V1.5 2024 03 04 run

.github/actions/install-cmdstan/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Epinowcast
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

.github/actions/install-cmdstan/action.yaml

@@ -0,0 +1,53 @@
+# MIT Licensed action vendored from
+# https://github.com/epinowcast/actions
+
+name: 'Install CmdStan with caching'
+description: 'Install CmdStan with caching'
+inputs:
+  cmdstan-version:
+    description: 'CmdStan version to install (use "latest" for the latest version)'
+    required: false
+    default: 'latest'
+  num-cores:
+    description: 'Number of cores to use for building CmdStan'
+    required: false
+    default: '1'
+
+runs:
+  using: 'composite'
+  steps:
+    - name: Determine CmdStan Version (Unix)
+      if: runner.os != 'Windows' && inputs.cmdstan-version == 'latest'
+      run: |
+        chmod +x ${{ github.action_path }}/scripts/get-latest-release.sh
+        ${{ github.action_path }}/scripts/get-latest-release.sh
+      shell: bash
+
+    - name: Determine CmdStan Version (Windows)
+      if: runner.os == 'Windows' && inputs.cmdstan-version == 'latest'
+      run: ${{ github.action_path }}\scripts\get-latest-release.ps1
+      shell: pwsh
+
+    - name: Set CmdStan Version (Specified)
+      if: inputs.cmdstan-version != 'latest'
+      run: echo "CMDSTAN_VERSION=${{ inputs.cmdstan-version }}" >> $GITHUB_ENV
+      shell: bash
+
+    - name: Restore Cache
+      id: cache-cmdstan
+      uses: actions/cache@v4
+      with:
+        path: '~/.cmdstan/cmdstan-${{ env.CMDSTAN_VERSION }}'
+        key: ${{ runner.os }}-cmdstan-${{ env.CMDSTAN_VERSION }}
+
+    - name: Check the CmdStan toolchain and repair it if required
+      if: steps.cache-cmdstan.outputs.cache-hit != 'true'
+      run: |
+        Rscript -e 'cmdstanr::check_cmdstan_toolchain(fix = TRUE)'
+      shell: bash
+
+    - name: Install CmdStan using cmdstanr
+      if: steps.cache-cmdstan.outputs.cache-hit != 'true'
+      run: |
+        Rscript -e 'cmdstanr::install_cmdstan(version = "${{ env.CMDSTAN_VERSION }}", cores = ${{ inputs.num-cores }})'
+      shell: bash

.github/actions/install-cmdstan/scripts/get-latest-release.ps1

@@ -0,0 +1,27 @@
+# PowerShell script to fetch the latest CmdStan release version with retry logic
+
+# Initialize retry parameters
+$max_attempts = 5
+$wait_time = 5 # seconds
+
+for ($attempt = 1; $attempt -le $max_attempts; $attempt++) {
+    try {
+        $response = Invoke-RestMethod -Uri "https://api.github.com/repos/stan-dev/cmdstan/releases/latest" -ErrorAction Stop
+        $version = $response.tag_name -replace '^v', ''
+
+        if (-not [string]::IsNullOrWhiteSpace($version)) {
+            "CMDSTAN_VERSION=$version" | Out-File -Append -FilePath $env:GITHUB_ENV
+            Write-Host "CmdStan latest version: $version"
+            break
+        }
+    } catch {
+        Write-Host "Attempt $attempt of $max_attempts failed. Retrying in $wait_time seconds..."
+        Start-Sleep -Seconds $wait_time
+        $wait_time = $wait_time * 2
+    }
+}
+
+if ([string]::IsNullOrWhiteSpace($version)) {
+    Write-Host "Failed to fetch CmdStan version after $max_attempts attempts."
+    exit 1
+}

.github/actions/install-cmdstan/scripts/get-latest-release.sh

@@ -0,0 +1,46 @@
+#!/bin/bash
+
+# Detect the operating system and install jq
+if [[ "$OSTYPE" == "linux-gnu"* ]]; then
+    sudo apt-get update
+    sudo apt-get install -y jq
+elif [[ "$OSTYPE" == "darwin"* ]]; then
+    brew install jq
+else
+    echo "Unsupported OS for this script"
+    exit 1
+fi
+
+# Function to get the latest CmdStan version using GitHub API
+get_latest_version() {
+    local retries=3
+    local wait_time=5
+    local status=0
+    local version=""
+
+    for ((i=0; i<retries; i++)); do
+        version=$(curl -s https://api.github.com/repos/stan-dev/cmdstan/releases/latest | jq -r '.tag_name' | tr -d 'v')
+        status=$?
+        if [ $status -eq 0 ] && [ -n "$version" ]; then
+            echo $version
+            return 0
+        fi
+        sleep $wait_time
+        wait_time=$((wait_time*2))
+    done
+
+    return 1
+}
+
+# Fetch the latest release version of CmdStan
+version=$(get_latest_version)
+
+if [ $? -ne 0 ] || [ -z "$version" ]; then
+    echo "Failed to fetch the latest CmdStan version"
+    exit 1
+fi
+
+# Pass the version to the GitHub environment
+echo "CMDSTAN_VERSION=$version" >> $GITHUB_ENV
+
+echo "CmdStan latest version: $version"

.github/workflows/r-cmd-check.yaml

@@ -0,0 +1,27 @@
+name: R CMD check project package
+
+on:
+  pull_request:
+  push:
+    branches: [main]
+
+jobs:
+  build-and-check:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: r-lib/actions/setup-r@v2
+      with:
+        r-version: 'release'
+        use-public-rspm: true
+        extra-repositories: 'https://mc-stan.org/r-packages/'
+    - uses: r-lib/actions/setup-r-dependencies@v2
+      with:
+        working-directory: cfaforecastrenewalww
+        needs: check
+    - name: "Install cmdstan via cmdstanr"
+      uses: ./.github/actions/install-cmdstan
+    - uses: r-lib/actions/check-r-package@v2
+      with:
+        working-directory: cfaforecastrenewalww
+        error-on: '"error"'

