-
Notifications
You must be signed in to change notification settings - Fork 13
162 lines (140 loc) · 4.97 KB
/
build.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
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
name: Python package
on: [push, pull_request]
jobs:
linting:
name: Run linting/pre-commit checks
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v4
with:
python-version: '3.10'
- run: pip install pre-commit
- run: pre-commit --version
- run: pre-commit install
- run: pre-commit run --all-files
unit-tests:
needs: [linting]
runs-on: ${{ matrix.platform }}
strategy:
max-parallel: 4
matrix:
platform: [ubuntu-latest, windows-latest, macos-latest]
python-version: ['3.8', '3.9', '3.10', '3.11']
env:
PLATFORM: ${{ matrix.platform }}
steps:
- uses: actions/checkout@v4
- name: Install poetry
run: |
python -m pip install --upgrade pip
pip install poetry
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
cache: poetry
- name: Install dependencies
run: poetry install --with=dev
- name: Setup passwordless SSH access to localhost for tests
# Adapted from https://stackoverflow.com/a/60367309/6388696
if: runner.os == 'Linux'
run: |
ssh-keygen -t ed25519 -f ~/.ssh/testkey -N ''
cat > ~/.ssh/config <<EOF
Host localhost
User $USER
HostName 127.0.0.1
IdentityFile ~/.ssh/testkey
EOF
echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys
chmod og-rw ~
ssh -o 'StrictHostKeyChecking no' localhost id
- name: Test with pytest
run: poetry run pytest --cov=milatools --cov-report=xml --cov-append
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v3
with:
file: ./coverage.xml
flags: unittests
env_vars: PLATFORM,PYTHON
name: codecov-umbrella
fail_ci_if_error: false
mock-slurm-integration-tests:
name: integration tests with a mock slurm cluster
needs: [unit-tests]
runs-on: ${{ matrix.platform }}
strategy:
max-parallel: 5
matrix:
# TODO: We should ideally also run this with Windows/Mac clients and a Linux
# server. Unsure how to set that up with GitHub Actions though.
platform: [ubuntu-latest]
python-version: ['3.8', '3.9', '3.10', '3.11']
# For the action to work, you have to supply a mysql
# service as defined below.
services:
mysql:
image: mysql:8.0
env:
MYSQL_ROOT_PASSWORD: root
ports:
- "8888:3306"
options: --health-cmd="mysqladmin ping" --health-interval=10s --health-timeout=5s --health-retries=3
steps:
- uses: actions/checkout@v4
# NOTE: Replacing this with our customized version of
# - uses: koesterlab/setup-slurm-action@v1
- uses: ./.github/custom_setup_slurm_action
- name: Test if the slurm cluster is setup correctly
run: srun --nodes=1 --ntasks=1 --cpus-per-task=1 --mem=1G --time=00:01:00 hostname
- name: Setup passwordless SSH access to localhost for tests
# Adapted from https://stackoverflow.com/a/60367309/6388696
run: |
ssh-keygen -t ed25519 -f ~/.ssh/testkey -N ''
cat > ~/.ssh/config <<EOF
Host localhost
User $USER
HostName 127.0.0.1
IdentityFile ~/.ssh/testkey
EOF
echo -n 'from="127.0.0.1" ' | cat - ~/.ssh/testkey.pub > ~/.ssh/authorized_keys
chmod og-rw ~
ssh -o 'StrictHostKeyChecking no' localhost id
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v5
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install poetry
poetry install --with=dev
- name: Launch integration tests
run: poetry run pytest --slow --cov=milatools --cov-report=xml --cov-append -vvv --log-level=DEBUG
timeout-minutes: 5
env:
SLURM_CLUSTER: localhost
- name: Upload coverage reports to Codecov
uses: codecov/codecov-action@v3
with:
file: ./coverage.xml
flags: integrationtests
env_vars: PLATFORM,PYTHON
name: codecov-umbrella
fail_ci_if_error: false
real-slurm-integration-tests:
name: integration tests with a real SLURM cluster
needs: [mock-slurm-integration-tests]
strategy:
max-parallel: 1
matrix:
# TODO: We should ideally also run this with Windows/Mac clients and a Linux
# server. Unsure how to set that up with GitHub Actions though.
python-version: ['3.11']
cluster: ['mila']
uses: ./.github/workflows/testing.yml
with:
cluster: ${{ matrix.cluster }}
python-version: ${{ matrix.python-version }}
secrets: inherit