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
|
name: NEURON Code Coverage
concurrency:
group: ${{ github.workflow }}#${{ github.ref }}
cancel-in-progress: true
on:
push:
branches:
- master
- release/**
pull_request:
branches:
- master
- release/**
# TODO : https://github.com/neuronsimulator/nrn/issues/1063
# paths-ignore:
# - '**.md'
# - '**.rst'
# - 'docs/**'
env:
PY_MIN_VERSION: '3.9'
PY_MAX_VERSION: '3.12'
jobs:
coverage:
runs-on: ubuntu-22.04
name: Code Coverage
timeout-minutes: 45
steps:
- name: Install apt packages
run: |
sudo apt-get install build-essential doxygen lcov libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf gpg
shell: bash
- name: Setup Caliper profiler
run: |
git clone https://github.com/LLNL/Caliper.git
cd Caliper
mkdir build && cd build
cmake ..
make && sudo make install
- name: Set up Python@${{ env.PY_MIN_VERSION }}
uses: actions/setup-python@v5
with:
python-version: ${{ env.PY_MIN_VERSION }}
- name: Set up Python@${{ env.PY_MAX_VERSION }}
uses: actions/setup-python@v5
with:
python-version: ${{ env.PY_MAX_VERSION }}
- uses: actions/checkout@v4
with:
fetch-depth: 2
- name: Install Python@${{ env.PY_MIN_VERSION }} dependencies
working-directory: ${{runner.workspace}}/nrn
run: |
python${PY_MIN_VERSION} -m pip install --upgrade pip -r nrn_requirements.txt
- name: Install Python@${{ env.PY_MAX_VERSION }} dependencies
working-directory: ${{runner.workspace}}/nrn
run: |
python${PY_MAX_VERSION} -m pip install --upgrade pip -r nrn_requirements.txt
- name: Build & Test
id: build-test
shell: bash
working-directory: ${{runner.workspace}}/nrn
run: |
export SHELL="/bin/bash"
# Compiler setup
export CC=gcc
export CXX=g++
# Python setup
export PYTHON_MIN=$(which $PYTHON_MIN_NAME);
export PYTHON_MAX=$(which $PYTHON_MAX_NAME);
mkdir build && cd build;
# CMake options & flags
export COVERAGE_FLAGS="--coverage -O0 -fno-inline -g";
export CMAKE_OPTION="-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PROFILING=ON";
cmake $CMAKE_OPTION -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX -DNRN_ENABLE_TESTS=ON -DCMAKE_C_FLAGS="${COVERAGE_FLAGS}" -DCMAKE_CXX_FLAGS="${COVERAGE_FLAGS}" ..;
# Coverage
# The Linux runners apparently have 2 cores, but jobs were being killed when we did not specify this explicitly.
# https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources
# By default we get a modern version of CMake that understands --parallel.
cmake --build . --parallel 2
(cd ..; lcov --capture --initial --directory . --no-external --output-file build/coverage-base.info)
export PATH=`pwd`/bin:$PATH;
ctest -VV;
(cd ..; lcov --capture --directory . --no-external --output-file build/coverage-run.info)
lcov --add-tracefile coverage-base.info --add-tracefile coverage-run.info --output-file coverage-combined.info
# Download codecov script and perform integrity checks
curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --import # One-time step
curl -Os https://uploader.codecov.io/latest/linux/codecov
curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM
curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig
gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM
shasum -a 256 -c codecov.SHA256SUM
chmod +x codecov
# Prefer auto-discovery for now. Specify reports once all python testing is unified under single report (-f option).
./codecov
env:
MATRIX_EVAL: "CC=gcc CXX=g++"
PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
# This step will set up an SSH connection on tmate.io for live debugging.
# To enable it, you have to:
# * add 'live-debug-coverage' to your PR title
# * push something to your PR branch (note that just re-running the pipeline disregards the title update)
- name: live debug session on failure (manual steps required, check `.github/coverage.yml`)
if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage')
uses: mxschmitt/action-tmate@v3
|
