API argument changes in EnsemblDb3

arg
changeset	old_name	new_name	summary	file
116:6ab6e42a2cdb	rsync_listdir(..)	rsync_listdir(.., remote_path, ..)	ENH: user can specify remote path for rsync download fixes #10	ensembldb3/download.py
120:7577e60f9ed1	get_features(..)	get_features(.., limit=None, ..)	ENH: added limit argument to Genome.get_features and _Region.get_features	ensembldb3/region.py
127:bad1318b704a	amend_species(..)	amend_species(.., synonym='', ..)	ENH: Species now accomodates synonymns for species names	ensembldb3/species.py
130:276c1ba24260	__init__(..)	__init__(.., gene_tree_root=None, ..)	ENH: now support exporting gene and species trees	ensembldb3/related_region.py
130:276c1ba24260	__init__(..)	__init__(.., method_clade_id=None, ..)	ENH: now support exporting gene and species trees	ensembldb3/related_region.py
1:05d8cbcd4ce1	makeLocation(.., End, ..)	makeLocation(.., end, ..)	fixed imports, attribute names and got most compara tests passing	ensembldb/genome.py
1:05d8cbcd4ce1	__init__(.., Start, ..)	__init__(.., start, ..)	fixed imports, attribute names and got most compara tests passing	ensembldb/assembly.py
1:05d8cbcd4ce1	makeLocation(.., Start, ..)	makeLocation(.., start, ..)	fixed imports, attribute names and got most compara tests passing	ensembldb/genome.py
1:05d8cbcd4ce1	getRegion(.., Start, ..)	getRegion(.., start, ..)	fixed imports, attribute names and got most compara tests passing	ensembldb/genome.py
1:05d8cbcd4ce1	__init__(.., End, ..)	__init__(.., end, ..)	fixed imports, attribute names and got most compara tests passing	ensembldb/assembly.py
20:307115d17063	__init__(.., Location, ..)	__init__(.., location, ..)	Location to location	ensembldb/region.py
24:e1a6b2660000	get_genes_matching(.., Symbol, ..)	get_genes_matching(.., symbol, ..)	Symbol attribute to symbol	ensembldb/genome.py
24:e1a6b2660000	get_variation(.., Symbol, ..)	get_variation(.., symbol, ..)	Symbol attribute to symbol	ensembldb/genome.py
24:e1a6b2660000	__init__(.., Symbol, ..)	__init__(.., symbol, ..)	Symbol attribute to symbol	ensembldb/region.py
25:ad142eb6278a	__init__(.., Species, ..)	__init__(.., species, ..)	Species attribute to species	ensembldb/genome.py
25:ad142eb6278a	get_syntenic_regions(.., Species, ..)	get_syntenic_regions(.., species, ..)	Species attribute to species	ensembldb/compara.py
34:5c43b47a0327	run(..)	run(.., numprocs, ..)	ENH: add mulptiple process support for download	ensembldb/download.py
38:7df9b6b79bcd	reduce_dirnames(.., debug=True, ..)	reduce_dirnames(.., debug=False, ..)	code tidy	ensembldb/download.py
3:d680ef4ae915	__init__(.., Release, ..)	__init__(.., release, ..)	global rename of Release attribute/args to release	many files..
4:95a4376bbd11	makeLocation(.., CoordName, ..)	makeLocation(.., coord_name, ..)	global rename of CoordName attribute/args to coord_name	ensembldb/genome.py
4:95a4376bbd11	getRegion(.., CoordName, ..)	getRegion(.., coord_name, ..)	global rename of CoordName attribute/args to coord_name	ensembldb/genome.py
4:95a4376bbd11	__init__(.., CoordName, ..)	__init__(.., coord_name, ..)	global rename of CoordName attribute/args to coord_name	many files..
4:95a4376bbd11	getSyntenicRegions(.., CoordName, ..)	getSyntenicRegions(.., coord_name, ..)	global rename of CoordName attribute/args to coord_name	ensembldb/compara.py
50:bced7db85607	install_one_db(..)	install_one_db(.., verbose=False, ..)	hack to fix strange "table does not exist" issue plus other enhancements	ensembldb/admin.py
50:bced7db85607	InstallTable(..)	InstallTable(.., verbose=False, ..)	hack to fix strange "table does not exist" issue plus other enhancements	ensembldb/admin.py
53:20b892ddc06f	install_one_db(..)	install_one_db(.., force_verwrite=False, ..)	ENH: don't install dbases if already installed	ensembldb/admin.py
62:0ad8b9113e7a	install(.., mysql, ..)	install(.., mysqlcfg, ..)	ENH: take advantage of user specified ENSEMBLDBRC	ensembldb/admin.py
62:0ad8b9113e7a	install_one_db(..)	install_one_db(.., mysqlcfg, ..)	ENH: take advantage of user specified ENSEMBLDBRC	ensembldb/admin.py
62:0ad8b9113e7a	InstallTable(..)	InstallTable(.., mysqlcfg, ..)	ENH: take advantage of user specified ENSEMBLDBRC	ensembldb/admin.py
65:6bd4c90d7834	drop(.., mysql, ..)	drop(.., mysqlcfg, ..)	FIX: update drop command for new mysql config option name	ensembldb/admin.py
75:f68539f8f6af	get_genes_matching(.., Description, ..)	get_genes_matching(.., description, ..)	Description to description	ensembldb/genome.py
76:62ebe17df74e	__init__(.., StableId, ..)	__init__(.., stableid, ..)	StableId to stableid	ensembldb/region.py
77:b376c55b44f1	__init__(.., Rank, ..)	__init__(.., rank, ..)	Rank to rank	ensembldb/region.py
78:3ed4b1a8a2e0	get_variation(.., Effect, ..)	get_variation(.., effect, ..)	Variation.Effect changed to effect	ensembldb/genome.py
78:3ed4b1a8a2e0	__init__(.., Effect, ..)	__init__(.., effect, ..)	Variation.Effect changed to effect	ensembldb/region.py
79:be354cfa17a5	__init__(.., Members, ..)	__init__(.., members, ..)	RelatedRegion.Members to members	ensembldb/related_region.py
80:7befdb218794	__init__(.., Relationships, ..)	__init__(.., relationships, ..)	Relationships to relationships	ensembldb/related_region.py