initial commit

.github/.gitignore

@@ -0,0 +1,2 @@
+*.html
+!*.yaml

.github/actions/pre-commit/action.yaml

@@ -0,0 +1,22 @@
+name: pre-commit
+description: run pre-commit
+inputs:
+  extra_args:
+    description: options to pass to pre-commit run
+    required: false
+    default: '--all-files'
+runs:
+  using: composite
+  steps:
+  - run: python -m pip install pre-commit
+    shell: bash
+  - run: python -m pip freeze --local
+    shell: bash
+  - uses: actions/cache@v4
+    with:
+      path: |
+        ~/.cache/pre-commit
+        ~/.cache/R/renv
+      key: pre-commit-3|${{ env.pythonLocation }}|${{ hashFiles('.pre-commit-config.yaml') }}
+  - run: pre-commit run --show-diff-on-failure --color=always ${{ inputs.extra_args }}
+    shell: bash

.github/workflows/pre-commit.yaml

@@ -0,0 +1,16 @@
+name: pre-commit
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  pre-commit:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: actions/setup-python@v5
+      with:
+        python-version: '3.12'
+    - uses: ./.github/actions/pre-commit

.gitignore

@@ -0,0 +1,45 @@
+# https://books.ropensci.org/targets/projects.html#extra-reproducibility
+_targets/
+targets.log
+.Rproj.user
+.Rhistory
+.Rdata
+.httr-oauth
+.DS_Store
+*.Rproj
+*.swp
+*.yaml
+
+# Don't track compiled model executable
+
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp_hierarchical_w_dispersion
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_phi
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_phi_varying_C
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp_hierarchical
+cfaforecastrenewalww/inst/stan/renewal_ww_hosp_site_level_inf_dynamics
+
+# Don't track data!
+diagnostic_report.html
+repo_data
+input
+output
+
+scratch/EDA.html
+# compiled test executables
+test/test_expgamma_lpdf
+
+# Test results
+*.Rcheck
+
+# Compiled package
+*.tar.gz
+
+# emacs tempfile
+*#
+*~
+.#*
+.~*
+
+# R tempfiles
+Rplots.pdf

.lintr

@@ -0,0 +1,9 @@
+linters: linters_with_defaults(
+    object_usage_linter = NULL,
+    line_length_linter(length = 100),
+    cyclocomp_linter = NULL
+  )
+exclusions: list(
+    ".Rprofile"
+  )
+encoding: "UTF-8"

.secrets.baseline

@@ -0,0 +1,112 @@
+{
+  "version": "1.4.0",
+  "plugins_used": [
+    {
+      "name": "ArtifactoryDetector"
+    },
+    {
+      "name": "AWSKeyDetector"
+    },
+    {
+      "name": "AzureStorageKeyDetector"
+    },
+    {
+      "name": "Base64HighEntropyString",
+      "limit": 4.5
+    },
+    {
+      "name": "BasicAuthDetector"
+    },
+    {
+      "name": "CloudantDetector"
+    },
+    {
+      "name": "DiscordBotTokenDetector"
+    },
+    {
+      "name": "GitHubTokenDetector"
+    },
+    {
+      "name": "HexHighEntropyString",
+      "limit": 3.0
+    },
+    {
+      "name": "IbmCloudIamDetector"
+    },
+    {
+      "name": "IbmCosHmacDetector"
+    },
+    {
+      "name": "JwtTokenDetector"
+    },
+    {
+      "name": "KeywordDetector",
+      "keyword_exclude": ""
+    },
+    {
+      "name": "MailchimpDetector"
+    },
+    {
+      "name": "NpmDetector"
+    },
+    {
+      "name": "PrivateKeyDetector"
+    },
+    {
+      "name": "SendGridDetector"
+    },
+    {
+      "name": "SlackDetector"
+    },
+    {
+      "name": "SoftlayerDetector"
+    },
+    {
+      "name": "SquareOAuthDetector"
+    },
+    {
+      "name": "StripeDetector"
+    },
+    {
+      "name": "TwilioKeyDetector"
+    }
+  ],
+  "filters_used": [
+    {
+      "path": "detect_secrets.filters.allowlist.is_line_allowlisted"
+    },
+    {
+      "path": "detect_secrets.filters.common.is_ignored_due_to_verification_policies",
+      "min_level": 2
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_indirect_reference"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_likely_id_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_lock_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_not_alphanumeric_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_potential_uuid"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_prefixed_with_dollar_sign"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_sequential_string"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_swagger_file"
+    },
+    {
+      "path": "detect_secrets.filters.heuristic.is_templated_secret"
+    }
+  ],
+  "results": {},
+  "generated_at": "2023-09-24T19:52:08Z"
+}

CONTRIBUTING.md

@@ -4,11 +4,11 @@ questions or doubts, don't be afraid to send them our way. We appreciate all
 contributions, and we are looking forward to fostering an open, transparent, and
 collaborative environment.
 
-Before contributing, we encourage you to also read or [LICENSE](https://github.com/CDCgov/template/blob/master/LICENSE),
-[README](https://github.com/CDCgov/template/blob/master/README.md), and
-[code-of-conduct](https://github.com/CDCgov/template/blob/master/code-of-conduct.md)
+Before contributing, we encourage you to also read or [LICENSE](LICENSE),
+[README](README.md), and
+[code-of-conduct](code-of-conduct.md)
 files, also found in this repository. If you have any inquiries or questions not
-answered by the content of this repository, feel free to [contact us](mailto:surveillanceplatform@cdc.gov).
+answered by the content of this repository, feel free to [contact us](https://www.cdc.gov/forecast-outbreak-analytics/contact-us.html)
 
 ## Public Domain
 This project is in the public domain within the United States, and copyright and
@@ -18,21 +18,11 @@ submitting a pull request you are agreeing to comply with this waiver of
 copyright interest.
 
 ## Requesting Changes
-Our pull request/merging process is designed to give the CDC Surveillance Team
-and other in our space an opportunity to consider and discuss any suggested
-changes. This policy affects all CDC spaces, both on-line and off, and all users
-are expected to abide by it.
 
 ### Open an issue in the repository
 If you don't have specific language to submit but would like to suggest a change
 or have something addressed, you can open an issue in this repository. Team
 members will respond to the issue as soon as possible.
 
 ### Submit a pull request
-If you would like to contribute, please submit a pull request. In order for us
-to merge a pull request, it must:
-   * Be at least seven days old. Pull requests may be held longer if necessary
-     to give people the opportunity to assess it.
-   * Receive a +1 from a majority of team members associated with the request.
-     If there is significant dissent between the team, a meeting will be held to
-     discuss a plan of action for the pull request.
+If you would like to contribute, please submit a pull request. We will review it and accept, decline, or suggest changes as appropriate.

LICENSE

@@ -1,4 +1,4 @@
-                                 Apache License
+                              Apache License
                            Version 2.0, January 2004
                         http://www.apache.org/licenses/