15 June 2016

I started my Outreachy internship with clear and precise timeline, which was part of my application.

Reality ruined it. I haven’t planned to get ill or to spend too much time figuring out what’s wrong with Vagrant.

That’s what my initial timeline looks like:

And that’s what I’ve done for now:

In each case I’ve added README.test with basic description how to test package manually. It partially replicates man for package, but in some cases I try to mention things like “this programs takes exactly 6 or 7 parameters” or “writes diagnostic messages or errors in input file to stderr - it’s normal when these messages appear”.

And yes, I’ve managed to fix my first bug!

Comparing What I Have Done vs. Ideal Timeline, it seems that I’m almost in time.

But at planning stage I thought I would have enough time to read related articles and could do tests for more that 2 packages per week.

Nope! Because some packages are more complex and require more time to spend comparing to other. Some of the reasons are:

  • complex built system,
  • different submodules involved in call with different parameters,
  • package dependencies,
  • etc.

Last package I worked on - pdb2pqr - is a huge pipeline, which has a collection of tests accompanying source code. But I haven’t made these tests work yet. To run them via autopkgtest requires to install them with additional scons files to proper locations. I haven’t figured out yet what files should I install to make installed tests work, and decided to check everything is ok first.

It turned out that with one specific parameter all goes wrong, because some files are not installed. Well, I fixed that and checked again. It turned out that during call with the same specific parameter program also uses networkx library. Well, I added it to debian/control as package dependency (but still not sure if I should add it to ‘Recommends’ or ‘Depends’ list). I decided to stop there, with 3 tests added and 4 lintian warnings removed. And to look again several days later.

Next package to look at should be Predictprotein or r-cran-bio3d. First one seems to require older version of perl (and I’ll probably have to figure out how to mention it in debian/control file), second is too complex, and I’ll have to refresh my R skills, yay! But it definitely will be very time-consuming. I even plan to make blog post on how to use it and probably try to write some .Rmd script.

For now, I’ve made a good very good decision to figure out how to work with package located in SVN repository, without waiting if someone moves it to Git for me.

Next possible good decision is already planned: to make small Atom plugin (or bash script, or whatever - it can be anything, but I like to edit files in Atom) to create ‘template’ files with repeated content for packages I start working on, to open these new template files in Atom (or open existing files, if they already present).

Hope this future decision - to automate repeated parts - will make my timeline look pessimistic rather than realistic.

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