-
Notifications
You must be signed in to change notification settings - Fork 3
329 lines (286 loc) · 11 KB
/
ci.yaml
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
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
# ==================================================================================================
# Header
# ==================================================================================================
name: CI
on: [push, pull_request]
# ==================================================================================================
# Jobs
# ==================================================================================================
jobs:
# ==========================================================================
# CI Matrix
# ==========================================================================
ci:
runs-on: ${{ matrix.os }}
strategy:
fail-fast: false
# -------------------------------------------------------
# matrix
# -------------------------------------------------------
matrix:
os:
# https://docs.github.com/en/actions/using-workflows/workflow-syntax-for-github-actions#choosing-github-hosted-runners
- ubuntu-20.04
- ubuntu-22.04
- macos-11
- macos-12
compiler:
- gcc-7
- gcc-8
- gcc-9
- gcc-10
- gcc-11
- gcc-12
- gcc-13
# - llvm-5
- llvm-6
- llvm-7
- llvm-8
- llvm-9
- llvm-10
- llvm-11
- llvm-12
- llvm-13
- llvm-14
- llvm-15
- llvm-16
- llvm-17
# -------------------------------------------------------
# exclude
# -------------------------------------------------------
exclude:
# Newer GCC versions are not available on all Ubuntu
- os: ubuntu-20.04
compiler: gcc-12
- os: ubuntu-20.04
compiler: gcc-13
- os: ubuntu-20.04
compiler: llvm-13
- os: ubuntu-20.04
compiler: llvm-14
- os: ubuntu-20.04
compiler: llvm-15
- os: ubuntu-20.04
compiler: llvm-16
- os: ubuntu-20.04
compiler: llvm-17
# Older GCC versions are not supported by Ubuntu any more
- os: ubuntu-22.04
compiler: gcc-7
- os: ubuntu-22.04
compiler: gcc-8
# llvm-9 causes weird segfauls on Ubuntu, which do not seem to be our fault.
# Need to investiage further at some point. We used setup-cpp locally to install
# the very same version of llvm-9, and got tons of segfauls for all kind of functions...
- os: ubuntu-20.04
compiler: llvm-9
- os: ubuntu-22.04
compiler: llvm-9
# Older GCC versions are also not supported by MacOS 12 any more.
# Also excluding a broken current one for now... Fix later!
- os: macos-12
compiler: gcc-7
- os: macos-12
compiler: gcc-8
- os: macos-12
compiler: gcc-13
# We also currently exclude clang from macos, as it fails with different types of
# linker errors. As this is merely a problem in the setup, we defer solving this for now.
# Wildcards do not work here, so we have to list them all... :-(
- os: macos-11
compiler: llvm-5
- os: macos-11
compiler: llvm-6
- os: macos-11
compiler: llvm-7
- os: macos-11
compiler: llvm-8
- os: macos-11
compiler: llvm-9
- os: macos-11
compiler: llvm-10
- os: macos-11
compiler: llvm-11
- os: macos-11
compiler: llvm-12
- os: macos-11
compiler: llvm-13
- os: macos-11
compiler: llvm-14
- os: macos-11
compiler: llvm-16
- os: macos-11
compiler: llvm-17
- os: macos-12
compiler: llvm-5
- os: macos-12
compiler: llvm-6
- os: macos-12
compiler: llvm-7
- os: macos-12
compiler: llvm-8
- os: macos-12
compiler: llvm-9
- os: macos-12
compiler: llvm-10
- os: macos-12
compiler: llvm-11
- os: macos-12
compiler: llvm-12
- os: macos-12
compiler: llvm-13
# - os: macos-12
# compiler: llvm-14
# - os: macos-12
# compiler: llvm-15
- os: macos-12
compiler: llvm-16
- os: macos-12
compiler: llvm-17
# -------------------------------------------------------
# include
# -------------------------------------------------------
include:
