Set up skeleton API package

.Rbuildignore

@@ -21,3 +21,7 @@
 ^\.covrignore$
 ^\.github$
 \.*gcov$
+^codecov\.yml$
+^.*\.Rproj$
+^\.Rproj\.user$
+^_pkgdown\.yml$

.gitattributes

@@ -0,0 +1 @@
+R/porcelain.R linguist-generated=true

.github/workflows/R-CMD-check.yaml

@@ -8,6 +8,8 @@ on:
 
 name: R-CMD-check
 
+permissions: read-all
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
@@ -47,3 +49,6 @@ jobs:
       - uses: r-lib/actions/check-r-package@v2
         with:
           upload-snapshots: true
+          build_args: 'c("--no-manual","--compact-vignettes=gs+qpdf")'
+          # TODO: add error on NOTE once {daedalus} fns are used
+          # currently not added due to NOTE on {daedalus} import without use

.github/workflows/lint-changed-files.yaml

@@ -0,0 +1,52 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  workflow_dispatch:
+  pull_request:
+    branches: [main, master]
+    paths:
+      - '**.R'
+      - '**.Rmd'
+      - '**/.lintr'
+      - '**/.lintr.R'
+
+name: lint-changed-files
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  lint-changed-files:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::gh
+            any::lintr
+            any::purrr
+            any::cyclocomp
+          needs: check
+
+      - name: Install package
+        run: R CMD INSTALL .
+
+      - name: Extract and lint files changed by this PR
+        run: |
+          files <- gh::gh("/repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/files")
+          changed_files <- purrr::map_chr(files, "filename")
+          all_files <- list.files(recursive = TRUE)
+          exclusions_list <- as.list(setdiff(all_files, changed_files))
+          lintr::lint_package(exclusions = exclusions_list)
+        shell: Rscript {0}
+        env:
+          LINTR_ERROR_ON_LINT: true

.github/workflows/test-coverage.yaml

@@ -8,6 +8,8 @@ on:
 
 name: test-coverage
 
+permissions: read-all
+
 jobs:
   test-coverage:
     runs-on: ubuntu-latest
@@ -24,23 +26,32 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::covr
+          extra-packages: any::covr, any::xml2
           needs: coverage
 
       - name: Test coverage
         run: |
-          covr::codecov(
+          cov <- covr::package_coverage(
             quiet = FALSE,
             clean = FALSE,
             install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
           )
+          covr::to_cobertura(cov)
         shell: Rscript {0}
 
+      - uses: codecov/codecov-action@v4
+        with:
+          fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }}
+          file: ./cobertura.xml
+          plugin: noop
+          disable_search: true
+          token: ${{ secrets.CODECOV_TOKEN }}
+
       - name: Show testthat output
         if: always()
         run: |
           ## --------------------------------------------------------------------
-          find ${{ runner.temp }}/package -name 'testthat.Rout*' -exec cat '{}' \; || true
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
         shell: bash
 
       - name: Upload test results

.github/workflows/update-citation-cff.yaml

@@ -0,0 +1,59 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/master/examples
+# The action runs when:
+# - The DESCRIPTION or inst/CITATION are modified
+# - Can be run manually
+# For customizing the triggers, visit https://docs.github.com/en/actions/learn-github-actions/events-that-trigger-workflows
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - DESCRIPTION
+      - inst/CITATION
+      - .github/workflows/update-citation-cff.yaml
+  workflow_dispatch:
+
+name: Update CITATION.cff
+permissions:
+  contents: write
+  pull-requests: write
+
+jobs:
+  update-citation-cff:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    steps:
+      - uses: actions/checkout@v4
+      - uses: r-lib/actions/setup-r@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: |
+            any::cffr
+            any::V8
+
+      - name: Update CITATION.cff
+        run: |
+
+          library(cffr)
+
+          # Customize with your own code
+          # See https://docs.ropensci.org/cffr/articles/cffr.html
+
+          # Write your own keys
+          mykeys <- list()
+
+          # Create your CITATION.cff file
+          cff_write(keys = mykeys)
+
+        shell: Rscript {0}
+      - name: Create Pull Request
+        uses: peter-evans/create-pull-request@v6
+        with:
+          commit-message: Update `CITATION.cff`
+          title: Update `CITATION.cff`
+          body: |
+            This pull request updates the citation file, ensuring all authors are credited and there are no discrepancies.
+
+            Please verify the changes before merging. 
+          branch: update-citation-cff

.lintr

@@ -1,6 +1,20 @@
-linters: linters_with_defaults(
-    object_length_linter = NULL,
-    object_usage_linter = NULL,
-    cyclocomp_linter = NULL
-    )
-exclusions: list("tests/testthat.R", "R/cpp11.R")
+linters: all_linters(
+	indentation_linter = NULL, # unstable as of lintr 3.1.0
+	extraction_operator_linter = NULL # allow R6 syntax from {porcelain}
+	)
+exclusions: list(
+	"R/porcelain.R" = list(
+		object_name_linter = Inf # allow fn name `__porcelain__`
+	),
+	"tests/testthat.R" = list(
+		unused_import_linter = Inf,
+		undesirable_function_linter = Inf # allow library() calls
+	),
+	"tests/testthat/test-main.R" = list(
+		implicit_integer_linter = Inf # allow port notation without integer L
+	),
+	"vignettes" = list(
+		undesirable_function_linter = Inf
+	),
+	"R/cpp11.R"
+	)

