Adds remote-access refgetstore and fai index capability

README.md

@@ -27,16 +27,24 @@ This repository is a work in progress, and still in early development. This repo
 
 ## Installation
 
-To install any component of `gtars`, you must have the rust toolchain installed. You can install it by [following the instructions](https://www.rust-lang.org/tools/install).
+To install `gtars`, you must first [install the rust toolchain](https://www.rust-lang.org/tools/install).
 
 ### Command-line interface
+
 You may build the cli binary locally by navigating to `gtars-cli` and using `cargo build --release`. This will create a binary in `target/release/gtars` at the top level of the workspace. You can then add this to your path, or run it directly.
 
 Alternatively, you can run `cargo install --path gtars-cli` from the top level of the workspace. This will install the binary to your cargo bin directory (usually `~/.cargo/bin`).
 
+We feature-gate binary dependencies maximize compatibility and minimize install size. You can specify features during installation like so:
+
+```
+cargo install --path gtars-cli gtars-cli --features "uniwig tokenizers"
+```
+
 Finally, you can download precompiled binaries from the [releases page](https://github.com/databio/gtars/releases).
 
 ### Python bindings
+
 You can install the Python bindings via pip. First, ensure you have a recent version of pip installed. Then run:
 
 ```bash
@@ -50,6 +58,11 @@ from gtars import __version__
 print(__version__)
 ```
 
+### Dev Python bindings
+
+
+
+
 ## Usage
 
 `gtars` provides several useful tools. There are 3 ways to use `gtars`. 

gtars-core/src/models/region_set.rs

@@ -22,7 +22,9 @@ use bigtools::{BedEntry, BigBedWrite};
 use crate::models::Region;
 #[cfg(feature = "http")]
 use crate::utils::get_dynamic_reader_from_url;
-use crate::utils::{get_chrom_sizes, get_dynamic_reader};
+use crate::utils::get_dynamic_reader;
+#[cfg(feature = "bigbed")]
+use crate::utils::get_chrom_sizes;
 
 ///
 /// RegionSet struct, the representation of the interval region set file,

gtars-core/src/utils.rs

@@ -2,14 +2,19 @@ use std::collections::HashMap;
 use std::ffi::OsStr;
 use std::fs::File;
 use std::io::prelude::*;
-use std::io::{BufRead, BufReader, Cursor};
+use std::io::{BufRead, BufReader};
+#[cfg(feature = "http")]
+use std::io::Cursor;
 use std::path::{Path, PathBuf};
 use std::str::FromStr;
 
 use anyhow::{Context, Result};
-use flate2::read::{GzDecoder, MultiGzDecoder};
+#[cfg(feature = "http")]
+use flate2::read::GzDecoder;
+use flate2::read::MultiGzDecoder;
 #[cfg(feature = "http")]
 use reqwest::blocking::Client;
+#[cfg(feature = "http")]
 use std::error::Error;
 
 use crate::models::region::Region;

gtars-python/README.md

@@ -0,0 +1,45 @@
+# gtars
+
+This is a Python package that wraps the `gtars` crate so you can call gtars code from Python.
+
+Documentation for Python bindings is hosted at: https://docs.bedbase.org/gtars/
+
+## Brief instructions
+
+To install the development version, you'll have to build it locally. The easy way to build/install is to do this, which reads the configuration in `pyproject.toml` for easy building/installing:
+
+```
+python -m pip install -e .
+```
+
+Or, you can have more control over it in two steps using `maturin` directly.
+Build Python bindings like this:
+
+```console
+cd gtars-python
+python_version=$(python --version | awk '{print $2}' | cut -d '.' -f1-2 )
+maturin build --interpreter $python_version  --release
+```
+
+
+Then install the local wheel that was just built:
+
+```console
+gtars_version=`grep '^version =' Cargo.toml | cut -d '"' -f 2`
+python_version_nodot=$(python --version | awk '{print $2}' | cut -d '.' -f1-2 | tr -d '.')
+ll ../target/wheels/gtars*
+wheel_path=$(find ../target/wheels/gtars-${gtars_version}-cp${python_version_nodot}-cp${python_version_nodot}-manylinux*.whl)
+echo $wheel_path
+pip install --force-reinstall ${wheel_path}
+```
+
+
+## Importing into python
+
+Once installed, you can import and use the package in Python. For example:
+
+```
+from gtars import refget
+sc = refget.digest_fasta("../tests/data/fasta/base.fa")
+sc2 = refget.load_fasta("../tests/data/fasta/base.fa")
+```