Lint (#13)

* Lint

* Add build workflow

.github/workflows/publish.yml

@@ -0,0 +1,72 @@
+---
+name: Publish
+
+on:
+ push:
+ tags:
+ - "0.*"
+
+jobs:
+ linux:
+ runs-on: "ubuntu-latest"
+ environment: pypi
+ strategy:
+ fail-fast: true
+ matrix:
+ python-version: [ "3.9", "3.10", "3.11" ]
+
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v3
+
+ - name: Create publish script
+ run: |
+ cat <<EOF > publish.sh
+ #!/bin/bash
+ docker run --rm -v $(pwd):/io ghcr.io/pyo3/maturin \
+ build --interpreter ${{ matrix.python-version }} --release --strip
+ #docker run --rm -v $(pwd):/io -e MATURIN_PYPI_TOKEN="\$1" \
+ # ghcr.io/pyo3/maturin publish --interpreter ${{ matrix.python-version }}
+ EOF
+ chmod +x publish.sh
+
+ - name: Publish optrs
+ run: |
+ ./publish.sh "${{ secrets.OPT_RS_UPLOAD_TOKEN }}"
+
+ - name: Publish optrs-api
+ run: |
+ cd api
+ ../publish.sh "${{ secrets.OPT_RS_API_UPLOAD_TOKEN }}"
+
+ mac:
+ runs-on: "macos-latest"
+ strategy:
+ fail-fast: true
+ matrix:
+ python-version: [ "3.9", "3.10", "3.11" ]
+
+ steps:
+ - name: Checkout repository
+ uses: actions/checkout@v3
+
+ - name: Setup Python
+ uses: actions/setup-python@v4
+ with:
+ python-version: ${{ matrix.python-version }}
+
+ - name: Install maturin
+ run: pip install maturin
+
+ - name: Publish optrs
+ env:
+ MATURIN_PYPI_TOKEN: ${{ secrets.OPT_RS_UPLOAD_TOKEN }}
+ run: |
+ maturin build --release --strip --universal2 #&& maturin publish
+
+ - name: Publish optrs-api
+ env:
+ MATURIN_PYPI_TOKEN: ${{ secrets.OPT_RS_API_UPLOAD_TOKEN }}
+ run: |
+ cd api
+ maturin build --release --strip --universal2 #&& maturin publish

.github/workflows/test.yml

@@ -1,26 +1,28 @@
+---
+name: Test
+
 on:
  push:
  branches: [ main ]
  pull_request:
 
-name: Test
-
 jobs:
  test:
- name: Test
+ runs-on: ubuntu-latest
  env:
  PROJECT_NAME_UNDERSCORE: optrs
  CARGO_INCREMENTAL: 0
  RUSTFLAGS: -Zprofile -Ccodegen-units=1 -Copt-level=0 -Clink-dead-code -Coverflow-checks=off -Zpanic_abort_tests -Cpanic=abort
  RUSTDOCFLAGS: -Cpanic=abort
- runs-on: ubuntu-latest
+
  steps:
- - uses: actions/checkout@v2
+ - uses: actions/checkout@v3
  - uses: actions-rs/toolchain@v1
  with:
  profile: minimal
  toolchain: nightly
  override: true
+
  - name: Cache dependencies
  uses: actions/cache@v2
  env:
@@ -34,18 +36,21 @@ jobs:
  ~/.cargo/registry/cache
  target
  key: ${{ runner.os }}-build-${{ env.cache-name }}-${{ hashFiles('Cargo.lock') }}
+
  - name: Generate test result and coverage report
  run: |
  cargo install cargo2junit grcov;
  cargo test $CARGO_OPTIONS --bins -- -Z unstable-options --format json | cargo2junit > results.xml;
  zip -0 ccov.zip `find . \( -name "$PROJECT_NAME_UNDERSCORE*.gc*" \) -print`;
  grcov ccov.zip -s . -t lcov --llvm --ignore-not-existing --ignore "/*" --ignore "tests/*" -o lcov.info;
+
  - name: Upload test results
  uses: EnricoMi/publish-unit-test-result-action@v1
  with:
  check_name: Test Results
  github_token: ${{ secrets.GITHUB_TOKEN }}
  files: results.xml
+
  - name: Upload to CodeCov
  uses: codecov/codecov-action@v1
  with:

.pre-commit-config.yaml

@@ -0,0 +1,30 @@
+---
+repos:
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.4.0
+ hooks:
+ - id: trailing-whitespace
+ - id: end-of-file-fixer
+ - id: check-toml
+
+ - repo: https://github.com/t-young31/pre-commit-hooks
+ rev: 0.1.3
+ hooks:
+ - id: stale-version
+
+ - repo: https://github.com/doublify/pre-commit-rust
+ rev: v1.0
+ hooks:
+ - id: fmt
+ - id: cargo-check
+
+ - repo: local
+ hooks:
+ - id: clippy
+ name: clippy
+ description: Lint rust sources
+ entry: cargo clippy
+ language: system
+ args: [ "--", "-A", "warnings"]
+ types: [ rust ]
+ pass_filenames: false

Cargo.toml

@@ -1,13 +1,13 @@
 [package]
 name = "optrs"
-version = "0.1.0"
+version = "0.1.1"
 edition = "2021"
 authors = ["Tom Young"]
 license = "MIT OR Apache-2.0"
 keywords = ["optimization", "chemistry"]
 repository = "https://github.com/t-young31/opt-rs"
 homepage = "https://github.com/t-young31/opt-rs"
-description = "Forcefield molecule optimization"
+description = "Molecular molecule optimization with forcefields"
 readme = "README.md"
 
 [[bin]]

README.md

@@ -5,7 +5,7 @@
 **optrs** is a lightweight molecular mechanics optimisation code written in rust.
 
 ***
-### Installation 
+### Installation
 Install the binary with
 
 ```bash
@@ -22,7 +22,7 @@ Optimise a molecule provided as a [.xyz](https://en.wikipedia.org/wiki/XYZ_file_
 optrs molecule.xyz
 ```
 
-which will generate _opt.xyz_ in working directory. 
+which will generate _opt.xyz_ in working directory.
 [API examples](https://github.com/t-young31/opt-rs/tree/main/api/examples).
 
 ***

api/Cargo.toml

@@ -1,6 +1,6 @@
 [package]
 name = "optrs"
-version = "0.1.0"
+version = "0.1.1"
 edition = "2021"
 authors = ["Tom Young"]