-
Notifications
You must be signed in to change notification settings - Fork 642
245 lines (221 loc) · 8.8 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
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
name: Nextflow CI
# read more here: https://help.github.com/en/articles/workflow-syntax-for-github-actions#on
# Note: We don't use the `on: path` option for docs,
# because the Build steps are *required* tests.
# Instead, we trigger + skip the tests if the only changes
# are in the docs folder. GitHub treats this as passing.
on:
push:
branches:
- 'master'
- 'test*'
- 'dev*'
- 'STABLE-*'
pull_request:
types: [opened, reopened, synchronize]
workflow_dispatch:
jobs:
build:
name: Build
runs-on: ubuntu-latest
timeout-minutes: 90
strategy:
fail-fast: false
matrix:
java_version: [17, 23]
steps:
- name: Checkout
uses: actions/checkout@v4
with:
fetch-depth: 1
submodules: true
- name: Get the commit message
id: get_commit_message
run: |
if [ "${{ github.event_name }}" = "pull_request" ]; then
echo "GitHub event=pull_request"
COMMIT_SHA=${{ github.event.pull_request.head.sha }}
COMMIT_MESSAGE=$(curl -s \
-H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message')
echo "Commit message=$COMMIT_MESSAGE" | head -n 1
echo "commit_message=$COMMIT_MESSAGE" | head -n 1 >> $GITHUB_OUTPUT
else
echo "GitHub event=${{ github.event_name }}"
echo "Commit message=${{ github.event.head_commit.message }}" | head -n 1
echo "commit_message=${{ github.event.head_commit.message }}" | head -n 1 >> $GITHUB_OUTPUT
fi
- name: Get changed files
id: changed-files
uses: tj-actions/changed-files@v43
with:
files_ignore: docs/**
- name: List all changed files
env:
ALL_CHANGED_FILES: ${{ steps.changed-files.outputs.all_changed_files }}
run: |
for file in ${ALL_CHANGED_FILES}; do
echo "$file was changed"
done
- name: Setup env
if: steps.changed-files.outputs.any_changed == 'true'
run: |
rm -f $HOME/.gitconfig;
mkdir -p "$HOME/.nextflow";
echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
env:
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
- name: Setup Java ${{ matrix.java_version }}
if: steps.changed-files.outputs.any_changed == 'true'
uses: actions/setup-java@v4
with:
java-version: ${{matrix.java_version}}
distribution: 'temurin'
architecture: x64
cache: gradle
- name: Compile
if: steps.changed-files.outputs.any_changed == 'true'
run: make assemble
- name: Test
if: steps.changed-files.outputs.any_changed == 'true'
run: |
env | sort
# configure test env
if [[ "$GOOGLE_SECRET" ]]; then
echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
fi
# run tests
make test
env:
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
- name: Publish tests report
uses: actions/upload-artifact@v4
if: steps.changed-files.outputs.any_changed == 'true' && always()
with:
name: report-unit-tests-jdk-${{ matrix.java_version }}
path: |
**/build/reports/tests/test
outputs:
any_changed: ${{ steps.changed-files.outputs.any_changed }}
commit_message: ${{ steps.get_commit_message.outputs.commit_message }}
test:
if: ${{ !contains(needs.build.outputs.commit_message, '[ci fast]') && needs.build.outputs.any_changed == 'true' }}
needs: build
