-
Notifications
You must be signed in to change notification settings - Fork 24
387 lines (334 loc) · 13.5 KB
/
unix_unit_tests.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
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
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
name: MHKiT-MATLAB Unix Unit Tests
on:
push:
branches: [ master, develop ]
pull_request:
branches: [ master, develop ]
jobs:
cache_population:
strategy:
fail-fast: false
matrix:
os: [ubuntu-latest]
python-version: ["3.10"]
matlab-version: [R2022b]
runs-on: ${{ matrix.os }}
env:
mhkit-python-dir: "MHKiT-Python"
MHKIT_PYTHON_VERSION: '0.7.0'
steps:
- name: Install & Setup Miniconda
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: latest
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: mhkit_conda_env
channels: conda-forge
- name: "Conda install netcdf4, hdf5"
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4
# conda install netcdf4 hdf5
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
- name: Check out MHKiT-MATLAB
uses: actions/checkout@v4
# - name: Check out MHKiT-Python
# uses: actions/checkout@v4
# with:
# repository: "MHKiT-Software/MHKiT-Python"
# path: ${{env.mhkit-python-dir}}
# - name: pip install mhkit module from source
# shell: bash -l {0}
# run: |
# conda activate mhkit_conda_env
# pip install -e .
# working-directory: ${{env.mhkit-python-dir}}
- name: pip install mhkit from pypi
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip install mhkit==$MHKIT_PYTHON_VERSION
- name: pip install mhkit-python-utils module from source
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip install -e .
- name: Pin scipy version
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip uninstall -y scipy
pip install scipy==1.10.1
- name: List installed pip modules
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip freeze
# Create the cache and add a dummy file
# The dummy file ensures that the artifact download
- name: Setup mhkit_webread_cache
shell: bash -l {0}
run: |
mkdir mhkit_webread_cache
touch mhkit_webread_cache/test.txt
echo "Hello World" > mhkit_webread_cache/test.txt
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v2
with:
release: ${{ matrix.matlab-version }}
# OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu
- name: Configure MATLAB Python Environment
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") > run.m
- name: Add MATLAB test commands
shell: bash
run: echo "version,
addpath(genpath('mhkit')),
import matlab.unittest.TestSuite,
import matlab.unittest.TestRunner,
testFolder = ['mhkit' filesep 'tests'],
suite = TestSuite.fromFolder(testFolder),
runner = TestRunner.withTextOutput,
results = runner.run(suite),
assertSuccess(results)" >> run.m
- name: Output run.m
shell: bash
run: cat run.m
- name: Run MATLAB Unit Tests
uses: matlab-actions/run-command@v2
with:
command: run
startup-options: -noFigureWindows
- name: Save mhkit_webread_cache directory as an artifact
uses: actions/upload-artifact@v4
with:
# GitHub Action "Name" of artifact
name: mhkit_webread_cache
# Filesystem path of directory
path: mhkit_webread_cache
main:
needs: cache_population
strategy:
fail-fast: false
# Expecting 2 * 4 * 7 - (13 * 2) = 30 jobs
matrix:
os: [macos-13, ubuntu-latest]
python-version: [3.8, 3.9, "3.10", 3.11]
# Note: It is preferred to use an actual release name as opposed to 'latest'
matlab-version: [R2021b, R2022a, R2022b, R2023a, R2023b, R2024a]
mhkit-python-version: ["0.7.0"]
exclude:
- python-version: "3.10" # cache_population job
matlab-version: R2022b
os: ubuntu-latest
- matlab-version: R2024a # Non compatiable versions of Python and MATLAB
python-version: 3.8
- matlab-version: R2023b
python-version: 3.8
- matlab-version: R2023a
python-version: 3.11
- matlab-version: R2022b
python-version: 3.11
- matlab-version: R2022a
python-version: 3.11
- matlab-version: R2022a
python-version: "3.10"
- matlab-version: R2021b
python-version: 3.11
- matlab-version: R2021b
python-version: "3.10"
- matlab-version: R2021a
python-version: 3.11
- matlab-version: R2021a
python-version: "3.10"
- matlab-version: R2021a
python-version: 3.9
- matlab-version: R2020b
python-version: 3.11
- matlab-version: R2020b
python-version: "3.10"
