chore: sync prod->main

* pin to rocker/tidyverse:4.2
* update Dockerfile to use pak and rspm for package installation
* add workflow_dispatch button

* simplify caching (r-lib/setup-r-dependencies caches by default)
* switch to Ubuntu latest
* keep R on 4.2

first attempt at fixing broken backfill build

[Refactor] Add type hints to `geomap.py` and a small test refactor

feat: add aggregate_by_weighted_sum to geomapper

Weekday adjustment to use Clarabel instead of ECOS

* all linters now use the same configuration file
* add `make format` command to format all code
* make sure all indicators pass with the new config
* update the template files as well
* add a new darker format job to CI
* add python package caching
* update README

feat: unify linter settings across indicators and add incremental formatting

Replace deprecated pkg_resources

* to make nssp run in staging

* add nssp to Jenkinsfile

* nssp_token name change

* et code

* Update nssp/delphi_nssp/run.py

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/README.md

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/DETAILS.md

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/delphi_nssp/__main__.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/pull.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/run.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* readme update

* column names mapping + signals name standardization to fit with other available sources and signals"

* improve readability

* Add type_dict constant

* more type_dict

* add more unit test pull

* data for unit test of pull

* hrr + msa geos

* use enumerate for clarity

* set nssp sircal max_age to 13 days

* set nssp sircal max_age to 15 days, to account for nighttime run

* add validation to params

* Update nssp/DETAILS.md

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/constants.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* et code

* Update nssp/delphi_nssp/run.py

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/README.md

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/DETAILS.md

Co-authored-by: David Weber <david.weber2@pm.me>

* Update nssp/delphi_nssp/__main__.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/pull.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/run.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* readme update

* column names mapping + signals name standardization to fit with other available sources and signals"

* improve readability

* Add type_dict constant

* more type_dict

* add more unit test pull

* data for unit test of pull

* hrr + msa geos

* use enumerate for clarity

* to make nssp run in staging

* add nssp to Jenkinsfile

* nssp_token name change

* set nssp sircal max_age to 15 days, to account for nighttime run

* set nssp sircal max_age to 13 days

* add validation to params

* Update nssp/DETAILS.md

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* Update nssp/delphi_nssp/constants.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* nssp correlation rmd and general notebook folder

* making Black happy

* update to new geomapper function

* following 120 line convention everywhere

* happy linter

* happy black formatter in nssp

* drop unneeded nssp tests

* updates borked old tests, caught by @dshemetov

* rebase woes and version consistency

* Update nssp-params-prod.json.j2 min/max lag to 13

* Update params.json.template min/max lag to 7 and 13

* missed column renames for geo_mapper, unneeded index

* lint+fix: update from linter changes
* add make format to nssp Makefile
* run make format on nssp

* ci: update ci to lint nssp

* lint: linter happy

* lint: pydocstyle happy

* lint: pydocstyle happy

* pct_visits to pct_ed_visits

---------

Co-authored-by: David Weber <david.weber2@pm.me>
Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>
Co-authored-by: Dmitry Shemetov <dshemetov@ucdavis.edu>

* Format county fips to all be 5 digits with leading zeros + Add test

* Update test_pull.py wordings

* linter

)

* remove clarabel spec in weekday, pin claims_hosp cvxpy to <=1.4 and doctor_visits cvxpy to >=1.5

* add solver as param spec

* Update update_sensor.py

* linter

* linter

* default to clarabel. ecos for hosp admissions

* linter

* Update claims_hosp/setup.py

Co-authored-by: george <george.haff@gmail.com>

* Apply suggestions from George's review

Co-authored-by: george <george.haff@gmail.com>

* linter

* linter

* linter

* add test get params legacy

* fix test get params legacy

* linter

---------

Co-authored-by: george <george.haff@gmail.com>

* add patching code

* add documentation

* linter

* fix dir name

* Update get_latest_claims_name.py

* remove patch var, use only issue"

* issue -> issue_date for clarity

* fix logger

* unit test

* fix unit test

* lint

* Update doctor_visits/delphi_doctor_visits/patch.py

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

* add download and get_latest_claims_name tests

* Update test_get_latest_claims_name.py test file name

---------

Co-authored-by: nmdefries <42820733+nmdefries@users.noreply.github.com>

Co-authored-by: David Weber <david.weber2@pm.me>

Move pipeline manual to repo

* fix doctor_visits log location (updated to be in shared system indicators log directory)
* Update doctor_visits export_dir

Co-authored-by: minhkhul <118945681+minhkhul@users.noreply.github.com>