diff --git a/.github/workflows/R-CMD-check-macOS.yml b/.github/workflows/R-CMD-check-macOS.yml deleted file mode 100644 index aa5a4d1aa..000000000 --- a/.github/workflows/R-CMD-check-macOS.yml +++ /dev/null @@ -1,56 +0,0 @@ -############################################################################## -# GitHub Actions Workflow to test the R interface of volesti -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## - -on: [push, pull_request] - -name: R-CMD-check-macOS - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: macOS-latest, r: 'devel'} - - {os: macOS-latest, r: 'release'} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - name: Install dependencies - run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat'))"; - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: cd cran_gen/; - Rscript genCRANpkg.R; - cd cran_package; - Rscript -e "library(rcmdcheck)" -e "rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')" - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/.github/workflows/R-CMD-check-ubuntu.yml b/.github/workflows/R-CMD-check-ubuntu.yml deleted file mode 100644 index 5d6e70a2b..000000000 --- a/.github/workflows/R-CMD-check-ubuntu.yml +++ /dev/null @@ -1,66 +0,0 @@ -############################################################################## -# GitHub Actions Workflow to test the R interface of volesti -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## - -on: [push, pull_request] - -name: R-CMD-check-ubuntu - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - # - {os: macOS-latest, r: 'devel'} - # - {os: macOS-latest, r: 'release'} - # - {os: windows-latest, r: 'devel'} - # - {os: windows-latest, r: 'release'} -# - {os: ubuntu-latest, r: 'devel'} # error in "Run r-lib/actions/setup-r@master" -# - {os: ubuntu-latest, r: 'release'} ##[error]Error in library(devtools) : there is no package called ‘devtools’ -# - {os: ubuntu-18.04, r: 'release'} ##[error]Error in library(devtools) : there is no package called ‘devtools’ - - {os: ubuntu-16.04, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: 'oldrel', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.5', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.4', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - {os: ubuntu-16.04, r: '3.3', rspm: "https://packagemanager.rstudio.com/cran/__linux__/xenial/latest"} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - name: Install dependencies - run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat'))"; - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: cd cran_gen/; - Rscript genCRANpkg.R; - cd cran_package; - Rscript -e "library(rcmdcheck)" -e "rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')" - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/.github/workflows/R-CMD-check-windows.yml b/.github/workflows/R-CMD-check-windows.yml deleted file mode 100644 index ea3da6bfa..000000000 --- a/.github/workflows/R-CMD-check-windows.yml +++ /dev/null @@ -1,56 +0,0 @@ -############################################################################## -# GitHub Actions Workflow to test the R interface of volesti -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## - -on: [push, pull_request] - -name: R-CMD-check-windows - -jobs: - R-CMD-check: - runs-on: ${{ matrix.config.os }} - - name: ${{ matrix.config.os }} (${{ matrix.config.r }}) - - strategy: - fail-fast: false - matrix: - config: - - {os: windows-latest, r: 'devel'} - - {os: windows-latest, r: 'release'} - - env: - R_REMOTES_NO_ERRORS_FROM_WARNINGS: true - RSPM: ${{ matrix.config.rspm }} - GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} - - steps: - - uses: actions/checkout@v2 - - - uses: r-lib/actions/setup-r@master - with: - r-version: ${{ matrix.config.r }} - - - uses: r-lib/actions/setup-pandoc@master - - - name: Install dependencies - run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat'))" - - - name: Check - env: - _R_CHECK_CRAN_INCOMING_REMOTE_: false - run: cd cran_gen/; - Rscript genCRANpkg.R; - cd cran_package; - Rscript -e "library(rcmdcheck)" -e "rcmdcheck::rcmdcheck(args = c('--no-manual', '--as-cran'), error_on = 'warning', check_dir = 'check')" - - - name: Upload check results - if: failure() - uses: actions/upload-artifact@master - with: - name: ${{ runner.os }}-r${{ matrix.config.r }}-results - path: check diff --git a/.github/workflows/cmake-clang.yml b/.github/workflows/cmake-clang.yml deleted file mode 100644 index 5bcb2014f..000000000 --- a/.github/workflows/cmake-clang.yml +++ /dev/null @@ -1,29 +0,0 @@ -############################################################################## -# GitHub