
|2x2.5/geos5/isoprene     
|2 x 2.5 G5 fullchem w/ Caltech isoprene scheme
|-align="left"
|2x2.5/geos5/standard     
|2 x 2.5 G5 fullchem standard (43 tracers)
|}
 
 
{| border=1 cellspacing=0 cellpadding=5 width="70%"
|-align="left"
|width="25%" |4x5/geos4/SOA         
|width="75%" |4 x 5  G4 fullchem w/ SOA simulation
|-align="left"
|4x5/geos4/dicarbonyls 
|4 x 5  G4 fullchem w/ dicarbonyls option
|-align="left"
|4x5/geos4/isoprene     
|4 x 5  G4 fullchem w/ Caltech isoprene scheme
|-align="left"
|4x5/geos4/standard     
|4 x 5  G4 fullchem standard (43 tracers)
|}
 
 
{| border=1 cellspacing=0 cellpadding=5 width="70%"
|-align="left"
|width="25%" |4x5/geos5/SOA         
|width="75%" |4 x 5  G5 fullchem w/ SOA simulation
|-align="left"
|4x5/geos5/dicarbonyls 
|4 x 5  G5 fullchem w/ dicarbonyls option
|-align="left"
|4x5/geos5/isoprene     
|4 x 5  G5 fullchem w/ Caltech isoprene scheme
|-align="left"
|4x5/geos5/standard     
|4 x 5  G5 fullchem standard (43 tracers)
|}
 
 
{| border=1 cellspacing=0 cellpadding=5 width="70%"
|-align="left"
|width="25%" |benchmark               
|width="75%" |4 x 5  G5 1-month benchmark simulation
|}
 
 
<tt>LOCAL-DIR-NAME</tt> is the name of the local directory on your disk into which the GEOS-Chem source code files will be placed.
 
=== Ignoring files ===
 
Git also allows you to ignore certain types of files that we don't need to track (e.g. anything that can be built from the source code).  These typically include:
 
* Object files <tt>(*.o)</tt>
* Library files <tt>(*.a)</tt>
* Module files <tt>(*.mod)</tt>
* Autosave files <tt>(*~)</tt>
* Executable files <tt>(geos, geostomas)</tt>
 
You can tell Git that you don't want these files to be tracked by editing the .git/info/exclude file in your source code directory.  Open this file in your favorite text editor and edit it to look like this:
 
# git-ls-files --others --exclude-from=.git/info/exclude
# Lines that start with '#' are comments.
# For a project mostly in C, the following would be a good set of
# exclude patterns (uncomment them if you want to use them):
*.[oa]
*.mod
*~
geos
geostomas
 
== Viewing the revision history ==
 
The best way to examine the contents of your Git-backed GEOS-Chem source code is to use the '''gitk''' viewer.  There are two ways to do this:
 
(1) Change into the Code.v8-03-01 directory and start '''gitk''' as follows:
 
cd Code.v8-03-01
gitk &
 
(2) Or if you are using the '''git gui''' GUI browser ([[#Making revisions|more on that below]]), you can invoke '''gitk''' from the '''Repository/Visualize master's History''' menu item.
 
At the top left of the '''gitk''' screen, you will see the graph of revisions.  Each dot represents a commit, along with the log message that accompanied each commit. 
 
Note that the most recent commit (i.e. the line at the very top), there are 2 green boxes at the top, one named '''master''' and one named '''origin''':
 
;origin: This was the state of the repository on the remote server when you checked it out for the first time.  Therefore, this is the "pristine", unchanged code that you got from the download.
;master: This is the current state of the local repository now.  Since we haven't done anything to the code yet, the '''master''' and '''origin''' point to the same commit.
 
If you click on any of the commits in the top left window, in the window below, you will see the log message and a list of changes to the source code.  The old code is marked in RED and the new code is marked in GREEN.  At right you will also see a list of files that were changed during the commit.
 
So it's really easy to see how the code has evolved with '''gitk'''.
 
