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JOSS review comments -- redux #109

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Aug 26, 2020
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c208a36
moved install dependencies bit
lincoln-harris Aug 24, 2020
8fdf8a3
updated USAGE.md path
lincoln-harris Aug 24, 2020
18fd26c
added adnl explanation for report_coverage option
lincoln-harris Aug 24, 2020
401e8e9
fixed csv vs json output issues
Aug 24, 2020
865d0ea
merge branch 'joss-review-redux' of https://github.com/czbiohub/cereb…
Aug 24, 2020
5f39fe7
updated issue report href
lincoln-harris Aug 24, 2020
3b0fbe3
updated report_coverage explanation
lincoln-harris Aug 24, 2020
286a306
further updates to USAGE.md
lincoln-harris Aug 24, 2020
d2b42c9
to -> and
lincoln-harris Aug 24, 2020
f6d1b69
nl
lincoln-harris Aug 24, 2020
f22ba7b
proper test VCF path in USAGE.md
lincoln-harris Aug 24, 2020
966dffc
moved windows exception in README.md
lincoln-harris Aug 24, 2020
bb83815
experimental -> tumor
lincoln-harris Aug 24, 2020
ad8485c
update paper.md
lincoln-harris Aug 24, 2020
b048b8f
update readme
lincoln-harris Aug 24, 2020
783b9ed
`germline-filter`
lincoln-harris Aug 24, 2020
6ef4dde
vs -> vs.
lincoln-harris Aug 24, 2020
f5edfe6
commented out types comparison stdout in utils.py
Aug 24, 2020
8a17b04
changed up germline filter option names
Aug 24, 2020
02aac26
update README
lincoln-harris Aug 24, 2020
b1c596a
small change to gf docstring
Aug 24, 2020
7dc711d
renamed gl-filt test dirs
Aug 24, 2020
04bc3c9
updated maynard ref
lincoln-harris Aug 25, 2020
77aba3c
docker (recommended)
lincoln-harris Aug 25, 2020
1b5d316
2019->2020
lincoln-harris Aug 25, 2020
1cabcf4
introduced WSL
lincoln-harris Aug 25, 2020
824fed2
added bio-informatics classifier in setup.py
Aug 25, 2020
b342788
cerebra -> `cerebra`
lincoln-harris Aug 25, 2020
f874165
adding separate Dependencies and Install (users vs developers) sections
lincoln-harris Aug 25, 2020
d9e5acc
dependencies hlink
lincoln-harris Aug 25, 2020
4af8344
pypi not recommended
lincoln-harris Aug 25, 2020
9368f13
`venv`
lincoln-harris Aug 25, 2020
77218cd
see CONTRIBUTING.md for more
lincoln-harris Aug 25, 2020
7a171b2
pypi install is not recommended
lincoln-harris Aug 25, 2020
9086622
updated INSTALL.md
lincoln-harris Aug 25, 2020
208825b
updated dependencies hlink
lincoln-harris Aug 25, 2020
1bd74dd
bolded
lincoln-harris Aug 25, 2020
d5c35b2
tumor/normal in USAGE.md
lincoln-harris Aug 25, 2020
daa2040
updates to USAGE.md
lincoln-harris Aug 25, 2020
916645d
wip
lincoln-harris Aug 25, 2020
7e20fd5
maynard 2020
lincoln-harris Aug 25, 2020
276b177
removed -e from makefile
lincoln-harris Aug 25, 2020
4b1889b
adding in issue templates
Aug 25, 2020
cee518b
update bugreport
lincoln-harris Aug 25, 2020
529e6c6
update bugreport
lincoln-harris Aug 25, 2020
3510bb8
removing bug_report.md and feature_request.md
lincoln-harris Aug 25, 2020
451e1bd
uncommented adnl sections in .travis.yml
lincoln-harris Aug 25, 2020
ba58b0a
changed pip install instruct in developer install
lincoln-harris Aug 25, 2020
358e87b
pip install in readme
lincoln-harris Aug 25, 2020
d6cb644
flake8 -> `flake8`
lincoln-harris Aug 25, 2020
6f33854
removed local dev guidelines from contributing.md
lincoln-harris Aug 25, 2020
9815ea6
changes to contributing.md
lincoln-harris Aug 25, 2020
a8c24ff
got rid of make coverage in .travis.yml
lincoln-harris Aug 25, 2020
d4a91f5
some changers
lincoln-harris Aug 26, 2020
d40de09
some spelling mistakes
lincoln-harris Aug 26, 2020
53d83b6
various spelling changes to README
lincoln-harris Aug 26, 2020
b8ae7d1
some revisions to REAME
lincoln-harris Aug 26, 2020
5e83fa5
changed intro to README
lincoln-harris Aug 26, 2020
dbae4da
lint
lincoln-harris Aug 26, 2020
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206 changes: 103 additions & 103 deletions .travis.yml
Original file line number Diff line number Diff line change
Expand Up @@ -23,117 +23,117 @@ matrix:
- pip3 install -r test_requirements.txt
- pip3 install .

