add readme and github workflow

.github/workflows/CI.yml → .github/workflows/cd.yaml

@@ -1,18 +1,13 @@
-# This file is autogenerated by maturin v1.4.0
-# To update, run
-#
-#    maturin generate-ci github
-#
-name: CI
+name: Release
 
 on:
   push:
     branches:
       - main
-      - master
     tags:
       - '*'
   pull_request:
+  merge_group:
   workflow_dispatch:
 
 permissions:
@@ -23,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        target: [x86_64, x86, aarch64, armv7, s390x, ppc64le]
+        target: [x86_64, x86] # aarch64, armv7, s390x, ppc64le
     steps:
       - uses: actions/checkout@v3
       - uses: actions/setup-python@v4
@@ -33,7 +28,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          args: --release --out dist
           sccache: 'true'
           manylinux: auto
       - name: Upload wheels
@@ -57,7 +52,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          args: --release --out dist
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v3
@@ -79,7 +74,7 @@ jobs:
         uses: PyO3/maturin-action@v1
         with:
           target: ${{ matrix.target }}
-          args: --release --out dist --find-interpreter
+          args: --release --out dist
           sccache: 'true'
       - name: Upload wheels
         uses: actions/upload-artifact@v3

.github/workflows/ci.yaml

@@ -0,0 +1,27 @@
+name: Test
+
+on:
+  pull_request:
+  merge_group:
+  push:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Test
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.10'
+      - uses: actions-rs/toolchain@v1
+        with:
+          profile: minimal
+          toolchain: stable
+          components: rustfmt, clippy
+      - uses: Swatinem/rust-cache@v2
+      - run: cargo fmt --all --check
+      - run: cargo clippy --all-features -- -D warnings
+      - run: cargo test --all-features

Cargo.toml

@@ -2,13 +2,23 @@
 name = "xyz-parse"
 version = "0.1.0"
 edition = "2021"
+authors = ["Julian Popescu <[email protected]>"]
+license = "MIT OR Apache-2.0"
+readme = "README.md"
+homepage = "https://github.com/aqora-io/xyz-parse"
+documentation = "https://docs.rs/xyz-parse/"
+repository = "https://github.com/aqora-io/xyz-parse"
+description = "Simple parser for the XYZ file format"
+keywords = ["xyz", "chemistry", "parser", "parse"]
+categories = ["parsing"]
 
 [lib]
+path = "src/lib.rs"
 name = "xyz_parse"
 crate-type = ["cdylib"]
 
 [features]
-default = ["python"]
+default = []
 python = ["pyo3"]
 
 [dependencies]

README.md

@@ -0,0 +1,14 @@
+# xyz-parse
+
+A parser for the [XYZ file format](https://en.wikipedia.org/wiki/XYZ_file_format)
+
+The formatting of the .xyz file format is as follows:
+
+```rust
+<number of atoms>
+comment line
+<element> <X> <Y> <Z>
+...
+```
+
+Currently the parser does not support extended XYZ format, but may do so in the future

src/atom.rs

@@ -1,6 +1,7 @@
 use rust_decimal::Decimal;
 use std::{borrow::Cow, error::Error, fmt, str::FromStr};
 
+/// An error that can occur when parsing an [`Atom`]
 #[derive(Debug, Clone)]
 pub enum AtomParseError<'a> {
     InvalidCoordinate(Cow<'a, str>, rust_decimal::Error),
@@ -36,6 +37,7 @@ impl<'a> fmt::Display for AtomParseError<'a> {
 
 impl Error for AtomParseError<'static> {}
 
+/// An atom in a molecule
 #[derive(Debug, Clone, Default, PartialEq, Eq)]
 pub struct Atom<'a> {
     pub symbol: Cow<'a, str>,

src/lib.rs

@@ -1,3 +1,16 @@
+//! A parser for the [XYZ file format](https://en.wikipedia.org/wiki/XYZ_file_format)
+//!
+//! The formatting of the .xyz file format is as follows:
+//!
+//! ```
+//! <number of atoms>
+//! comment line
+//! <element> <X> <Y> <Z>
+//! ...
+//! ```
+//!
+//! Currently the parser does not support extended XYZ format, but may do so in the future
+
 mod atom;
 mod molecule;
 mod xyz;
@@ -9,6 +22,7 @@ pub use atom::*;
 pub use molecule::*;
 pub use xyz::*;
 
+/// Parse an [`Xyz`] string
 pub fn parse_xyz(s: &str) -> Result<Xyz, XyzParseError> {
     Xyz::parse(s)
 }

src/molecule.rs

@@ -1,6 +1,7 @@
 use crate::atom::{Atom, AtomParseError};
 use std::{borrow::Cow, error::Error, fmt, str::FromStr};
 
+/// An error that can occur when parsing a [`Molecule`]
 #[derive(Debug, Clone)]
 pub enum MoleculeParseError<'a> {
     NoAtomNumber,
@@ -57,6 +58,7 @@ impl Error for MoleculeParseError<'static> {
     }
 }
 
+/// A molecule
 #[derive(Debug, Clone, Default, PartialEq, Eq)]
 pub struct Molecule<'a> {
     pub comment: Cow<'a, str>,

src/xyz.rs

@@ -1,6 +1,7 @@
 use crate::molecule::{Molecule, MoleculeParseError};
 use std::{error::Error, fmt, str::FromStr};
 
+/// An error that can occur while parsing an [`Xyz`]
 #[derive(Debug, Clone)]
 pub enum XyzParseError<'a> {
     InvalidMolecule(usize, MoleculeParseError<'a>),
@@ -32,6 +33,7 @@ impl Error for XyzParseError<'static> {
     }
 }
 
+/// A list of molecules
 #[derive(Debug, Clone, Default, PartialEq, Eq)]
 pub struct Xyz<'a> {
     pub molecules: Vec<Molecule<'a>>,
@@ -88,6 +90,7 @@ mod tests {
     use super::*;
     use crate::{atom::Atom, molecule::Molecule};
     use rust_decimal::Decimal;
+    use std::borrow::Cow;
 
     const PYRIDINE: &str = r#"11