…etect (#134) * chore: run fusen::sepuku() to drop fusen workflow Removes dev/flat_*.Rmd and dev/config_fusen.yaml, strips the "Generated by {fusen}" banners from R/, tests/, and vignettes/. Updates CLAUDE.md to no longer describe the fusen workflow. * feat(detect): parse R code via AST to close detection gaps Rewrite att_from_rscript() to walk the R syntax tree rather than regex-match source text. This closes several gaps reported on GitHub: - #120/#132: false positives from `::` inside string literals or comments (xpath `following-sibling::td`, CSS `label::after`, `sprintf('%s::plot()', ...)`) are now ignored. - #128: `use("pkg", ...)` (R >= 4.4) is now detected. - #129: named-arg forms are supported: `library(package = "pkg")`, `require(lib.loc = ..., package = ...)`, `requireNamespace("pkg", lib.loc = ...)`, `getFromNamespace("fn", "pkg")`, `loadNamespace()`, `asNamespace()`, `attachNamespace()`, `getNamespace()`, `packageVersion()`. Fixture `tests/testthat/f_edge_cases.R` and new test file `tests/testthat/test-edge-cases.R` document the cases. The regex path is kept as a fallback for snippets that fail to parse. * feat(vignettes): quarto-aware engine detection (#131) When vignettes are `.qmd`, att_from_rmds() now contributes `quarto` instead of (or alongside) `rmarkdown` to the vignette dependency list. Mixed .Rmd + .qmd directories contribute both engines. `knitr` is kept in both cases since Quarto uses the knitr engine for R chunks. Closes #131. * feat(rmd): auto-detect `inside_rmd` via knitr options (#106) `att_from_rmd()` and `att_from_rmds()` now default `inside_rmd = NULL` and auto-detect whether they are being called from inside a knit session by looking at `knitr::opts_knit$get("out.format")`. Users no longer have to reason about this flag for the common case. Backwards compatible: explicit TRUE/FALSE is still honored. Closes #106. * docs: update NEWS, regenerate Rd, ignore CLAUDE.md in build - Document the detection-gap fixes and fusen removal in NEWS.md. - Regenerate man/*.Rd with roxygen2 7.3.3. - Add CLAUDE.md to .Rbuildignore so R CMD check stays clean. - Rename a fixture library() target from `dplyr` to `findedge0` to stop the "unstated dependencies in tests" warning. `R CMD check` now returns 0 errors / 0 warnings / 0 notes. * fix: warn instead of silently ignore readLines errors in att_from_rscript Agent-Logs-Url: https://github.com/ThinkR-open/attachment/sessions/a9033401-4988-4a12-a5c9-8c9f73d52493 Co-authored-by: VincentGuyader <10470699+VincentGuyader@users.noreply.github.com> * fix(rmd): default `inside_rmd` to `NULL` to match documented auto-detect The roxygen doc already stated `NULL` (auto-detect) as the default, but `att_amend_desc()` and the deprecated `att_to_description()` still hard-coded `FALSE`. Align the defaults with the documented behavior. * docs(claude): clarify that the `{fusen}` workflow has been removed * fix(tests): expect `inside_rmd: ~` in saved yaml config The default of `att_amend_desc(inside_rmd = ...)` changed from `FALSE` to `NULL` (01c615c) but `test-amend_with_config.R` still compared the serialized yaml against "inside_rmd: no". `yaml::write_yaml()` turns `NULL` into "~", so all 3 snapshot assertions failed on every CI job. Update the expected snapshots to match the new default. * fix(detect): harden AST walker and narrow detection scope Follow-up to the audit of #134: - Walker: handle "empty" call arguments (e.g. `x[, 1]`, `yaml_options[!names(...) %in% ...]`, missing `else` branches). The previous walker crashed with `argument "el" is missing, with no default` on any script containing them, which meant most real R files silently fell back to the legacy regex detector. A new `walk_elem()` helper inspects each sub-expression as a promise and skips empty symbols without forcing them into a local binding. - `att_from_rscript()` gains an `encoding` argument (default `getOption("encoding")`) instead of hardcoding UTF-8. Avoids a regression for Latin-1 / Windows-1252 scripts on Windows. - Restrict `pkg_intro_calls` to the documented set (`library`, `require`, `requireNamespace`, `loadNamespace`, `use`, `getFromNamespace`). `packageVersion()`, `getNamespace()`, `asNamespace()`, `attachNamespace()` are intentionally *not* treated as dependency introducers — they are commonly used for feature detection and would otherwise silently expand `Imports`. - Emit a `warning()` when the AST parser fails and we fall back to the legacy regex detector, naming the offending file. Broken scripts are no longer silently degraded. - Replace `expect_silent()` around `att_from_rmd()` with explicit type and length