- matlab-version: R2020b
python-version: 3.9
# Specific versions of tests that fail consistently. Most likely due to the GitHub actions environment
# - matlab-version: R2024a # Python netcdf4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123413351
# python-version: 3.11
# os: macos-13
# - matlab-version: R2024a # Working!
# python-version: "3.10"
# os: macos-13
# - matlab-version: R2024a # Java Segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411604
# python-version: 3.9
# os: macos-13
# - matlab-version: R2023b # Python netcd4 pip build error: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412889
# python-version: 3.11
# os: macos-13
# - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123412352
# python-version: "3.10"
# os: macos-13
# - matlab-version: R2023b # Java segfault on Python initialization: https://github.com/MHKiT-Software/MHKiT-MATLAB/actions/runs/8789749433/job/24123411335
# python-version: 3.9
# os: macos-13
runs-on: ${{ matrix.os }}
env:
mhkit-python-dir: "MHKiT-Python"
MHKIT_PYTHON_VERSION: ${{ matrix.mhkit-python-version }}
steps:
- name: Check out MHKiT-MATLAB
uses: actions/checkout@v4
# - name: Check out MHKiT-Python
# uses: actions/checkout@v4
# with:
# repository: "MHKiT-Software/MHKiT-Python"
# path: ${{env.mhkit-python-dir}}
- name: Install & Setup Miniconda
uses: conda-incubator/setup-miniconda@v3
with:
miniconda-version: latest
auto-update-conda: true
python-version: ${{ matrix.python-version }}
activate-environment: mhkit_conda_env
channels: conda-forge
# This is necessary to fix any issues with netcdf4 and hdf5 headers
- name: "Conda install netcdf4, hdf5"
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
conda install numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4
# conda install netcdf4 hdf5
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
# - name: Setup Python ${{ matrix.python-version }}
# shell: bash -l {0}
# run: |
# conda create --name mhkit_conda_env python=${{ matrix.python-version }} numpy==1.24.4 cython pip pytest hdf5 libnetcdf cftime netcdf4 --strict-channel-priority
# conda activate mhkit_conda_env
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
# pip install -e . --no-deps --force-reinstall
# - name: Setup MHKiT Dependencies on macOS
# if: ${{ matrix.os == 'macos-13' }}
# run: brew install hdf5 netcdf
# - name: Setup MHKiT Dependencies on ubuntu
# run: sudo apt install libhdf5-serial-dev libnetcdf-dev
# if: ${{ matrix.os == 'ubuntu-latest' }}
# - name: Setup MHKiT Dependencies on ubuntu
# if: ${{ matrix.os == 'ubuntu-latest' }}
# run: |
# sudo apt update
# sudo apt upgrade
# sudo apt install build-essential
# - name: Print GCC Version
# if: ${{ matrix.os == 'ubuntu-latest' }}
# run: |
# gcc --version
# g++ --version
# - name: Setup MATLAB Path on Ubuntu
# if: ${{ matrix.os == 'ubuntu-latest' }}
# run: echo "export LD_LIBRARY_PATH=/usr/local/MATLAB/${{ matrix.matlab-version }}/sys/os/glnxa64" >> "$GITHUB_ENV"
- name: Setup MATLAB Path on Ubuntu
if: ${{ matrix.os == 'ubuntu-latest' }}
run: echo "LD_PRELOAD=/lib/x86_64-linux-gnu/libstdc++.so.6" >> "$GITHUB_ENV"
- name: Print Python executable
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
python -c "import sys; print(sys.executable)"
- name: Print Python Version
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
python --version
# - name: pip install mhkit module from source
# working-directory: ${{env.mhkit-python-dir}}
# shell: bash -l {0}
# run: |
# conda activate mhkit_conda_env
# export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
# pip install -e .
- name: pip install mhkit from pypi
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install mhkit==$MHKIT_PYTHON_VERSION
- name: pip upgrade netcdf4
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
export PATH="${CONDA_PREFIX}/bin:${CONDA_PREFIX}/Library/bin:$PATH" # so setup.py finds nc-config
pip install --upgrade netcdf4
- name: pip install mhkit-python-utils module from source
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip install -e .
- name: Pin scipy version
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip uninstall -y scipy
pip install scipy==1.10.1
- name: List installed pip modules
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
pip freeze
- name: Print MHKiT-Python Version
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
python -c "import mhkit; print(mhkit.__version__)"
- name: Verify MHKiT-Python Operation
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
python -c "import mhkit; [ED, AP] = mhkit.river.performance.circular(30); print(ED); print(AP);"
- name: Download mhkit_webread_cache artifact
uses: actions/download-artifact@v4
with:
name: mhkit_webread_cache
path: mhkit_webread_cache
- name: Display structure mhkit_webread_cache
run: ls -R
working-directory: .
- name: Set up MATLAB
uses: matlab-actions/setup-matlab@v2
with:
release: ${{ matrix.matlab-version }}
- name: Add Python Dir to Path
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
printf "getenv('path')\nsetenv('path', ['%s;', getenv('path')])\ngetenv('path')\n" $(python -c "import sys; import os; print(os.path.dirname(sys.executable))") >> run.m
# OutOfProcess is required to properly call netcdf/hdf5 and works reliably on macos and ubuntu
- name: Configure MATLAB Python Environment
shell: bash -l {0}
run: |
conda activate mhkit_conda_env
printf 'pyenv(Version="%s", ExecutionMode="OutOfProcess")\n' $(python -c "import sys; print(sys.executable)") >> run.m
- name: Add MATLAB test commands
shell: bash
run: echo "version,
addpath(genpath('mhkit')),
import matlab.unittest.TestSuite,
import matlab.unittest.TestRunner,
testFolder = ['mhkit' filesep 'tests'],
suite = TestSuite.fromFolder(testFolder),
runner = TestRunner.withTextOutput,
results = runner.run(suite),
assertSuccess(results)" >> run.m
- name: Output run.m
shell: bash
run: cat run.m
# This is a good idea but does not work because you cannot explicitly set the python execution mode
# - name: Run MHKiT-MATLAB Unit Tests
# uses: matlab-actions/run-tests@v1
# with:
# select-by-folder: mhkit/tests
- name: Run MATLAB Unit Tests
uses: matlab-actions/run-command@v2
with:
command: run
startup-options: -noFigureWindows