Merge pull request #87 from t-kalinowski/la-updates

Linear algebra support + stricter name/arg validation

Author: t-kalinowski

AGENTS.md

@@ -6,7 +6,7 @@ This project is an R package that transpiles R functions to Fortran.
 R -q -e 'devtools::test()'
 ```
 
-- To run the full `R CMD check` locally:
+- To run the full `R CMD check` locally (this takes a long time):
 ```sh
 R -q -e 'rcmdcheck::rcmdcheck(error_on = "warning")'
 ```
@@ -16,6 +16,17 @@ R -q -e 'rcmdcheck::rcmdcheck(error_on = "warning")'
 R -q -e 'devtools::test_active_file("tests/testthat/test-dims2f.R")'
 ```
 
+- To run a subset of test files:
+```sh
+R -q -e 'devtools::test(filter = "regex")'
+```
+filter arg behavior: If not `NULL`, only tests with file names matching this regular expression will be executed. Matching is performed on the file name after it's stripped of "test-" and ".R".
+
+- To run full coverage and save zero-coverage JSON output:
+```sh
+R -q -e 'covr::package_coverage() -> cov; saveRDS(cov, "cov.rds"); z <- covr::zero_coverage(cov); jsonlite::toJSON(z, pretty = TRUE)'
+```
+
 - To see the generated C and Fortran code for an R function, use `r2f()`:
 ```sh
 R --no-save -q <<'EOF'
@@ -33,10 +44,13 @@ EOF
 
 - Never disable or skip tests.
 
-- When adding tests, prefer user-facing API tests (e.g. `expect_quick_identical()`); avoid asserting on generated Fortran/C translation strings.
+- When adding tests, strongly prefer tests that only excercise the public API (e.g. `expect_quick_identical()`); avoid asserting on generated Fortran/C translation strings unless explicitly asked. Avoid testing internal functions unless explicitly.
+
+- When writing tests, make sure that we test both C/Fortran code generation (typically reported accuratly by covr), as well as calling the generated function (not covered by covr). Our tests must excercise the actual generated function.
+
+- While troubleshooting and iterating towards a solution, you can run targeted single-file tests; After large refactors, always run the full test suite.
 
-- While troubleshooting and iterating towards a solution, you can run targeted single-file tests; before committing/pushing, always run the full test suite and `rcmdcheck`.
-- Before finishing a task, always run the full test suite and `rcmdcheck`.
+- Before opening a PR, always run `rcmdcheck`.
 
 - Prefer extending S7 classes with explicit properties over attaching arbitrary unchecked attributes.
 

NEWS.md

@@ -3,7 +3,15 @@
 - Added initial matrix/linear algebra handler support from base R, using the
   same BLAS/LAPACK as R: `%*%`, `t()`, `crossprod()`, `tcrossprod()`,
   `outer()` (with `FUN="*"`), `%o%`, `forwardsolve()`, `backsolve()`, `diag()`,
-  `t()`, `chol()`, `chol2inv()`, `solve()`, and `qr.solve()`.
+  `t()`, `chol()`, `chol2inv()`, `solve()`, and `qr.solve()`. This includes
+  support for:
+
+  - `drop()` for rank 0-2 inputs (including singleton matrices).
+  - `svd()` results via `$d`, `$u`, and `$v` (either from `s <- svd(x)` or
+    directly from `svd(x)$d`/`$u`/`$v`).
+  - `.Machine$double.eps`.
+  - `qr.solve()` using the LINPACK QR path (for better compatibility with
+    base R behavior).
 
   The plan is to add more functions in the future (#77, #79 @mns-nordicals)
 
@@ -79,6 +87,27 @@
 - Fixed a crash when compiling chained / fall-through assignments like
   `a <- b <- 1` (#60).
 
+- `quick()` now supports dotted symbols (e.g. `foo.bar`) for arguments, locals,
+  and loop variables. Conflicting names that map to the same Fortran symbol now
+  error (Fortran is case-insensitive).
+
+- Fixed C bridge size checks for dotted argument names used in
+  `declare(type(...))` size expressions (e.g. `type(x = double(foo.bar))`).
+
+- `quick()` now gives a helpful error message when a function argument is used
+  without being declared
+  (i.e. missing `declare(type(arg = ...))`).
+
+- Fixed an error in invalid subscript arity reporting, e.g. `x[1, 2, 3]` on a
+  matrix now errors cleanly instead of failing while formatting the message.
+
+- Vector-matrix recycling in arithmetic is now restricted to recycling
+  along the first axes only.
+
+- Local closures now support optional arguments with `NULL` defaults, with
+  validation to ensure optional arguments are initialized (via `is.null()`)
+  before use.
+
 # quickr 0.2.1
 
 - Added support for `!` and unary `-` and `+` (#49, @mns-nordicals)

R/aaa-utils.R

@@ -6,6 +6,42 @@ NULL
 
 `%||%` <- function(x, y) if (is.null(x)) y else x
 
+fortranize_name <- function(name, prefix = "v_") {
+  stopifnot(is_string(name), is_string(prefix), nzchar(prefix))
+  out <- gsub("[^A-Za-z0-9_]", "_", name)
+  if (!nzchar(out) || !grepl("^[A-Za-z]", out)) {
+    out <- paste0(prefix, out)
+  }
+  out
+}
+
+fortranize_expr_symbols <- function(expr) {
+  if (!is.symbol(expr) && !is.call(expr)) {
+    return(expr)
+  }
+  syms <- all.vars(expr)
+  if (!length(syms)) {
+    return(expr)
+  }
+  replacements <- setNames(
+    lapply(syms, \(sym) as.symbol(fortranize_name(sym))),
+    syms
+  )
+  substitute_(expr, list2env(replacements, parent = emptyenv()))
+}
+
+scope_fortran_symbol <- function(sym, scope) {
+  stopifnot(is.symbol(sym))
+  if (is.null(scope)) {
+    return(sym)
+  }
+  var <- get0(as.character(sym), scope)
+  if (inherits(var, Variable) && !is.null(var@name)) {
+    return(as.symbol(var@name))
+  }
+  sym
+}
+
 quickr_r_cmd <- function(
   os_type = .Platform$OS.type,
   r_home = R.home,