-
Notifications
You must be signed in to change notification settings - Fork 136
151 lines (139 loc) · 5.69 KB
/
Copy pathGithubActionTests.yml
File metadata and controls
151 lines (139 loc) · 5.69 KB
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
name: PR Tests
on: [pull_request]
concurrency:
group: ${{ github.workflow }}-${{ github.ref }}
cancel-in-progress: true
jobs:
qc:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- uses: astral-sh/ruff-action@v3
name: ruff check
- uses: astral-sh/ruff-action@v3
name: ruff format
with:
args: "format --check --diff"
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Install dependencies
run: |
export BIOCONDA_DISABLE_BUILD_PREP=1
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
bash install-and-set-up-conda.sh
eval "$(conda shell.bash hook)"
conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
conda activate bioconda
conda install -y -c conda-forge ty
- name: ty check
run: |
eval "$(conda shell.bash hook)"
conda activate bioconda
ty check .
test-linux:
name: Linux tests
runs-on: ubuntu-latest
strategy:
matrix:
py_test_marker:
- not long_running_1 and not long_running_2
- long_running_1
- long_running_2
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Install bioconda-utils
run: |
export BIOCONDA_DISABLE_BUILD_PREP=1
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
bash install-and-set-up-conda.sh
eval "$(conda shell.bash hook)"
conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
conda activate bioconda
conda list
python -m pip install --no-deps --no-build-isolation .
- name: Build docker container
run: |
docker build -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest ./
docker history quay.io/bioconda/bioconda-utils-build-env-cos7:latest
docker run --rm -t quay.io/bioconda/bioconda-utils-build-env-cos7:latest sh -lec 'type -t conda && conda info --verbose && conda list'
docker build -t quay.io/bioconda/bioconda-utils-test-env-cos7:latest -f ./Dockerfile.test ./
- name: Run tests '${{ matrix.py_test_marker }}'
run: |
eval "$(conda shell.bash hook)"
conda activate bioconda
if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
py.test --durations=0 test/ -v --log-level=DEBUG --tb=native -m '${{ matrix.py_test_marker }}'
else
echo "Skipping pytest - only docs modified"
fi
test-macosx:
name: OSX tests
runs-on: macos-15-intel
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Install bioconda-utils
run: |
export BIOCONDA_DISABLE_BUILD_PREP=1
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
bash install-and-set-up-conda.sh
eval "$(conda shell.bash hook)"
conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
conda list
conda activate bioconda
python -m pip install --no-deps --no-build-isolation .
- name: Run tests
run: |
eval "$(conda shell.bash hook)"
conda activate bioconda
if git diff --name-only origin/master...HEAD | grep -vE ^docs; then
py.test --durations=0 test/ -v --log-level=DEBUG -k "not docker" --tb=native
else
echo "Skipping pytest - only docs modified"
fi
autobump-test:
name: autobump test
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Install bioconda-utils
run: |
export BIOCONDA_DISABLE_BUILD_PREP=1
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{common,install-and-set-up-conda,configure-conda}.sh
bash install-and-set-up-conda.sh
eval "$(conda shell.bash hook)"
conda create -n bioconda --quiet --yes --file test-requirements.txt --file bioconda_utils/bioconda_utils-requirements.txt
conda activate bioconda
conda list
python -m pip install --no-deps --no-build-isolation .
- name: Test autobump
run: |
eval "$(conda shell.bash hook)"
conda activate bioconda
git clone --depth 1 https://github.com/bioconda/bioconda-recipes.git
cd bioconda-recipes
git config user.name Autobump
git config user.email bioconda@users.noreply.github.com
mkdir /tmp/artifacts
bioconda-utils autobump \
--packages "a*" \
--unparsed-urls /tmp/artifacts/unparsed_urls.txt \
--failed-urls /tmp/artifacts/failed_urls.txt \
--recipe-status /tmp/artifacts/status.txt \
--create-pr \
--no-check-pinnings \
--no-check-pending-deps \
--no-follow-graph \
--exclude bioconductor-* \
--commit-as BiocondaBot 47040946+BiocondaBot@users.noreply.github.com \
--max-updates 5 \
--dry-run