Merge 'develop' in 'topics/in-house-linear-program-solver'

MICS-Lab · Oct 9, 2024 · 207bb05 · 207bb05
2 parents 099ddca + e105f2a
commit 207bb05
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diff --git a/.github/workflows/build-test-gha-branches.yml b/.github/workflows/build-test-gha-branches.yml
@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-20.04
     strategy:
       matrix:
-        python_version: ['3.8', '3.12']
+        python_version: ['3.8', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -63,11 +63,17 @@ jobs:
       - name: Check the wheel
         run: twine check dist/*.whl
 
+      - name: Upload the wheel to GitHub Actions artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheel-dist-${{ matrix.python_version }}-linux
+          path: dist
+
   build-for-windows:
     runs-on: windows-2019
     strategy:
       matrix:
-        python_version: ['3.8', '3.12']
+        python_version: ['3.8', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -131,11 +137,17 @@ jobs:
       - name: Check the wheel
         run: twine check (get-item dist\*.whl)
 
+      - name: Upload the wheel to GitHub Actions artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheel-dist-${{ matrix.python_version }}-windows
+          path: dist
+
   build-for-macos:
     runs-on: macos-12
     strategy:
       matrix:
-        python_version: ['3.8', '3.12']
+        python_version: ['3.8', '3.13']
     env:
       MACOSX_DEPLOYMENT_TARGET: 12.0
     steps:
@@ -182,6 +194,12 @@ jobs:
       - name: Check the wheel
         run: twine check dist/*.whl
 
+      - name: Upload the wheel to GitHub Actions artifacts
+        uses: actions/upload-artifact@v4
+        with:
+          name: wheel-dist-${{ matrix.python_version }}-macos
+          path: dist
+
   check:
     runs-on: ${{ matrix.os }}
     needs:
@@ -200,15 +218,15 @@ jobs:
           - macos-12
           - macos-13
           # No macos-14: we don't support M1 chips
-        python_version: ['3.8', '3.12']
+        python_version: ['3.8', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python_version }}
       # DO NOT install any other dependencies, to test that the wheels are self-contained
 
-      - name: Dowload the wheels from GitHub Actions artifacts
+      - name: Download the wheels from GitHub Actions artifacts
         uses: actions/download-artifact@v4
         with:
           pattern: wheel-dist-${{ matrix.python_version }}-*

diff --git a/.github/workflows/distribute-pre-release.yml b/.github/workflows/distribute-pre-release.yml
@@ -39,7 +39,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -112,7 +112,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -202,7 +202,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     env:
       MACOSX_DEPLOYMENT_TARGET: 12.0
     steps:
@@ -277,7 +277,7 @@ jobs:
           - macos-12
           - macos-13
           # No macos-14: we don't support M1 chips
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -338,7 +338,7 @@ jobs:
       - name: Download the wheels from GitHub Actions artifacts
         uses: actions/download-artifact@v4
         with:
-          name: wheel-dist-3.10-linux
+          name: wheel-dist-3.13-linux
           path: docker
       - name: Build the Docker image
         run: docker build --pull --no-cache --build-arg lincs_version=$(echo ${{ github.ref_name }} | sed 's/^v//') --tag jacquev6/lincs:$(echo ${{ github.ref_name }} | sed 's/^v//') docker

diff --git a/.github/workflows/distribute-release.yml b/.github/workflows/distribute-release.yml
@@ -37,7 +37,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -110,7 +110,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -200,7 +200,7 @@ jobs:
       - make-source-dist
     strategy:
       matrix:
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     env:
       MACOSX_DEPLOYMENT_TARGET: 12.0
     steps:
@@ -275,7 +275,7 @@ jobs:
           - macos-12
           - macos-13
           # No macos-14: we don't support M1 chips
-        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12']
+        python_version: ['3.8', '3.9', '3.10', '3.11', '3.12', '3.13']
     steps:
       - name: Install Python
         uses: actions/setup-python@v5
@@ -336,7 +336,7 @@ jobs:
       - name: Download the wheels from GitHub Actions artifacts
         uses: actions/download-artifact@v4
         with:
-          name: wheel-dist-3.10-linux
+          name: wheel-dist-3.13-linux
           path: docker
       - name: Build the Docker image
         run: docker build --pull --no-cache --build-arg lincs_version=$(echo ${{ github.ref_name }} | sed 's/^v//') --tag jacquev6/lincs:$(echo ${{ github.ref_name }} | sed 's/^v//') docker

diff --git a/development/Dockerfile b/development/Dockerfile
@@ -88,7 +88,7 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
       sudo
 
