Exceptions

From drussel@gmail.com Mon Oct 20 00:24:44 2008 From: Daniel Russel To: imp-dev@salilab.org Subject: Re: [IMP-dev] [IMP-commits] r770 - trunk/doc Date: Mon, 20 Oct 2008 00:24:35 -0700 Message-ID: <3109EDF0-9C37-42AD-BD8C-267E98B8E666@gmail.com> In-Reply-To: <200810200707.m9K77wxV025293@cowbell.compbio.ucsf.edu> MIME-Version: 1.0 Content-Type: multipart/mixed; boundary="===============5962241131028050757==" --===============5962241131028050757== Content-Type: text/plain; charset="utf-8" Content-Transfer-Encoding: quoted-printable Looks good except I think that sending paches to impdev is not a great =20 way to raise changes for discussion. An English description and =20 proposed function signatures (if non trivial functions are propsed) is =20 probably more useful ((and both patches and English is a bit much) On Oct 20, 2008, at 12:07 AM, Notification of IMP commits wrote: > Author: ben(a)SALILAB.ORG > Date: 2008-10-20 00:07:58 -0700 (Mon, 20 Oct 2008) > New Revision: 770 > > Modified: > trunk/doc/usage.xml > Log: > Document > - commit writes for kernel and modules > - modules outside of the IMP repository > - namespace macros > - code maturity > - finding and fixing bugs > > > Modified: trunk/doc/usage.xml > =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D= =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D > --- trunk/doc/usage.xml 2008-10-20 05:38:34 UTC (rev 769) > +++ trunk/doc/usage.xml 2008-10-20 07:07:58 UTC (rev 770) > @@ -152,11 +152,21 @@ > There are also two "general purpose" modules: the misc filename> > module, which contains miscellaneous features which are > generally not used by other modules, and > -the core module, which contains general-=20 > purpose features > -and upon which many other modules depend. The misc filename> module > -can be used for features that do not neatly fit into a specialized =20 > module, > -such as code that implements proposed new methodologies. > +the core module, which contains features =20 > expected to be > +used by almost everybody, and upon which many other modules depend. > +The misc module can be used for features that =20 > do not > +neatly fit into a specialized module, such as code that implements =20 > proposed > +new methodologies. > > + > + > +It is also possible to create your IMP modules outside of IMP =20 > itself. This > +is ideal if you have different licensing requirements, your code is =20 > very > +experimental, or you do not want to share your source code, for =20 > example. > +Of course, if you go down this route, you must do your own book =20 > keeping to > +make sure that the IMP kernel and any modules you depend on are =20 > correctly built > +before your own. > + > > > > @@ -233,7 +243,7 @@ > > Exceptions > Exceptions are classes, so name as for classes, above. Do not =20 > use > -exception specfications, but do document the possible exceptions =20 > thrown by > +exception specifications, but do document the possible exceptions =20 > thrown by > a function with the Doxygen \exception command. > > > @@ -297,6 +307,11 @@ > Avoids namespace pollution, and removes any ambiguity. > > > +Use the provided macros such as

IMP_BEGIN_NAMESPACE code> and
> +IMP_END_NAMESPACE to begin and end the namespace for =20
> the kernel
> +or a module.
> +