assertions, and verify the `knitr::opts_knit` auto-detect expression directly rather than re-running the purl pipeline through `system()`. The previous tests were flaky on CI because knitr/purl and `system()` both write to stdout. - Update `test-rscript.R` expectation for `escape_newline.R`: the former assertion (`c("rmarkdown", "glue", "knitr")`) relied on regex false positives inside glue string literals. With AST detection, only `glue` is a real call (via `glue::glue_collapse`); the other two must not be detected. Regenerated `man/*.Rd` with roxygen2. * feat(detect): support fully-qualified intro calls and underscores in fallback - Walker now honours fully-qualified dependency-introducing calls such as `base::library(pkg)`, `base::require(pkg)`, `base::requireNamespace("pkg")`, `base::loadNamespace("pkg")`, and `methods::getFromNamespace(fn, "pkg")`. Previously only the outer namespace was recorded; the inner package was missed. - The legacy regex fallback now accepts `_` in package names. Previously `my_pkg::fn` was truncated to `pkg`, which hit GitHub-hosted packages as soon as a file failed to parse (the fallback is invoked per file, so a single syntax error upstream could corrupt the whole detection). - Roxygen `@details` updated to describe both the new fully-qualified behaviour and the parse-failure fallback warning. - Two new unit tests under `test-edge-cases.R` cover the qualified-call path and the underscore-preserving fallback. * test(dev): add manual detection edge-case harness A ~450-line R script exercising every dependency-detection situation we could enumerate: standard `pkg::fn` and `library()/require()` variants, R >= 4.4 `use()`, `getFromNamespace`, named and positional package args, string literals (xpath, CSS, C++, URLs, sprintf, multiline, raw r"(...)"), comments, empty/missing subscripts, control flow, closures, formulas, S4/R6, `quote/bquote/substitute/expression`, `eval(quote(...))`, deep/wide nesting, semicolons, whitespace around `::`, fully-qualified intro calls (`base::library(pkg)`) and known-limitation cases (e.g. `library(symbol, character.only = TRUE)` captures the symbol, not the string it points to). Two comment blocks at the bottom enumerate EXPECTED_TRUE_POSITIVES and EXPECTED_FALSE_POSITIVES so a maintainer can diff against `att_from_rscript()` output after any change to the detector. Force-added despite `dev/.gitignore: *.R` — the harness is shared maintenance-time infrastructure, not a personal scratchpad, and the `dev/` directory is already `.Rbuildignore`d so it is not shipped to CRAN. * chore: bump version to 1.0.0 Major version bump to mark the new AST-based dependency detector and the set of user-visible changes captured in NEWS.md since 0.4.5: parse-tree detection, `use()`/`getFromNamespace` support, fully-qualified intro calls (`base::library(pkg)`), quarto-aware vignette engine selection, `inside_rmd` auto-detect, and the removal of the `{fusen}` maintenance workflow. * refactor(detect): address Copilot review on walk_elem + @return docs - `walk_elem()`: drop the redundant `missing(el)` guard (the helper is always called with `args[[i]]`, so the arg is always supplied) and reword the comment to state the actual invariant: the element is received as a function argument rather than bound locally, which is what keeps R from forcing the missing-arg value. Copilot review comment on R/att_from_rscripts.R:104. - `att_from_rmds()` `@return`: the old roxygen said "knitr and rmarkdown are added by default". Since we now conditionally pick `quarto`/`rmarkdown` based on the files actually present in the vignette directory, reword the @return to describe the new engine-inference logic. Copilot review comment on man/att_from_rmds.Rd:37. Regenerated `man/att_from_rmds.Rd` with roxygen2. * docs(news): restructure 1.0.0 entry and add walker-robustness fix - Group bullets by topic (detection foundation / new patterns / robustness / vignettes / maintenance) so reviewers and users can scan the change set without reading every line. - Add the previously-missing entry for the AST walker's safe handling of empty call arguments (`x[, 1]`, empty `switch` alternatives, missing `else` branches). Without that fix the walker crashed on almost any realistic script. - Tighten issue references: only keep issue numbers next to bullets whose fix is actually tested and shipped in this release (#106, #120, #128, #131, #132). #129 is partially addressed so it is no longer claimed as closed in NEWS.

Uh oh!

att_amend_desc seems to detect dependencies from css rules ? #132

Description

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions