Skip to content
This repository was archived by the owner on Mar 20, 2023. It is now read-only.

Commit 9c40afb

Browse files
alexsavulescualexsavulescu
authored
CoreNEURON CI via Github Actions (#433)
CI_BRANCHES:NEURON_BRANCH=master
1 parent fa5744f commit 9c40afb

File tree

1 file changed

+162
-0
lines changed

1 file changed

+162
-0
lines changed

‎.github/workflows/coreneuron-ci.yml‎

Lines changed: 162 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,162 @@
1+
name: CoreNEURON CI
2+
3+
on:
4+
push:
5+
branches:
6+
- master
7+
- live-debug*
8+
pull_request:
9+
branches:
10+
- master
11+
12+
env:
13+
BUILD_TYPE: Release
14+
DEVELOPER_DIR: /Applications/Xcode_11.3.1.app/Contents/Developer
15+
DEFAULT_PY_VERSION: 3.8
16+
17+
jobs:
18+
ci:
19+
runs-on: ${{ matrix.os }}
20+
21+
name: ${{ matrix.os }} - ${{ toJson(matrix.config) }})
22+
23+
env:
24+
INSTALL_DIR: install
25+
SDK_ROOT: $(xcrun --sdk macosx --show-sdk-path)
26+
27+
strategy:
28+
matrix:
29+
os: [ ubuntu-16.04, macOS-10.15 ]
30+
config:
31+
- {cmake_option: "-DCORENRN_ENABLE_MPI=ON", documentation: ON }
32+
- {cmake_option: "-DCORENRN_ENABLE_MPI=OFF"}
33+
- {cmake_option: "-DCORENRN_ENABLE_SOA=ON"}
34+
- {cmake_option: "-DCORENRN_ENABLE_SOA=OFF"}
35+
- {use_nmodl: ON, py_version: 3.6.7}
36+
- {use_nmodl: ON}
37+
- {use_ispc: ON, py_version: 3.6.7}
38+
- {gcc_version: 9}
39+
fail-fast: false
40+
41+
steps:
42+
43+
- name: Install homebrew packages
44+
if: startsWith(matrix.os, 'macOS')
45+
run: |
46+
brew install coreutils bison flex boost openmpi
47+
shell: bash
48+
49+
- name: Install apt packages
50+
if: startsWith(matrix.os, 'ubuntu')
51+
run: |
52+
sudo apt-get install doxygen bison flex libboost-all-dev libopenmpi-dev openmpi-bin python3-dev python3-pip
53+
shell: bash
54+
55+
- name: Install specific apt packages
56+
if: startsWith(matrix.os, 'ubuntu') && matrix.config.gcc_version
57+
run: |
58+
sudo apt-get install g++-${GCC_VERSION}
59+
shell: bash
60+
env:
61+
GCC_VERSION: ${{ matrix.config.gcc_version }}
62+
63+
- name: Set up Python3
64+
uses: actions/setup-python@v2
65+
with:
66+
python-version: ${{ env.PYTHON_VERSION }}
67+
env:
68+
PYTHON_VERSION: ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}
69+
70+
- name: Install ISPC
71+
if: ${{ matrix.config.use_ispc == 'ON' }}
72+
working-directory: ${{runner.workspace}}
73+
run: |
74+
ispc_version="v1.12.0";
75+
if [ "${{ startsWith(matrix.os, 'ubuntu') }}" == "true" ]; then
76+
url_os="linux";
77+
ispc_version_suffix="b";
78+
else
79+
url_os="macOS";
80+
ispc_version_suffix="";
81+
fi;
82+
url="https://github.com/ispc/ispc/releases/download/${ispc_version}/ispc-${ispc_version}${ispc_version_suffix}-${url_os}.tar.gz";
83+
wget -O ispc.tar.gz $url;
84+
mkdir ispc && tar -xvzf ispc.tar.gz -C ispc --strip 1;
85+
- name: Install NMODL dependencies
86+
if: ${{ matrix.config.use_nmodl == 'ON' || matrix.config.use_ispc == 'ON' }}
87+
run: |
88+
python3 -m pip install --upgrade pip jinja2 pyyaml pytest "sympy<1.6";
89+
90+
- uses: actions/checkout@v2
91+
92+
