Nmparser

.Rbuildignore

@@ -24,3 +24,4 @@
 ^doc$
 ^Meta$
 ^_starlightr\.toml$
+^\.positai$

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

@@ -39,11 +39,25 @@ jobs:
         run: |
           git config --global url."https://${{ secrets.PRIVATE_REPO_ACCESS_TOKEN }}@github.com/".insteadOf "https://github.com/"
 
-      - uses: dtolnay/rust-toolchain@master
+      - uses: dtolnay/rust-toolchain@stable
         with:
           toolchain: ${{ matrix.config.rust-version }}
           targets: ${{ matrix.config.rust-target }}
 
+      - name: Ensure rustup cargo bin is first on PATH
+        if: runner.os != 'Windows'
+        run: echo "$HOME/.cargo/bin" >> $GITHUB_PATH
+
+      - name: Verify Rust toolchain
+        if: runner.os != 'Windows'
+        run: |
+          which rustup
+          which rustc
+          which cargo
+          rustup show
+          rustc --version
+          cargo --version
+
       # Add rust-cache for faster builds
       - name: Cache Rust dependencies
         uses: Swatinem/rust-cache@v2
@@ -95,7 +109,7 @@ jobs:
             echo "All system dependencies are present"
           fi
       - name: rv-sync
-        run: rv sync
+        run: rv sync -vvv
         if: runner.os != 'Windows'
 
       - name: rv-sync (Windows)

.github/workflows/pharos-dependency-check.yaml

@@ -15,14 +15,29 @@ jobs:
 
       - name: Check pharos dependency status
         run: |
-          # Get pharos branch from Cargo.toml
+          # Determine whether Cargo.toml pins pharos via branch or tag.
+          # Branch pin: compare lock commit to that branch's HEAD.
+          # Tag pin:    compare lock commit to main's HEAD (so we still get
+          #             notified when pharos advances past a release pin).
           BRANCH=$(grep -A 2 'git = "https://github.com/a2-ai/pharos"' src/rust/Cargo.toml | grep 'branch =' | sed 's/.*branch = "\([^"]*\)".*/\1/' | head -1)
+          TAG=$(grep -A 2 'git = "https://github.com/a2-ai/pharos"' src/rust/Cargo.toml | grep 'tag =' | sed 's/.*tag = "\([^"]*\)".*/\1/' | head -1)
 
-          # Get current and latest commits
           CURRENT=$(grep -A 1 'source = "git+https://github.com/a2-ai/pharos' src/rust/Cargo.lock | grep -o '#[a-f0-9]\{40\}' | head -1 | cut -c2-)
-          LATEST=$(git ls-remote https://github.com/a2-ai/pharos refs/heads/$BRANCH | cut -f1)
 
-          echo "Branch: $BRANCH"
+          if [ -n "$BRANCH" ]; then
+            TARGET_REF="refs/heads/$BRANCH"
+            TARGET_LABEL="branch $BRANCH"
+          elif [ -n "$TAG" ]; then
+            TARGET_REF="refs/heads/main"
+            TARGET_LABEL="main (pinned to tag $TAG)"
+          else
+            echo "::error::Could not determine pharos pin style (branch or tag) in Cargo.toml"
+            exit 1
+          fi
+
+          LATEST=$(git ls-remote https://github.com/a2-ai/pharos $TARGET_REF | cut -f1)
+
+          echo "Pin: $TARGET_LABEL"
           echo "Current: $CURRENT"
           echo "Latest: $LATEST"
 

