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Revision 396 - (view) (download) (annotate) - [select for diffs]
Modified Tue Feb 18 13:07:32 2014 UTC (5 years, 3 months ago) by markus
File length: 3943 byte(s)
Diff to previous 367 , to selected 155
This is the next intermediate commit.
Its main purpose is to make the package pass the cran checks so that further collaboration is not hindered.
Many of the functions I introduced and documented sparsely are not too probable to survive in their current 
form. 
The reason is the following:
Regarding design this version is in the middle of the path from the aspect oriented version I started with to the hierarchical version I have in mind and could maintain much easier.
E.g. I got rid of package.skeleton and inlinedocs now writes (most of ) the rd files.
This is not true for lists and similar stuff yet.
My final goal would be to get also rid of modify.Rd.file and move its functionality to the functions that now replace 
package.skeleton. 
If that is achieved we would be left with only two steps ( or "aspects").
1.) gather the information from the source into an environment
2.) pass the whole environment to the various Rd file writers that write the completed files instead of parsing the templates

The last step
3.) (filling the *.Rd files with  content)
    
would not be necessary any longer.

I also hope to simplify the first step considerably.
1.1)
When I started the most abstract thing we had to deal with was the list of objects.
This however does not contain generics, methods or classes.
To extract those you need the whole (populated) environment.
So step 1) will in future just populate an environment and leave the details to specialized functions. 
E.g. the (present) object list would then only be created by the function that writes Rd files for functions.
The function that document Methods dont need it.
At the moment the interfaces are in the process of change so that objects, the  environment , Methodlists, lists of Generics  are passed around for everyone to pick what he needs. This intermediate mess is not there to stay.

1.2) 
A second thing that caused a lot of work, was the parsing of the code files to produce the doc links.
I introduced a good deal of duplication here, that is however also not there to stay but a step towards reducing this kind of thing altogether but in tiny steps (seperately for classes methods and so on)
I would very much like to avoid parsing a setMethod (or setClass) statement altogether.
Presently this is necessary to find out the signature of the mehtod in question only to store the doc link relevant info  with the right key to rejoin it later with the other docs for that method.
The effort to do so is enormous. E.g. I have to reassemble the argument list of a setMethod( )call to be sure what is what in the following text. The sad thing is that the R parser does this (effortlessly) anyway when the environment is populated.
Therefore I propose to research the  srcref features in R, that would help us to find the src chunk of a method by asking the 
method object in the environment where it came from and find the preceding comments this way.

This is what I am driving towards.
So the apparent inconsistency is a reflection of ongoing design change.

To faciliate this migration I have also included some more unit tests (27 runit tests now) and some small helper scripts to run them continiously and in parallel whenever the tiniest bit of code in inlinedocs/R is touched. 
You find them in

...testfiles/mm. 

The tests duplicate a lot of code (thereby  asking  for a setup mehtod.) 
To use them as extended documentation I however prioritised readability and therefor made every test independent to understand.

