-
Notifications
You must be signed in to change notification settings - Fork 49
156 lines (141 loc) · 5.4 KB
/
github_actions.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
name: AlphaPulldown-CI-CD
on:
pull_request:
push:
branches:
- main
release:
types: [published]
workflow_dispatch:
jobs:
build-and-test:
runs-on: ubuntu-20.04
strategy:
fail-fast: false
matrix:
python-version: ["3.10", "3.11"]
install-type: ['user', 'developer']
steps:
- uses: webfactory/[email protected]
with:
ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
- uses: actions/checkout@v4
with:
submodules: recursive
- run: ls -la -R
- uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
cache: "pip"
- run: python -c "import sys; print(sys.version)"
- run: |
echo $CONDA/bin >> $GITHUB_PATH
echo "$GITHUB_WORKSPACE/alphapulldown" >> $GITHUB_PATH
- if: matrix.install-type == 'user'
run: |
conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif
eval "$(conda shell.bash hook)"
conda activate AlphaPulldown
conda install -c bioconda hmmer hhsuite
pip install alphapulldown==2.0.0b6
- if: matrix.install-type == 'developer'
run: |
conda create -n AlphaPulldown -c omnia -c bioconda -c conda-forge python==${{ matrix.python-version }} openmm==8.0 pdbfixer==1.9 kalign2 pytest importlib_metadata modelcif
eval "$(conda shell.bash hook)"
conda activate AlphaPulldown
conda install -c bioconda hmmer hhsuite
pip install -e .
pip install -e ColabFold --no-deps
pip install -e alphafold --no-deps
pip install -U "jax[cuda12]"
export PYTHONPATH=$PWD/AlphaLink2:$PYTHONPATH
# install dependencies for AlphaLink backend
# pip install torch==1.13.0+cu117 --extra-index-url https://download.pytorch.org/whl/cu117
# pip install setuptools==69.5.1 # Downgrade setuptools to avoid crashes when installing unicore
# git clone https://github.com/dptech-corp/Uni-Core.git
# cd Uni-Core
# python setup.py install --disable-cuda-ext
# cd .
python test/test_python_imports.py
- if: matrix.install-type == 'developer'
run: |
eval "$(conda shell.bash hook)"
conda activate AlphaPulldown
pytest -s test/test_custom_db.py
pytest -s test/test_remove_clashes_low_plddt.py
pytest -s test/test_modelcif.py
pytest -s test/test_features_with_templates.py
pytest -s test/test_post_prediction.py
export PYTHONPATH=$PWD/alphapulldown/analysis_pipeline:$PYTHONPATH
conda install -c bioconda biopandas
pip install pyrosetta-installer
python -c 'import pyrosetta_installer; pyrosetta_installer.install_pyrosetta()'
pytest -s test/test_pdb_analyser.py
pytest -s test/test_get_good_inter_pae.py
build-fold-container:
runs-on: ubuntu-latest
steps:
- uses: webfactory/[email protected]
with:
ssh-private-key: ${{ secrets.SSH_PRIVATE_KEY }}
- name: Checkout
uses: actions/checkout@v4
- name: Free disk space
run: |
rm -rf /opt/hostedtoolcache
- name: Login to Docker Hub
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Build and push fold container
if: github.event_name == 'push'
uses: docker/build-push-action@v5
with:
context: .
file: ./docker/pulldown.dockerfile
push: true
tags: ${{ secrets.DOCKER_USERNAME }}/fold:latest
ssh: default
- name: Build and push fold container with version
if: github.event_name == 'release' && github.event.action == 'published'
uses: docker/build-push-action@v5
with:
context: .
file: ./docker/pulldown.dockerfile
push: true
tags: ${{ secrets.DOCKER_USERNAME }}/fold:${{ github.event.release.tag_name }}
ssh: default
build-analysis-container:
runs-on: ubuntu-latest
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Free disk space
run: |
rm -rf /opt/hostedtoolcache
- name: Login to Docker Hub
uses: docker/login-action@v3
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v3
- name: Build and push analysis container
if: github.event_name == 'push'
uses: docker/build-push-action@v5
with:
context: .
file: ./docker/analysis.dockerfile
push: true
tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:latest
- name: Build and push analysis container with version
if: github.event_name == 'release' && github.event.action == 'published'
uses: docker/build-push-action@v5
with:
context: .
file: ./docker/analysis.dockerfile
push: true
tags: ${{ secrets.DOCKER_USERNAME }}/fold_analysis:${{ github.event.release.tag_name }}