.gitignore

@@ -15,3 +15,4 @@ lefthook.yaml
 ./pharos.toml
 /doc/
 /Meta/
+.positai

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: hyperion
 Title: Pharmaceutical Model Development and Workflow Tools
-Version: 0.4.2
+Version: 0.5.0
 Authors@R: c(
     person("Matt", "Smith", , "matthews@a2-ai.com", role = c("aut", "cre")),
     person("Vincent", "Prouillet", ,"vincent@a2-ai.com", role = c("aut")),
@@ -17,8 +17,7 @@ Description: Hyperion is an R interface to the pharos CLI for
 License: MIT + file LICENSE
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
-Config/rextendr/version: 0.4.2
+Config/rextendr/version: 0.5.0
 Config/build/never-clean: true
 Config/build/extra-sources: src/rust/Cargo.lock
 SystemRequirements: Cargo (Rust's package manager), rustc >= 1.65.0, xz
@@ -33,7 +32,6 @@ Suggests:
     withr
 VignetteBuilder: knitr
 Imports:
-    fs,
     cli,
     knitr,
     lifecycle,
@@ -42,3 +40,5 @@ Imports:
     tomledit
 Config/testthat/edition: 3
 URL: https://a2-ai.github.io/hyperion-docs, https://github.com/a2-ai/hyperion
+Config/roxygen2/version: 7.3.3
+RoxygenNote: 7.3.3

NAMESPACE

@@ -1,17 +1,17 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(base::`$`, hyperion_nonmem_model)
-S3method(base::`[[`, hyperion_nonmem_model)
-S3method(base::names, hyperion_nonmem_model)
-S3method(base::print, hyperion_model_metadata)
-S3method(base::print, hyperion_nonmem_dataset)
-S3method(base::print, hyperion_nonmem_model)
-S3method(base::print, hyperion_nonmem_summary)
-S3method(base::print, hyperion_nonmem_summary_not_run)
-S3method(base::print, hyperion_nonmem_summary_running)
-S3method(base::print, hyperion_nonmem_tree)
-S3method(base::print, parameter_audit)
-S3method(base::summary, hyperion_nonmem_model)
+S3method(base::`$`,hyperion_nonmem_model)
+S3method(base::`[[`,hyperion_nonmem_model)
+S3method(base::names,hyperion_nonmem_model)
+S3method(base::print,hyperion_model_metadata)
+S3method(base::print,hyperion_nonmem_dataset)
+S3method(base::print,hyperion_nonmem_model)
+S3method(base::print,hyperion_nonmem_summary)
+S3method(base::print,hyperion_nonmem_summary_not_run)
+S3method(base::print,hyperion_nonmem_summary_running)
+S3method(base::print,hyperion_nonmem_tree)
+S3method(base::print,parameter_audit)
+S3method(base::summary,hyperion_nonmem_model)
 S3method(knitr::knit_print,hyperion_model_metadata)
 S3method(knitr::knit_print,hyperion_nonmem_dataset)
 S3method(knitr::knit_print,hyperion_nonmem_model)
@@ -20,7 +20,7 @@ S3method(knitr::knit_print,hyperion_nonmem_summary_not_run)
 S3method(knitr::knit_print,hyperion_nonmem_summary_running)
 S3method(knitr::knit_print,hyperion_nonmem_tree)
 S3method(knitr::knit_print,parameter_audit)
-S3method(utils::str, hyperion_nonmem_model)
+S3method(utils::str,hyperion_nonmem_model)
 export(ModelComments)
 export(OmegaComment)
 export(SigmaComment)
@@ -32,13 +32,13 @@ export(are_models_in_lineage)
 export(audit_parameter_info)
 export(check_dataset)
 export(check_model)
+export(clear_metadata_file)
 export(compute_ci)
 export(compute_cv)
 export(compute_rse)
 export(copy_model)
 export(format_hyperion_decimal_string)
 export(format_hyperion_sigfig_string)
-export(format_omega_display_name)
 export(from_config_relative)
 export(get_comment)
 export(get_comment_type)
@@ -74,6 +74,7 @@ export(submit_model_to_slurm)
 export(transform_value)
 export(update_metadata_file)
 export(update_param_info)
+export(use_comments)
 export(use_type1_comments)
 if (getRversion() < "4.3.0") importFrom("S7", "@")
 importFrom(knitr,knit_print)

