Feat: prepare for pypi distribution

[dapineyro]

Overview

This PR adds the necessary changes to be able to upload this repository to PyPI.

Jira

https://lifebit.atlassian.net/browse/LP-30465

Changes

• The name of the module has changed from cloudos to cloudos_cli. This was necessary as there is already an unrelated cloudos repo in PyPI. This implies:
  • "cloudos" folder has renamed to "cloudos_cli"
  • When importing the module, the import expression should be import cloudos_cli.XXX
• Added GPLv3+ License: it allows free distribution, free usage (even for private users). The only restriction is to re-pack the software and sell it, which is not permitted.
• There were some modifications in setup.py to correctly build the repo for pip

Tests

Install from PIP

# Create a new venv
python -m venv ~/path/to/my/venvs/testpip
source ~/path/to/my/venvs/testpip/bin/activate
# update pip (just in case)
pip install --upgrade pip
# Install cloudos-cli
pip install cloudos-cli

Create some bash variables

CLOUDOS="https://cloudos.lifebit.ai"
MY_API_KEY="xxx"
WORKSPACE_ID="5c6d3e9bd954e800b23f8c62"
PROJECT_NAME="API jobs"
WORKFLOW_NAME="rnatoy"
P1="reads=s3://lifebit-featured-datasets/pipelines/rnatoy-data"
P2="genome=s3://lifebit-featured-datasets/pipelines/rnatoy-data/ggal_1_48850000_49020000.Ggal71.500bpflank.fa"
P3="annot=s3://lifebit-featured-datasets/pipelines/rnatoy-data/ggal_1_48850000_49020000.bed.gff"
JOB_NAME="Test_PIP_cloudos_cli"

Launch a job

cloudos job run \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID \
    --project-name "$PROJECT_NAME" \
    --workflow-name $WORKFLOW_NAME \
    -p $P1 \
    -p $P2 \
    -p $P3 \
    --job-name $JOB_NAME

Check job status

job_id="67b74a796ccfc5767c5794b7"
cloudos job status \
    --apikey $MY_API_KEY \
    --cloudos-url $CLOUDOS \
    --job-id $job_id

Get Job List CSV

cloudos job list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

Get workflow list CSV

cloudos workflow list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

Get projects list

cloudos project list \
    --cloudos-url $CLOUDOS \
    --apikey $MY_API_KEY \
    --workspace-id $WORKSPACE_ID

Import a module into Python script

python
import cloudos_cli.clos as cl

[danielboloc]

LGTM!