chore: initialize repository

.editorconfig

@@ -0,0 +1,27 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+charset = utf-8
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+
+[*.{py,rst,ini,rs,toml}]
+indent_style = space
+indent_size = 4
+
+[*.{html,css,scss,json,yml}]
+indent_style = space
+indent_size = 2
+
+[*.md]
+trim_trailing_whitespace = false
+
+[Makefile]
+indent_style = tab
+
+[nginx.conf]
+indent_style = space
+indent_size = 2

.github/workflows/conventional-prs.yml

@@ -0,0 +1,18 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+        with:
+          validateSingleCommit: true

.github/workflows/release-please.yml

@@ -0,0 +1,37 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    if: github.repository_owner == 'bihealth'
+    runs-on: ubuntu-latest
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: rust
+          package-name: mehari
+
+      - uses: actions/checkout@v2
+        if: ${{ steps.release.outputs.release_created }}
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        if: ${{ steps.release.outputs.release_created }}
+        with:
+          toolchain: stable
+          override: true
+
+      - uses: Swatinem/[email protected]
+        if: ${{ steps.release.outputs.release_created }}
+
+      - name: Publish crate
+        if: ${{ steps.release.outputs.release_created }}
+        uses: actions-rs/cargo@v1
+        with:
+          command: publish
+          args: --token ${{ secrets.CRATES_IO_TOKEN }}

.github/workflows/rust.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  Formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: rustfmt
+
+      - name: Check format
+        run: |
+          cargo fmt -- --check
+
+  Linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          lfs: true
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+          components: clippy
+
+      - name: Lint with clippy
+        uses: actions-rs/clippy-check@v1
+        with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+  Testing:
+    needs: Formatting
+    runs-on: ubuntu-latest
+
+    services:
+      # The tests need a postgres server;  the data will be loaded later
+      # after checkout.
+      postgres:
+        image: postgres
+        env:
+          POSTGRES_DB: uta
+          POSTGRES_USER: uta_admin
+          POSTGRES_PASSWORD: uta_admin
+        options: >-
+          --health-cmd pg_isready
+          --health-interval 10s
+          --health-timeout 5s
+          --health-retries 5
+        ports:
+          - 5432:5432
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v2
+        with:
+          lfs: 'true'
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+
+      - uses: Swatinem/[email protected]
+
+      - name: Run cargo-tarpaulin with fast tests
+        uses: actions-rs/[email protected]
+        with:
+          version: 0.21.0
+          args: "-- --test-threads 1"
+
+      - name: Codecov submission of fast test results
+        uses: codecov/codecov-action@v3
+        with:
+          verbose: true
+          fail_ci_if_error: true
+          token: ${{ secrets.CODECOV_TOKEN }}

.gitignore

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+/target
+#/Cargo.lock
+
+*~
+.*.sw?
+/.vscode
+
+*.lock
+
+
+# Added by cargo
+#
+# already existing elements were commented out
+
+#/target

CHANGELOG.md

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+# Changelog

Cargo.toml

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+[package]
+name = "mehari"
+version = "0.1.0"
+edition = "2021"
+authors = ["Manuel Holtgrewe <[email protected]>"]
+description = "Variant effect prediction all in Rust"
+license = "MIT"
+homepage = "https://github.com/bihealth/mehari"
+readme = "README.md"
+
+[[bin]]
+name = "mehari"
+
+[dependencies]

README.md

@@ -0,0 +1,8 @@
+[![CI](https://github.com/bihealth/mehari/actions/workflows/rust.yml/badge.svg)](https://github.com/bihealth/mehari/actions/workflows/rust.yml)
+
+# Mehari
+
+<img align="right" width="200" height="200" src="misc/camel.jpeg">
+
+Mehari is a software package for annotating VCF files with variant effect.
+The program uses [hgvs-rs](https://crates.io/crates/hgvs) for projecting genomic variants to transcripts and proteins and thus has high prediction quality.

src/main.rs

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+fn main() {
+    println!("Hello, world!");
+}