Week Notes: 2

Jan 31, 2022 07:20 · 671 words · 4 minutes read weekly-reviews

Free And Open Source(FOSS) Work

  • At Genenetwork, we switched to invoking guix shell for development purposes. In genenetwork2, we experienced a bunch of build failures because of a failing python-seaborn build. This is tracked in Guix upstream here. To work around this, we patched this in our channel here.
  • Fixed a build error in python-twint here.

  • A tip from work on using Guix channels:

    Unless you are doing a lot of changes to a specific channel(“guix-bioinformatics”), prefer to the use of the “module” as a guix channel rather than loading it manually with the “-L” flag.

  • Updated my channels file to:

      (cons*
   (channel
    (name 'guix-past)
    (url "https://gitlab.inria.fr/guix-hpc/guix-past")
    ;; The following lines allow 'guix pull' to authenticate
    ;; this channel.  It requires a recent Guix (July 2020)
    ;; and can be omitted with older versions.
    (introduction
     (make-channel-introduction
      "0c119db2ea86a389769f4d2b9c6f5c41c027e336"
      (openpgp-fingerprint
       "3CE4 6455 8A84 FDC6 9DB4  0CFB 090B 1199 3D9A EBB5"))))
   (channel
    (name 'gn-bioinformatics)
    (url "https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git")
    (branch "master"))
   %default-channels)

  • Something I learnt when trying to install gn-proxy (in racket): You can’t do a yes | raco pkg install; Instead, run: raco pkg install --auto.

  • Finally merged this.

  • Started insisting on “syncs” during stand-ups. Should people(myself included) feel the need to extensively talk about something, just schedule a sync with the necessary party. Sync is short for “synchronize”.

  • Based off a long mail thread, I documented some task that needs doing this week here.

  • Reviewed:

  • Scheduled a GN101 meet with Rob. Many contributors to our genenetwork eco-system have no background in Genetics or Biology. This meet will fill in those gaps to make things easier on the contributors; in addition to allow any of the GN2 stake-holders to voice any concerns around contributions they may have. I’ll be setting up a BigBlueButton instance for that this week.

  • If you have info manuals, in Emacs, do “C-h i m Guix RET i local-file RET” to get info on “local-file”. I want to get into the habit of using this interface more to look up documentation.

  • Paired with Zach on Saturday. Made guix shell work for him. Figured out the scope of what I wanted to work on this work; and also sync’d up on overlapping work.

Grad School

  • Un-installed GRETL. We used this in one of our classes(Time Series Analysis And Forecasting). I hate this s/w because it’s primarily a UI driven tool(though you can script with it). UI driven tools with many pop-ups are annoying to use in tiling window managers.
  • Made some progress in our group term paper. Started doing daily stand-ups.

Books

  • Skimmed “Semantic Web for the Working Ontologist” 2nd Ed by Dean Allemang and James Hendler. I’ll try reading this later during the year.
  • Started re-reading “The Art of Nonviolent Communication” and finished chapter 1 and 2.
  • Made some progress in: “How To Read A Book”.
  • Started reading: “Bad Science”.

Personal & Miscellaneous

  • I started an early morning waking-up routine where I wake up at 5:30 AM. Only day I woke up late(11:00 AM) was Thursday since I slept late the previous night.
  • I was running out of space because of repeated guix builds ad guix pulls. I deleted docker images and containers– all of them! This cleared up 34.97 GB of memory!
  • Got some insight from a friend on how he goes about designing programs and projects.
  • Created an office checklist in my Bullet Journal. The idea is to use this checklist every time I leave the house in order to prevent myself from forgetting anything important.
  • Tough week with my partner. I kept misgendering them and it hurt them alot. Now I get it– why misgendering is hurtful.
  • I listened to Kenyan Oldies albums:
    • E-Sir’s “Nimefika”
    • Jua Cali’s “Sekta”
    • Kleptomaniax’ “M4E(Maniax 4 Ever)”
  • Hanged out with dear ones at the office on Friday in the evening.
  • Checked up on another friend on Sunday and wound up playing “UnderCover” which was mad fun.