Actions Workflow for volesti to build tests with GCC -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## -name: clang-test - -on: [push, pull_request] - -jobs: - build: - name: ${{ matrix.compilers }} - strategy: - fail-fast: false - matrix: - compilers: [clang++-6.0, clang++-7, clang++-8, clang++-9] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v1 - - run: sudo apt-get update || true; - sudo apt-get install clang-6.0 clang-7 clang-8 clang-9 lp-solve; - rm -rf build; - mkdir build; - cd build; - cmake -D CMAKE_CXX_COMPILER=${{ matrix.compilers }} -D CMAKE_CXX_FLAGS=-fsanitize=memory -D CMAKE_CXX_FLAGS=-fsanitize=undefined -D CMAKE_CXX_FLAGS=-g -D DISABLE_NLP_ORACLES=ON ../test; - make; - ctest --verbose; diff --git a/.github/workflows/cmake-gcc.yml b/.github/workflows/cmake-gcc.yml deleted file mode 100644 index 7ea4e9d62..000000000 --- a/.github/workflows/cmake-gcc.yml +++ /dev/null @@ -1,28 +0,0 @@ -############################################################################## -# GitHub Actions Workflow for volesti to build tests with GCC -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## -name: gcc-test - -on: [push, pull_request] - -jobs: - build: - name: ${{ matrix.compilers }} - strategy: - fail-fast: false - matrix: - compilers: [g++-4.8, g++-5, g++-6, g++-7, g++-8, g++-9] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v1 - - run: sudo apt-get update || true; - sudo apt-get install ${{ matrix.compilers }} lp-solve; - rm -rf build; - mkdir build; - cd build; - cmake -D CMAKE_CXX_COMPILER=${{ matrix.compilers }} -D DISABLE_NLP_ORACLES=ON ../test; - make; diff --git a/.github/workflows/cmake-windows.disactivated b/.github/workflows/cmake-windows.disactivated deleted file mode 100644 index ad4a1a8dd..000000000 --- a/.github/workflows/cmake-windows.disactivated +++ /dev/null @@ -1,25 +0,0 @@ -############################################################################## -# GitHub Actions Workflow for volesti to build tests with GCC -# -# Copyright (c) 2020 Vissarion Fisikopoulos -# -# Licensed under GNU LGPL.3, see LICENCE file -############################################################################## -name: windows-test - -on: [push, pull_request] - -jobs: - build: - name: windows - runs-on: windows-latest - steps: - - uses: actions/checkout@v1 - - run: mkdir build; - cd build; - $url = "https://sourceforge.net/projects/lpsolve/files/lpsolve/5.5.2.5/lp_solve_5.5.2.5_dev_win64.zip/download"; - $output = "$lp_solve.zip"; - Invoke-WebRequest -Uri $url -OutFile $output -UserAgent ([Microsoft.PowerShell.Commands.PSUserAgent]::InternetExplorer); - unzip lp_solve.zip; - cmake ../test; - make; diff --git a/.github/workflows/testSDP.yml b/.github/workflows/testSDP.yml deleted file mode 100644 index 3f6d11f9d..000000000 --- a/.github/workflows/testSDP.yml +++ /dev/null @@ -1,30 +0,0 @@ -name: gcc-test-SDP - -on: [push, pull_request] - -jobs: - build: - name: ${{ matrix.compilers }} - strategy: - fail-fast: false - matrix: - compilers: [g++-4.8, g++-5, g++-6, g++-7, g++-8, g++-9] - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v1 - - run: sudo apt-get update || true; - sudo apt-get install ${{ matrix.compilers }} lp-solve; - sudo apt install gfortran libopenblas-dev liblapack-dev libarpack2-dev; - sudo apt install git; - sudo apt install libpthread-stubs0-dev; - git clone https://github.com/m-reuter/arpackpp; - cd arpackpp; - ./install-openblas.sh; - ./install-arpack-ng.sh; - cp -r external ../test/SDP; - cd ../; - rm -rf buildSDP; - mkdir buildSDP; - cd buildSDP; - cmake -D CMAKE_CXX_COMPILER=${{ matrix.compilers }} ../test/SDP; - make; diff --git a/README.md b/README.md index 322fc2d06..756e3e53b 100644 --- a/README.md +++ b/README.md @@ -1,12 +1,4 @@ -This is a branch of **VolEsti** that contains the supplementary code for the manuscript *"Geometric algorithms for sampling the flux space of metabolic networks"*. - -Authors: Apostolos Chalkis, Vissarion Fisikopoulos, Elias Tsigaridas, Haris Zafeiropoulos. - ---- - -![logo](doc/logo/volesti_logo.jpg) - -**VolEsti** is a `C++` library for volume approximation and sampling of convex bodies (*e.g.* polytopes) with an `R` and limited `python` interface. **VolEsti** is part of the [GeomScale](https://geomscale.github.io) project. +This is an R package based on [VolEsti](https://github.com/GeomScale/volume_approximation) library that serves as supplementary code for the paper [*"Geometric algorithms for sampling the flux space of metabolic networks"*](https://arxiv.org/abs/2012.05503). ### Dependencies