predictosaurus 0.7.3

Uncertainty aware haplotype based genomic variant effect prediction
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97

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

      - name: Install GSL
        run: sudo apt-get update && sudo apt-get install -y libgsl-dev

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
          toolchain: stable
          override: true
      
      - uses: Swatinem/rust-cache@v1.3.0

      - uses: actions-rs/cargo@v1
        with:
          command: test

  Coverage:
    needs:
      - Testing
    runs-on: ubuntu-latest
    steps:
      - name: Checkout repository
        uses: actions/checkout@v3

      - name: Install GSL
        run: sudo apt-get update && sudo apt-get install -y libgsl-dev

      - name: Install stable toolchain
        uses: actions-rs/toolchain@v1
        with:
          toolchain: stable
          override: true

      - name: Run cargo-tarpaulin
        run: |
          cargo install cargo-tarpaulin
          cargo tarpaulin --out Xml

      - name: Upload coverage reports to Codecov
        uses: codecov/codecov-action@v4
        env:
          CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

      - name: Archive code coverage results
        uses: actions/upload-artifact@v4
        with:
          name: code-coverage-report
          path: cobertura.xml