forked from bioconda/bioconda-recipes
-
Notifications
You must be signed in to change notification settings - Fork 0
169 lines (147 loc) · 5.57 KB
/
master.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
name: Upload
on:
push:
branches:
- master
jobs:
build-linux:
name: Linux Upload
if: github.repository == 'bioconda/bioconda-recipes'
runs-on: ubuntu-latest
strategy:
fail-fast: false
max-parallel: 13
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
- name: Set up bioconda-utils
run: bash install-and-set-up-conda.sh
# This script can be used to reconfigure conda to use the right channel setup.
- name: Configure conda
run: bash configure-conda.sh
- name: Build and upload
env:
QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# Mimic circleci
OSTYPE: "linux-gnu"
CI: "true"
run: |
set -ex
eval "$(conda shell.bash hook)"
conda activate bioconda
bioconda-utils handle-merged-pr recipes config.yml \
--repo bioconda/bioconda-recipes \
--git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
--quay-upload-target biocontainers \
--fallback build \
--artifact-source github-actions
build-osx-64:
name: OSX-64 Upload
if: github.repository == 'bioconda/bioconda-recipes'
runs-on: macos-13
strategy:
fail-fast: false
max-parallel: 4
steps:
- uses: actions/checkout@v4
with:
fetch-depth: 0
- name: set path
run: echo "/opt/mambaforge/bin" >> $GITHUB_PATH
- name: Fetch conda install script
run: |
wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
- name: Set up bioconda-utils
run: bash install-and-set-up-conda.sh
# This script can be used to reconfigure conda to use the right channel setup.
- name: Configure conda
run: bash configure-conda.sh
- name: Build and Test
env:
QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# Mimic circleci
OSTYPE: "darwin"
CI: "true"
run: |
set -e
eval "$(conda shell.bash hook)"
conda activate bioconda
# Sets up OSX SDK
run_conda_forge_build_setup
bioconda-utils handle-merged-pr recipes config.yml \
--repo bioconda/bioconda-recipes \
--git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
--fallback build \
--artifact-source github-actions
# Disabled due to concurrency limits on GHA for OSX. osx-arm64 builds are on CircleCI.
# build_and_upload-osx-arm64:
# name: OSX-ARM64 Upload
# if: github.repository == 'bioconda/bioconda-recipes'
# runs-on: macOS-14 # M1
# strategy:
# fail-fast: false
# max-parallel: 4
# steps:
# - uses: actions/checkout@v4
# with:
# fetch-depth: 0
# # bail if there's no osx-arm64 recipes
# - name: Check for Additional Platforms
# id: additional_platforms
# run: |
# result=$(./scripts/check-for-additional-platforms.sh "${GITHUB_SHA}~1 ${GITHUB_SHA}" "build_and_upload" "${GITHUB_JOB}")
# if [[ ${result} != "build" ]]
# then
# echo "No recipes using this platform, skipping rest of job."
# echo "skip_build=true" >> $GITHUB_OUTPUT
# fi
# - name: set path
# run: |
# echo "/opt/mambaforge/bin" >> $GITHUB_PATH
# - name: Fetch conda install script
# if: steps.additional_platforms.outputs.skip_build != 'true'
# run: |
# wget https://raw.githubusercontent.com/bioconda/bioconda-common/master/{install-and-set-up-conda,configure-conda,common}.sh
# - name: Set up bioconda-utils
# if: steps.additional_platforms.outputs.skip_build != 'true'
# run: bash install-and-set-up-conda.sh
# - name: Configure conda
# if: steps.additional_platforms.outputs.skip_build != 'true'
# run: bash configure-conda.sh
# - name: Build and Upload
# if: steps.additional_platforms.outputs.skip_build != 'true'
# env:
# QUAY_LOGIN: ${{ secrets.QUAY_LOGIN }}
# QUAY_OAUTH_TOKEN: ${{ secrets.QUAY_OAUTH_TOKEN }}
# ANACONDA_TOKEN: ${{ secrets.ANACONDA_TOKEN }}
# INVOLUCRO_AUTH: ${{ secrets.INVOLUCRO_AUTH }}
# GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
# # Mimic circleci
# OSTYPE: "darwin"
# CI: "true"
# run: |
# set -xe
# eval "$(conda shell.bash hook)"
# conda activate bioconda
# source common.sh
# # Sets up OSX SDK
# run_conda_forge_build_setup
# bioconda-utils handle-merged-pr recipes config.yml \
# --repo bioconda/bioconda-recipes \
# --git-range ${GITHUB_SHA}~1 ${GITHUB_SHA} \
# --fallback build \
# --artifact-source github-actions