WIP: argweavers 1.0

1. drop cmake while compile Rust
2. drop binaries wrapper for legacy C++
3. Make legacy R interface optional in Python

Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "argweavers"
-version = "0.9.0"
+version = "1.0.0"
 edition = "2021"
 authors = ["Tang Ziya <[email protected]>"]
 
@@ -12,23 +12,23 @@ crate-type = ["lib", "cdylib"]
 [dependencies]
 autocxx = "0.26.0"
 bio = { version = "1.5.0", features = ["phylogeny"] }
-clap = { version = "4.4.18", features = ["derive", "cargo"] }
+clap = { version = "4.5.1", features = ["derive", "cargo"] }
 csv = "1.3.0"
-cxx = "1.0.115"
+cxx = "1.0.117"
 flate2 = "1.0.28"
 libc = "0.2.153"
 log = "0.4.20"
 log4rs = "1.3.0"
 nom = "7.1.3"
 polars = { version = "0.37.0", features = ["lazy"] }
 pyo3 = { version = "0.20", features = ["abi3-py38", "extension-module", "multiple-pymethods"], optional = true }
-pyo3-polars = { version = "0.11.1", optional = true }
+pyo3-polars = { version = "0.11.3", optional = true }
 rust-htslib = { version = "0.46.0", features = ["libdeflate"] }
-serde = { version = "1.0.195", features = ["derive"] }
-tempfile = "3.9.0"
+serde = { version = "1.0.197", features = ["derive"] }
+tempfile = "3.10.0"
 
 [dev-dependencies]
-criterion = { version = "0.4", features = ["html_reports"] }
+criterion = { version = "0.5", features = ["html_reports"] }
 
 [[bench]]
 name = "my_benchmark"
@@ -44,7 +44,5 @@ extension-module = [
 
 [build-dependencies]
 autocxx-build = "0.26.0"
-cmake = "0.1"
 glob = "0.3.1"
-miette = { version = "5.10.0", features = ["fancy"] }
-pyo3-build-config = { version = "0.20.2", features = ["abi3-py38"], optional = true }
+pyo3-build-config = { version = "0.20.3", features = ["abi3-py38"], optional = true }

argweavers/bin.py

@@ -1,5 +1,4 @@
 """Wrapper for compiled binaries."""
-import pathlib
 import shutil
 import subprocess
 import sys
@@ -17,8 +16,7 @@ def __call__(self, args: _CMD = None, **kwargs) -> subprocess.CompletedProcess:
             ...
 
 
-_binaries = ["arg_likelihood", "arg_sample", "arg_summarize"]
-__all__ = _binaries + ["require_executable"]
+__all__ = ["require_executable"]
 
 arg_likelihood: "_BinaryWrapper"
 "Sampler for large ancestral recombination graphs"
@@ -27,8 +25,6 @@ def __call__(self, args: _CMD = None, **kwargs) -> subprocess.CompletedProcess:
 arg_summarize: "_BinaryWrapper"
 "Summarize the output of ARGweaver."
 
-_bin_dir = pathlib.Path(__file__).parent.parent / "bin"
-
 
 def _bin_wrapper(path: "Union[Path, str]", **kwargs) -> "_BinaryWrapper":
     def f(args=None, **kw):
@@ -45,13 +41,6 @@ def f(args=None, **kw):
     return f
 
 
-for _ in _binaries:
-    _bin = _bin_dir / _.replace("_", "-")
-    if not _bin.exists():
-        raise RuntimeError(f"Missing binary: {_bin}")
-    globals()[_] = _bin_wrapper(_bin, capture_output=False, return_process=False)
-
-
 def require_executable(executable: str, additional_message: str = "", **kwargs):
     """Require an executable to be available and return a wrapper for it.
 

argweavers/r.py

@@ -1,6 +1,10 @@
 """R interface for argweaver."""
+import importlib.util
 import typing
 
+if importlib.util.find_spec("rpy2") is None:
+    raise ImportError("rpy2 not installed, please install this package with `r` extra.")
+
 import rpy2.robjects as ro
 from rpy2.robjects import pandas2ri
 from rpy2.robjects.packages import importr

benches/my_benchmark.rs

@@ -23,7 +23,7 @@ fn ffi_read_sites() {
 
 fn read_sites() {
     let path = std::path::PathBuf::from("examples/sim1/sim1.sites");
-    let _sites = Sites::from_path(path).unwrap();
+    let _sites = Sites::from_path(&path).unwrap();
 }
 
 fn criterion_benchmark(c: &mut Criterion) {

build.rs

@@ -1,14 +1,9 @@
-use miette::IntoDiagnostic;
-
-fn main() -> miette::Result<()> {
+fn main() -> Result<(), Box<dyn std::error::Error>> {
     #[cfg(feature = "extension-module")]
     pyo3_build_config::add_extension_module_link_args();
-    cmake::build(".");
     let path = std::path::PathBuf::from("src");
     let mut b = autocxx_build::Builder::new("src/lib.rs", [&path]).build()?;
-    let source_files = glob::glob("src/argweaver/*.cpp")
-        .into_diagnostic()?
-        .map(|p| p.unwrap());
+    let source_files = glob::glob("src/argweaver/*.cpp")?.map(|x| x.unwrap());
     b.flag_if_supported("-std=c++14")
         .files(source_files)
         .flag("-w")

pyproject.toml

@@ -31,12 +31,14 @@ dependencies = [
     "numpy>=1.24.4",
     "polars>=0.20.9",
     "pyarrow>=15.0.0",
-    "rpy2>=3.5.15",
     "pandas>=2.0.3",
     "matplotlib>=3.7.5",
     "biopython>=1.83",
 ]
 
+[project.optional-dependencies]
+r = ["rpy2>=3.5.15"]
+
 [project.scripts]
 arg-likelihood = "argweavers.bin:arg_likelihood"
 arg-sample = "argweavers.bin:arg_sample"
@@ -64,7 +66,6 @@ htmlcov-serve = "python -m http.server --directory htmlcov"
 
 [tool.maturin]
 features = ["extension-module"]
-include = ["bin/*"]
 
 [[tool.mypy.overrides]]
 module = [