Bug #3195
closedCheck all documentation for 1.0 release
0%
Description
All of the documentation needs to be checked for accuracy and completeness before the 1.0 release, which is currently scheduled for April 25.
Updated by Chad Berkley about 16 years ago
Kirsten has found a bunch of actors that still have no documentation. Here's the current list:
AddPointToSVG (no documentation--IN BOTH HEIRARCHIES)
AlignmentEditor(Seaview) (no docs)
AnyofParameter (no docs)
ArchiveCounter (no docs)
ArrayAppend (no docs-- IN BOTH HEIRARCHIES)
ClustalWSeqAlign (no docs)
CopyFromNode (no docs)
CopyToNode (no docs)
CreateExpressionFromQuery (no docs)
CreateRequestFromResult (no docs)
EndPlanFile (no docs)
ExecuteOnNode (no docs)
GAMESSPlanFileGenerator (no docs)
GriddlesFileCopy (no docs)
HistogramPlotter (no docs)
JCOGGridFTP ("docs coming soon"; Jagan Kommineni)
JCOGProxyExec ("docs coming soon")
JCOGWorkflowExec ("docs coming soon")
JRunCIPRes (no docs)
JobCreator (no docs)
JobGetDirectory (no docs)
JobGetRealJobID (no docs)
JobManager (no docs)
JobRemover (no docs)
JobStatus (no docs)
JobSubmitter (no docs)
Logger (no docs)
MappedLogger (no docs)
MastOpalInput (no docs)
MemeOpalInput (no docs)
OnError (no docs)
OneofParameter (no docs)
PAUPConsensustrees (no docs)
RandomParameter (no docs)
RangePointsParameter (no docs)
RangeStepParameter (no docs)
RunCompositeActor (no docs)
SRBAddMetadata (no docs)
SRBSput (no docs)
SRBStreamPut (no docs)
SequenceScope (no docs)
ServerExecute (no docs)
SingleParemeter (no docs)
Sleep (no docs)
StartPlanFile (no docs)
Substitute (no docs)
SyncOnTerminator (no docs)
TempActor (no docs)
TriggeredEnumItem
Updated by Chad Berkley about 16 years ago
page 13: Kepler 1.0 is based on the Jan 31 ...
It's based on Ptolemy 7 beta 2
page 13: cheminformatics
is that the right word?
page 14: visual editor based on java
It's written in java, not based on it.
page 15: toplevel
should be "top level"
page 16: version 1 was released Feb 28, 2008
May 2, 2008 (at this point)
page 18: To create an anonymous...
The commands are not creating an account, they are using the anonymous account to
check out kepler from the CVS server. It should read something like
"To anonymously check out the Kepler source code..."
This section should probably also have the commands needed, i.e.
export CVS_RSH=ssh
export CVSROOT=:ext:anonymous@cvs.ecoinformatics.org:/cvs
cvs checkout kepler
page 19: documentation is in the kepler-docs module...
should this be in courier? Maybe just a side note or something
page 19: typo: ...account to be able to do register.
page 22: 296 MB
change to 300 MB
page 22: CPU 2 GHz
either this needs to be "CPU:..." or it should be "2 GHz CPU..."
page 22: it looks like there are some missing dashes after "Network connection..."
and "R software..."
page 23: the version of R that is distributed with kepler is now 2.6.2
page 24: screen shots say RC1 on them. might want to redo them.
page 24: wrong verison of R (2.4.0)
page 25: we are now distributing a version of kepler for the mac with R
page 25: download instructions for the mac installer are wrong. It will be
distributed as a jar file, which can be double clicked on, but there is
no decompression step. Also, no shortcut will appear on the desktop for the mac.
page 26: need to redo the linux installer section when that installer is done
page 26: the kepler icon will not be on the desktop for the mac. it will be
in Applications/Kepler. The user can drag it to the desktop or the dock if
he/she desires.
page 34: 2.4.3 seems to indicate that there is only a search field for data
when there is a search field for components too
page 35: the heading for 2.4.3.2 is widowed. it should be down on 36.
page 36: "The Kepler EarthGrid". This should be refered to as the EarthGrid,
not the "kepler earthgrid".
page 37: "~" is not a command, it's a shortcut or alias. the command to
move to your home dir is 'cd ~'
page 37: telling a user to "manually empty the cached version" is dangerous.