> +
> 
>
> 
> @@ -347,14 +362,50 @@
>
>


>
> -
> -Code review
> +
> +Adding code to IMP
>
> -To ensure code quality, additions to the IMP kernel should be =20
> reviewed
> -by the other developers. In general, this means posting a patch =20
> with some
> -explanation of the changes (e.g. suitable for the source control =20
> logs) to the
> -imp-dev(a)salilab.org mailing list. This is mandatory =20
> for
> -changes that:
> +
> +Choosing a module for your code
> +
> +
> +By far the easiest way to contribute to IMP is to create a module =20
> for your
> +specific problem domain. For example, restraints and optimizers =20
> specific to
> +ligands could go in a ligand module. Please =20
> contact Ben
> +to have a new module created. If you feel your code doesn't belong =20
> in its
> +own module, you can add it to the misc module =20
> instead.
> +If you feel your new functionality is of use to everybody and =20
> should live in the
> +core module, you should request this on the =20
> IMP mailing
> +list and have it approved by Ben, who has the final say on where =20
> code should
> +end up. This is partly to prevent the core =20
> module from
> +becoming too bloated with specialized code.
> +
> +
> +
> +Code should generally not be moved from one
> +module to another, unless there is an exceptionally good reason to =20
> do so. If
> +for some reason you do want to move things between modules, ask Ben =20
> to do it.
> +
> +
> +
> +
> +Defining your interfaces
> +
> +
> +Before you sit down and write your new code or change existing =20
> code, you
> +should think about the interfaces. These are the classes and their =20
> methods,
> +without any implementation. It is recommended that you discuss these
> +interfaces on the imp-dev(a)salilab.org mailing list =20
> before you
> +proceed with implementation, so that you do not duplicate work, =20
> others can
> +make valuable suggestions or point out problems, and people are =20
> made aware of
> +your contribution. If you want to add to or change the interfaces =20
> in the
> +kernel or the core module, this discussion is
> +mandatory, since potentially everybody could be affected by your =20
> changes. Any
> +issues raised by users with changes to the kernel or =20
> core
> +must be resolved to their satisfaction before the changes are made. =20
> For clarity,
> +the following should be considered changes that warrant discussion:
> +
> +
> 
> Change the API (e.g. remove or rename existing =20
> methods or
> classes, change the arguments taken by existing methods, change the =20
> behavior
> @@ -364,10 +415,25 @@
> Remove or modify existing test cases. listitem>
> 
>
> -For more minor changes, such as adding new tests, methods and/=20
> or classes
> -(which may change the ABI but not the API), documentation updates, =20
> etc.
> -review is not required but is recommended. para>
> +
> +Conversely, changes in internal implementation or documentation to =20
> any module,
> +or changes in the interfaces of your own modules or the
> +misc module, do not need to be announced, and =20
> neither does
> +the addition of new methods to existing classes, although it may be =20
> helpful
> +to tell people about such changes.
> +
>
> +
> +
> +
> +Creating a patch
> +
> +
> +Generally speaking, to add code to IMP, your changes should be made =20
> to your
> +checkout of the IMP repository, and then a patch generated by using =20
> the
> +svn di command.
> +
> +
> Patches should contain a related set of changes. For example, =20
> a patch
> which adds a new method foo, a new testcase =20
> for
> foo, and some documentation for the
> @@ -384,17 +450,97 @@
> other effects is better than nothing.)
>
> Rationale:
> -Other developers may have external applications and their own in-=20
> progress work
> -which may be adversely affected by your changes. There may also be =20
> disagreement
> -about a change, so discussing it on the mailing list first assures =20
> that a
> -consensus is first reached, rather than other developers later =20
> reverting the
> -change. It is much easier to review a patch if it is small and =20
> contains only
> -relevant changes, and in addition it can generally be applied to =20
> source control
> -virtually unchanged if the code is OK. Test cases also help to =20
> document the
> +It is much easier for others to understand your patch's changes if =20
> it is small
> +and contains only relevant changes. Test cases also help to =20
> document the
> intent of code changes, as well as making sure that the new =20
> additions are not
> accidentally broken in future.
> 
>
> +
> +
> +
> +Committing a patch
> +
> +
> +Once your patch is complete and you have run the testcases to make =20
> sure you
> +didn't break anything, and reviewed the patch to check your work, =20
> it can be
> +committed to the source control system, provided that any interface =20
> changes
> +have been discussed if =20
> required.
> +How this is done depends on whether you have commit rights for the =20
> affected
> +module(s). If you do, you can simply use svn ci. =20
> If you do
> +not, send the patch to the owner of the module for integration, =20
> with a brief
> +description of your changes for the source control logs:
> +
> +
> +
> +IMP kernel
> +
> +All changes to the IMP kernel, since they affect everybody, must be =20
> approved
> +by Ben. Send your patch to imp-dev(a)salilab.org for =20
> integration.
> +
> +
> +
> +
> +core and misc modules
> +
> +Anybody can commit to these modules after approval; ask Ben to get =20
> your
> +account activated.
> +
> +
> +
> +
> +Other modules
> +
> +Domain-specific modules all have a responsible owner, and it is up =20
> to them
> +whether they want to allow others commit rights. Email them and ask =20
> for
> +commit rights (a sysadmin can add these), or send them your patch for
> +integration. If in doubt, post it on the imp-=20
> dev(a)salilab.org
> +mailing list.
> +
> +
> +
> +
> +
> +
> +Code maturity
> +
> +IMP is a work shared by many developers, and they would prefer not =20
> to have
> +spend time working around problems introduced by others elsewhere =20
> in the code.
> +Therefore, it is expected that any code committed to IMP should at =20
> least
> +compile. Any test cases you write for your code should also be =20
> expected to
> +pass, or at least if they do not, you should quickly fix things so =20
> that they
> +do. (As a rule of thumb, your changes should not break the nightly =20
> builds
> +for more than 3 consecutive days; if they do, your changes risk =20
> being reverted.)
> +
> +
> +
> +It is fine to add code to IMP that is not yet fully complete or =20
> ready for
> +others to use (provided that it compiles and tests, as above). =20
> However, any
> +such classes or methods should be marked in their Doxygen comments as
> +immature.
> +
> +
> +
> +
> +
> +Finding and fixing bugs in IMP
> +
> +If you find a bug in IMP, please report it on the
> +IMP bug tracker. =20
> This will
> +ensure it does not get lost. The best way to report a bug is to =20
> provide a
> +short script file that demonstrates the problem.
> +
> +
> +
> +If you create a patch which fixes a bug, please cite the bug ID in =20
> the commit
> +log for that patch. The patch should also include a testcase which =20
> triggers
> +the bug, so that we can ensure your fix for the bug does not break =20
> in future.
> +In many cases, the demonstration script in the bug report can be =20
> trivially
> +adapted into a test case.
> +
> +
> +
> +
> 
>
> 
>
> _______________________________________________
> IMP-commits mailing list
> IMP-commits(a)salilab.org
> https://salilab.org/mailman/listinfo/imp-commits

