Allow parameterizing via env vars

[nsheff]

Here I have an example of some code that allows a database-backed Python object to be parameterized either via constructor, or via ENV vars:

https://github.com/refgenie/seqcolapi/blob/fa889f818e1858573cb261077fd737af905178af/seqcolapi/scconf.py#L79-L94

I have found this convenient, because to use it I just do something like:

source settings.env
python

Then

db = RDBDict()

which is quite nice, and also cloud-friendly. I have found myself wanting to do this with pipestat. Would it be possible to make the constructor work like this so it can be configured via ENV vars?

I know it's a little different since there's a pipestat config file, and there's nothing like that here.

I wonder if priority_get could help;

https://github.com/databio/yacman/blob/5db6323a6469347abfa16a590fc8b48d21b7b16f/yacman/yacman_future.py#L358-L389

[donaldcampbelljr]

Is this actually already possible? Looks as though we are using priority_get to potentially use any environment variables:

pipestat/pipestat/pipestat.py

Lines 187 to 210 in e7d4237

	self.cfg[SCHEMA_PATH] = self.cfg[CONFIG_KEY].priority_get(
	"schema_path", env_var=ENV_VARS["schema"], override=schema_path
	)
	self.process_schema(schema_path)
	self.cfg[RECORD_IDENTIFIER] = self.cfg[CONFIG_KEY].priority_get(
	"record_identifier", env_var=ENV_VARS["record_identifier"], override=record_identifier
	)
	self.cfg[PIPELINE_NAME] = (
	self.cfg[SCHEMA_KEY].pipeline_name
	if self.cfg[SCHEMA_KEY] is not None
	else pipeline_name
	)
	self.cfg[PROJECT_NAME] = self.cfg[CONFIG_KEY].priority_get(
	"project_name", env_var=ENV_VARS["project_name"], override=project_name
	)
	self.cfg[SAMPLE_NAME_ID_KEY] = self.cfg[CONFIG_KEY].priority_get(
	"record_identifier",
	env_var=ENV_VARS["sample_name"],
	override=record_identifier,
	)

[donaldcampbelljr]

I did confirm that this works fine. The only snag I ran into was sourcing my .env file. I found a package that assisted with this in Python.
https://github.com/theskumar/python-dotenv

Example of Code, assuming main.py and .env are parallel:

from pipestat import PipestatManager
from dotenv import load_dotenv

load_dotenv()
psm1=PipestatManager()
psm1.report(values={"number_of_things":3})