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Merge pull request #1 from icbi-lab/master
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federicomarini authored Dec 11, 2020
2 parents 14ba869 + 6586736 commit cfeb095
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2 changes: 2 additions & 0 deletions .Rbuildignore
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^appveyor\.yml$
^.*\.Rproj$
^\.Rproj\.user$
^README\.Rmd$
^cran-comments\.md$
^NEWS\.md$
^\.travis\.yml$
^\.github
77 changes: 77 additions & 0 deletions .conda/meta.yaml
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{% set name = "r-immunedeconv" %}

package:
name: {{ name }}
version: "develop"

source:
path: ".."

build:
script: $R CMD INSTALL --build .
number: 0
noarch: generic
rpaths:
- lib/R/lib/
- lib/

requirements:
host:
- r-base
- r-dplyr >=0.7
- r-magrittr >=1.5
- r-readr >=1.1
- r-readxl >=1.0
- r-testit >=0.7
- r-tibble >=1.4.2
- r-data.tree >=0.7
- r-limsolve >=1.5.5.1
- r-e1071 >=1.6
- bioconductor-biobase
- bioconductor-biocgenerics
- bioconductor-biocparallel
- bioconductor-preprocesscore
- bioconductor-gsva
- bioconductor-sva
- bioconductor-gseabase
- r-xcell >=1.2
- r-epic >=1.1
- r-mcpcounter
run:
- r-base
- r-dplyr >=0.7
- r-magrittr >=1.5
- r-readr >=1.1
- r-readxl >=1.0
- r-testit >=0.7
- r-tibble >=1.4.2
- r-data.tree >=0.7
- r-limsolve >=1.5.5.1
- r-e1071 >=1.6
- bioconductor-biobase
- bioconductor-biocgenerics
- bioconductor-biocparallel
- bioconductor-preprocesscore
- bioconductor-gsva
- bioconductor-sva
- bioconductor-gseabase
- r-xcell >=1.2
- r-epic >=1.1
- r-mcpcounter

test:
commands:
- '$R -e "library(''immunedeconv'')"'

about:
home: https://github.com/icbi-lab/immunedeconv
license: BSD_3_clause
summary: "collection of methods for immune cell deconvolution of bulk RNA-seq samples."
license_family: BSD
license_file: LICENSE.md

extra:
recipe-maintainers:
- grst
identifiers:
- doi:10.1101/463828
4 changes: 4 additions & 0 deletions .gitattributes
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* text=auto
data/* binary
vignettes/* text=lf
R/* text=lf
41 changes: 41 additions & 0 deletions .github/workflows/conda.yml
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name: conda

on:
push:
branches: [master]
pull_request:
branches: [master]

jobs:
tests:
runs-on: ${{ matrix.os }}
name: conda ${{ matrix.os }}
strategy:
fail-fast: false
matrix:
os: ["ubuntu-latest", "macos-latest"]

steps:
- uses: actions/checkout@v2

- name: Setup Minoconda
uses: goanpeca/setup-miniconda@v1
with:
auto-update-conda: true

- name: Set-up channels and install conda build
run: |
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
conda install -y conda-build conda-verify
shell: bash

- name: build and test package
run: |
cd .conda
conda build . --no-anaconda-upload
shell: bash



136 changes: 136 additions & 0 deletions .github/workflows/test.yml
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name: tests

on:
push:
branches: [master]
pull_request:
branches: [master]

jobs:
tests:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (R ${{ matrix.config.R }})
strategy:
fail-fast: false
matrix:
config:
- {R: "3.4", os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {R: "3.5", os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {R: "3.6", os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
- {R: "4.0", os: ubuntu-16.04, rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"}
# Currently trouble running with various R version on windows (some dependencies fail to install,
# it's different ones every day...)
# - {R: "3.4", os: windows-latest}
# - {R: "3.5", os: windows-latest}
- {R: "3.6", os: windows-latest}
# - {R: "4.0", os: windows-latest}
- {R: "3.4", os: macos-latest}
- {R: "3.5", os: macos-latest}
- {R: "3.6", os: macos-latest}
- {R: "4.0", os: macos-latest}

env:
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
RSPM: ${{ matrix.config.rspm }}

steps:
- uses: actions/checkout@v2

- name: Setup R
uses: r-lib/actions/setup-r@v1
with:
r-version: ${{ matrix.config.R }}

- name: Setup pandoc
uses: r-lib/actions/setup-pandoc@v1

- name: Query dependencies
shell: Rscript {0}
run: |
install.packages('remotes', repos='https://cloud.r-project.org')
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
# Rscript -e "deps <- devtools::dev_package_deps(dependencies = NA); remotes::install_deps(dependencies = TRUE, upgrade='never'); if (!all(deps$$package %in% installed.packages())) { message('missing: ', paste(setdiff(deps$$package, installed.packages()), collapse=', ')); q(status = 1, save = 'no')}"
- name: Cache R packages
if: runner.os != 'Windows'
uses: actions/cache@v1
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ runner.os }}-r-${{ matrix.config.R }}-1-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ runner.os }}-r-${{ matrix.config.R }}-1-

