Merge branch 'coin-or:master' into master

.coin-or/Dependencies

@@ -1,12 +1,14 @@
-Data/Sample       https://github.com/coin-or-tools/Data-Sample master
-Data/miplib3      https://github.com/coin-or-tools/Data-miplib3 master
+ThirdParty/Glpk   https://github.com/coin-or-tools/ThirdParty-Glpk master
+ThirdParty/Mumps  https://github.com/coin-or-tools/ThirdParty-Mumps stable/3.0
+Data/Sample       https://github.com/coin-or-tools/Data-Sample 1.2
+Data/miplib3      https://github.com/coin-or-tools/Data-miplib3 1.2
 CoinUtils         https://github.com/coin-or/CoinUtils master
 Osi               https://github.com/coin-or/Osi master
 Clp               https://github.com/coin-or/Clp master
 Cgl               https://github.com/coin-or/Cgl master
 Alps              https://github.com/coin-or/CHiPPS-ALPS stable/1.6
 Bcps              https://github.com/coin-or/CHiPPS-BiCePS stable/0.95
-Blis              https://github.com/coin-or/CHiPPS-BLIS master
+Blis              https://github.com/coin-or/CHiPPS-BLIS stable/0.95
 SYMPHONY          https://github.com/coin-or/SYMPHONY master
 Cbc               https://github.com/coin-or/Cbc master
 

.coin-or/config.yml

@@ -20,28 +20,36 @@ Description:
     - Optimization deterministic linear discrete
   PaperCite: https://doi.org/10.1007/s12532-020-00183-6
 Dependencies:
+  - Description: ThirdParty wrapper for building Glpk
+    URL: https://github.com/coin-or-tools/ThirdParty-Glpk
+    Version: master
+    Required: Optional
+  - Description: ThirdParty wrapper for building Mumps
+    URL: https://github.com/coin-or-tools/ThirdParty-Mumps
+    Version: 3.0
+    Required: Optional
   - Description: Sample data files
-    URL: https://projects.coin-or.org/svn/Data/Sample/stable/1.2
+    URL: https://github.com/coin-or-tools/Data-Sample
     Version: 1.2
     Required: Required
-  - Description: miplib3 data files
-    URL: https://projects.coin-or.org/svn/Data/miplib3/stable/1.2
+  - Description: Miplib3 data files
+    URL: https://github.com/coin-or-tools/Data-miplib3
     Version: 1.2
     Required: Required
   - Description: COIN-OR Utilities
-    URL: https://projects.coin-or.org/svn/CoinUtils/stable/2.11/CoinUtils
+    URL: https://github.com/coin-or/CoinUtils
     Version: master
     Required: Required
   - Description: Open Solver Interface
-    URL: https://projects.coin-or.org/svn/Osi/stable/0.108/Osi
+    URL: https://github.com/coin-or/Osi
     Version: master
     Required: Required
   - Description: COIN-OR Linear Programming Solver
-    URL: https://projects.coin-or.org/svn/Clp/stable/1.17/Clp
+    URL: https://github.com/coin-or/Clp
     Version: master
     Required: Required
   - Description: Cut Generation Library
-    URL: https://projects.coin-or.org/svn/Cgl/stable/0.60/Cgl
+    URL: https://github.com/coin-or/Cgl
     Version: master
     Required: Required
   - Description: Abstract Library for Parallel Search
@@ -54,14 +62,14 @@ Dependencies:
     Required: Required
   - Description: BiCePS Linear Integer Solver
     URL: https://github.com/coin-or/CHiPPS-BLIS
-    Version: master
+    Version: 0.95
     Required: Required
   - Description: SYMPHONY Mip Solver
     URL: https://github.com/coin-or/SYMPHONY
     Version: master
     Required: Required
   - Description: COIN-OR Branch-and-cut
-    URL: https://projects.coin-or.org/svn/Cbc/stable/2.10/Cbc
+    URL: https://github.com/coin-or/Cbc
     Version: master
     Required: Required
   - Description: Basic Linear Algebra Subroutines (BLAS)