D    pkg/inlinedocs/inst/scratch/inlinedocsTest
D    pkg/inlinedocs/inst/scratch/tw_testIndent.R
D    pkg/inlinedocs/inst/etc/default-function.R
D    pkg/inlinedocs/inst/etc/users.org
D    pkg/inlinedocs/inst/etc/anne-parse.R
D    pkg/inlinedocs/inst/etc/make.R
D    pkg/inlinedocs/inst/etc/tags
D    pkg/inlinedocs/inst/etc/inner.function
D    pkg/inlinedocs/inst/etc/parseRd.R
D    pkg/inlinedocs/inst/etc/anne.R
D    pkg/inlinedocs/inst/etc/minimalErrorPkg
D    pkg/inlinedocs/inst/etc/author.from.author.R
AM   pkg/inlinedocs/inst/testfiles/csall.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.NamespaceExample.R
A    pkg/inlinedocs/inst/testfiles/mm/srcref.example.R
D    pkg/inlinedocs/inst/testfiles/mm/package.skeleton.R
AM   pkg/inlinedocs/inst/testfiles/mm/cisall.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.Infrastructure.R
D    pkg/inlinedocs/inst/testfiles/mm/runit.OperatorDoc.R
AM   pkg/inlinedocs/inst/testfiles/mm/continousRunner.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.AddExampleCodeFromExternalTest.R
A    pkg/inlinedocs/inst/testfiles/mm/help.R
M    pkg/inlinedocs/inst/testfiles/mm/Itest.R
A    pkg/inlinedocs/inst/testfiles/mm/findGenericsAndMethodsWithSrcrefs.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.ClassDoc.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.MethodExample.R
M    pkg/inlinedocs/inst/testfiles/mm/isolatedTestRunner.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.FunctionExample.R
M    pkg/inlinedocs/inst/testfiles/mm/isall.R
AM   pkg/inlinedocs/inst/testfiles/mm/cITest.sh
M    pkg/inlinedocs/inst/testfiles/mm/runit.MethodDoc.R
A    pkg/inlinedocs/inst/testfiles/mm/runit.RepairUsage.R
A    pkg/inlinedocs/inst/testfiles/lastrun
M    pkg/inlinedocs/R/package.skeleton.dx.R
M    pkg/inlinedocs/R/test.R
M    pkg/inlinedocs/R/parsers.R
M    pkg/inlinedocs/R/utils.R
M    pkg/inlinedocs/R/testhelpers.R
M    pkg/inlinedocs/DESCRIPTION
A    pkg/inlinedocs/man/writeMethodRdFiles.Rd
A    pkg/inlinedocs/man/MethodsWithSrcRefForGen.Rd
M    pkg/inlinedocs/man/removeAliasesfrom.Rd.file.Rd
A    pkg/inlinedocs/man/methSrc.Rd
A    pkg/inlinedocs/man/mm.examples.from.testfile.Rd
M    pkg/inlinedocs/man/modify.Rd.file.Rd
A    pkg/inlinedocs/man/sigString.Rd
A    pkg/inlinedocs/man/writeFunctionRdFiles.Rd
A    pkg/inlinedocs/man/removeComma.Rd
A    pkg/inlinedocs/man/rewriteSetMethodArgs.Rd
M    pkg/inlinedocs/man/print.allfun.Rd
A    pkg/inlinedocs/man/extra.class.docs.Rd
A    pkg/inlinedocs/man/pp.Rd
M    pkg/inlinedocs/man/package.skeleton.dx.Rd
A    pkg/inlinedocs/man/definition.from.source.Rd
A    pkg/inlinedocs/man/writePackageRdFile.Rd
A    pkg/inlinedocs/man/extract.docs.Rd
M    pkg/inlinedocs/man/apply.parsers.Rd
A    pkg/inlinedocs/man/z[-methods.Rd
M    pkg/inlinedocs/man/combine.character.Rd
A    pkg/inlinedocs/man/hiddenClasses.Rd
M    pkg/inlinedocs/man/combine.Rd
