Don't install scoringutils in the vignette

The vignette should use the scoringutils package made available
via covidHubUtils, rather than trying to install it again (which
can cause an "unload" error).

First pass at removing some the explicit dependency install in the R CHECK workflow

Also removed tidyverse dependency in align.R as part of this cleanup.

Remove RSocrata install

I don't *think* we're downloading anything from Socrata in this package

remove here and textshaping installs from the github workflows

Remove the extraneous "remotes" install in the github workflows

We still have #406 to get the covidHubUtils workflows in better alignment
with those in the hubverse, but for now we're focused on cleaning up workflow installs
per # 404 by either moving them to DESCRIPTION (if they're used) or
deleting them (if they're not).

Fixup to reinstate the specific version for scoringutils

Move covidData to a first-class dependency (rather than 'suggests')

Removing some of the explicit dependency installs from github
workflows broke things, because covidData wasn't being installed
with the command install_deps(NA). Since covidData is used by
covidHubUtils, let's make sure it's always installed and try to
avoid ad-hoc package installation in CI.

Fix vignette errors by making sure the packages in "suggests" are
installed

Remove explicit installs of zoltr and covidData

Let's see what happens when we remove the build steps that install
zoltr and covidData (since these two packages are already listed
as dependencies in covidHubUtils)

fixup PR feedback

Try making sure the package itself is installed

Streamline dependency installs in pkgdown.yaml

.github/workflows/pkgdown.yaml

@@ -21,14 +21,8 @@ jobs:
 
       - name: Install dependencies
         run: |
-          install.packages(c("remotes","devtools", "rmarkdown","tidyverse","DT","here", "pkgdown", "textshaping"))
-          devtools::install_github("epiforecasts/scoringutils")
-          remotes::install_deps(dependencies = NA)
-        shell: Rscript {0}
-
-      - name: Install zoltr
-        run: |
-          devtools::install_github("reichlab/zoltr")
+          install.packages(c("devtools"))
+          remotes::install_deps(dependencies = TRUE)
           devtools::install()
         shell: Rscript {0}
 

.github/workflows/pr_unittest.yaml

@@ -21,13 +21,8 @@ jobs:
           key: r-${{ hashFiles('DESCRIPTION') }}
       - name: Install dependencies
         run: |
-          install.packages(c("remotes","devtools", "rmarkdown","tidyverse","DT","here","RSocrata"))
-          devtools::install_github("epiforecasts/[email protected]")
-          remotes::install_deps(dependencies = NA)
-        shell: Rscript {0}
-      - name: Install zoltr
-        run: |
-          devtools::install_github("reichlab/zoltr")
+          install.packages(c("devtools"))
+          remotes::install_deps(dependencies = TRUE)
           devtools::install()
         shell: Rscript {0}
       - name: Run unit tests
@@ -85,7 +80,7 @@ jobs:
         shell: Rscript {0}
       - name: Render vignettes
         run: |
-          rmarkdown::render("vignettes/covidHubUtils-overview.Rmd")
+          devtools::build_vignettes()
         shell: Rscript {0}
 
 

.github/workflows/r_cmd_check.yaml

@@ -20,23 +20,10 @@ jobs:
           key: r-${{ hashFiles('DESCRIPTION') }}
       - name: Install dependencies
         run: |
-          install.packages(c("remotes","devtools","rmarkdown","tidyverse","DT","here","RSocrata"))
+          install.packages(c("devtools"))
           devtools::install_github("epiforecasts/[email protected]")
-          remotes::install_deps(dependencies = NA)
+          devtools::install_deps(dependencies = TRUE)
         shell: Rscript {0}
-      - name: Install zoltr
-        run: |
-          devtools::install_github("reichlab/zoltr")
-          devtools::install()
-        shell: Rscript {0}
-      - name: Checkout covidData
-        uses: actions/checkout@v3
-        with:
-          repository: reichlab/covidData
-          path: covidData
-      - name: Install covidData
-        run: make recent_data
-        working-directory: ./covidData/code/data-processing
       - name: Check
         run: |
           devtools::check(args = c("--no-tests", "--no-manual", "--no-vignettes"),error_on = "error")

DESCRIPTION

@@ -52,6 +52,7 @@ Description:
     https://covid19forecasthub.org/.
 License: MIT
 Imports:
+    covidData,
     dplyr (>= 0.8.4),
     tibble (>= 2.1.3),
     tidyr (>= 1.0.2),
@@ -86,12 +87,13 @@ LazyData: true
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.2.3
 VignetteBuilder: knitr
-Suggests: 
-    testthat,
-    covidData,
+Suggests:
+    DT,
     knitr,
-    rmarkdown
+    mockery,
+    testthat
 Remotes:
+    reichlab/covidData,
     reichlab/zoltr,
     epiforecasts/[email protected]
 Depends: 

tests/testthat/test-align.R

@@ -1,6 +1,7 @@
-library(tidyverse)
 library(covidHubUtils)
 library(testthat)
+library(tibble)
+library(tidyr)
 
 
 #     Aug/Sep 2021
@@ -51,7 +52,7 @@ test_that("original columns preserved and new columns are correct", {
         )
     )
     reference_dates <- as.Date(c(
-        "2021-08-14", 
+        "2021-08-14",
         "2021-08-14",
         "2021-08-16",
         "2021-08-21",

vignettes/covidHubUtils-overview.Rmd

@@ -67,12 +67,12 @@ We have identified two central use cases for downloading data using `load_foreca
 
 2. Downloading all available forecasts for selected models that are submitted on a set of dates. This is achieved by using a vector of dates in `dates` parameter.
 
-Below are some examples of reading in data. We start by loading the `covidHubUtils` package and the `tidyverse`.
+Below are some examples of reading in data. We start by loading the `covidHubUtils` package.
 
 ```{r message=FALSE}
 library(covidHubUtils)
 library(doParallel)
-library(tidyverse)
+library(ggplot2)
 theme_set(theme_bw())
 ```
 
@@ -433,7 +433,6 @@ The inputs to the `scored_forecasts()` include a `forecasts` data frame created
 
 The `scoringutils` package provides a collection of metrics and proper scoring rules that make it simple to score forecasts against the true observed values. 
 ``` {r}
-# devtools::install_github("epiforecasts/[email protected]")
 library(scoringutils)
 ```