_targets.R

@@ -759,14 +759,22 @@ list(
   ),
 
   # Format data for the hub ----------------------------------------------------
+  tar_target(
+    name = loc_model_map_submission,
+    command = get_loc_model_map(
+      df_of_filepaths_id,
+      hosp_only_states
+    ),
+    deployment = "main"
+  ),
   tar_target(
     name = df_of_filepaths,
     command = get_submission_filepath_df(
       prod_model_type = prod_model_type,
-      hosp_only_states = hosp_only_states,
+      loc_model_map = loc_model_map_submission,
       df_of_filepaths_inf_dyn = df_of_filepaths_id,
       df_of_filepaths_agg = df_of_filepaths_us,
-      df_of_filepaths_hosp_only = df_of_filepaths_ho,
+      df_of_filepaths_hosp_only = df_of_filepaths_ho
     ),
     deployment = "main"
   ),
@@ -797,11 +805,17 @@ list(
   ),
   tar_target(
     name = table_of_state_model_designations,
-    command = get_summarized_table(
-      hub_submission_df,
-      full_diagnostics_df,
-      hosp_only_states,
-      repo_file_path
+    command = do.call(
+      get_summarized_table,
+      c(
+        list(
+          hub_submission_df = hub_submission_df,
+          full_diagnostics_df = full_diagnostics_df,
+          hosp_only_states = hosp_only_states,
+          repo_file_path = repo_file_path
+        ),
+        config_vars_id
+      )
     ),
     deployment = "main"
   ),
@@ -876,14 +890,28 @@ list(
   ),
 
   # Generate "would-be" submissions from each model type -----------------------
+  tar_target(
+    name = is_submitted_forecast,
+    command = FALSE,
+    deployment = "main"
+  ),
+  tar_target(
+    name = loc_model_map_ho,
+    command = get_loc_model_map(
+      df_of_filepaths_ho |> dplyr::filter(location != "US"),
+      hosp_only_states,
+      us_model_type = "hospital admissions only"
+    ),
+    deployment = "main"
+  ),
   tar_target(
     name = df_of_filepaths_hosp_only,
     command = get_submission_filepath_df(
       prod_model_type = "hospital admissions only",
-      hosp_only_states = c(),
+      loc_model_map = loc_model_map_ho,
       df_of_filepaths_inf_dyn = df_of_filepaths_id,
       df_of_filepaths_agg = df_of_filepaths_us,
-      df_of_filepaths_hosp_only = df_of_filepaths_ho,
+      df_of_filepaths_hosp_only = df_of_filepaths_ho
     ),
     deployment = "main"
   ),
@@ -896,8 +924,8 @@ list(
         submitting_model_name = "cfa-wwrenewal_hosp_only",
         submission_file_path = submission_file_path,
         repo_file_path = repo_file_path, # We won't write to the repo
-        prod_run = FALSE, # This is not what we're submitting, even if it is part of a
-        # production run
+        prod_run = is_submitted_forecast, # This is not what we're submitting,
+        # even if it is part of a production run
         is_for_public_repo = FALSE
       )
     ),
@@ -938,14 +966,21 @@ list(
     ),
     deployment = "main"
   ),
+  tar_target(
+    name = loc_model_map_ww,
+    command = get_loc_model_map(df_of_filepaths_id,
+      hosp_only_states = c()
+    ),
+    deployment = "main"
+  ),
   tar_target(
     name = df_of_filepaths_ww,
     command = get_submission_filepath_df(
       prod_model_type = prod_model_type,
-      hosp_only_states = c(),
+      loc_model_map = loc_model_map_ww,
       df_of_filepaths_inf_dyn = df_of_filepaths_id,
       df_of_filepaths_agg = df_of_filepaths_us,
-      df_of_filepaths_hosp_only = df_of_filepaths_ho,
+      df_of_filepaths_hosp_only = df_of_filepaths_ho
     ),
     deployment = "main"
   ),
@@ -958,8 +993,8 @@ list(
         submitting_model_name = "cfa-wwrenewal_all_ww",
         submission_file_path = submission_file_path,
         repo_file_path = repo_file_path, # we won't write to the repo
-        prod_run = FALSE, # This is not what we're submitting, even if it is part of a
-        # production run
+        prod_run = is_submitted_forecast, # This is not what we're submitting,
+        # even if it is part of a production run
         is_for_public_repo = FALSE
       )
     ),

cfaforecastrenewalww/DESCRIPTION

@@ -70,10 +70,12 @@ Suggests:
     covidcast,
     httr,
     knitr,
-    withr
+    withr,
+    testthat
 Additional_repositories: https://mc-stan.org/r-packages/
 SystemRequirements: CmdStan (>=2.34.1)
 RoxygenNote: 7.3.1
 Encoding: UTF-8
 LazyData: true
 Config/testthat/edition: 3
+Config/Needs/check: rcmdcheck, testthat

cfaforecastrenewalww/NAMESPACE

@@ -33,6 +33,7 @@ export(get_hosp_reporting_delay)
 export(get_ind_m)
 export(get_ind_m_cum_sum)
 export(get_init_fun)
+export(get_loc_model_map)
 export(get_low_case_count_diagnostic)
 export(get_metadata)
 export(get_metadata_yaml)