# Test with the latest of both compilers and OSs
- os: ubuntu-latest
compiler: gcc
- os: ubuntu-latest
compiler: llvm
# - os: macos-latest
# compiler: gcc
# - os: macos-latest
# compiler: llvm
# We test AppleClang as well, as a special case.
# - os: macos-10.15
# compiler: apple
- os: macos-11
compiler: apple
- os: macos-12
compiler: apple
# ==========================================================================
# Steps
# ==========================================================================
steps:
- name: Checkout
uses: actions/[email protected]
# -------------------------------------------------------
# Setup
# -------------------------------------------------------
- name: Setup C++
# Reference: https://github.com/marketplace/actions/setup-cpp-c-c
uses: aminya/[email protected]
if: matrix.compiler != 'apple'
with:
compiler: ${{ matrix.compiler }}
cmake: true
make: true
- name: Setup C++ - AppleClang
if: matrix.compiler == 'apple'
run: |
brew install cmake
# -------------------------------------------------------
# Dependencies
# -------------------------------------------------------
- name: Install Dependencies - Ubuntu
if: runner.os == 'linux'
# 1: htslib dependencies, see https://github.com/samtools/htslib/blob/develop/INSTALL
# 2: clang on ubuntu 22 is not properly set up, we need libtinfo5,
# see https://github.com/aminya/setup-cpp/issues/149
run: |
sudo apt-get install autoconf automake zlib1g-dev libbz2-dev liblzma-dev
sudo apt-get install libtinfo5
- name: Install Dependencies - MacOS
if: runner.os == 'macos'
# - Install simple dependencies of htslib
# - For our test script, we might need gdate, see https://apple.stackexchange.com/a/47181
# This is not used at the moment, but we keep it here for the future.
# - switch xcode mode, see https://stackoverflow.com/a/67654877
run: |
brew install autoconf automake libdeflate
brew install coreutils
if [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
# -------------------------------------------------------
# Configure
# -------------------------------------------------------
- name: Configure
run: |
# Need to set the xcode patch here as well, as job steps don't keep status.
if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
# For static builds, set the according CMake option
export GRENEDALF_BUILD_STATIC=""
if [[ "${{ matrix.os }}" == "ubuntu-22.04" ]] && [[ "${{ matrix.compiler }}" == "gcc-13" ]]; then
export GRENEDALF_BUILD_STATIC="-DGRENEDALF_BUILD_STATIC=ON"
fi
cmake -S . -B ./build ${GRENEDALF_BUILD_STATIC}
# -------------------------------------------------------
# Build
# -------------------------------------------------------
- name: Build
run: |
# Weird workarounds. On some CI builds, this is needed somehow for LLVM under Ubuntu.
if [[ "${RUNNER_OS}" != "macOS" ]] && [[ ! -f /usr/bin/gmake ]]; then
sudo ln -s /usr/bin/make /usr/bin/gmake
fi
# Need to set the xcode patch here as well, as job steps don't keep status.
if [[ "${RUNNER_OS}" == "macOS" ]] && [[ "${{ matrix.compiler }}" == gcc* ]]; then
echo "Patching xcode gcc issues"
sudo xcode-select --switch /Library/Developer/CommandLineTools
fi
cmake --build ./build -- -j 2
- name: Upload Logs
if: always()
uses: actions/upload-artifact@v4
with:
name: logs-${{ matrix.os }}-${{ matrix.compiler }}
path: |
build/**/*.log
# -------------------------------------------------------
# Upload Binaries
# -------------------------------------------------------
# We upload the static binaries for the most important systems.
# These are the ones that we want to publish with release versions.
- name: Upload Binaries
if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple'
uses: actions/upload-artifact@v4
with:
name: binary-${{ matrix.os }}
path: |
bin/grenedalf
# -------------------------------------------------------
# Test
# -------------------------------------------------------
# For the same versions that we use for the binaries above,
# we also run the test case, comparing grenedalf against our independent implementation.
# This covers Ubuntu and two Mac versions, so hopefully good enough.
- name: Python Setup
if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple'
uses: actions/setup-python@v2
with:
python-version: 3.8
- name: Install Test Dependencies
if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple'
run: |
# Install the dependencies for the tests
pip install -r test/pip.txt
# Verify the installation
pip list
python --version
- name: Run Test
if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple'
run: |
cd test
./run.sh
cd ..
- name: Upload Tests
if: ( matrix.os == 'ubuntu-22.04' && matrix.compiler == 'gcc-13' ) || matrix.compiler == 'apple'
uses: actions/upload-artifact@v4
with:
name: test-${{ matrix.os }}
path: |
test