resolve conflicts

GeomScale · Oct 14, 2023 · bd0fbb5 · bd0fbb5
2 parents 44d7d17 + ac68063
commit bd0fbb5
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Showing 140 changed files with 16,646 additions and 4,899 deletions.
diff --git a/.github/workflows/R-CMD-check-macOS.yml b/.github/workflows/R-CMD-check-macOS.yml
@@ -30,13 +30,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install dependencies
         run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat', 'downloader', 'xfun'))";
@@ -51,7 +51,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         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
@@ -31,18 +31,18 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - run: sudo apt-get update || true;
-             sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev;
+             sudo apt install build-essential libcurl4-gnutls-dev libxml2-dev libssl-dev libgit2-dev libfontconfig1-dev libharfbuzz-dev libfribidi-dev;
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install dependencies
-        run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat', 'downloader', 'xfun'))";
+        run: Rscript -e "install.packages(c('testthat', 'pkgload', 'rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'downloader', 'xfun', dependencies=TRUE))";
 
       - name: Check
         env:
@@ -54,7 +54,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         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
@@ -29,13 +29,13 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Install dependencies
         run: Rscript -e "install.packages(c('devtools', dependencies=TRUE))" -e "install.packages(c('rcmdcheck', 'devtools', 'Rcpp', 'RcppEigen', 'BH', 'testthat', 'downloader', 'xfun'))"
@@ -50,7 +50,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v2
         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
@@ -1,7 +1,7 @@
 ##############################################################################
-# GitHub Actions Workflow for volesti to build tests with GCC
+# GitHub Actions Workflow for volesti to build tests with Clang
 #
-# Copyright (c) 2020-2021 Vissarion Fisikopoulos
+# Copyright (c) 2020-2022 Vissarion Fisikopoulos
 #
 # Licensed under GNU LGPL.3, see LICENCE file
 ##############################################################################
@@ -11,19 +11,29 @@ on: [push, pull_request]
 
 jobs:
   build:
-    name: ${{ matrix.compilers }}
+    name: ${{ matrix.config.os }} - ${{ matrix.config.compiler }}
     strategy:
           fail-fast: false
           matrix:
-            compilers: [clang++-6.0, clang++-7, clang++-8, clang++-9, clang++-10]
-    runs-on: ubuntu-latest
+            config:
+              - {os: ubuntu-22.04, compiler_pkg: clang-11, compiler: clang++-11}
+              - {os: ubuntu-22.04, compiler_pkg: clang-12, compiler: clang++-12}
+              - {os: ubuntu-22.04, compiler_pkg: clang-13, compiler: clang++-13}
+              - {os: ubuntu-22.04, compiler_pkg: clang-14, compiler: clang++-14}
+              #- {os: ubuntu-22.04, compiler_pkg: clang-15, compiler: clang++-15}
+              - {os: ubuntu-20.04, compiler_pkg: clang-8, compiler: clang++-8}
+              - {os: ubuntu-20.04, compiler_pkg: clang-9, compiler: clang++-9}
+              - {os: ubuntu-20.04, compiler_pkg: clang-10, compiler: clang++-10}
+              - {os: ubuntu-20.04, compiler_pkg: clang-11, compiler: clang++-11}
+              - {os: ubuntu-20.04, compiler_pkg: clang-12, compiler: clang++-12}
+    runs-on: ${{ matrix.config.os }}
     steps:
       - uses: actions/checkout@v1
       - run: sudo apt-get update || true;
-             sudo apt-get install clang-6.0 clang-7 clang-8 clang-9 clang-10 lp-solve;
+             sudo apt-get install ${{ matrix.config.compiler_pkg }} lp-solve;
              rm -rf build;
              mkdir build;
              cd build;
-             cmake -D CMAKE_CXX_COMPILER=${{ matrix.compilers }} -D CMAKE_CXX_FLAGS=-fsanitize=memory -D CMAKE_CXX_FLAGS=-fsanitize=undefined -D CMAKE_CXX_FLAGS=-g -D DISABLE_NLP_ORACLES=ON -D USE_MKL=OFF ../test;
+             cmake -D CMAKE_CXX_COMPILER=${{ matrix.config.compiler }} -D CMAKE_CXX_FLAGS=-fsanitize=memory -D CMAKE_CXX_FLAGS=-fsanitize=undefined -D CMAKE_CXX_FLAGS=-g -D DISABLE_NLP_ORACLES=ON -D USE_MKL=OFF ../test;
              make;
-             ctest --verbose;
+             ctest --verbose;
diff --git a/.github/workflows/cmake-examples.yml b/.github/workflows/cmake-examples.yml
@@ -0,0 +1,40 @@
+##############################################################################
+# GitHub Actions Workflow for volesti to build tests with GCC
+#
+# Copyright (c) 2020-2022 Vissarion Fisikopoulos
+#
+# Licensed under GNU LGPL.3, see LICENCE file
+##############################################################################
+name: cmake-examples
+
+on: [push, pull_request]
+
+jobs:
+  build:
+    name: ${{ matrix.config.os }} - ${{ matrix.config.compiler }}
+    strategy:
+          fail-fast: false
+          matrix:
+            config:
+              - {os: ubuntu-22.04, compiler_pkg: clang-11, compiler: clang++-11}
+              - {os: ubuntu-22.04, compiler_pkg: g++-11, compiler: g++-11}
+    runs-on: ${{ matrix.config.os }}
+    steps:
+      - uses: actions/checkout@v1
+      - run: sudo apt-get update || true;
+             sudo apt-get install ${{ matrix.config.compiler_pkg }} lp-solve libomp-dev libopenblas-dev libarpack2-dev;
+      - name: Build examples
+        run: |
+          cd examples
+          for dir in */; do
+            if [ "$dir" != "EnvelopeProblemSOS/" ] && [ "$dir" != "python_utilities/" ]; then
+              echo
+              echo "Building examples in $dir ....................."
+              cd "$dir"
+              mkdir build && cd build
+              cmake -DCMAKE_CXX_COMPILER=${{ matrix.config.compiler }} -DUSE_MKL=OFF ..
+              make
+              cd ../..
+            fi
+          done
+
diff --git a/.github/workflows/cmake-gcc.yml b/.github/workflows/cmake-gcc.yml
@@ -11,19 +11,28 @@ on: [push, pull_request]
 
