Merge branch 'master' into feature/custom-decomp

.github/workflows/build_wheels.yml

@@ -1,9 +1,23 @@
-name: Build
+name: Build wheels
 
 on:
-  push:
-    tags: 
-      - 'v[0-9]+.[0-9]+.[0-9]+'
+  workflow_dispatch:
+      inputs:
+          # scip_version:
+          #     type: string
+          #     description: SCIPOptSuite deployment version
+          #     required: true
+          #     default: "v0.4.0"
+          upload_to_pypi:
+              type: boolean
+              description: Should upload
+              required: false
+              default: true
+          test_pypi:
+              type: boolean
+              description: Use Test PyPI
+              required: false
+              default: true
 
 jobs:
   build_wheels:
@@ -16,7 +30,7 @@ jobs:
             arch: x86_64
           - os: macos-14
             arch: arm64
-          - os: macos-latest
+          - os: macos-13
             arch: x86_64
           - os: windows-latest
             arch: AMD64
@@ -27,41 +41,63 @@ jobs:
       - uses: actions/checkout@v4
 
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.16.5
+        uses: pypa/cibuildwheel@v2.21.1
         env:
           CIBW_ARCHS: ${{ matrix.arch }}
           CIBW_TEST_REQUIRES: pytest
           CIBW_TEST_COMMAND: "pytest {project}/tests"
+          CIBW_MANYLINUX_*_IMAGE: manylinux_2_28
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: wheels-${{ matrix.os}}-${{ matrix.arch }}
           path: ./wheelhouse/*.whl
 
   build_sdist:
     name: Build source distribution
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Build sdist
         shell: bash -l {0}
         run: pipx run build --sdist
 
-      - uses: actions/upload-artifact@v3
+      - uses: actions/upload-artifact@v4
         with:
+          name: source-distribution
           path: dist/*.tar.gz
 
-  upload_pypi:
+  merge_artifacts:
+    name: Merge Artifacts
     needs: [build_wheels, build_sdist]
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/download-artifact@v3
+      - name: Merge Artifacts
+        uses: actions/upload-artifact/merge@v4
+
+  upload_pypi:
+    needs: [build_wheels, build_sdist, merge_artifacts]
+    runs-on: ubuntu-latest
+    if: github.event.inputs.upload_to_pypi == 'true'
+    steps:
+      - uses: actions/download-artifact@v4
         with:
-          name: artifact
+          name: merged-artifacts
           path: dist
 
       - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event.inputs.test_pypi == 'false'
         with:
           user: __token__
           password: ${{ secrets.PYPI_API_TOKEN }}
           verbose: true
+
+      - uses: pypa/gh-action-pypi-publish@release/v1
+        if: github.event.inputs.test_pypi == 'true'
+        with:
+          repository-url: https://test.pypi.org/legacy/
+          user: __token__
+          password: ${{ secrets.TESTPYPI_API_TOKEN }}
+          verbose: true
+

.github/workflows/coverage.yml

@@ -1,6 +1,6 @@
 name: Run tests with coverage
 env:
-  version: 9.0.0
+  version: 9.1.0
 
 on:
   push:

.github/workflows/generate_docs.yml

@@ -0,0 +1,16 @@
+name: Generate documentation
+
+on:
+  workflow_dispatch:
+      inputs: {}
+
+jobs:
+  generate-documentation:
+    runs-on: ubuntu-20.04
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Generate documentation
+        run: |
+          sudo apt-get install doxygen graphviz
+          bash -ex generate-docs.sh "${{ secrets.GITHUB_TOKEN }}" "gh-pages"

.github/workflows/integration-test.yml

@@ -1,13 +1,16 @@
 name: Integration test
 
 env:
-  version: 9.0.0
+  version: 9.2.0
 
 # runs on branches and pull requests; doesn't run on tags.
 on:
   push:
     branches:
       - 'master'
+  pull_request:
+    branches:
+      - 'master'
 
 jobs:
 
@@ -54,7 +57,7 @@ jobs:
 
       - name: Download dependencies (SCIPOptSuite)
         shell: powershell
-        run: wget https://github.com/scipopt/scip/releases/download/$(echo "v${{env.version}}" | tr -d '.')/SCIPOptSuite-${{ env.version }}-win64-VS15.exe -outfile scipopt-installer.exe
+        run: wget https://github.com/scipopt/scip/releases/download/$(echo "v${{env.version}}" | tr -d '.')/SCIPOptSuite-${{ env.version }}-win64.exe -outfile scipopt-installer.exe
 
       - name: Install dependencies (SCIPOptSuite)
         shell: cmd
@@ -90,33 +93,13 @@ jobs:
     steps:
       - uses: actions/checkout@v3
 