A    pkg/inlinedocs/man/writeMethodTableRdFiles.Rd
M    pkg/inlinedocs/man/findGeneric.Rd
M    pkg/inlinedocs/man/inlinedocs-package.Rd
A    pkg/inlinedocs/man/getMethodName.Rd
M    pkg/inlinedocs/man/extract.docs.setClass.Rd
A    pkg/inlinedocs/man/exportedFunctions.Rd
M    pkg/inlinedocs/man/extra.code.docs.Rd
M    pkg/inlinedocs/man/make.package.and.check.Rd
A    pkg/inlinedocs/man/allClasses.Rd
M    pkg/inlinedocs/man/save.test.result.Rd
A    pkg/inlinedocs/man/writeClassRdFiles.Rd
A    pkg/inlinedocs/man/exported.Rd
M    pkg/inlinedocs/man/get_S3_primitive_generics.Rd
M    pkg/inlinedocs/man/test.file.Rd
M    pkg/inlinedocs/man/extract.file.parse.Rd
A    pkg/inlinedocs/man/z[_method__listOfMethods_logical.Rd
A    pkg/inlinedocs/man/methodDocName.Rd
A    pkg/inlinedocs/man/exportedClasses.Rd
M    pkg/inlinedocs/man/extract.docs.file.Rd
A    pkg/inlinedocs/man/GenHasAnyMethodWithSrc.Rd
M    pkg/inlinedocs/man/getKnownS3generics.Rd
M    pkg/inlinedocs/man/is_primitive_in_base.Rd
A    pkg/inlinedocs/man/MethodHasSrc.Rd
M    pkg/inlinedocs/man/fixPackageFileNames.Rd
A    pkg/inlinedocs/man/trimmedNonEmptyLines.Rd
A    pkg/inlinedocs/man/getMethodSrc.Rd
A    pkg/inlinedocs/man/methodTable.Rd
A    pkg/inlinedocs/man/MethodSignatureHasOnlyExportedClasses.Rd
M    pkg/inlinedocs/man/replace.one.Rd
A    pkg/inlinedocs/man/CompareTrimmedNonEmptyLines.Rd
M    pkg/inlinedocs/man/get_internal_S3_generics.Rd
M    pkg/inlinedocs/man/forfun.Rd
A    pkg/inlinedocs/man/mmPromptMethods.Rd
M    pkg/inlinedocs/man/getSource.Rd
A    pkg/inlinedocs/man/documentableMeths.Rd
A    pkg/inlinedocs/man/pe.Rd
A    pkg/inlinedocs/man/GenHasAnyExposedMethod.Rd
M    pkg/inlinedocs/man/leadingS3generic.Rd
A    pkg/inlinedocs/man/exportedGenerics.Rd
M    pkg/inlinedocs/man/decomment.Rd
A    pkg/inlinedocs/man/createObjects.Rd
A    pkg/inlinedocs/man/GenHasSrc.Rd
A    pkg/inlinedocs/man/exportedDocumentableMeths.Rd
M    pkg/inlinedocs/man/prefixed.lines.Rd
M    pkg/inlinedocs/man/forall.Rd
A    pkg/inlinedocs/man/title.from.firstline.Rd
M    pkg/inlinedocs/man/kill.prefix.whitespace.Rd
M    pkg/inlinedocs/man/combine.NULL.Rd
M    pkg/inlinedocs/man/combine.list.Rd
A    pkg/inlinedocs/man/extra.method.docs.Rd
A    pkg/inlinedocs/man/inherit.docs.Rd
M    pkg/inlinedocs/man/extract.xxx.chunks.Rd
M    pkg/inlinedocs/man/do.not.generate.Rd
A    pkg/inlinedocs/man/extract.docs.setMethod.Rd
A    pkg/inlinedocs/man/methSig.Rd
A    pkg/inlinedocs/man/manMan
A    pkg/inlinedocs/man/manMan/descfile.names.Rd
A    pkg/inlinedocs/man/manMan/default.parsers.Rd
A    pkg/inlinedocs/man/manMan/lonely.Rd
A    pkg/inlinedocs/man/manMan/nondesc.parsers.Rd
A    pkg/inlinedocs/man/manMan/non.descfile.names.Rd
A    pkg/inlinedocs/man/manMan/forall.parsers.Rd
A    pkg/inlinedocs/man/manMan/forfun.parsers.Rd
A    pkg/inlinedocs/man/manMan/prefix.Rd
M    pkg/inlinedocs/NAMESPACE
M    pkg/inlinedocs/NEWS

