fix: restore coverage workflow and README badges

.github/workflows/test-coverage.yaml

@@ -0,0 +1,71 @@
+# 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:
+  push:
+    branches: [main, master]
+  pull_request:
+    branches: [main, master]
+
+name: test-coverage
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  test-coverage:
+    runs-on: ubuntu-latest
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::covr, any::xml2
+          needs: coverage
+
+      - name: Test coverage
+        run: |
+          cov <- covr::package_coverage(
+            quiet = FALSE,
+            clean = FALSE,
+            install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
+          )
+          print(cov)
+          pct <- round(covr::percent_coverage(cov), 2)
+          cat(sprintf("Overall coverage: %s%%\n", pct))
+          writeLines(as.character(pct), "coverage-percent.txt")
+          covr::to_cobertura(cov)
+        shell: Rscript {0}
+
+      - name: Report coverage percent
+        run: |
+          echo "Overall package coverage: $(cat coverage-percent.txt)%"
+
+      - uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7
+        with:
+          fail_ci_if_error: true
+          files: ./cobertura.xml
+          plugins: noop
+          disable_search: true
+          use_oidc: true
+
+      - name: Show testthat output
+        if: always()
+        run: |
+          ## --------------------------------------------------------------------
+          find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
+        shell: bash
+
+      - name: Upload test results
+        if: failure()
+        uses: actions/upload-artifact@v7
+        with:
+          name: coverage-test-failures
+          path: ${{ runner.temp }}/package

README.md

@@ -3,6 +3,8 @@
 <!-- badges: start -->
 [![R-CMD-check](https://github.com/bbuchsbaum/templateflow/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/bbuchsbaum/templateflow/actions/workflows/R-CMD-check.yaml)
 [![pkgdown](https://github.com/bbuchsbaum/templateflow/actions/workflows/pkgdown.yaml/badge.svg)](https://bbuchsbaum.github.io/templateflow/)
+[![test-coverage](https://github.com/bbuchsbaum/templateflow/actions/workflows/test-coverage.yaml/badge.svg)](https://github.com/bbuchsbaum/templateflow/actions/workflows/test-coverage.yaml)
+[![Codecov test coverage](https://codecov.io/gh/bbuchsbaum/templateflow/branch/main/graph/badge.svg)](https://app.codecov.io/gh/bbuchsbaum/templateflow?branch=main)
 <!-- badges: end -->
 
 R client for the [TemplateFlow](https://www.templateflow.org/) archive of neuroimaging templates.

