-
Notifications
You must be signed in to change notification settings - Fork 88
125 lines (121 loc) · 3.46 KB
/
linux.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
name: linux
on: [pull_request, push]
defaults:
run:
shell: bash -l {0}
jobs:
docs:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: mamba-org/setup-micromamba@main
with:
environment-file: .github/snakePipesEnvCI.yml
condarc: |
channels:
- conda-forge
- bioconda
- defaults
channel_priority: 'strict'
cache-downloads: true
- name: Install snakePipes
run: |
micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
- name: docs
run: |
micromamba activate snakePipes_CI
cd docs
make html
flake:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: mamba-org/setup-micromamba@main
with:
environment-file: .github/snakePipesEnvCI.yml
condarc: |
channels:
- conda-forge
- bioconda
- defaults
channel_priority: 'strict'
cache-downloads: true
- name: Install snakePipes
run: |
micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
- name: flake
run: |
micromamba activate snakePipes_CI
flake8 --ignore=E501,E722,E402 --exclude tests,docs/conf.py,build/lib/snakePipes/shared/tools/three_prime_seq,snakePipes/shared/tools/three_prime_seq .
CI:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: mamba-org/setup-micromamba@main
with:
environment-file: .github/snakePipesEnvCI.yml
condarc: |
channels:
- conda-forge
- bioconda
- defaults
channel_priority: 'strict'
cache-downloads: true
- name: Install snakePipes
run: |
micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
- name: CI
run: |
micromamba activate snakePipes_CI
./.ci_stuff/test_dag.sh
- name: pytest
run: |
micromamba activate snakePipes_CI
pytest --verbosity=2
createEnvs:
needs: CI
strategy:
fail-fast: false
matrix:
envs: [
'CONDA_SHARED_ENV',
'CONDA_CREATE_INDEX_ENV',
'CONDA_RNASEQ_ENV',
'CONDA_RMATS_ENV',
'CONDA_scRNASEQ_ENV',
'CONDA_seurat3_ENV',
'CONDA_loompy_ENV',
'CONDA_alevinqc_ENV',
'CONDA_eisaR_ENV',
'CONDA_DNA_MAPPING_ENV',
'CONDA_CHIPSEQ_ENV',
'CONDA_ATAC_ENV',
'CONDA_HIC_ENV',
'CONDA_WGBS_ENV',
'CONDA_DSS_ENV',
'CONDA_RMD_ENV',
'CONDA_PREPROCESSING_ENV',
'CONDA_NONCODING_RNASEQ_ENV',
'CONDA_SAMBAMBA_ENV',
'CONDA_pysam_ENV'
]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- uses: mamba-org/setup-micromamba@main
with:
environment-file: .github/snakePipesEnvCI.yml
condarc: |
channels:
- conda-forge
- bioconda
- defaults
channel_priority: 'strict'
cache-downloads: true
- name: install snakePipes
run: |
micromamba run -n snakePipes_CI python -m pip install . --no-deps --ignore-installed -vvv
- name: createEnvs
run: |
micromamba activate snakePipes_CI
snakePipes createEnvs --autodetectCondaEnvDir --force --only ${{matrix.envs}}