Hi all,
I have a few general questions about best practices in tool development and would like to collect a few opinions. Maybe the Intergalactic Utilities Commission can discuss some points at their first meeting.
1. How to handle dependencies that are not guaranteed to exist for a large time. Sometimes I'm very sceptical about whether upstream will keep every software version for the next X years, which I will define in my tools, e.g. some ftp server for binaries or some beta-versions of actually used software (bowtie2?). Is it possible/wished to create a repository for such software?
2. How to handle different compiler versions or other system level changes? For example with the new gcc-4.7 some 'include'-definitions changed and because of that bowtie2 is not compiling any more. Should we add a feature to ship patches in our tools for such simple workarounds? Or should we rather wait for a new upstream version and not support our tool on such systems?
3. Should we standardize the version numbering of tools to reflect if a update is important or not? For example something like foo.bar.baz. With: foo = major tool-dependency changing: expected result changes bar = minor tool-dependency changing due to bug fixing: results can change but it is not expected baz = no expected changes in the result due to wrapper changes (help-text, adding of new parameters, etc.).
I think in the end we need to decide how much effort do we put into reproducibility over the next X years and how do we guarantee that, either as Community or as Intergalactic Utilities Commission.
What did you think? Björn
[1] http://gcc.gnu.org/gcc-4.7/porting_to.html