.coin-or/generate_readme

@@ -20,24 +20,43 @@ create_variables $SCRIPT_DIR/config.yml
 
 make_header
 
-echo "MibS is a solver for stochastic mixed integer bilevel linear optimization problems. For an
-introduction to bilevel optimization, see [this slide
+echo "MibS is a solver for stochastic mixed integer bilevel linear optimization 
+problems. For an introduction to bilevel optimization, see [this slide
 deck](http://coral.ie.lehigh.edu/~ted/files/talks/BILEVEL-IWOBIP16.pdf). A
 somewhat outdated but still useful introduction to MibS is
 [here](http://coral.ie.lehigh.edu/~ted/files/talks/BILEVEL-INFORMS11.pdf). 
-A paper that contains a complete technical description of the algorithms in MibS is 
-[here](http://coral.ie.lehigh.edu/~ted/files/papers/MIBLP16.pdf).
+A paper that contains a complete technical description of the algorithms in 
+MibS is [here](http://coral.ie.lehigh.edu/~ted/files/papers/MIBLP16.pdf). 
+A paper that discusses the cuts employed by MibS is 
+[here](http://coral.ie.lehigh.edu/~ted/files/papers/MibSCuts20.pdf).
+
+More detailed documentation is available [here](https://coin-or.github.io/MibS).
 "
 
 make_build_info_no_packages
 
 echo "## USING
 
+### Modelling Systems
+
+MibS has interfaces to the following modelling systems that allow the user to
+conveniently build the bilevel model in a high-level modelling language and
+pass the model to MibS through the interface for solution.
+
+- Pyomo (Python) through the
+[PAO](https://pao.readthedocs.io/en/latest/index.html#) package,
+see [here](https://pao.readthedocs.io/en/latest/solvers.html)
+- JuMP (Julia) through the [BilevelJuMP](https://github.com/joaquimg/BilevelJuMP.jl) package, see
+[here](https://github.com/joaquimg/BilevelJuMP.jl/blob/master/docs/src/examples/MibS_example1.jl)
+for an example. 
+
+### Command Line
+
 To solve a deterministic mixed integer bilevel linear optimization problem,
 you must provide both an MPS file and an auxiliary information file that
 specifies which variables and constraints are associated with the each level
-(see
-[here](http://coral.ise.lehigh.edu/wp-content/uploads/2016/02/MibS_inputFile.pdf)).
+(see a description of the file format
+[here](https://coin-or.github.io/MibS/input.html)).
 Then call \`mibs\` like this: 
 \`\`\` 
 <build_or_install_dir>/bin/mibs -Alps_instance file.mps -MibS_auxiliaryInfoFile aux_file.txt 
@@ -77,8 +96,15 @@ linear optimization problems. To solve these problems, there are two ways:
     [src/mibsStochastic.par.in].
 "
 
-make_links
+    echo "
+## Project Links
 
+ * [Additional documentation](https://coin-or.github.io/MibS)
+ * [Code of Conduct](https://www.coin-or.org/code-of-conduct/)
+ * [COIN-OR Web Site](http://www.coin-or.org/)
+ * [Discussion forum](https://github.com/coin-or/$Description_Slug/discussions)
+ * [Report a bug](https://github.com/coin-or/$Description_Slug/issues/new)
+" 
 echo "## ACKNOWLEDGEMENT
 
 MibS was developed with support from

.github/workflows/linux-ci.yml

@@ -7,7 +7,7 @@ on:
       - 'stable/*'
   pull_request:
     branches:
-      - '*'
+      - '**'
   release:
     types:
       - created
@@ -18,40 +18,39 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-18.04, ubuntu-20.04]
+        os: [ubuntu-20.04, ubuntu-22.04]
         build_static: [true, false]
         flags: [ADD_CXXFLAGS=-fvisibility=hidden]
         download_requirements: [sudo apt install -y -qq gfortran liblapack-dev libmetis-dev libnauty2-dev]
         include:
-          - os: macos-10.15
+          - os: macos-12
             build_static: false
-            flags: CC=clang CXX=clang++ OSX=10.15
+            flags: CC=clang CXX=clang++ OSX=12
             download_requirements: brew install metis bash
-          - os: macos-10.15
+          - os: macos-12
             build_static: false
-            flags: CC=gcc-9 CXX=g++-9 OSX=10.15
+            flags: CC=gcc-11 CXX=g++-11 OSX=12
             download_requirements: brew install metis bash
-          - os: macos-10.15
+          - os: macos-12
             build_static: false
-            flags: CC=gcc-10 CXX=g++-10 OSX=10.15
+            flags: CC=gcc-12 CXX=g++-12 OSX=12
             download_requirements: brew install metis bash
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: ${{ github.event.repository.name }}
       - name: Install required packages from package manager
         run: ${{ matrix.download_requirements }}
       - name: Checkout coinbrew
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: coin-or/coinbrew
           path: coinbrew
       - name: Build project
         run: |
           export ${{ matrix.flags }}
           ADD_ARGS=()
-          ADD_ARGS+=( --no-prompt )
           ADD_ARGS+=( --skip='ThirdParty/Metis ThirdParty/Mumps ThirdParty/Blas ThirdParty/Lapack' )
           ADD_BUILD_ARGS=()
           ADD_BUILD_ARGS+=( --tests main --enable-relocatable )
@@ -71,7 +70,7 @@ jobs:
           cp ${{ github.event.repository.name }}/LICENSE dist/
           tar -czvf release.tar.gz -C dist .
       - name: Checkout package name generation script
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: coin-or-tools/platform-analysis-tools
           path: tools
@@ -86,7 +85,7 @@ jobs:
           echo "platform_string=${platform_str}" >> $GITHUB_ENV
       - name: Upload Artifact
         if: ${{ github.event_name == 'pull_request'}}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ github.event.repository.name }}-${{ github.head_ref }}-${{ env.platform_string }}.tar.gz
           path: release.tar.gz

