Merge pull request #48 from databio/dev

Release `v0.1.0` - Fender stratocaster

Author: nleroy917

.github/workflows/CI.yml

@@ -27,7 +27,7 @@ jobs:
       - name: Build wheels
         uses: PyO3/maturin-action@v1
         with:
-          working-directory: ./bindings
+          working-directory: ./bindings/python
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
@@ -36,7 +36,7 @@ jobs:
         uses: actions/upload-artifact@v3
         with:
           name: wheels
-          path: ./bindings/dist
+          path: ./bindings/python/dist
 
   windows:
     runs-on: windows-latest
@@ -55,12 +55,12 @@ jobs:
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
-          working-directory: ./bindings
+          working-directory: ./bindings/python
       - name: Upload wheels
         uses: actions/upload-artifact@v3
         with:
           name: wheels
-          path: ./bindings/dist
+          path: ./bindings/python/dist
 
   macos:
     runs-on: macos-latest
@@ -78,12 +78,12 @@ jobs:
           target: ${{ matrix.target }}
           args: --release --out dist --find-interpreter
           sccache: 'true'
-          working-directory: ./bindings
+          working-directory: ./bindings/python
       - name: Upload wheels
         uses: actions/upload-artifact@v3
         with:
           name: wheels
-          path: ./bindings/dist
+          path: ./bindings/python/dist
 
   sdist:
     runs-on: ubuntu-latest
@@ -94,12 +94,12 @@ jobs:
         with:
           command: sdist
           args: --out dist
-          working-directory: ./bindings
+          working-directory: ./bindings/python
       - name: Upload sdist
         uses: actions/upload-artifact@v3
         with:
           name: wheels
-          path: ./bindings/dist
+          path: ./bindings/python/dist
 
   release:
     name: Release
@@ -113,13 +113,13 @@ jobs:
       - uses: actions/download-artifact@v3
         with:
           name: wheels
-          path: ./bindings/dist
+          path: ./bindings/python/dist
       - name: List contents
         run: |
           echo "Contents of dist/"
-          ls -l ./bindings/dist/
+          ls -l ./bindings/python/dist/
       - name: Publish to PyPI
         uses: PyO3/maturin-action@v1
         with:
           command: upload
-          args: --non-interactive --skip-existing ./bindings/dist/*
+          args: --non-interactive --skip-existing ./bindings/python/dist/*

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

@@ -0,0 +1,42 @@
+on:
+  push:
+    branches:
+      - master
+  pull_request:
+    branches:
+      - master
+
+name: R-CMD-check
+
+jobs:
+  R-CMD-check:
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.os }} (R-${{ matrix.config.r }} rust-${{ matrix.config.rust-version }})
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          #  - {os: windows-latest, r: 'release', rust-version: 'stable-msvc', rust-target: 'x86_64-pc-windows-gnu'}
+          - {os: macOS-latest,   r: 'release', rust-version: 'stable'}
+          - {os: ubuntu-latest,  r: 'release', rust-version: 'stable'}
+          - {os: ubuntu-latest,  r: 'devel',   rust-version: 'stable'}
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+    steps:
+      - uses: actions/checkout@v2
+      - uses: dtolnay/rust-toolchain@master
+        with:
+          toolchain: ${{ matrix.config.rust-version }}
+          targets: ${{ matrix.config.rust-target }}
+      - uses: r-lib/actions/setup-pandoc@v2
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: rcmdcheck
+          working-directory: ${{ github.workspace }}/bindings/r
+      - uses: r-lib/actions/check-r-package@v2
+        with:
+          working-directory: ${{ github.workspace }}/bindings/r

.gitignore

@@ -14,6 +14,14 @@ Cargo.lock
 *.pdb
 
 .venv
-
+/.idea/genimtools.iml
+/.idea/modules.xml
+/.idea/.gitignore
+/.idea/vcs.xml
 # this is for "act"
-bin/
+bin/
+/.idea/gtars.iml
+/gtars/tests/data/test1.bw
+
+.DS_Store
+.Rhistory

.vscode/settings.json

@@ -1,6 +1,7 @@
 {
     "rust-analyzer.linkedProjects": [
         "./gtars/Cargo.toml",
-        "./bindings/Cargo.toml",
+        "./bindings/python/Cargo.toml",
+        "./bindings/r/src/rust/Cargo.toml",
     ]
 }

bindings/.gitignore bindings/python/.gitignore

@@ -1,6 +1,6 @@
 [package]
 name = "gtars-py"
-version = "0.0.15"
+version = "0.1.0"
 edition = "2021"
 
 # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html
@@ -10,7 +10,7 @@ crate-type = ["cdylib"]
 
 [dependencies]
 anyhow = "1.0.82"
-gtars = { path = "../gtars" }
+gtars = { path = "../../gtars" }
 pyo3 = { version = "0.21", features=["anyhow", "extension-module"] }
 numpy = "0.21"
 # pyo3-tch = { git = "https://github.com/LaurentMazare/tch-rs" }

bindings/Cargo.toml bindings/python/Cargo.toml

@@ -0,0 +1,18 @@
+use pyo3::prelude::*;
+
+use gtars::igd::search::igd_search;
+
+#[pyclass(name="IGD")]
+pub struct IGD;
+
+#[pymethods]
+impl IGD {
+
+    #[classmethod]
+    pub fn search(database_path: String, query_file_path: String) {
+
+        igd_search(&database_path, &query_file_path).unwrap();
+
+
+    }
+}

bindings/README.md bindings/python/README.md

@@ -5,6 +5,7 @@ mod ailist;
 mod models;
 mod tokenizers;
 mod utils;
+mod igd;
 
 pub const VERSION: &str = env!("CARGO_PKG_VERSION");
 

bindings/gtars/__init__.py bindings/python/gtars/__init__.py

@@ -65,9 +65,17 @@ pub fn read_tokens_from_gtok(filename: &str) -> PyResult<Vec<u32>> {
     Ok(tokens)
 }
 
+#[pyfunction]
+pub fn read_tokens_from_gtok_as_strings(filename: &str) -> PyResult<Vec<String>> {
+    let tokens = gtars::io::read_tokens_from_gtok(filename)?;
+    let tokens = tokens.iter().map(|t| t.to_string()).collect();
+    Ok(tokens)
+}
+
 #[pymodule]
 pub fn utils(_py: Python, m: &Bound<'_, PyModule>) -> PyResult<()> {
     m.add_wrapped(wrap_pyfunction!(write_tokens_to_gtok))?;
     m.add_wrapped(wrap_pyfunction!(read_tokens_from_gtok))?;
+    m.add_wrapped(wrap_pyfunction!(read_tokens_from_gtok_as_strings))?;
     Ok(())
 }

bindings/gtars/__init__.pyi bindings/python/gtars/__init__.pyi

@@ -0,0 +1,2 @@
+^src/\.cargo$
+^LICENSE\.md$

bindings/gtars/ailist/__init__.py bindings/python/gtars/ailist/__init__.py

@@ -0,0 +1,13 @@
+Package: gtars
+Title: Performance critical genomic interval analysis using Rust, in R
+Version: 0.0.0.9000
+Authors@R: 
+    person("Nathan", "LeRoy", , "[email protected]", role = c("aut", "cre"),
+           comment = c(ORCID = "0000-0002-7354-7213"))
+Description: Performance-critical tools to manipulate, analyze, and process genomic interval data. Primarily focused on building tools for geniml - our genomic machine learning python package. 
+License: MIT + file LICENSE
+Encoding: UTF-8
+Roxygen: list(markdown = TRUE)
+RoxygenNote: 7.3.2
+Config/rextendr/version: 0.3.1.9001
+SystemRequirements: Cargo (Rust's package manager), rustc

bindings/gtars/ailist/__init__.pyi bindings/python/gtars/ailist/__init__.pyi

@@ -0,0 +1,2 @@
+YEAR: 2024
+COPYRIGHT HOLDER: gtars authors

bindings/gtars/models/__init__.py bindings/python/gtars/models/__init__.py

@@ -0,0 +1,21 @@
+# MIT License
+
+Copyright (c) 2024 gtars authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

bindings/gtars/models/__init__.pyi bindings/python/gtars/models/__init__.pyi

@@ -0,0 +1,7 @@
+# Generated by roxygen2: do not edit by hand
+
+export(r_igd_create)
+export(r_igd_search)
+export(read_tokens_from_gtok)
+export(write_tokens_to_gtok)
+useDynLib(gtars, .registration = TRUE)

bindings/gtars/tokenizers/__init__.py bindings/python/gtars/tokenizers/__init__.py

