forked from deeptools/HiCExplorer
-
Notifications
You must be signed in to change notification settings - Fork 0
/
azure-pipelines.yml
94 lines (89 loc) · 3.5 KB
/
azure-pipelines.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
pr:
autoCancel: true
jobs:
- job: 'Linux'
timeoutInMinutes: 0
pool:
vmImage: 'ubuntu-latest'
strategy:
matrix:
Python36:
python.version: '3.6'
Python37:
python.version: '3.7'
Python38:
python.version: '3.8'
steps:
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
hash -r
displayName: Add conda to PATH
- bash: |
conda config --set always_yes yes --set changeps1 no
conda info -a
conda create -n hicexplorer --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
source activate hicexplorer
conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
conda install --yes -c conda-forge -c bioconda nose
conda install --yes pathlib
conda install --yes -c defaults -c conda-forge -c bioconda configparser
python setup.py install
displayName: installing dependencies
- script: |
source activate hicexplorer
flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712,W504
displayName: linting
- script: |
source activate hicexplorer
py.test hicexplorer/test/test_pytest_collected_items.py --doctest-modules --capture=sys
py.test hicexplorer --doctest-modules --ignore=hicexplorer/test/
displayName: doc_test_and_number_of_cases
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py
py.test hicexplorer/test/general/test_hicTADClassifier.py
py.test hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest
- job: 'OSX'
timeoutInMinutes: 0
pool:
vmImage: 'macOS-10.14'
strategy:
matrix:
Python36:
python.version: '3.6'
Python37:
python.version: '3.7'
Python38:
python.version: '3.8'
steps:
- bash: |
echo "##vso[task.prependpath]$CONDA/bin"
hash -r
displayName: Add conda to PATH
- bash: |
conda config --set always_yes yes --set changeps1 no
conda info -a
conda create -n hicexplorer --yes -c conda-forge -c bioconda python=$(python.version) --file requirements.txt
source activate hicexplorer
conda install --yes -c conda-forge -c bioconda pytest flake8 pytest-xdist pytest-forked
conda install --yes -c conda-forge -c bioconda nose
conda install --yes pathlib
conda install --yes -c defaults -c conda-forge -c bioconda configparser
python setup.py install
displayName: installing dependencies
- script: |
source activate hicexplorer
flake8 . --exclude=.venv,.build,planemo_test_env,build --ignore=E501,F401,F403,E402,F999,F405,E712,W504
displayName: linting
- script: |
source activate hicexplorer
py.test hicexplorer/test/test_pytest_collected_items.py --doctest-modules --capture=sys
py.test hicexplorer --doctest-modules --ignore=hicexplorer/test/
displayName: doc_test_and_number_of_cases
- script: |
source activate hicexplorer
py.test hicexplorer/test/general/ --doctest-modules --capture=sys -n 4 --ignore=hicexplorer/test/general/test_hicTADClassifier.py --ignore=hicexplorer/test/general/test_hicTrainTADClassifier.py
py.test hicexplorer/test/general/test_hicTADClassifier.py
py.test hicexplorer/test/general/test_hicTrainTADClassifier.py
displayName: pytest