- name: Install Python3 documentation dependencies
93+
if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
94+
working-directory: ${{runner.workspace}}/CoreNeuron
95+
run: |
96+
python3 -m pip install --upgrade pip
97+
python3 -m pip install --upgrade -r docs/docs_requirements.txt
98+
99+
- name: Build and Test
100+
id: build-test
101+
shell: bash
102+
working-directory: ${{runner.workspace}}/CoreNeuron
103+
run: |
104+
if [ -n "$GCC_VERSION" ]; then
105+
export CXX="g++-${GCC_VERSION}" CC="gcc-${GCC_VERSION}";
106+
fi
107+
108+
if [[ "${{ startsWith(matrix.os, 'macOS') }}" = "true" ]]; then
109+
git submodule update --init -- external/Random123
110+
export PATH=${{runner.workspace}}/CoreNeuron/external/Random123:/usr/local/opt/flex/bin:/usr/local/opt/bison/bin:$PATH;
111+
export CXX=g++;
112+
export CC=gcc;
113+
fi
114+
115+
echo "------- Build, Test and Install -------"
116+
mkdir build && cd build
117+
if [[ "$USE_ISPC" == "ON" ]]; then
118+
cmake -DCORENRN_ENABLE_ISPC=ON -DCMAKE_ISPC_COMPILER=${{runner.workspace}}/ispc/bin/ispc -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
119+
elif [[ "$USE_NMODL" == "ON" ]]; then
120+
cmake -DCORENRN_ENABLE_NMODL=ON -DCORENRN_NMODL_FLAGS="sympy --analytic" -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
121+
else
122+
cmake ${cmake_option} -DCMAKE_INSTALL_PREFIX=$INSTALL_DIR -DPYTHON_EXECUTABLE=$(which python3) ..;
123+
fi
124+
make
125+
ctest --output-on-failure
126+
make install
127+
env:
128+
cmake_option: ${{ matrix.config.cmake_option }}
129+
USE_ISPC: ${{ matrix.config.use_ispc }}
130+
USE_NMODL: ${{ matrix.config.use_nmodl }}
131+
INSTALL_DIR: ${{ runner.workspace }}/install
132+
GCC_VERSION: ${{ matrix.config.gcc_version }}
133+
PYTHON_VERSION: ${{ matrix.config.py_version || env.DEFAULT_PY_VERSION }}
134+
135+
# This step will set up an SSH connection on tmate.io for live debugging.
136+
# To trigger it, simply prefix your branch name with `live-debug`
137+
# i.e.: live-debug-hocfix
138+
- name: live debug session on failure
139+
if: failure() && startsWith(github.ref, 'refs/heads/live-debug')
140+
uses: mxschmitt/action-tmate@v3
141+
142+
- name: Documentation
143+
if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.config.documentation == 'ON' }}
144+
id: documentation
145+
working-directory: ${{runner.workspace}}/CoreNeuron
146+
run: |
147+
echo "------- Build Doxygen Documentation -------";
148+
pushd build;
149+
make docs;
150+
echo "-------- Disable jekyll --------";
151+
pushd docs;
152+
touch .nojekyll;
153+
echo ::set-output name=status::done
154+
155+
# - name: Deploy 🚀
156+
# uses: JamesIves/[email protected]
157+
# if: steps.documentation.outputs.status == 'done'
158+
# with:
159+
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
160+
# BRANCH: gh-pages # The branch the action should deploy to.
161+
# FOLDER: ${{runner.workspace}}/nrn/build/docs # The folder the action should deploy.
162+
# CLEAN: false # Automatically remove deleted files from the deploy branch

0 commit comments

Comments
 (0)