runs-on: ubuntu-latest
timeout-minutes: 90
strategy:
fail-fast: false
matrix:
java_version: [17, 23]
test_mode: ["test_integration", "test_docs", "test_aws", "test_azure", "test_google", "test_wave"]
steps:
- name: Checkout
uses: actions/checkout@v4
with:
fetch-depth: 1
submodules: true
- name: Setup env
run: |
rm -f $HOME/.gitconfig;
mkdir -p "$HOME/.nextflow";
echo "providers.github.auth='$NXF_GITHUB_ACCESS_TOKEN'" > "$HOME/.nextflow/scm"
env:
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
- name: Setup Java ${{ matrix.java_version }}
uses: actions/setup-java@v4
with:
java-version: ${{matrix.java_version}}
distribution: 'temurin'
architecture: x64
cache: gradle
- name: Run tests
run: |
env | sort
# configure test env
if [[ "$GOOGLE_SECRET" ]]; then
echo $GOOGLE_SECRET | base64 -d > $PWD/google_credentials.json
export GOOGLE_APPLICATION_CREDENTIALS=$PWD/google_credentials.json
fi
cat $HOME/.nextflow/scm
make clean assemble install
bash test-ci.sh
env:
TEST_JDK: ${{ matrix.java_version }}
TEST_MODE: ${{ matrix.test_mode }}
GRADLE_OPTS: '-Dorg.gradle.daemon=false'
TOWER_ACCESS_TOKEN: ${{ secrets.TOWER_ACCESS_TOKEN }}
AWS_DEFAULT_REGION: eu-west-1
AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
NXF_BITBUCKET_ACCESS_TOKEN: ${{ secrets.NXF_BITBUCKET_ACCESS_TOKEN }}
NXF_GITHUB_ACCESS_TOKEN: ${{ secrets.NXF_GITHUB_ACCESS_TOKEN }}
NXF_GITLAB_ACCESS_TOKEN: ${{ secrets.NXF_GITLAB_ACCESS_TOKEN }}
NXF_AZURE_REPOS_TOKEN: ${{ secrets.NXF_AZURE_REPOS_TOKEN }}
GOOGLE_SECRET: ${{ secrets.GOOGLE_SECRET }}
AZURE_STORAGE_ACCOUNT_NAME: nfazurestore
AZURE_STORAGE_ACCOUNT_KEY: ${{ secrets.AZURE_STORAGE_ACCOUNT_KEY }}
AZURE_BATCH_ACCOUNT_NAME: nfbatchtest
AZURE_BATCH_ACCOUNT_KEY: ${{ secrets.AZURE_BATCH_ACCOUNT_KEY }}
- name: Tar integration tests
if: always()
run: tar -cvf integration-tests.tar tests/checks
- name: Publish tests report
uses: actions/upload-artifact@v4
if: always()
with:
name: report-${{ matrix.test_mode }}-jdk-${{ matrix.java_version }}
path: |
validation/**/*
validation/**/.*
integration-tests.tar
test-e2e:
if: ${{ contains(needs.build.outputs.commit_message,'[e2e stage]') || contains(needs.build.outputs.commit_message,'[e2e prod]') }}
needs: build
runs-on: ubuntu-latest
timeout-minutes: 10
permissions:
actions: write # Allow writing to actions
contents: write # Allow writing to repository contents
steps:
- name: Checkout
uses: actions/checkout@v4
with:
fetch-depth: 1
submodules: true
- name: Setup Java 17
uses: actions/setup-java@v4
with:
java-version: 17
distribution: 'temurin'
architecture: x64
cache: gradle
- name: Setup env
run: |
wget -q -O wave https://github.com/seqeralabs/wave-cli/releases/download/v1.4.1/wave-1.4.1-linux-x86_64
chmod +x wave
mv wave /usr/local/bin/
echo "COMMIT_MESSAGE=\"${{ needs.build.outputs.commit_message }}\"" >> $GITHUB_ENV
- name : Docker Login to Seqera public CR
uses : docker/login-action@v3
with :
registry : "public.cr.seqera.io"
username : "public-cr-admin"
password : ${{ secrets.SEQERA_PUBLIC_CR_PASSWORD }}
- name: Launch tests
run: |
cd test-e2e
bash run.sh
env:
GITHUB_TOKEN: ${{ secrets.AUTOMATION_GITHUB_TOKEN }}
GRADLE_OPTS: '-Dorg.gradle.daemon=false'