# - os: linux
# python: "3.8-dev"
# install:
# - pip3 install -r requirements.txt
# - pip3 install -r test_requirements.txt
# - pip3 install .
- os: linux
python: "3.8-dev"
install:
- pip3 install -r requirements.txt
- pip3 install -r test_requirements.txt
- pip3 install .

# - os: linux
# python: "3.9-dev"
# install:
# - pip3 install -r requirements.txt
# - pip3 install -r test_requirements.txt
# - pip3 install .
- os: linux
python: "3.9-dev"
install:
- pip3 install -r requirements.txt
- pip3 install -r test_requirements.txt
- pip3 install .

# - os: linux
# python: "pypy3"
# install:
# - pip3 install -r requirements.txt
# - pip3 install -r test_requirements.txt
# - pip3 install .
- os: linux
python: "pypy3"
install:
- pip3 install -r requirements.txt
- pip3 install -r test_requirements.txt
- pip3 install .

# - name: "Python 3.6.6 OSX"
# os: osx
# language: generic
# env: PYTHON=3.6.6'
# before_install:
# - brew update
# - brew install openssl
# - brew install zlib
# - brew outdated pyenv || brew upgrade pyenv
# - brew install pyenv-virtualenv
# - pyenv install 3.6.6
# - export PYENV_VERSION=3.6.6
# - export PATH="/Users/travis/.pyenv/shims:${PATH}"
# - pyenv virtualenv venv
# - source /Users/travis/.pyenv/versions/venv/bin/activate
# - python --version
# install:
# - python -m pip install -U pip
# - sudo pip install setuptools
# - sudo pip install -r requirements.txt -e .
# - sudo pip install -r test_requirements.txt -e .
- name: "Python 3.6.6 OSX"
os: osx
language: generic
env: PYTHON=3.6.6'
before_install:
- brew update
- brew install openssl
- brew install zlib
- brew outdated pyenv || brew upgrade pyenv
- brew install pyenv-virtualenv
- pyenv install 3.6.6
- export PYENV_VERSION=3.6.6
- export PATH="/Users/travis/.pyenv/shims:${PATH}"
- pyenv virtualenv venv
- source /Users/travis/.pyenv/versions/venv/bin/activate
- python --version
install:
- python -m pip install -U pip
- sudo pip install setuptools
- sudo pip install -r requirements.txt -e .
- sudo pip install -r test_requirements.txt -e .