@@ -0,0 +1,38 @@
+# Generated by extendr: Do not edit by hand
+
+# nolint start
+
+#
+# This file was created with the following call:
+#   .Call("wrap__make_gtars_wrappers", use_symbols = TRUE, package_name = "gtars")
+
+#' @usage NULL
+#' @useDynLib gtars, .registration = TRUE
+NULL
+
+`__init__` <- function() invisible(.Call(wrap____init__))
+
+#' Write tokens to a gtok file
+#' @export
+#' @param filename A string representing the path to the gtok file.
+read_tokens_from_gtok <- function(filename) .Call(wrap__r_read_tokens_from_gtok, filename)
+
+#' Write tokens to a gtok file
+#' @export
+#' @param filename A string representing the path to the gtok file.
+#' @param tokens The tokens to write.
+write_tokens_to_gtok <- function(filename, tokens) invisible(.Call(wrap__r_write_tokens_to_gtok, filename, tokens))
+
+#' Create an IGD database from a directory of bed files
+#' @param output_path String path where the IGD database will be saved
+#' @param filelist String path to either a text file containing paths to bed files, or a directory containing bed files
+#' @param db_name String name for the database (will be used in output filenames)
+rextendr_igd_create <- function(output_path, filelist, db_name) .Call(wrap__rextendr_igd_create, output_path, filelist, db_name)
+
+#' Search igd with a bed file
+#' @param database_path A string representing the path to the database igd file.
+#' @param query_path A string representing the path to the query bed file.
+rextendr_igd_search <- function(database_path, query_path) .Call(wrap__rextendr_igd_search, database_path, query_path)
+
+
+# nolint end

bindings/gtars/tokenizers/__init__.pyi bindings/python/gtars/tokenizers/__init__.pyi

@@ -0,0 +1,73 @@
+#' @useDynLib gtars, .registration = TRUE
+NULL
+
+#' @title Create IGD Database
+#' 
+#' @description Creates an IGD (Indexed Genomic Data) database from a collection of BED files.
+#' 
+#' @param output_path Character string specifying the directory where the IGD database will be saved
+#' @param filelist Character string specifying either:
+#'   - Path to a text file containing paths to BED files (one per line)
+#'   - Path to a directory containing BED files
+#'   - "-" or "stdin" to read paths from standard input
+#' @param db_name Character string specifying the name for the database (will be used in output filenames).
+#'   Defaults to "igd_database"
+#' 
+#' @return NULL invisibly on success
+#' 
+#' @examples
+#' \dontrun{
+#' # Create database with default name
+#' igd_create("path/to/output", "path/to/bed/files")
+#' }
+#' 
+#' @export
+r_igd_create <- function(output_path, filelist, db_name = "igd_database") {
+  # Input validation
+  if (!is.character(output_path) || length(output_path) != 1) {
+    stop("output_path must be a single character string")
+  }
+  if (!is.character(filelist) || length(filelist) != 1) {
+    stop("filelist must be a single character string")
+  }
+
+  # Call Rust function
+  .Call(wrap__rextendr_igd_create, output_path, filelist, db_name)
+
+  invisible(NULL)
+}
+
+
+#' @title Search IGD Database
+#' 
+#' @description Searches an IGD database for region overlaps with an input BED file
+#' 
+#' @param database_path path to .igd database
+#' @param query_path path to .bed file
+#' 
+#' @return dataframe of overlap hits
+#' 
+#' @examples
+#' \dontrun{
+#' }
+#' 
+#' @export
+r_igd_search <- function(database_path, query_path) {
+  
+  # Input validation
+  if (!is.character(database_path) || length(database_path) != 1) {
+    stop("database_path must be a single character string")
+  }
+  if (!is.character(query_path) || length(query_path) != 1) {
+    stop("query_path must be a single character string")
+  }
+  
+  # Call Rust function
+  chr_vector <- .Call(wrap__rextendr_igd_search, database_path, query_path)
+  
+  split_result <- strsplit(chr_vector, split = '\t')
+  df <- data.frame(matrix(unlist(split_result[-1]), nrow = length(chr_vector)-1, byrow = TRUE))
+  colnames(df) <- split_result[[1]]
+  
+  invisible(df)
+}