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From ben@salilab.org Mon Oct 20 00:28:33 2008
From: Ben Webb 
To: imp-dev@salilab.org
Subject: Re: [IMP-dev] [IMP-commits] r770 - trunk/doc
Date: Mon, 20 Oct 2008 00:28:33 -0700
Message-ID: <48FC3321.3000903@salilab.org>
In-Reply-To: <3109EDF0-9C37-42AD-BD8C-267E98B8E666@gmail.com>
MIME-Version: 1.0
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Daniel Russel wrote:
> Looks good except I think that sending paches to impdev is not a great  
> way to raise changes for discussion. An English description and  
> proposed function signatures (if non trivial functions are propsed) is  
> probably more useful ((and both patches and English is a bit much)

Exactly - that's what I say, isn't it? Maybe the text is misleading in
some way? I just say "discuss these interfaces on the imp-dev mailing
list" not the implementations. Or perhaps you're referring to a
different part of the text?

	Ben
-- 
ben(a)salilab.org                      http://salilab.org/~ben/
"It is a capital mistake to theorize before one has data."
	- Sir Arthur Conan Doyle

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From drussel@gmail.com Mon Oct 20 00:30:59 2008
From: Daniel Russel 
To: imp-dev@salilab.org
Subject: Re: [IMP-dev] [IMP-commits] r770 - trunk/doc
Date: Mon, 20 Oct 2008 00:30:55 -0700
Message-ID: 
In-Reply-To: <48FC3321.3000903@salilab.org>
MIME-Version: 1.0
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> Daniel Russel wrote:
>> Looks good except I think that sending paches to impdev is not a  
>> great
>> way to raise changes for discussion. An English description and
>> proposed function signatures (if non trivial functions are propsed)  
>> is
>> probably more useful ((and both patches and English is a bit much)
>
> Exactly - that's what I say, isn't it? Maybe the text is misleading in
> some way? I just say "discuss these interfaces on the imp-dev mailing
> list" not the implementations. Or perhaps you're referring to a
> different part of the text?
The deleted part :-) I need to go to sleep.

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