vsoch

package main

import (
	"fmt"
)

type Fruit struct {
	Name string
	Color	string
}

vsoch

name: generate-site

on:
  pull_request: []
  push:   
    branches:
      - "main"

jobs:
  Update:

vsoch

vsoch

% clingo dinosaur.lp
% These are blanket facts, statements that each of these is living
% I think these are called atoms
living(vanessa).
living(fernando).
living(maria).

% This tells use size of arms for each living thing
armsize(vanessa, "small").
armsize(fernando, "large").

vsoch

from django.contrib.auth import REDIRECT_FIELD_NAME
from django.shortcuts import render, resolve_url
from myapp.settings import cfg
from myapp import settings
from urllib.parse import urlparse

import uuid


def login_is_required(

vsoch

# This is a small script (that typically I copy paste) on a Google Cloud instance
# to set up an environment to mimic a worker. It includes installing snakemake,
# retrieving a package with the working directory (which typically has the 
# version of snakemake I aim to develop or debug, and then interactively debugging
# or doing this.

sudo apt-get install -y wget bzip2 ca-certificates gnupg2 git
wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
sudo chown -R $USER /opt
bash Miniconda3-latest-Linux-x86_64.sh -b -p /opt/conda 

vsoch

#!/usr/bin/env python

# This is a helper script for the Google Life Sciences instance to be able to:
# 1. download a blob from storage, which is required at the onset of the Snakemake
#     gls.py download <bucket> <source> <destination>
# workflow step to obtain the working directory. 
# 2. Upload logs back to storage (or some specified directory of files)
#    gls.py save <bucket> <source-dir> <destination-dir>
#    gls.py save <bucket> /google/logs/output source/logs

vsoch

FROM ubuntu:16.04
LABEL version="1.0"

ENTRYPOINT [ "/singularity" ]

RUN mkdir -p /APPS /PROFILES
RUN chmod 0777 /APPS /PROFILES
RUN dpkg --add-architecture i386
RUN apt-get update && apt-get -y install wget less vim software-properties-common python3-software-properties apt-transport-https winbind
RUN wget https://dl.winehq.org/wine-builds/Release.key

vsoch

Airflow Feedback

This is feedback about contribution to Apache Airflow.

Background

I first opened up a pull request in early March 2019 to add a Singularity operator to airflow. I am fairly experienced with Singularity (but not Airflow) so largely my strategy was to use an existing operator (Docker) as an example, and go from there. The interaction felt more controlled than usual because I was required to open a JIRA issue, but this wasn't terrible and is understandable for a larger community. A reviewer was very quick

vsoch

#!/bin/bash

# Suggested by Github actions to be strict
# Taken from https://www.github.com/vsoch/pull-request-action
set -e
set -o pipefail

################################################################################
# Global Variables (we can't use GITHUB_ prefix)
################################################################################