gtars 0.0.15__tar.gz

gtars-0.0.15/PKG-INFO

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+Metadata-Version: 2.3
+Name: gtars
+Version: 0.0.15
+Classifier: Programming Language :: Rust
+Classifier: Programming Language :: Python :: Implementation :: CPython
+Classifier: Programming Language :: Python :: Implementation :: PyPy
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM
+
+# gtars
+This is a python wrapper around the `gtars` crate. It provides an easy interface for using `gtars` in python. It is currently in early development, and as such, it does not have a lot of functionality yet, but new tools are being worked on right now.
+
+## Installation
+You can get `gtars` from PyPI:
+```bash
+pip install gtars
+```
+
+## Usage
+Import the package, and use the tools:
+```python
+import gtars as gt
+
+gt.prune_universe(...)
+```
+## Developer docs
+Write the develop docs here...

gtars-0.0.15/README.md

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+[![codecov](https://codecov.io/gh/databio/gtars/branch/master/graph/badge.svg)](https://codecov.io/gh/databio/gtars)
+[![crates.io](https://img.shields.io/crates/v/gtars?&logo=rust)](https://crates.io/crates/gtars)
+
+<h1 align="center">
+<img src="gtars/docs/logo.svg" alt="gtars logo" height="100px">
+</h1>
+
+`gtars` is a rust crate that provides a set of tools for working with genomic interval data. Its primary goal is to provide processors for our python package, [`geniml`](https:github.com/databio/geniml), a library for machine learning on genomic intervals. However, it can be used as a standalone library for working with genomic intervals as well.
+
+`gtars` provides three things:
+
+1. A rust library crate.
+2. A command-line interface, written in rust.
+3. A Python package that provides bindings to the rust library.
+
+## Repository organization (for developers)
+
+This repo is organized like so:
+
+1. A rust library crate (`/gtars/lib.rs`) that provides functions, traits, and structs for working with genomic interval data.
+2. A rust binary crate (in `/gtars/main.rs`), a small, wrapper command-line interface for the library crate.
+3. A rust crate (in `/bindings`) that provides Python bindings, and a resulting Python package, so that it can be used within Python.
+
+This repository is a work in progress, and still in early development.
+
+## Installation
+To install `gtars`, you must have the rust toolchain installed. You can install it by following the instructions [here](https://www.rust-lang.org/tools/install).
+
+You may build the binary locally using `cargo build --release`. This will create a binary in `target/release/gtars`. You can then add this to your path, or run it directly.
+
+## Usage
+`gtars` is very early in development, and as such, it does not have a lot of functionality yet. However, it does have a few useful tools. To see the available tools, run `gtars --help`. To see the help for a specific tool, run `gtars <tool> --help`.
+
+Alternatively, you can link `gtars` as a library in your rust project. To do so, add the following to your `Cargo.toml` file:
+```toml
+[dependencies]
+gtars = { git = "https://github.com/databio/gtars" }
+```
+
+## Testing
+To run the tests, run `cargo test`.
+
+## Contributing
+### New internal library crate tools
+If you'd like to add a new tool, you can do so by creating a new module within the src folder.
+
+### New public library crate tools
+If you want this to be available to users of `gtars`, you can add it to the `gtars` library crate as well. To do so, add the following to `src/lib.rs`:
+```rust
+pub mod <tool_name>;
+```
+
+### New binary crate tools
+Finally, if you want to have command-line functionality, you can add it to the `gtars` binary crate. This requires two steps:
+1. Create a new `cli` using `clap` inside the `interfaces` module of `src/cli.rs`:
+```rust
+pub fn make_new_tool_cli() -> Command {
+
+}
+```
+
+2. Write your logic in a wrapper function. This will live inside the `functions` module of `src/cli.rs`:
+```rust
+// top of file:
+use tool_name::{ ... }
+
+// inside the module:
+pub fn new_tool_wrapper() -> Result<(), Box<dyn Error>> {
+    // your logic here
+}
+```
+
+Please make sure you update the changelog and bump the version number in `Cargo.toml` when you add a new tool.
+
+### VSCode users
+If you are using VSCode, make sure you link to the `Cargo.toml` inside the `.vscode` folder, so that `rust-analyzer` can link it all together:
+```json
+{
+    "rust-analyzer.linkedProjects": [
+        "./vocab/Cargo.toml",
+        "./Cargo.toml"
+        "./new-tool/Cargo.toml"
+    ]
+}
+```

gtars-0.0.15/bindings/.gitignore

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+/target
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+.pytest_cache/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+.venv/
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+include/
+man/
+venv/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+pip-selfcheck.json
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+.DS_Store
+
+# Sphinx documentation
+docs/_build/
+
+# PyCharm
+.idea/
+
+# VSCode
+.vscode/
+
+# Pyenv
+.python-version