forked from NationalGenomicsInfrastructure/TACA
-
Notifications
You must be signed in to change notification settings - Fork 0
130 lines (115 loc) · 3.9 KB
/
lint-code.yml
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
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
name: Lint code
on: [push, pull_request]
jobs:
# Use ruff to check for code style violations
ruff-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11.5"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install ruff
- name: ruff --> Check for style violations
# Configured in pyproject.toml
run: ruff check .
# Use ruff to check code formatting
ruff-format:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11.5"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install ruff
- name: ruff --> Check code formatting
run: ruff format --check .
# Use mypy for static type checking
mypy-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repo
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11.5"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install mypy
# Start by installing type stubs
- name: mypy --> Install stubs
run: echo -e "y" | mypy --install-types . || exit 0
- name: mypy --> Static type checking
# Configured in pyprojet.toml
run: mypy .
# Use pipreqs to check for missing dependencies
pipreqs-check:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: "3.11.5"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install -r requirements.txt
pip install -r requirements-dev.txt
- name: Run pipreqs
run: |
pipreqs --savepath pipreqs.txt taca 2>&1 | tee pipreqs_output.log
if grep -q 'WARNING: Package .* does not exist or network problems' pipreqs_output.log; then
missing_packages=$(grep 'WARNING: Package .* does not exist or network problems' pipreqs_output.log | sed -E 's/.*Package "(.*)" does not exist.*/\1/')
echo "ERROR: Add unresolved packages to requirements. Missing package(s): $missing_packages. Example: '<pkg> @ git+https://github.com/<author>/<repo>.git'"
exit 1
fi
- name: Compare requirements
run: |
# Extract and sort package names
awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' requirements.txt | tr '[:upper:]' '[:lower:]' | sort -u > requirements.compare
awk -F'(=|==|>|>=|<|<=| @ )' '{print $1}' pipreqs.txt | tr '[:upper:]' '[:lower:]' | sort -u > pipreqs.compare
# Compare package lists
if cmp -s requirements.compare pipreqs.compare
then
echo "Requirements are the same"
exit 0
else
echo "Requirements are different"
echo ""
echo "=== current requirements.txt ==="
echo ""
cat requirements.compare
echo ""
echo "=== pipreqs requirements ==="
echo ""
cat pipreqs.compare
exit 1
fi
# Use Prettier to check various file formats
prettier:
runs-on: ubuntu-latest
steps:
- name: Checkout repository
uses: actions/checkout@v4
- name: Setup node
uses: actions/setup-node@v4
with:
node-version: "20"
- name: Install Prettier
run: npm install -g prettier
- name: Run Prettier --check
run: prettier --check .