== Making revisions ==
 
=== Using the GUI browser ===
 
We recommend using the '''git gui''' for source code management.  Start this in your <tt>Code.v8-03-01</tt> subdirectory:
 
cd Code.v8-03-01
git gui &
 
On the left there are 2 windows:
 
;'''Unstaged Changes''': An unstaged change is a modification that Git does not know about yet.  If you modified any files since the last commit, then they should be displayed in this window.  Also, right above this window you will find the name of the current checked-out branch.
;'''Staged Changes''': These are changes that Git will add to the repository the very next time you make a commit.
 
In general, anytime you need to modify the source code, you should NOT do it on the '''master''' branch.  You should create a new branch for your modifications.  Then you can test your modifications ad nauseum until you are sure that everything is functioning as it should.  When your modifications are complete, you can merge them back into the '''master''' branch.  Then the branch you created can be [[#Deleting branches|deleted]]. 
 
The advantage of this approach is that if you ever need to start over from scratch, you can just go back to the '''master''' branch and you will get back the state of the code before your modifications were added.
 
=== Creating branches ===
 
To create a new branch, go to the '''Branch/Create''' on the menu (or type '''CTRL-N''').  You will get a dialog box that prompts you for the new branch name.  Type a unique name and then click OK. 
 
You should pick names that have meaning to you.  Some good branch names are:
 
* Bug_fix_sulfate_mod
* CO2_simulation
* KPP_with_isoprene
* Methane_simulation
 
etc.  To switch between branches, go to '''Branch/Checkout''' on the menu and pick the name of the branch you would like to switch to.  The current branch name will be displayed just below the menu at top left.
 
Once you have created your branch and have checked it out, then you may begin making modifications to the source code with your favorite text editor.
 
=== Committing ===
 
With Git, you should commit frequently, such as when you have completed making revisions to a file or group of files.  Commits that are made on one branch will not affect the other branches. 
 
Committing is best done with the '''git gui'''.  Basically you follow these steps:
 
# To force the '''git gui''' to show the latest changes, you can pick '''Commit/Rescan''' from the menu (or type the F5 key).
# You should get a list of files in the '''Unstaged Changes''' window.  Clicking on the icons on the left of the file names will send them to the '''Staged Changes''' window.  Once they are in the '''Staged Changes''' this means that Git will add them to the repository on the very next commit. Note: Clicking on the icon of the files in the '''Staged Changes''' moves back the file to the '''Unstaged Changes''' window.
# Type a '''Commit message''' in the bottom right window.  [http://spheredev.org/wiki/Git_for_the_lazy#Writing_good_commit_messages See this example of a good commit message].  Some pointers are:
## The first line should only be 50 characters or less and succinctly describe the commit
## Then leave a blank line
## Then add more in-depth text that describes the commit
## Then click on the '''Signed-off by''' button.  This will add your name, email address, and a timestamp.
# There are two radio buttons above the '''Commit message''' window.
##New commit: This is the default.  Assumes we are making a totally new commit.
##Amend last commit: If for whatever reason we need to update the last commit message, pick this button.
# Then when your commit message is done, you can click on the '''Commit''' button.
 
Then if you [[#Viewing the revision history|start the '''gitk''' viewer]], your new commit should be visible.
 
=== Merging ===
 
When you are ready to merge your changes back into the mainline '''master''' branch, then you can follow this procedure.
 
# Switch back to the '''master''' branch by selecting '''Branch/Checkout''' from the menu (or type  '''CTRL-O''').  You will be given a dialog box of available branches.  Select '''master''' and press OK.
# From the menu, pick '''Merge/Local Merge''' (or '''CTRL-M''').
 
This should merge your changes back into '''master'''.  If you then use the [[#Viewing the revision history|the '''gitk''' viewer]], then the merge you just made should be visible.
 
=== Tagging ===
 
Git also allows you to tag a particular commit with an alphanumeric string for easy reference.  This tag will allow users to just refer to the tag name using '''git pull'''. 
 
Tagging is best done outside of the '''git gui'''.  You can just type:
 
git tag GEOS-Chem v8-03-01
git tag GEOS-Chem v8-03-01-patched
 
etc. at the Unix command line.
 
NOTE: Tagging is something that typically only the GEOS-Chem support team will do.
 
