Monthly Archives: March 2023

git logo

Checking out a remote git branch

If you are working on git, sometimes you create a branch on one machine, and then want to get that on your remote machine.

Step 1. Create a branch on the remote machine called rob

git checkout -b rob

Do some work, make some changes, commit some code.

Now I am working on a remote machine in the same repo, but I want my rob branch. Easy!

Git fetch just makes sure we are upto date.

Git branch -v -a lists all remote branches, and provides more information about each. You should see the branch listed as remotes/origin/rob but you don’t need the remotes/origin part.

Git switch allows you to move into the existing remote branch

git fetch
git branch -v -a
git switch rob
Jupyter

Installing The Littlest Jupyter Hub

  1. Start an instance using nectar or jetstream
  2. You don’t need a user account. Possibly
  3. Install jupyterhub:
curl -L https://tljh.jupyter.org/bootstrap.py | sudo python3 -  --admin rob
  1. Allow users to create usernames and passwords:
tljh-config set auth.type nativeauthenticator.NativeAuthenticator
tljh-config reload
  1. Create a username using the web interface
  2. Authorize those users:
add /hub/authorize to your URL. e.g.
http://203.101.227.65/hub/authorize
  1. Install R and Python
apt install r-base nodejs
  1. Start R and install ir-kernel
$ R
> install.packages('IRkernel')
> IRkernel::installspec(user = FALSE)
> quit()

Usermanagement:

If you are having issues with user management you can cheat and get into the SQLIte database

sqlite3  /opt/tljh/state/jupyterhub.sqlite
#find the schema for the user tables
.tables
.schema users_info

CREATE TABLE users_info (
        id INTEGER NOT NULL,
        username VARCHAR(128) NOT NULL,
        password BLOB NOT NULL,
        is_authorized BOOLEAN,
        login_email_sent BOOLEAN,
        email VARCHAR(128),
        has_2fa BOOLEAN,
        otp_secret VARCHAR(16),
        PRIMARY KEY (id)
);

Find out about a user:

select * from users_info;

Authorise a user:

update users_info set is_authorized=1 where username='rob';

select * from users_info;

Should be good to go now!

Calculate the SHA256 checksum

If you create a conda recipe you need to calculate the sha256 checksum. This is a quick post to explain how to do that.

We often submit things to PyPi and then use the PyPi versions to create conda installations. The beauty of this approach is that if you update the PyPi installation, you don’t need to do anything else: the conda bot will automagically notice the new version and update for you. Procrastination pays off again! We talk about this in our PhiSpy blog post.

In the bioconda recipe we usually use this to point to a specific PyPi package for conda to install:

{% set name = "pyctv_taxonomy" %}
{% set version = "0.25" %}
{% set sha256 = "332e54fed6640f61e5c4722c62b9df633921358ba0eb8daf6230711970da2ad9" %}

package:
  name: "{{ name|lower }}"
  version: '{{ version }}'

source:
  url: "https://pypi.io/packages/source/{{ name[0] }}/{{ name }}/{{ name }}-{{ version }}.tar.gz"
  sha256: '{{ sha256 }}'

Note that we have the name (which is lower case) and the version number, and the URL is constructed from the first character of the name, the name, and the name-version.tar.gz. So in this case, the URL would be https://pypi.io/packages/source/p/pyctv_taxonomy/pyctv_taxonomy-0.25.tar.gz

Now there are a couple of ways we can generate the sha256 sum:

URL=<code>https://pypi.io/packages/source/p/pyctv_taxonomy/pyctv_taxonomy-0.25.tar.gz</code>
wget -qO- $URL | shasum -a 256

or

URL=<code>https://pypi.io/packages/source/p/pyctv_taxonomy/pyctv_taxonomy-0.25.tar.gz</code>
curl -sL $URL | openssl sha256

In this case, they both give the same answer:

332e54fed6640f61e5c4722c62b9df633921358ba0eb8daf6230711970da2ad9