- name: Install system dependencies
if: runner.os == 'Linux'
env:
RHUB_PLATFORM: linux-x86_64-ubuntu-gcc
run: |
sudo apt-get -y update && sudo apt-get install -y libcurl4-openssl-dev
# Rscript -e "remotes::install_github('r-hub/sysreqs')"
# sysreqs=$(Rscript -e "cat(sysreqs::sysreq_commands('DESCRIPTION'))")
# sudo -s eval "$sysreqs"
- name: Install dependencies
run: |
remotes::install_deps(dependencies = TRUE)
remotes::install_cran("rcmdcheck")
shell: Rscript {0}

- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}

- name: Check
env:
_R_CHECK_CRAN_INCOMING_: 0
_R_CHECK_DOC_SIZES_: 0
_R_CHECK_TESTS_NLINES_: 0
R_QPDF: "true" # /bin/true https://www.mail-archive.com/[email protected]/msg34816.html
run: |
R CMD build .
R CMD check --no-manual --as-cran immunedeconv*.tar.gz
shell: bash
# run: rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')
# shell: Rscript {0}

- name: Show testthat output
if: always()
run: find check -name 'testthat.Rout*' -exec cat '{}' \; || true
shell: bash

- name: Build docs
shell: Rscript {0}
run: pkgdown::build_site()

- name: Get target folder for page deploy from github ref
run: |
# get rid of "refs/"
tmp_target_dir=$(echo $github_ref | sed "s/^refs\///")
echo $tmp_target_dir
# get rid of "merge" at the end of ref for PRs
if [[ $tmp_target_dir = pull/* ]]
then
tmp_target_dir=$(echo $tmp_target_dir | sed "s/\/merge$//")
fi
# when on master, we want to deploy to the root dir (-> ".")
target_dir=$(echo $tmp_target_dir | sed "s/heads\/master/./")
echo $target_dir
echo "::set-env name=target_dir::$target_dir"
env:
github_ref: ${{ github.ref }}
shell: bash

- name: Deploy docs to gh-pages
if: ( matrix.config.os == 'ubuntu-16.04' ) && ( matrix.config.R == '3.6' )
uses: JamesIves/github-pages-deploy-action@releases/v3
with:
ACCESS_TOKEN: ${{ secrets.ACCESS_TOKEN }}
BRANCH: gh-pages # The branch the action should deploy to.
FOLDER: docs # The folder the action should deploy.
TARGET_FOLDER: ${{ env.target_dir }}
CLEAN: true
CLEAN_EXCLUDE: '["heads", "pull", "tags"]'


17 changes: 0 additions & 17 deletions .travis.yml

This file was deleted.

76 changes: 76 additions & 0 deletions CODE_OF_CONDUCT.md
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# Contributor Covenant Code of Conduct

## Our Pledge

In the interest of fostering an open and welcoming environment, we as
contributors and maintainers pledge to making participation in our project and
our community a harassment-free experience for everyone, regardless of age, body
size, disability, ethnicity, sex characteristics, gender identity and expression,
level of experience, education, socio-economic status, nationality, personal
appearance, race, religion, or sexual identity and orientation.

## Our Standards

Examples of behavior that contributes to creating a positive environment
include:

* Using welcoming and inclusive language
* Being respectful of differing viewpoints and experiences
* Gracefully accepting constructive criticism
* Focusing on what is best for the community
* Showing empathy towards other community members

Examples of unacceptable behavior by participants include:

* The use of sexualized language or imagery and unwelcome sexual attention or
advances
* Trolling, insulting/derogatory comments, and personal or political attacks
* Public or private harassment
* Publishing others' private information, such as a physical or electronic
address, without explicit permission
* Other conduct which could reasonably be considered inappropriate in a
professional setting

## Our Responsibilities

Project maintainers are responsible for clarifying the standards of acceptable
behavior and are expected to take appropriate and fair corrective action in
response to any instances of unacceptable behavior.

Project maintainers have the right and responsibility to remove, edit, or
reject comments, commits, code, wiki edits, issues, and other contributions
that are not aligned to this Code of Conduct, or to ban temporarily or
permanently any contributor for other behaviors that they deem inappropriate,
threatening, offensive, or harmful.

## Scope

This Code of Conduct applies both within project spaces and in public spaces
when an individual is representing the project or its community. Examples of
representing a project or community include using an official project e-mail
address, posting via an official social media account, or acting as an appointed
representative at an online or offline event. Representation of a project may be
further defined and clarified by project maintainers.

## Enforcement

Instances of abusive, harassing, or otherwise unacceptable behavior may be
reported by contacting the project team at [email protected]. All
complaints will be reviewed and investigated and will result in a response that
is deemed necessary and appropriate to the circumstances. The project team is
obligated to maintain confidentiality with regard to the reporter of an incident.
Further details of specific enforcement policies may be posted separately.

Project maintainers who do not follow or enforce the Code of Conduct in good
faith may face temporary or permanent repercussions as determined by other
members of the project's leadership.

## Attribution

This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
available at https://www.contributor-covenant.org/version/1/4/code-of-conduct.html

[homepage]: https://www.contributor-covenant.org

For answers to common questions about this code of conduct, see
https://www.contributor-covenant.org/faq
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