 # Python versions
-ENV LINCS_DEV_PYTHON_VERSIONS="3.8 3.9 3.10 3.11 3.12"
+ENV LINCS_DEV_PYTHON_VERSIONS="3.8 3.9 3.10 3.11 3.12 3.13"
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
     --mount=type=cache,target=/var/lib/apt,sharing=locked \
     --mount=type=bind,from=download-get-pip,source=/download,target=/download \
@@ -101,18 +101,13 @@ RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
  && add-apt-repository ppa:deadsnakes/ppa \
  && apt-get update \
  && DEBIAN_FRONTEND=noninteractive apt-get install --yes --no-install-recommends \
-      $(for python_version in $non_default_python_versions; do echo "python$python_version-dev python$python_version-distutils python$python_version-venv"; done) \
+      $(for python_version in $non_default_python_versions; do echo python$python_version-dev; echo python$python_version-distutils; echo python$python_version-venv; done | grep -v python3.13-distutils) \
  && for python_version in $non_default_python_versions $default_python_version; do python$python_version /download/get-pip.py || exit 1; done
 
 # Boost
 RUN --mount=type=bind,from=download-boost,source=/download,target=/download,readwrite \
     set -x \
- && cd /download/boost \
- && (for version in $LINCS_DEV_PYTHON_VERSIONS; do echo "using python : $version ;"; done) >tools/build/src/user-config.jam \
- && ./bootstrap.sh --with-libraries=python \
- && ./b2 $(for version in $LINCS_DEV_PYTHON_VERSIONS; do echo "python=$version"; done) \
- && cp -r /download/boost/boost /usr/local/include \
- && cp -r /download/boost/stage/lib/* /usr/local/lib
+ && cp -r /download/boost/boost /usr/local/include
 
 # NVidia packages
 RUN --mount=type=cache,target=/var/cache/apt,sharing=locked \
@@ -158,11 +153,12 @@ RUN --mount=type=bind,from=download-patchelf,source=/download,target=/download \
     set -x \
  && cp /download/patchelf/bin/patchelf /usr/local/bin
 
-# Python packages: runtime dependencies
+# Python packages: install and runtime dependencies
 RUN --mount=type=cache,target=/root/.cache/pip,sharing=locked \
     for python_version in $LINCS_DEV_PYTHON_VERSIONS; do python$python_version -m pip install \
       click~=8.1 \
       matplotlib~=3.7 \
+      setuptools~=75.1 \
       six~=1.16 \
     || exit 1; done
 

diff --git a/doc-sources/changelog.rst b/doc-sources/changelog.rst
@@ -7,7 +7,7 @@ Changelog
 Version 2.0.0 (2024-XX-YY)
 ==========================
 
-- Support Python 3.12
+- Support Python 3.12 and 3.13
 
 - Drop support for macOS 11 (`not supported by GitHub Actions anymore <https://github.blog/changelog/2024-05-20-actions-upcoming-changes-to-github-hosted-macos-runners/>`_)
 

diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -1,9 +1,9 @@
-FROM python:3.10-slim AS dist
+FROM python:3.13-slim AS dist
 RUN mkdir /dist
 ARG lincs_version
 COPY lincs-$lincs_version-cp310-cp310-manylinux_2_31_x86_64.whl /dist
 
-FROM python:3.10-slim
+FROM python:3.13-slim
 ARG lincs_version
 RUN --mount=type=bind,from=dist,source=/dist,target=/dist pip install --find-links /dist --only-binary lincs lincs==$lincs_version
 CMD ["bash"]
diff --git a/integration-tests/c++-library-is-usable/c++-library-is-usable.ipynb b/integration-tests/c++-library-is-usable/c++-library-is-usable.ipynb
@@ -169,6 +169,38 @@
       "\n",
       "name,\"Physics grade\",\"Literature grade\",category\n",
       "Alice,11,12,Good\n",
+      "Bob,9,11,Bad\n",
+      "Python 3.13\n",
+      "kind: classification-problem\n",
+      "format_version: 1\n",
+      "criteria:\n",
+      "  - name: Physics grade\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 20\n",
+      "  - name: Literature grade\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 20\n",
+      "ordered_categories:\n",
+      "  - name: Bad\n",
+      "  - name: Good\n",
+      "\n",
+      "kind: ncs-classification-model\n",
+      "format_version: 1\n",
+      "accepted_values:\n",
+      "  - kind: thresholds\n",
+      "    thresholds: [10]\n",
+      "  - kind: thresholds\n",
+      "    thresholds: [10]\n",
+      "sufficient_coalitions:\n",
+      "  - kind: weights\n",
+      "    criterion_weights: [0.400000006, 0.699999988]\n",
+      "\n",
+      "name,\"Physics grade\",\"Literature grade\",category\n",
+      "Alice,11,12,Good\n",
       "Bob,9,11,Bad\n"
      ]
     }