 jobs:
   build:
-    name: ${{ matrix.compilers }}
+    name: ${{ matrix.config.os }} - ${{ matrix.config.compiler }}
     strategy:
           fail-fast: false
           matrix:
-            compilers: [g++-5, g++-6, g++-7, g++-8, g++-9, g++-10]
-    runs-on: ubuntu-18.04
+            config:
+              - {os: ubuntu-22.04, compiler: g++-9}
+              - {os: ubuntu-22.04, compiler: g++-10}
+              - {os: ubuntu-22.04, compiler: g++-11}
+              - {os: ubuntu-22.04, compiler: g++-12}
+              #- {os: ubuntu-22.04, compiler: g++-13}
+              - {os: ubuntu-20.04, compiler: g++-7}
+              - {os: ubuntu-20.04, compiler: g++-8}
+              - {os: ubuntu-20.04, compiler: g++-9}
+              - {os: ubuntu-20.04, compiler: g++-10}
+    runs-on: ${{ matrix.config.os }}
     steps:
       - uses: actions/checkout@v1
       - run: sudo apt-get update || true;
-             sudo apt-get install ${{ matrix.compilers }} lp-solve;
+             sudo apt-get install ${{ matrix.config.compiler }} lp-solve;
              rm -rf build;
              mkdir build;
              cd build;
-             cmake -D CMAKE_CXX_COMPILER=${{ matrix.compilers }} -D DISABLE_NLP_ORACLES=ON -D USE_MKL=OFF ../test;
+             cmake -D CMAKE_CXX_COMPILER=${{ matrix.config.compiler }} -D DISABLE_NLP_ORACLES=ON -D USE_MKL=OFF ../test;
              make;
              ctest --verbose;
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -0,0 +1,27 @@
+name: Docs
+on: [push, pull_request]
+
+jobs:
+  notebooks:
+    name: "Build the docs"
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Set up Python
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.8
+
+      - name: Install dependencies
+        run: |
+          sudo apt-get install doxygen
+          python -m pip install -U pip
+          python -m pip install -r docs/requirements.txt
+
+      - name: Build the docs
+        run: |
+          python -m pip install -U setuptools
+          python -m pip install -U pillow mock alabaster commonmark recommonmark sphinx sphinx-rtd-theme readthedocs-sphinx-ext
+          cd docs
+          python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html
diff --git a/.gitignore b/.gitignore
@@ -1,6 +1,7 @@
 test/build
 external/_deps
 examples/build
+.vscode
 test/Testing/Temporary/CTestCostData.txt
 *.log
 .Rproj.user