-      - name: Cache dependencies (SCIPOptSuite)
-        id: cache-scip
-        uses: actions/cache@v2
-        with:
-          path: |
-            ${{ runner.workspace }}/scipoptsuite
-            ~/Library/Caches/Homebrew/tbb--*
-              /usr/local/opt/tbb*
-            ~/Library/Caches/Homebrew/downloads/*--tbb-*
-            ~/Library/Caches/Homebrew/boost--*
-              /usr/local/opt/boost*
-            ~/Library/Caches/Homebrew/downloads/*--boost-*
-          key: ${{ runner.os }}-scipopt-${{ env.version }}-${{ hashFiles('**/lockfiles') }}
-          restore-keys: |
-            ${{ runner.os }}-scipopt-${{ env.version }}-
-
       - name: Install dependencies (SCIPOptSuite)
-        if: steps.cache-scip.outputs.cache-hit != 'true'
         run: |
           brew install tbb boost bison
-          wget --quiet --no-check-certificate https://github.com/scipopt/scip/releases/download/$(echo "v${{env.version}}" | tr -d '.')/scipoptsuite-${{ env.version }}.tgz
-          tar xfz scipoptsuite-${{ env.version }}.tgz
-          cd scipoptsuite-${{ env.version }}
-          mkdir build
-          cd build
-          cmake .. -DCMAKE_BUILD_TYPE=Debug -DCMAKE_INSTALL_PREFIX=${{ runner.workspace }}/scipoptsuite -DIPOPT=off -DSYM=none -DTPI=tny -DREADLINE=off
-          make install -j
+          wget --quiet --no-check-certificate https://github.com/scipopt/scip/releases/download/$(echo "v${{env.version}}" | tr -d '.')/SCIPOptSuite-${{ env.version }}-Darwin.sh
+          chmod +x SCIPOptSuite-${{ env.version }}-Darwin.sh
+          ./SCIPOptSuite-${{ env.version }}-Darwin.sh --skip-license --include-subdir
+          mv SCIPOptSuite-${{ env.version }}-Darwin ${{ runner.workspace }}/scipoptsuite
 
       - name: Setup python ${{ matrix.python-version }}
         uses: actions/setup-python@v4

.gitignore

@@ -81,6 +81,7 @@ instance/
 
 # Sphinx documentation
 docs/_build/
+docs/_autosummary/
 
 # PyBuilder
 target/

.readthedocs.yaml

@@ -0,0 +1,16 @@
+version: 2
+
+sphinx:
+  builder: html
+  configuration: docs/conf.py
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.11"
+
+formats: all
+
+python:
+  install:
+    - requirements: docs/requirements.txt

CHANGELOG.md

@@ -2,9 +2,61 @@
 
 ## Unreleased
 ### Added
+- Added categorical data example
+- Added printProblem to print problem to stdout
+- Added stage checks to presolve, freereoptsolve, freetransform
+- Added primal_dual_evolution recipe and a plot recipe
+### Fixed
+- Added default names to indicator constraints
+### Changed
+- GitHub actions using Mac now use precompiled SCIP from latest release
+### Removed
+
+## 5.2.1 - 2024.10.29
+### Added
+- Expanded Statistics class to more problems.
+- Created Statistics class
+- Added parser to read .stats file
+- Release checklist in `RELEASE.md`
+- Added Python definitions and wrappers for SCIPstartStrongbranch, SCIPendStrongbranch SCIPgetBranchScoreMultiple, 
+  SCIPgetVarStrongbranchInt, SCIPupdateVarPseudocost, SCIPgetVarStrongbranchFrac, SCIPcolGetAge, 
+  SCIPgetVarStrongbranchLast, SCIPgetVarStrongbranchNode, SCIPallColsInLP, SCIPcolGetAge
+- Added getBipartiteGraphRepresentation
+- Added helper functions that facilitate testing
+- Added Python definitions and wrappers for SCIPgetNImplVars, SCIPgetNContVars, SCIPvarMayRoundUp,
+  SCIPvarMayRoundDown, SCIPcreateLPSol, SCIPfeasFloor, SCIPfeasCeil, SCIPfeasRound, SCIPgetPrioChild,
+  SCIPgetPrioSibling
+- Added additional tests to test_nodesel, test_heur, and test_strong_branching
+- Migrated documentation to Readthedocs
+- `attachEventHandlerCallback` method to Model for a more ergonomic way to attach event handlers
+- Added Model method: optimizeNogil
+- Added Solution method: getOrigin, retransform, translate
+- Added SCIP.pxd: SCIP_SOLORIGIN, SCIPcopyOrigVars, SCIPcopyOrigConss, SCIPsolve nogil, SCIPretransformSol, SCIPtranslateSubSol, SCIPsolGetOrigin, SCIPhashmapCreate, SCIPhashmapFree
+- Added additional tests to test_multi_threads, test_solution, and test_copy
+### Fixed
+- Fixed too strict getObjVal, getVal check
+### Changed
+- Changed createSol to now have an option of initialising at the current LP solution
+- Unified documentation style of scip.pxi to numpydocs
+### Removed
+
+## 5.1.1 - 2024-06-22
+### Added
+- Added SCIP_STATUS_DUALLIMIT and SCIP_STATUS_PRIMALLIMIT
+- Added SCIPprintExternalCodes (retrieves version of linked symmetry, lp solver, nl solver etc)
+- Added recipe with reformulation for detecting infeasible constraints
+- Wrapped SCIPcreateOrigSol and added tests 
+- Added verbose option for writeProblem and writeParams
+- Expanded locale test
+- Added methods for creating expression constraints without adding to problem
+- Added methods for creating/adding/appending disjunction constraints
 - Added check for pt_PT locale in test_model.py
+- Added SCIPgetOrigConss and SCIPgetNOrigConss Cython bindings. 
+- Added transformed=False option to getConss, getNConss, and getNVars
 ### Fixed
+- Fixed locale errors in reading
 ### Changed
+- Made readStatistics a standalone function
 ### Removed
 
 ## 5.0.1 - 2024-04-05
@@ -14,6 +66,7 @@
 - Add SCIP function SCIPgetTreesizeEstimation and wrapper getTreesizeEstimation
 - New test for model setLogFile
 ### Fixed
+- Fixed locale fix
 - Fixed model.setLogFile(None) error
 - Add recipes sub-package
 - Fixed "weakly-referenced object no longer exists" when calling dropEvent in test_customizedbenders