NEWS.md

@@ -1,3 +1,66 @@
+# hyperion 0.5.0
+
+## Breaking changes
+
+- `get_model_lineage()` signature changed. Old: `get_model_lineage(model_dir)`
+  (required a directory or model object). New: `get_model_lineage(model = NULL,
+  from = NULL, to = NULL)`.
+  - No-arg call returns the whole project lineage tree, rooted at the directory
+    containing `pharos.toml`.
+  - `model` returns ancestors and descendants of one model.
+  - `from`/`to` filter the tree downstream / upstream / to the slice between
+    two models.
+  - The `model_dir` argument no longer exists.
+- `copy_model()` `description` is now required (was `description = NULL`).
+- R-side raw comment parsing is removed. All comment parsing is owned by
+  pharos. The "raw" mode documentation, parsing pipeline, and transform
+  keyword mapping are gone from `get_model_parameter_info()`. `NA` names are
+  acceptable when pharos cannot parse a comment; `summary()` falls back to
+  NONMEM names in that case. Raw parsing mode is most similar to `type2` 
+  comments in pharos.
+- `use_type1_comments()` is soft-deprecated in favor of `use_comments()`.
+  It still works but emits a `.Deprecated()` warning and delegates.
+
+## New features
+
+- `clear_metadata_file()` — new exported function. Selectively clears
+  `based_on`, `copied_from`, and/or `tags` in a model's metadata file;
+  unspecified fields are preserved.
+- `copy_model()` gains `based_on` and `tags` arguments so metadata can be
+  populated at copy time rather than via a follow-up `set_metadata_file()`.
+- `set_metadata_file()` gains `copied_from` to record mechanical-copy
+  provenance separately from `based_on`.
+- `hyperion.config_dir` option — explicit override for where `pharos.toml` is
+  resolved from. Status is surfaced in the package-load options message.
+- `use_comments(type = c("type1", "type2"))` — single entry point for setting
+  comment parsing type in `pharos.toml`. The new `"type2"` mode is a flexible
+  structured grammar; `"type1"` remains strict structured. Replaces
+  `use_type1_comments()`.
+- `summary()` includes `model_file` in its output.
+- `read_ext_file()` accepts a `hyperion_nonmem_model` object in addition to
+  the previously-supported path forms.
+- `get_model_lineage(verbose = TRUE)` renders the lineage as a flat table
+  with Model, Parent, Description, Tags, Model Hash, and Dataset Hash columns
+  instead of the tree view.
+
+## Bug fixes
+
+- `.ext` parameter columns are sanitized to syntactic R names (e.g.
+  `IIV (CL)` → `IIV_CL`), so returned data frames no longer require backtick
+  quoting.
+- `.grd` gradient column names are similarly sanitized; the surrounding
+  `GRD(...)` wrapper is stripped before sanitization.
+- Fixed `clear_metadata_file()` so previously-set values are actually cleared
+  (prior behavior left stale fields in place).
+- `read_model()` reports parsing diagnostics for malformed NONMEM control
+  streams, backed by a new pharos parser aimed at better control-stream
+  coverage.
+- `$EST FILE=` overrides are now honored when locating `.ext` files in
+  `get_parameters()`, `read_ext_file()`, `get_run_status()`, and
+  `copy_model()` parameter updates. Previously these always used
+  `{model}.ext` regardless of where NONMEM was actually writing estimates.
+
+
 # hyperion 0.4.2
 
 ## Bug fixes

R/comments-audit.R

@@ -44,7 +44,7 @@ audit_parameter_info <- function(info) {
 #' @param x A parameter_audit object
 #' @param ... Additional arguments (ignored)
 #' @return Invisible copy of x
-#' @rawNamespace S3method(base::print, parameter_audit)
+#' @exportS3Method base::print parameter_audit
 print.parameter_audit <- function(x, ...) {
   cli::cli_text("")
   cli::cli_h1("Parameter Info Audit")