# - name: "Python 3.7.7 OSX"
# os: osx
# language: generic
# env: PYTHON=3.7.7'
# before_install:
# - brew update
# - brew install openssl
# - brew install zlib
# - brew outdated pyenv || brew upgrade pyenv
# - brew install pyenv-virtualenv
# - pyenv install 3.7.7
# - export PYENV_VERSION=3.7.7
# - export PATH="/Users/travis/.pyenv/shims:${PATH}"
# - pyenv virtualenv venv
# - source /Users/travis/.pyenv/versions/venv/bin/activate
# - python --version
# install:
# - python -m pip install -U pip
# - sudo pip install setuptools
# - sudo pip install -r requirements.txt -e .
# - sudo pip install -r test_requirements.txt -e .
- name: "Python 3.7.7 OSX"
os: osx
language: generic
env: PYTHON=3.7.7'
before_install:
- brew update
- brew install openssl
- brew install zlib
- brew outdated pyenv || brew upgrade pyenv
- brew install pyenv-virtualenv
- pyenv install 3.7.7
- export PYENV_VERSION=3.7.7
- export PATH="/Users/travis/.pyenv/shims:${PATH}"
- pyenv virtualenv venv
- source /Users/travis/.pyenv/versions/venv/bin/activate
- python --version
install:
- python -m pip install -U pip
- sudo pip install setuptools
- sudo pip install -r requirements.txt -e .
- sudo pip install -r test_requirements.txt -e .

# - name: "Python 3.8.2 OSX"
# os: osx
# language: generic
# env: PYTHON=3.8.2'
# before_install:
# - brew update
# - brew install openssl
# - brew install zlib
# - brew outdated pyenv || brew upgrade pyenv
# - brew install pyenv-virtualenv
# - pyenv install 3.8.2
# - export PYENV_VERSION=3.8.2
# - export PATH="/Users/travis/.pyenv/shims:${PATH}"
# - pyenv virtualenv venv
# - source /Users/travis/.pyenv/versions/venv/bin/activate
# - python --version
# install:
# - python -m pip install -U pip
# - sudo pip install setuptools
# - sudo pip install -r requirements.txt -e .
# - sudo pip install -r test_requirements.txt -e .
- name: "Python 3.8.2 OSX"
os: osx
language: generic
env: PYTHON=3.8.2'
before_install:
- brew update
- brew install openssl
- brew install zlib
- brew outdated pyenv || brew upgrade pyenv
- brew install pyenv-virtualenv
- pyenv install 3.8.2
- export PYENV_VERSION=3.8.2
- export PATH="/Users/travis/.pyenv/shims:${PATH}"
- pyenv virtualenv venv
- source /Users/travis/.pyenv/versions/venv/bin/activate
- python --version
install:
- python -m pip install -U pip
- sudo pip install setuptools
- sudo pip install -r requirements.txt -e .
- sudo pip install -r test_requirements.txt -e .

# - name: "Python 3.8.0 Windows"
# os: windows
# language: shell
# before_install:
# - choco install python --version 3.8.0
# - python -m pip install --upgrade pip
# env: PATH=/c/Python38:/c/Python38/Scripts:$PATH
# install:
# - python -m pip install -U pip # maybe dont need this
# - pip install setuptools
# - pip install -r requirements.txt -e .
# - pip install -r test_requirements.txt -e .
- name: "Python 3.8.0 Windows"
os: windows
language: shell
before_install:
- choco install python --version 3.8.0
- python -m pip install --upgrade pip
env: PATH=/c/Python38:/c/Python38/Scripts:$PATH
install:
- python -m pip install -U pip # maybe dont need this
- pip install setuptools
- pip install -r requirements.txt -e .
- pip install -r test_requirements.txt -e .

# allow_failures:
# - python: "3.8-dev"
# - python: "3.9-dev"
# - python: "pypy3"
# - os: windows
allow_failures:
- python: "3.8-dev"
- python: "3.9-dev"
- python: "pypy3"
- os: windows

script:
- make test
- make coverage
- make lint
# - make coverage
# - make lint

after_script:
- pip3 install codecov
- codecov
#after_script:
# - pip3 install codecov
# - codecov
2 changes: 1 addition & 1 deletion Makefile
Original file line number Diff line number Diff line change
Expand Up @@ -16,4 +16,4 @@ lint:

install:
pip install -r requirements.txt
pip install -e .
pip install .
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