Clean up generated code#7
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RyanMarcus merged 1 commit intoMay 27, 2026
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Clean up generated code by adding some spacing and sorting includes Update contributors
nh13
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this pull request
in fg-labs/prmi
May 28, 2026
…src/upstream/ Establishes the Cargo workspace shape that the v0.1 stack will build on: * Root `Cargo.toml` declares `prmi` + `prmi-sys` members and a shared `workspace.dependencies` block. * `prmi/Cargo.toml` ships the upstream-dependency set (log, byteorder, rayon, plus the rmi_lib-inherited indicatif/json/bytesize/superslice/ tabular crates that Marcus's source references). * `prmi/src/lib.rs` is a stub declaring `pub mod upstream;`. Fulcrum- authored modules (encoding, fasta, sa, sidecar, train, index, cli) land in subsequent PRs. * `prmi-sys/Cargo.toml` + `prmi-sys/src/lib.rs` are placeholders so the workspace member set is stable from PR #1 onward; the actual FFI surface lands in PR #7 (`feat/v0.1-prmi-sys`). Marcus's primitives move from the original repo layout (`src/`, `rmi_lib/`, `tests/`) into `prmi/src/upstream/`: * `prmi/src/upstream/models/` — LinearModel, LinearSplineModel, LogLinearModel, RobustLinearModel, RMITrainingData, Model trait, ModelInput, ModelParam, TrainingKey, stdlib/utils helpers. Fulcrum extensions added (`weighted_slr`, `LinearModel::new_weighted`, `LinearSplineModel::new_weighted`) for the upcoming priors PR. * `prmi/src/upstream/train/` — `lower_bound_correction.rs` (with the Fulcrum Option-returning accessors `next_real`/`prev_real`/ `next_index_real`/`prev_index_real` plus the `*_is_real` bools that disambiguate sentinel entries), `two_layer.rs` (kept verbatim, unused by the Fulcrum trainer but preserved for upstream parity), `mod.rs`. * `prmi/src/upstream/mod.rs` re-exports the model primitives and marks the module `#[allow(clippy::all, unused_*, dead_code)]` so inherited code does not pollute the workspace lint surface. Per-file copyright headers (`// Copyright Ryan Marcus 2020` plus `// Modified by Fulcrum Genomics 2026` where applicable) identify inherited vs new code. `LICENSE-FORK-NOTICE.md` documents the lineage. Pruned from Marcus's original layout (replaced by prmi v0.1 design): * `src/main.rs`, `src/load.rs` — the standalone `rmi` optimizer binary. * `rmi_lib/src/{cache_fix, codegen, optimizer}.rs` — codegen + tuning machinery for the upstream binary, not used by the prmi trainer. * `rmi_lib/src/models/{balanced_radix, cubic_spline, histogram, normal, radix}.rs` — RMI model variants outside prmi's v0.1 scope. * `rmi_lib/src/train/multi_layer.rs` — multi-layer trainer; prmi's cleanroom trainer (PR #4a) is single-L1-L2. * `tests/` — Marcus's RMI binary CLI tests; prmi tests in PR #2+. * `.drone.yml`, `COPYING`, `example_param_grid.json` — Marcus's CI config (replaced by `.github/workflows/ci.yml` in PR #8) and optimizer-specific artefacts. Workspace builds clean (`cargo build --workspace`) and the 3 unit tests inherited from upstream models pass.
nh13
referenced
this pull request
in fg-labs/prmi
May 28, 2026
…src/upstream/ (#2) Establishes the Cargo workspace shape that the v0.1 stack will build on: * Root `Cargo.toml` declares `prmi` + `prmi-sys` members and a shared `workspace.dependencies` block. * `prmi/Cargo.toml` ships the upstream-dependency set (log, byteorder, rayon, plus the rmi_lib-inherited indicatif/json/bytesize/superslice/ tabular crates that Marcus's source references). * `prmi/src/lib.rs` is a stub declaring `pub mod upstream;`. Fulcrum- authored modules (encoding, fasta, sa, sidecar, train, index, cli) land in subsequent PRs. * `prmi-sys/Cargo.toml` + `prmi-sys/src/lib.rs` are placeholders so the workspace member set is stable from PR #1 onward; the actual FFI surface lands in PR #7 (`feat/v0.1-prmi-sys`). Marcus's primitives move from the original repo layout (`src/`, `rmi_lib/`, `tests/`) into `prmi/src/upstream/`: * `prmi/src/upstream/models/` — LinearModel, LinearSplineModel, LogLinearModel, RobustLinearModel, RMITrainingData, Model trait, ModelInput, ModelParam, TrainingKey, stdlib/utils helpers. Fulcrum extensions added (`weighted_slr`, `LinearModel::new_weighted`, `LinearSplineModel::new_weighted`) for the upcoming priors PR. * `prmi/src/upstream/train/` — `lower_bound_correction.rs` (with the Fulcrum Option-returning accessors `next_real`/`prev_real`/ `next_index_real`/`prev_index_real` plus the `*_is_real` bools that disambiguate sentinel entries), `two_layer.rs` (kept verbatim, unused by the Fulcrum trainer but preserved for upstream parity), `mod.rs`. * `prmi/src/upstream/mod.rs` re-exports the model primitives and marks the module `#[allow(clippy::all, unused_*, dead_code)]` so inherited code does not pollute the workspace lint surface. Per-file copyright headers (`// Copyright Ryan Marcus 2020` plus `// Modified by Fulcrum Genomics 2026` where applicable) identify inherited vs new code. `LICENSE-FORK-NOTICE.md` documents the lineage. Pruned from Marcus's original layout (replaced by prmi v0.1 design): * `src/main.rs`, `src/load.rs` — the standalone `rmi` optimizer binary. * `rmi_lib/src/{cache_fix, codegen, optimizer}.rs` — codegen + tuning machinery for the upstream binary, not used by the prmi trainer. * `rmi_lib/src/models/{balanced_radix, cubic_spline, histogram, normal, radix}.rs` — RMI model variants outside prmi's v0.1 scope. * `rmi_lib/src/train/multi_layer.rs` — multi-layer trainer; prmi's cleanroom trainer (PR #4a) is single-L1-L2. * `tests/` — Marcus's RMI binary CLI tests; prmi tests in PR #2+. * `.drone.yml`, `COPYING`, `example_param_grid.json` — Marcus's CI config (replaced by `.github/workflows/ci.yml` in PR #8) and optimizer-specific artefacts. Workspace builds clean (`cargo build --workspace`) and the 3 unit tests inherited from upstream models pass.
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Add #pragma once header guards to C++ output - this is the primary syntactic change as it allows for safe inclusion of the generated headers in multiple files.
Clean up generated code by adding some spacing and sorting includes - makes generated code (slightly) easier to read.
Update contributors.
A side-effect of the PR is to eliminate trailing whitespace in the touched files.