chore: initializing repository

.editorconfig

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+# 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/ISSUE_TEMPLATE/bug_report.md

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+---
+name: Bug report
+about: Create a report to help us improve
+title: ''
+labels: bug
+assignees: ''
+
+---
+
+<!--
+For general questions please use the Discussions section of the project:
+
+https://github.com/bihealth/varfish-server/discussions
+
+For bug reports and feature requests please open a ticket using the templates!
+-->
+
+**Describe the bug**
+A clear and concise description of what the bug is.
+
+**To Reproduce**
+Steps to reproduce the behavior:
+1. Go to '...'
+2. Click on '....'
+3. Scroll down to '....'
+4. See error
+
+**Expected behavior**
+A clear and concise description of what you expected to happen.
+
+**Screenshots**
+If applicable, add screenshots to help explain your problem.
+
+**Desktop (please complete the following information):**
+ - OS: [e.g. iOS]
+ - Browser [e.g. chrome, safari]
+ - Version [e.g. 22]
+
+**Smartphone (please complete the following information):**
+ - Device: [e.g. iPhone6]
+ - OS: [e.g. iOS8.1]
+ - Browser [e.g. stock browser, safari]
+ - Version [e.g. 22]
+
+**Additional context**
+Add any other context about the problem here.

.github/ISSUE_TEMPLATE/feature_request.md

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+---
+name: Feature request
+about: Suggest an idea for this project
+title: ''
+labels: enhancement
+assignees: ''
+
+---
+
+<!--
+For general questions please use the Discussions section of the project:
+
+https://github.com/bihealth/varfish-server/discussions
+
+For bug reports and feature requests please open a ticket using the templates!
+-->
+
+**Is your feature request related to a problem? Please describe.**
+A clear and concise description of what the problem is. Ex. I'm always frustrated when [...]
+
+**Describe the solution you'd like**
+A clear and concise description of what you want to happen.
+
+**Describe alternatives you've considered**
+A clear and concise description of any alternative solutions or features you've considered.
+
+**Additional context**
+Add any other context or screenshots about the feature request here.

.github/dependabot.yml

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+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "cargo"
+    directory: "/"
+    schedule:
+      interval: "weekly"

.github/workflows/automerge.yml

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+name: Dependabot auto-merge
+
+on: pull_request
+
+permissions:
+  contents: write
+
+jobs:
+  dependabot:
+    runs-on: ubuntu-latest
+    if: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - name: Enable auto-merge for Dependabot PRs
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          # GitHub provides this variable in the CI env. You don't
+          # need to add anything to the secrets vault.
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/conventional-prs.yml

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+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

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+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@v2
+        id: release
+        with:
+          release-type: rust
+          package-name: scarus
+
+      - uses: actions/checkout@v3
+        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/rust-cache@v2
+        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@v3
+
+      - 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@v3
+
+      - 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
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+        with:
+          lfs: true
+
+      - name: Install stable toolchain
+        uses: actions-rs/toolchain@v1
+        with:
+          toolchain: stable
+          override: true
+
+      - uses: Swatinem/rust-cache@v2
+
+      - name: Run cargo-tarpaulin
+        uses: actions-rs/[email protected]
+        with:
+          version: 0.21.0
+          args: "--skip-clean -- --test-threads 1"
+
+      - name: Codecov
+        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?
+

CHANGELOG.md

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+# Changelog

Cargo.toml

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+[package]
+name = "scarus"
+version = "0.1.0"
+edition = "2021"
+authors = ["Manuel Holtgrewe <[email protected]>"]
+description = "Automated evaluation of ACMG rules"
+license = "MIT"
+homepage = "https://github.com/bihealth/scarus"
+readme = "README.md"
+
+[[bin]]
+name = "scarus"
+path = "src/main.rs"
+
+[dependencies]
+anyhow = "1.0"
+clap-verbosity-flag = "2.0"
+clap = { version = "4.4", features = ["derive", "help"] }
+log = "0.4"
+thiserror = "1.0"
+tokio = { version = "1.33", features = ["full"] }
+tracing = "0.1"
+tracing-subscriber = "0.3"
+
+[dev-dependencies]
+anyhow = "1.0"
+clap-verbosity-flag = {version = "2.0"}
+clap = { version = "4.1", features = ["derive", "env"] }
+env_logger = "0.10"
+pretty_assertions = "1.3"
+temp_testdir = "0.2"
+test-log = "0.2"
+tracing-subscriber = {version = "0.3" }