diff --git a/integration-tests/python-module-is-executable/python-module-is-executable.ipynb b/integration-tests/python-module-is-executable/python-module-is-executable.ipynb
@@ -154,6 +154,35 @@
       "ordered_categories:\n",
       "  - name: Worst category\n",
       "  - name: Intermediate category 1\n",
+      "  - name: Best category\n",
+      "Python 3.13\n",
+      "# Reproduction command (with lincs version 2.0.0a3.dev0): lincs generate classification-problem 4 3 --random-seed 208978669\n",
+      "kind: classification-problem\n",
+      "format_version: 1\n",
+      "criteria:\n",
+      "  - name: Criterion 1\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 1\n",
+      "  - name: Criterion 2\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 1\n",
+      "  - name: Criterion 3\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 1\n",
+      "  - name: Criterion 4\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 1\n",
+      "ordered_categories:\n",
+      "  - name: Worst category\n",
+      "  - name: Intermediate category 1\n",
       "  - name: Best category\n"
      ]
     }

diff --git a/integration-tests/python-package-is-usable/python-package-is-usable.ipynb b/integration-tests/python-package-is-usable/python-package-is-usable.ipynb
@@ -169,6 +169,38 @@
       "\n",
       "name,\"Physics grade\",\"Literature grade\",category\n",
       "Alice,11,12,Good\n",
+      "Bob,9,11,Bad\n",
+      "Python 3.13\n",
+      "kind: classification-problem\n",
+      "format_version: 1\n",
+      "criteria:\n",
+      "  - name: Physics grade\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 20\n",
+      "  - name: Literature grade\n",
+      "    value_type: real\n",
+      "    preference_direction: increasing\n",
+      "    min_value: 0\n",
+      "    max_value: 20\n",
+      "ordered_categories:\n",
+      "  - name: Bad\n",
+      "  - name: Good\n",
+      "\n",
+      "kind: ncs-classification-model\n",
+      "format_version: 1\n",
+      "accepted_values:\n",
+      "  - kind: thresholds\n",
+      "    thresholds: [10]\n",
+      "  - kind: thresholds\n",
+      "    thresholds: [10]\n",
+      "sufficient_coalitions:\n",
+      "  - kind: weights\n",
+      "    criterion_weights: [0.400000006, 0.699999988]\n",
+      "\n",
+      "name,\"Physics grade\",\"Literature grade\",category\n",
+      "Alice,11,12,Good\n",
       "Bob,9,11,Bad\n"
      ]
     }

diff --git a/...ation-tests/shared-object-does-not-contain-main/shared-object-does-not-contain-main.ipynb b/...ation-tests/shared-object-does-not-contain-main/shared-object-does-not-contain-main.ipynb
@@ -29,6 +29,10 @@
       "Python 3.12\n",
       "/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o: in function `_start':\n",
       "(.text+0x24): undefined reference to `main'\n",
+      "collect2: error: ld returned 1 exit status\n",
+      "Python 3.13\n",
+      "/usr/bin/ld: /usr/lib/gcc/x86_64-linux-gnu/9/../../../x86_64-linux-gnu/Scrt1.o: in function `_start':\n",
+      "(.text+0x24): undefined reference to `main'\n",
       "collect2: error: ld returned 1 exit status\n"
      ]
     }

diff --git a/lincs/liblincs/linear-programming/test-bug-0005-gpu-behaves-differently-from-cpu.cpp b/lincs/liblincs/linear-programming/test-bug-0005-gpu-behaves-differently-from-cpu.cpp
@@ -0,0 +1,31 @@
+// Copyright 2023-2024 Vincent Jacques
+
+#include "testing.hpp"
+
+
+TEST_CASE("Bug") {
+  test([](auto& linear_program) -> std::optional<float> {
+    {
+      std::vector<typename std::remove_reference_t<decltype(linear_program)>::variable_type> v;
+      v.push_back(linear_program.create_variable());
+      v.push_back(linear_program.create_variable());
+      v.push_back(linear_program.create_variable());
+      linear_program.mark_all_variables_created();
+      linear_program.set_objective_coefficient(v[0], -2.6169455);
+      linear_program.set_objective_coefficient(v[1], -0.56562924);
+      linear_program.set_objective_coefficient(v[2], -2.6307747);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[0], 1);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[1], 1);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[2], 1);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[0], 0.3803965).set_coefficient(v[1], -0.9824758).set_coefficient(v[2], 0.4877367);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[0], 0.57658184).set_coefficient(v[1], -0.8118078).set_coefficient(v[2], 0.014208794);
+      linear_program.create_constraint().set_bounds(-1, 1).set_coefficient(v[0], 0.85147953).set_coefficient(v[1], -0.5650891).set_coefficient(v[2], 0.15271592);
+    }
+    const auto solution = linear_program.solve();
+    if (solution) {
+      return solution->cost;
+    } else {
+      return std::nullopt;
+    }
+  });
+}