#--------------------
# Basic GO cvs setup:
#--------------------

# set an environment variable to change your default text editor to emacs
setenv EDITOR "emacs"

# set an environment variable to use ssh with cvs:
setenv CVS_RSH ssh

# alias to change ssh password
alias sshpassword 'ssh -t [username]@ext.geneontology.org passwd'

# cvs checkout and update commands
# the final '-d' will add new folders and the '-P' will remove empty directories.
alias cvs 'cvs -q -d :ext:[username]@ext.geneontology.org:/share/go/cvs'
alias cvsco 'cvs -q -d :ext:jenclark@ext.geneontology.org:/share/go/cvs co -A go' 
alias cvsup 'cvs -q -d :ext:jenclark@ext.geneontology.org:/share/go/cvs update -d -P -A'
alias update 'update -d -P -A'

#-----------------------------------------
# To check and commit OBO flatfiles to cvs
#-----------------------------------------

# copy pre-edit file to personal archive 'old'
alias cpo 'cp go/ontology/gene_ontology_edit.obo go/ontology/old/gene_ontology_edit.obo'
	
# diff between working copy and pre-changes copy.
alias do 'diff go/ontology/gene_ontology_edit.obo go/ontology/old/gene_ontology_edit.obo'
	
#diff between cvs copy and edited working copy
alias dcvso 'cvs -q -d :ext:[username]@ext.geneontology.org:/share/go/cvs diff go/ontology/gene_ontology_edit.obo | more'

# update 
alias upo 'cvs -q -d :ext:[username]@ext.geneontology.org:/share/go/cvs update -d -P go/ontology/gene_ontology_edit.obo'

# commit 
alias cvso 'cvs ci go/ontology/gene_ontology_edit.obo'

# cvs log commands (to show all log messages on the gene_ontology_edit.obo file)
alias logo 'cvs log go/ontology/gene_ontology_edit.obo | more'


#-----------------------------------
# Other useful GO cvs setup commands
#-----------------------------------

# to see whether your working copy is the same release as the most up to date cvs copy
alias statall 'cvs status go/ontology/gene_ontology_edit.obo' 

# to open the go.numbers file in emacs
alias en 'emacs go/numbers/go_numbers' 

# to open the synonyms file in emacs
alias es 'emacs go/synonyms/Synonyms.txt'

# alias to checkout go with verbose output 
alias verbose 'cvs -t -d :ext:[username]@ext.geneontology.org:/share/go/cvs checkout go'