I don't think we should ever tell a user to delete stuff from the .kepler
directory.
page 39: the 2.4.4 is widowed
page 41: should probably say "see ptolemy docs" when referring to changing
an actor to a class
page 42: is there a screenshot missing? the navigation area section
seems empty
page 59: the font size gets strangely small above figure 3.14
page 60: figure 3.15, the caption is half bold, half normal
page 60: the chart is widowed
page 62: the text type in the table changes to courier in the arrayType
description
page 73: 4.2.2 heading has two sizes of fonts
page 80: the caption for figure 4.10 is orphaned on the next page
page 81: $kepler should be kepler
page 85: figure 4.15 caption refers to the "kepler earthgrid". should just be
"earthgrid"
page 89: kepler earthgrid
made it to page 103. continue the rest tomorrow.
Updated by Christopher Brooks about 16 years ago
Chad wrote:
page 13: Kepler 1.0 is based on the Jan 31 ...
It's based on Ptolemy 7 beta 2
Kepler 1.0 is based on Ptolemy II 7.0.2
page 22: CPU 2 GHz
either this needs to be "CPU:..." or it should be "2 GHz CPU..."
BTW - I run Kepler on a 1.8Ghz laptop and it is fine. I don't
know if this needs to be changed though.
Updated by Chad Berkley about 16 years ago
page 115: figure 5.17 looks kinda bad. the pull out box needs to be redone.
page 122: reference to the "kepler earthgrid"
page 124: "easily enlarged". I don't think this is the right terminology.
Maybe "easily appended" or something.
page 128: "Components Access area". I haven't seen the library refered to
like this before. I think it's kind of confusing.
page 129: Array Max is widowed.
page 130: Data Query is widowed
page 131: directors is widowed
page 133: GAMES is TBD in red
page 134: image processing is widowed
page 135: select is widowed
page 138: units is widowed
page 142: Tools/Create composite actor does not do the same thing as dragging
a composite from the library. this should be made clear. the "create composite
actor" menu creates a composite actor from whatever components are highlighted
on the canvas.
page 157: 5.5.2.1 is widowed
page 165: kepler earthgrid
left off at page 170.
Updated by Chad Berkley about 16 years ago
need to update http://www.kepler-project.org/Wiki.jsp?page=Documentation
Updated by Chad Berkley about 16 years ago
page 170: heading of table is widowed
page 181: kepler earthgrid
page 181: table header widowed
page 183: in the description of EML, I think we should say that even though
EML was developed by the ecological community, it is a broad specification
that can easily be used by other domains.
page 183: kepler earthgrid
page 184: "all of the mechanical issues" this phrase seems out of place. maybe
just simplify the phrase a bit.
page 186: table 6.2. need a space between "actors" and "only" in the namespace row
page 197: widowed table
page 206: widowed table
page 213: typo: streches should be stretches
page 221: maybe need a note telling windows users that they may have to install
3rd party software to make scp work.
page 233: SRBQueryMetedata should be SRBQueryMetadata
page 267: R is included with the Mac. Not with linux, though.
left off at page 276
Updated by Chad Berkley about 16 years ago
page 280: The page ends with "can be found here:" but the path after the colon
is not a link.
page 303: include a URL for the ENM demos
page 306: the heading for the PIW workflow is widowed
page 313: we are not yet supporting JDK6. They need to get Java 5
http://java.sun.com/javase/downloads/index_jdk5.jsp
page 314: We do not use the Ptolemy coding style in kepler. This link should
be removed and possibly replaced with the sun java coding best practices:
http://java.sun.com/docs/codeconv/
page 325: section 10.2.2 it needs to be made clear that to use the compilation
mathod that is described, the user must be using the nightly build or some other
pre-compiled development version of kepler. the build/kepler.jar file will
not exist in a source only checkout.
page 336: "...that includes source code" should be "...that includes executable code"
the .class file is not source.
page 337: R is now included with the mac
page 340: it looks like this section is incomplete. there is a small outline at
the bottom of the page.
page 395: EcoGrid should be EarthGrid (or EarthGrid formerly the EcoGrid)
Done with User Manual review.
Updated by Chad Berkley about 16 years ago
finished reviewing the GSG. I checked my changes into CVS with track changes on.
Updated by Kirsten Menger-Anderson about 16 years ago
I've incorporated Chad's User Manual and GSG feedback and created new PDF files of the docs for the 1.0.0 release. Also updated the doc wiki page.
One thing that came up during this process is that not all of the workflows used in screenshots in the User Manual are in the /demos directory (e.g., SRB and a Maxent workflow used to illustrate the ExternalExecution actor--others as well). It would be nice if these workflows were more easily accessible to users (most are in the workflows directory). I do not currently have a complete list of workflows, but perhaps this can be a todo for the next release?
Updated by Chad Berkley almost 16 years ago
I have now reviewed all documentation. Kirstin is making changes and will have the pdf files for the release hopefully by wednesday.