=== Deleting branches ===
 
Once you have merged your changes back into the '''master''' branch, you may delete the branch you just created.  In the '''git gui''', go to the '''Branch/Delete''' menu item.  You will be given a dialog box where you can select the name of the branch you wish to delete.
 
== Sharing your revisions with others (and vice versa) ==
 
One of the really nice features of Git is that it can create '''patch files''', or files which contain a list of changes that can be imported into someone else's local Git repository.  Using patch files totally obviates the need of having to merge differences between codes manually.
 
=== Creating a patch file to share with others ===
 
To create a patch file of your '''master''' branch, type the following text:
 
git format-patch master --stdout > my-patch-file.diff
 
This will pipe the output from the '''git format-patch''' command to a file named by you.  You can then include the patch file as an email attachment and send it to other GEOS-Chem users, or the GEOS-Chem Support Team.
 
NOTE: You can create a patch file from other branches by just supplying the name of the branch (i.e. replace the text <tt>master</tt> in the above example w/ the name of the branch whose revisions you want to share).
 
=== Reading a patch file into your local repository ===
 
Other users can also send you their source code revisions as patch files.  To ingest their changes into your local Git repository you should first [[#Creating branches|make a new branch]].  Follow this procedure:
# Pick '''Branch/Create''' from the menu (or type '''CTRL-N''').  Give your branch a descriptive name like <tt>Updates_from_xxxx</tt>" that will serve as a mnemonic.
# Pick '''Branch/Checkout''' from the menu (or type '''CTRL-O''') and switch to the branch you just created.
# To ingest the other person's source code changes, type:
 
      git am < their-patch-file.diff
 
You can then test the other person's revisions in the separate branch until you are sure they are OK.  Then you can [[#Merging|merge them back into the '''master''' branch]] as described above.
 
== Getting updates from the remote repository ==
 
When a new GEOS-Chem version is released, we recommend that you [[#Downloading a new GEOS-Chem version|download it into a new local directory]] with the '''git clone''' command.
 
However, there may be times when "patches" (i.e. minor updates to fix bugs or other issues) need to be applied to an existing GEOS-Chem version.  The easiest way to obtain patches is to use the '''git pull''' command, as follows:
 
# Change to your local code directory (e.g. <tt>Code.v8-03-01</tt>)
# [[#Creating branches|Make a new branch]] named '''patch''' (or something similar).
# [[#Creating branches|Check out]] the '''patch''' branch.  Now we are ready to obtain the updates from the remote server.
# Use the '''git pull''' command to download the updated files, as follows:
## Jacob group users type: <tt>git pull /as/pub/git/bmy/gamap2 master</tt>
## All others users type:  <tt>git pull git://git.as.harvard.edu/bmy/GEOS-Chem master</tt>
# Test: compilation and few time steps to make sure everything is fine
# [[#Creating branches|Check out]] the '''master''' branch.
# [[#Merging|Merge]] the '''patch''' branch into your '''master''' branch.
# [[#Deleting branches|Delete]] the '''patch''' branch.
 
This will merge the changes from the '''master''' branch of the remote repository into your '''master''' branch.
 
--[[User:Bmy|Bob Y.]] 13:04, 16 March 2010 (EDT)
 
== In summary ==
 
We recommend using the '''git gui''' because of its user-friendly interface.  The following operations are best done from the GUI interface:
 
# [[#Creating branches|Creating and checking out branches ]]
# [[#Committing|Committing code]]
# [[#Merging|Merging code]]
# [[#Deleting branches|Deleting branches]]
# [[#Viewing the revision history|Examining revision history]] (you may also use '''gitk''' as standalone)
 
The following operations are best done from the command line:
 
# <tt>git clone</tt>:&nbsp; [[#Initial download|Initial download of repository]]
# <tt>git push</tt>:&nbsp; Send changes to a remote repository
# <tt>git pull</tt>:&nbsp; [[#Getting updates from the remote repository|Get changes from a remote repository]]
# <tt>git tag</tt>:&nbsp; [[#Tagging|Attach a label to a particular commit]]
# <tt>git format-patch</tt>:&nbsp; [[#Creating a patch file to share with others|Create a patch]]
 
--[[User:Bmy|Bob Y.]] 10:14, 19 March 2010 (EDT)

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