DESCRIPTION

@@ -1,17 +1,33 @@
 Package: daedalus.api
-Title: Package Title Here
-Version: 0.1.0
+Title: Serve the 'daedalus' model via an API
+Version: 0.0.1
 Authors@R: c(
-    person("First", "Last", , "email@example.com", role = c("aut", "cre")),
+    person("Pratik", "Gupte", , "p.gupte24@imperial.ac.uk", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0001-5294-7819")),
     person("Imperial College of Science, Technology and Medicine", role = "cph")
   )
-Description: Description of the pacakge in more than one full sentence.
+Description: API server for the 'daedalus' model, using 'porcelain' and
+    'plumber'.
 License: MIT + file LICENSE
-URL: https://github.com/j-idea/daedalus.api
-BugReports: https://github.com/j-idea/daedalus.api/issues
-Suggests:
+URL: https://github.com/jameel-institute/daedalus.api
+BugReports: https://github.com/jameel-institute/daedalus.api/issues
+Imports: 
+    daedalus,
+    docopt,
+    jsonlite,
+    lgr,
+    porcelain
+Suggests: 
+    httr,
+    mockery,
+    spelling,
     testthat (>= 3.0.0)
+Remotes:
+    jameel-institute/daedalus,
+    reside-ic/porcelain
 Config/testthat/edition: 3
 Encoding: UTF-8
-Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+Language: en-GB
+Roxygen: list(markdown = TRUE, roclets = c("rd", "namespace",
+    "porcelain::porcelain_roclet"))
+RoxygenNote: 7.3.2

LICENSE.md

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 Imperial College of Science, Technology and Medicine
+
+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.

NAMESPACE

@@ -1 +1,3 @@
 # Generated by roxygen2: do not edit by hand
+
+export(api)

R/api.R

@@ -0,0 +1,32 @@
+##' Create an daedalus.api server, a porcelain object
+##'
+##' @title Create daedalus.api
+##'
+##' @param validate Logical, indicating if validation should be done
+##'   on responses.  This should be `FALSE` in production
+##'   environments.  See [porcelain::porcelain] for details
+##'
+##' @param log_level Logging level to use. Sensible options are "off",
+##'   "info" and "all".
+##'
+##' @return A [porcelain::porcelain] object. Notably this does *not*
+##'   start the server
+##'
+##' @export
+api <- function(validate = NULL, log_level = "info") {
+  logger <- make_logger(log_level)
+  api <- porcelain::porcelain$new(validate = validate, logger = logger)
+  api$include_package_endpoints()
+  api
+}
+
+##' @porcelain GET / => json(root)
+root <- function() {
+  versions <- c(
+    list(
+      daedalus = utils::packageVersion("daedalus"),
+      daedalus.api = utils::packageVersion("daedalus.api")
+    )
+  )
+  lapply(versions, function(v) scalar(as.character(v)))
+}

R/daedalus.api-package.R

@@ -0,0 +1,6 @@
+#' @keywords internal
+"_PACKAGE"
+
+## usethis namespace: start
+## usethis namespace: end
+NULL

R/logging.R

@@ -0,0 +1,9 @@
+## See reside-266, might move this into porcelain
+make_logger <- function(log_level) {
+  logger <- lgr::get_logger("daedalus.api", reset = TRUE)
+  logger$set_propagate(FALSE)
+  logger$set_threshold(log_level)
+  appender <- lgr::AppenderConsole$new(layout = lgr::LayoutJson$new())
+  logger$add_appender(appender, name = "json")
+  logger
+}

R/main.R

@@ -0,0 +1,21 @@
+parse_main <- function(args = commandArgs(TRUE)) {
+  usage <- "Usage:
+daedalus.api [options]
+
+Options:
+  --log-level=LEVEL  Log-level (off, info, all) [default: info]
+  --validate         Enable json schema validation
+  --port=PORT        Port to run api on [default: 8001]"
+  dat <- docopt::docopt(usage, args)
+  list(
+    log_level = dat$log_level,
+    validate = dat$validate,
+    port = as.integer(dat$port)
+  )
+}
+
+
+main <- function(args = commandArgs(TRUE)) {
+  dat <- parse_main(args)
+  api(dat$validate, dat$log_level)$run("0.0.0.0", port = dat$port)
+}

R/util.R

@@ -1,3 +1,7 @@
-`%||%` <- function(x, y) { # nolint
-  if (is.null(x)) y else x
+scalar <- function(x) {
+  jsonlite::unbox(x)
+}
+
+package_version_string <- function(name) {
+  as.character(utils::packageVersion(name))
 }