From 289ef16343afef8969e1b954b09869021eaaaa73 Mon Sep 17 00:00:00 2001 From: xiangli313 Date: Tue, 6 Feb 2024 10:10:31 +0000 Subject: [PATCH] add installation instruction --- DESCRIPTION | 2 +- NEWS.md | 4 ++++ README.Rmd | 6 ++++++ README.md | 8 +++++++- 4 files changed, 18 insertions(+), 2 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 27ddbcb..eaba27d 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: vimpact Title: Vaccine Impact Calculation -Version: 0.1.0 +Version: 0.1.2 Authors@R: c(person(given = "Rich", family = "FitzJohn", diff --git a/NEWS.md b/NEWS.md index 516fc38..e45031b 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,7 @@ +# vimpact 0.1.2 + +* Add to readme installation instruction. + # vimpact 0.1.1 * Able to recognise different no-vaccination scenario types. diff --git a/README.Rmd b/README.Rmd index cb56224..52b8c34 100644 --- a/README.Rmd +++ b/README.Rmd @@ -8,6 +8,12 @@ Support code for impact calculations. +## Installation +Package can be installed via +``` +devtools::install_github("vimc/vimpact") +``` + ## Running tests which rely on PostgreSQL database Some require a PostgreSQL database. These tests will be skipped by default when running locally. To enable them, run the `./scripts/test_db_start.sh` script to run up a Postgres db within a docker container. When finished testing locally run `./scripts/test_db_stop.sh` to stop the container. diff --git a/README.md b/README.md index 9f10157..52b8c34 100644 --- a/README.md +++ b/README.md @@ -8,11 +8,17 @@ Support code for impact calculations. +## Installation +Package can be installed via +``` +devtools::install_github("vimc/vimpact") +``` + ## Running tests which rely on PostgreSQL database Some require a PostgreSQL database. These tests will be skipped by default when running locally. To enable them, run the `./scripts/test_db_start.sh` script to run up a Postgres db within a docker container. When finished testing locally run `./scripts/test_db_stop.sh` to stop the container. -You can connect directly to the Postgres db by running `./scripts/connect_db.sh`. +You can connect directly to the Postgres db by running `./scripts/connect_db.sh` ## Running tests which rely on Montagu database Some tests require access to montagu database. You need to make the montagu science db password available as an env var for these tests to run. You can do this by getting the password from the vault and adding it to `~/.Renviron` as MONTAGU_PASSWORD=. Tests will be skipped if montagu science db password does not exist. `tests/testthat/helper-vimpact.R` will use `.Renviron` to handle db access. `helper-generate_test_data.R` extracts minimal needed data from montagu, and creates an in-memory database against which vimpact functions are run. `vimpact-test-data` stores test data (copied artefacts from github.com/vimc/montagu-reports/oneoff-collate-vimpact-test-data, and uploaded to github.com/vimc/vimpact-test-data). vimpact outputs must be equivalent to the test data for passing tests.