Revision 367 - (view) (download) (annotate) - [select for diffs]
Modified Thu Oct 25 10:07:37 2012 UTC (6 years, 7 months ago) by tomaschwutz
File length: 3920 byte(s)
Diff to previous 359 , to selected 155
tryCatch around parse in gen.Rd, workaround on accessor functions failures

Revision 359 - (view) (download) (annotate) - [select for diffs]
Modified Mon Apr 9 21:55:16 2012 UTC (7 years, 2 months ago) by tdhock
File length: 3875 byte(s)
Diff to previous 344 , to selected 155
as-cran for tests

Revision 344 - (view) (download) (annotate) - [select for diffs]
Modified Fri Apr 6 08:36:23 2012 UTC (7 years, 2 months ago) by tdhock
File length: 3829 byte(s)
Diff to previous 307 , to selected 155
copy NAMESPACE from silly package to avoid WARNING

Revision 307 - (view) (download) (annotate) - [select for diffs]
Modified Fri Oct 21 11:37:19 2011 UTC (7 years, 7 months ago) by tdhock
File length: 3787 byte(s)
Diff to previous 275 , to selected 155
test errors reported more clearly

Revision 275 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 27 11:55:21 2011 UTC (8 years ago) by tdhock
File length: 3718 byte(s)
Diff to previous 274 , to selected 155
disable recursive R CMD check

Revision 274 - (view) (download) (annotate) - [select for diffs]
Modified Fri May 27 10:14:41 2011 UTC (8 years ago) by tdhock
File length: 3373 byte(s)
Diff to previous 249 , to selected 155
try to debug cran err

Revision 249 - (view) (download) (annotate) - [select for diffs]
Modified Thu Apr 7 13:58:27 2011 UTC (8 years, 2 months ago) by tdhock
File length: 3329 byte(s)
Diff to previous 247 , to selected 155
docs for make.package.and.check

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Modified Thu Apr 7 13:22:13 2011 UTC (8 years, 2 months ago) by tdhock
File length: 3134 byte(s)
Diff to previous 239 , to selected 155
verbose arg for make.package.and.check

Revision 239 - (view) (download) (annotate) - [select for diffs]
Modified Mon Mar 28 16:07:28 2011 UTC (8 years, 2 months ago) by tdhock
File length: 3113 byte(s)
Diff to previous 204 , to selected 155
check and test

Revision 204 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 16:48:22 2011 UTC (8 years, 3 months ago) by tdhock
File length: 2867 byte(s)
Diff to previous 203 , to selected 155
alternate syntax parser testfile

Revision 203 - (view) (download) (annotate) - [select for diffs]
Modified Fri Feb 18 15:59:29 2011 UTC (8 years, 3 months ago) by tdhock
File length: 2856 byte(s)
Diff to previous 202 , to selected 155
Unit tests accept .parsers variable

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Modified Fri Feb 18 15:54:00 2011 UTC (8 years, 3 months ago) by tdhock
File length: 2845 byte(s)
Diff to previous 156 , to selected 155
check outer list in unit tests

Revision 156 - (view) (download) (annotate) - [select for diffs]
Modified Fri Oct 29 13:06:55 2010 UTC (8 years, 7 months ago) by tdhock
File length: 2611 byte(s)
Diff to previous 155
R CMD check for each testfile

Revision 155 - (view) (download) (annotate) - [selected]
Modified Fri Oct 29 12:12:58 2010 UTC (8 years, 7 months ago) by tdhock
File length: 1817 byte(s)
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erase browser

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Modified Fri Oct 29 12:11:52 2010 UTC (8 years, 7 months ago) by tdhock
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parsefun and extract.docs.fun consolidated into extract.xxx.chunks in ongoing effort to make parser functions more readable and modular

Revision 138 - (view) (download) (annotate) - [select for diffs]
Modified Tue Oct 19 22:51:59 2010 UTC (8 years, 7 months ago) by tdhock
File length: 1817 byte(s)
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update examples to pass new more stringent parser checks

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Modified Fri Jun 18 16:32:29 2010 UTC (9 years ago) by tdhock
File length: 1393 byte(s)
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fermat-inline test, extract.docs.fun now uses nondesc.parsers as the parser list

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Modified Fri Jun 18 09:40:30 2010 UTC (9 years ago) by tdhock
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test.file verbose, tags test, save.test.result doc

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Modified Mon Jun 7 12:33:37 2010 UTC (9 years ago) by tdhock
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test for sublogo

Revision 110 - (view) (download) (annotate) - [select for diffs]
Added Mon Jun 7 12:08:54 2010 UTC (9 years ago) by tdhock
File length: 932 byte(s)
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unit test for extract.docs.file

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