tests/testthat/test_cli_coverage.R

@@ -0,0 +1,123 @@
+# Additional CLI branches not covered by test_cli*.R --------------------------
+
+test_that("tf_cli get lists matching files without downloading present assets", {
+  tmp <- file.path(tempdir(), "tf-cli-get-branch")
+  if (dir.exists(tmp)) unlink(tmp, recursive = TRUE, force = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE, force = TRUE), add = TRUE)
+
+  # Seed a real non-empty JSON asset so get short-circuits before network I/O.
+  tpl_dir <- file.path(tmp, "tpl-TestTpl")
+  dir.create(tpl_dir, recursive = TRUE)
+  asset <- file.path(tpl_dir, "tpl-TestTpl_desc-ref_template_description.json")
+  writeLines('{"Name":"TestTpl"}', asset)
+
+  withr::with_options(
+    list(templateflow.test.forcebundled = TRUE),
+    {
+      cfg <- tf_default_config(root = tmp)
+      cache <- TemplateFlowCache(config = cfg)
+      cache$layout <- tf_build_layout(tmp)
+      client <- structure(list(cache = cache), class = "TemplateFlowClient")
+
+      testthat::local_mocked_bindings(
+        tf_cli_make_client = function(root, autoupdate) client,
+        .package = "templateflow"
+      )
+
+      output <- capture.output({
+        paths <- tf_cli(c("--root", tmp, "get", "TestTpl", "--suffix", "template_description"))
+      })
+      expect_true(length(paths) >= 1)
+      expect_true(any(grepl("template_description", paths)) ||
+        any(grepl("template_description", output)))
+    }
+  )
+})
+
+test_that("tf_cli get errors without a template argument", {
+  expect_error(tf_cli(c("get")), class = "tf_cli_error")
+})
+
+test_that("tf_cli cite and cite --bibtex print citations", {
+  tmp <- file.path(tempdir(), "tf-cli-cite-branch")
+  if (dir.exists(tmp)) unlink(tmp, recursive = TRUE, force = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE, force = TRUE), add = TRUE)
+
+  out_plain <- capture.output(tf_cli(c("--root", tmp, "cite", "MNI152Lin")))
+  expect_true(length(out_plain) >= 1)
+
+  # Keep --bibtex offline: stub DOI conversion at the package boundary.
+  testthat::local_mocked_bindings(
+    tf_to_bibtex = function(doi, timeout) paste0("@article{stub,\n  url = {", doi, "}\n}"),
+    .package = "templateflow"
+  )
+  out_bib <- capture.output(tf_cli(c("--root", tmp, "cite", "MNI152Lin", "--bibtex")))
+  expect_true(any(grepl("@article|doi|MNI|template|http", out_bib, ignore.case = TRUE)))
+})
+
+test_that("tf_cli cite errors without a template argument", {
+  expect_error(tf_cli(c("cite")), class = "tf_cli_error")
+})
+
+test_that("tf_cli meta errors for unknown fields and missing template", {
+  tmp <- file.path(tempdir(), "tf-cli-meta-branch")
+  if (dir.exists(tmp)) unlink(tmp, recursive = TRUE, force = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE, force = TRUE), add = TRUE)
+
+  expect_error(tf_cli(c("meta")), class = "tf_cli_error")
+  expect_error(
+    tf_cli(c("--root", tmp, "meta", "MNI152Lin", "--field", "DefinitelyMissing")),
+    class = "tf_cli_error"
+  )
+})
+
+test_that("tf_cli doctor --fix removes zero-byte and XML error files", {
+  tmp <- file.path(tempdir(), "tf-cli-doctor-fix")
+  if (dir.exists(tmp)) unlink(tmp, recursive = TRUE, force = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE, force = TRUE), add = TRUE)
+
+  client <- TemplateFlowClient(root = tmp)
+  zero <- file.path(tmp, "tpl-MNI152Lin", "zero-stub.nii.gz")
+  dir.create(dirname(zero), recursive = TRUE, showWarnings = FALSE)
+  file.create(zero)
+
+  xml <- file.path(tmp, "tpl-MNI152Lin", "bad.xml")
+  file.copy(testthat::test_path("data", "error_response.xml"), xml, overwrite = TRUE)
+
+  output <- capture.output(tf_cli(c("--root", tmp, "doctor", "--fix")))
+  expect_true(any(grepl("Removed|zero-byte|XML", output, ignore.case = TRUE)))
+  expect_false(file.exists(zero))
+  expect_false(file.exists(xml))
+})
+
+test_that("tf_cli parses --autoupdate and rejects invalid values", {
+  tmp <- file.path(tempdir(), "tf-cli-autoupdate")
+  if (dir.exists(tmp)) unlink(tmp, recursive = TRUE, force = TRUE)
+  on.exit(unlink(tmp, recursive = TRUE, force = TRUE), add = TRUE)
+
+  expect_output(
+    tf_cli(c("--root", tmp, "--autoupdate", "off", "config")),
+    "TEMPLATEFLOW_AUTOUPDATE=off"
+  )
+  expect_error(
+    tf_cli(c("--root", tmp, "--autoupdate", "maybe", "config")),
+    class = "tf_cli_error"
+  )
+  expect_error(tf_cli(c("--root")), class = "tf_cli_error")
+  expect_error(tf_cli(c("--autoupdate")), class = "tf_cli_error")
+})
+
+test_that("tf_cli update --help and refresh --help print usage", {
+  expect_true(any(grepl("Usage:", capture.output(tf_cli(c("update", "--help"))))))
+  expect_true(any(grepl("Usage:", capture.output(tf_cli(c("refresh", "--help"))))))
+  expect_true(any(grepl("Usage:", capture.output(tf_cli(c("doctor", "--help"))))))
+  expect_true(any(grepl("Usage:", capture.output(tf_cli(c("cite", "--help"))))))
+  expect_true(any(grepl("Usage:", capture.output(tf_cli(c("get", "--help"))))))
+})
+
+test_that("tf_cli flag without value errors", {
+  expect_error(
+    tf_cli(c("--root", tempdir(), "ls", "MNI152Lin", "--suffix")),
+    class = "tf_cli_error"
+  )
+})