.github/workflows/windows-ci.yml

@@ -7,7 +7,7 @@ on:
       - 'stable/*'
   pull_request:
     branches:
-      - '*'
+      - '**'
   release:
     types:
       - created
@@ -24,18 +24,16 @@ jobs:
           { os: windows-2019, arch: x86_64, msystem: mingw64, debug: false, suffix: "" },
           { os: windows-2019, arch: i686, msystem: mingw32, debug: true, suffix: "-dbg" },
           { os: windows-2019, arch: i686, msystem: mingw32, debug: false, suffix: "" },
-          { os: windows-2019, arch: msvc, msystem: mingw64, debug: true, suffix: "-mdd" },
           { os: windows-2019, arch: msvc, msystem: mingw64, debug: false, suffix: "-md" },
-          { os: windows-2016, arch: msvc, msystem: mingw64, debug: true, suffix: "-mdd" },
-          { os: windows-2016, arch: msvc, msystem: mingw64, debug: false, suffix: "-md" },
+          { os: windows-2022, arch: msvc, msystem: mingw64, debug: false, suffix: "-md" },
         ]
     steps:
       - name: Checkout source
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           path: ${{ github.event.repository.name }}
       - name: Checkout coinbrew
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: coin-or/coinbrew
           path: coinbrew
@@ -60,7 +58,6 @@ jobs:
       - name: Build project
         run: |
           ADD_ARGS=()
-          ADD_ARGS+=( --no-prompt )
           ADD_ARGS+=( --skip='ThirdParty/Metis ThirdParty/Mumps ThirdParty/Blas ThirdParty/Lapack' )
           ADD_BUILD_ARGS=()
           ADD_BUILD_ARGS+=( --build=x86_64-w64-mingw32 --tests main --enable-relocatable )
@@ -74,7 +71,7 @@ jobs:
           cp ${{ github.event.repository.name }}/LICENSE dist/
         shell: msys2 {0}
       - name: Upload failed build directory
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         if: failure()
         with:
           name: ${{ matrix.os}}-{{ matrix.arch }}-debug=${{ matrix.debug }}-failedbuild
@@ -92,7 +89,7 @@ jobs:
         if: ${{ matrix.arch != 'msvc' }}
       - name: Upload artifact
         if: ${{ github.event_name == 'pull_request'}}
-        uses: actions/upload-artifact@v2
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ github.event.repository.name }}-${{ github.head_ref }}-${{ env.package_suffix }}
           path: dist

CHANGELOG

@@ -1,11 +1,32 @@
 MibS Change Log
-
+
+## 1.1.0
+
+ * General improvements and fixes to cut generation
+ * Improvements to efficiency of feasibility checking and solving upper bounding problem.
+ * Introduce generalized version of increasing objective cut
+ * Introduce watermelon IC
+ * Improvements to structure detection
+ * This is the version used in the published revision of  the [paper](http://dx.doi.org/10.1007/s12532-020-00183-6)
+
+## 1.0.0
+
+ * Adding support for name-based file format
+ * Improving robustness
+ * Better default parameters setting
+ * General refactoring and cleaning up
+
 ## 0.95.1
 
  * Updates for new experiments in updated draft.
  * Changed parameter names to match paper
  * Fixed bug in linking solution pool	
 
-##0.95.0
+## 0.95.0
 
- * Version used for initial draft of [paper](http://coral.ie.lehigh.edu/~ted/files/papers/MIBLP16.pdf)	
+ * Version used for initial draft of [paper](http://coral.ie.lehigh.edu/~ted/files/papers/MIBLP16.pdf)
+ * Added linking solution pool
+
+## 0.9.0 
+
+ * First official release!