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Port over the existing tests and set up CI #11

Merged
merged 108 commits into from
Jul 12, 2024
Merged

Port over the existing tests and set up CI #11

merged 108 commits into from
Jul 12, 2024

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kaitejohnson
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@kaitejohnson kaitejohnson commented Jul 8, 2024 •
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This PR moves over the existing testing infrastructure from https://github.com/CDCgov/wastewater-informed-covid-forecasting, and modifies the tests as needed to fit the new functions. It also sets up CI to run the tests every time there is a PR into main or prod. Other scope creep things it does:

  • adds documentation to the data using data.R
  • includes some but not complete set of examples for exported functions

Definitely need to figure out how to set up caching because the r-cmd-check is taking on the order of 20 min to fail :( I think this can be a separate issue though.

Do we want to set up any other CI? For example, I know @zsusswein set up code-cov (we would not do well right now....) and also a check to make sure that the change log( NEWS.md) was updated every time a PR merges to main

Need to have main merged in once #5 is merged

kaitejohnson and others added 30 commits June 26, 2024 10:06
@kaitejohnson
remove extra files
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@kaitejohnson
add a .gitignore with R and data stuff
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@kaitejohnson
add git ignore from cfa-repo-template
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@kaitejohnson
make .github folder mirror cfa-repo-template
f66494a
@kaitejohnson
remove attributes
d19fe05
@kaitejohnson
add bare bones componets of an R package
eeb3fe6
@kaitejohnson
update description
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@kaitejohnson
add description of package
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@kaitejohnson
Update README.md
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@kaitejohnson
fix pre-commit
fcd6b15
@kaitejohnson
Merge branch 'format-as-package' of https://github.com/CDCgov/ww-infe…
00fac5b 
…rence-model into format-as-package
@kaitejohnson
pre-commit on readme
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@kaitejohnson
attempt to set up pkgdown
d8167b6
@kaitejohnson
correct path to deps
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@kaitejohnson
remove call to package
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@kaitejohnson
Create CODEOWNERS
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@kaitejohnson
Create CONTRIBUTING.md
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@kaitejohnson
Create NEWS.md
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@kaitejohnson
Create SUPPORT.md
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@kaitejohnson
add stan model and start of vignette
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@kaitejohnson
start of generating simulated data
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add parameters, package, more documentation to gen simulated data
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add in functions for getting delay distributions
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add functions needed for generating simulated data
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add simulated data as package data
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@kaitejohnson
add some initial pre-processing functions from other packages
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@kaitejohnson
add functions to preprocess wastewater data
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@kaitejohnson
add minimal hosp data preprocessing
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@kaitejohnson
add internal package data for covid GI and delay
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@kaitejohnson
add functions to create stan data, modify model to be more generally …
c732701 
…based on count data rather than only hosp
@kaitejohnson kaitejohnson marked this pull request as ready for review July 11, 2024 14:02
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Fixing up a few things but think this is almost ready @dylanhmorris however, I don't the pkgdown is working correctly. When I go to Settings >Pages it says that it was deployed 2 weeks ago, and I think it should have been deployed with the latest merge to main?

Edit: added main to pkgdown.yaml, and presuming this should fix it. This is ready for review. Note I moved the COVID delay distributions to delay_distribs.R to keep them as internal package functions.

dylanhmorris
dylanhmorris requested changes Jul 11, 2024
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@dylanhmorris this is ready for re-review

dylanhmorris
dylanhmorris requested changes Jul 12, 2024
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A few things

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@dylanhmorris dylanhmorris mentioned this pull request Jul 12, 2024
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dylanhmorris reviewed Jul 12, 2024
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Minor wording suggestion

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dylanhmorris approved these changes Jul 12, 2024
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Provided the CI checks pass this LGTM!

@kaitejohnson kaitejohnson merged commit 371748c into main Jul 12, 2024
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@kaitejohnson kaitejohnson deleted the 9-port-over-tests branch July 12, 2024 20:02
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