scisoftdev-tmp-HiPOP 1.0.2__tar.gz

scisoftdev_tmp_hipop-1.0.2/.github/workflows/ci.yaml

@@ -0,0 +1,53 @@
+name: Continuous integration checks
+
+on:
+  push:
+    branches:
+      - 'feature/**' # TODO remove feature/* once the workflow is stable
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  build-and-test:
+    name: Build & run tests (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: # See https://docs.github.com/en/actions/reference/runners/github-hosted-runners
+          - ubuntu-latest  # Arch: x64
+          - windows-latest # Arch: x64
+          - macos-latest   # Arch: arm64
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.10'
+
+      - name: Install OpenMP (macOS only)
+        if: runner.os == 'macOS'
+        # AppleClang has no OpenMP by default, thus it must be installed separately.
+        # The environment variable OpenMP_ROOT is then exported for subsequent steps
+        # (CMake uses this variable as a search hint).
+        run: |
+          brew install libomp
+          echo "OpenMP_ROOT=$(brew --prefix libomp)" >> "$GITHUB_ENV"
+
+      - name: C++ core library - Configure
+        run: cmake -S . -B build-cpponly -G Ninja
+
+      - name: C++ core library - Build
+        run: cmake --build build-cpponly
+
+      - name: C++ core library - Run tests
+        run: ctest --test-dir build-cpponly --output-on-failure --no-tests=error
+
+      - name: Python wrapper - Build & install
+        run: pip install --group dev .
+
+      - name: Python wrapper - Run tests
+        run: pytest

scisoftdev_tmp_hipop-1.0.2/.github/workflows/deploy.yaml

@@ -0,0 +1,89 @@
+name: Deploy to PyPI
+
+on:
+  push:
+    branches:
+      - 'feature/**' # TODO remove feature/* once the workflow is stable
+  # TODO define the trigger with EMobLab once the workflow is stable
+
+jobs:
+
+  build-wheels:
+    name: Build wheels (${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: # See https://docs.github.com/en/actions/reference/runners/github-hosted-runners
+          - ubuntu-latest  # Arch: x64
+          # TODO re-enable - windows-latest # Arch: x64
+          # TODO re-enable - macos-14       # Arch: arm64
+          # Do not use the latest macOS runner to ensure backward compatibility.
+          # See comment on MACOSX_DEPLOYMENT_TARGET in pyproject.toml for more details.
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.x' # The exact Python version is not important here.
+
+      - name: Build wheels
+        run: |
+          pip install --group distrib
+          python -m cibuildwheel
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: wheels-${{ matrix.os }}
+          path: ./wheelhouse/*.whl
+
+  build-sdist:
+    name: Build source distribution
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v7
+
+      - uses: actions/setup-python@v7
+        with:
+          python-version: '3.x' # The exact Python version is not important here.
+
+      - name: Build sdist
+        run: |
+          pip install --group distrib
+          python -m build --sdist
+
+      - uses: actions/upload-artifact@v7
+        with:
+          name: sdist
+          path: ./dist/*.tar.gz
+
+  publish:
+    name: Publish to PyPI
+    runs-on: ubuntu-latest
+    needs:
+      - build-wheels
+      - build-sdist
+    # TODO keep? if: github.event_name == 'release'
+
+    environment:
+      name: pypi-env
+      url: https://pypi.org/project/scisoftdev-tmp-HiPOP # TODO fix project name in URL
+
+    permissions:
+      id-token: write # Required for authentication through OIDC.
+
+    steps:
+      - uses: actions/download-artifact@v8
+        with:
+          path: dist
+          merge-multiple: true
+
+      - name: Debug # TODO to remove
+        run: |
+          ls -al dist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

scisoftdev_tmp_hipop-1.0.2/.gitignore

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+# Keep the following list of files/directories to exclude from version control as small as possible.
+# Only patterns relevant for the current project should appear in this list.
+
+# Python bytecode directories
+__pycache__/
+
+# Output directories for Python distribution files (wheels & source distributions)
+/dist/
+/wheelhouse/
+
+# Python virtual environments (usual names)
+env/
+venv/
+.env/
+.venv/
+env[_\-]*/
+venv[_\-]*/
+.env[_\-]*/
+.venv[_\-]*/
+
+# CMake build directories (usual names)
+build/
+build[_\-]*/
+
+# MacOS files
+.DS_Store
+
+# IDE files
+.vscode/
+.idea/

scisoftdev_tmp_hipop-1.0.2/CMakeLists.txt

@@ -0,0 +1,50 @@
+cmake_minimum_required(VERSION 3.19)
+
+project(HiPOP
+    VERSION 0.0.3 # TODO synchronize version number with pyproject.toml
+    DESCRIPTION "High Performance Optimal Path module"
+    HOMEPAGE_URL "https://github.com/EMob-Lab/HiPOP"
+    LANGUAGES CXX
+)
+
+option(HIPOP_WITH_PYTHON "Compile Python wrapper" OFF) # Disabled by default, so that pybind11 is not required then.
+option(HIPOP_WITH_TESTS "Compile HiPOP tests (for core library)" ON)
+option(HIPOP_WITH_EXAMPLES "Compile HiPOP examples (for core library)" ON)
+
+# Default build configuration.
+# Can be overriden with `-DCMAKE_BUILD_TYPE=<Debug|RelWithDebInfo|Release|...>` when calling CMake.
+if(NOT CMAKE_BUILD_TYPE)
+    set(CMAKE_BUILD_TYPE Release)
+endif()
+message(STATUS "CMAKE_BUILD_TYPE set to [${CMAKE_BUILD_TYPE}]")
+
+# Default C++ standard for all the targets in the project.
+# Can be overriden with `-DCMAKE_CXX_STANDARD=...` when calling CMake (but should be at least the default value).
+if(NOT CMAKE_CXX_STANDARD)
+    set(CMAKE_CXX_STANDARD 17)
+endif()
+message(STATUS "CMAKE_CXX_STANDARD set to [${CMAKE_CXX_STANDARD}]")
+
+# 3rd-party dependencies.
+find_package(OpenMP REQUIRED)
+if(HIPOP_WITH_PYTHON)
+    set(PYBIND11_FINDPYTHON ON) # See: https://pybind11.readthedocs.io/en/stable/cmake/#modes
+    find_package(pybind11 REQUIRED)
+endif()
+
+# Enable CTest and related testing features if requested
+# (must be done before adding the subdirectories).
+if(HIPOP_WITH_TESTS)
+    enable_testing()
+endif()
+
+# `cpp` subdirectory -> C++ library with related tests and examples, excluding the Python wrapper.
+message(STATUS "Building HiPOP core library")
+add_subdirectory(cpp)
+
+# `python` subdirectory -> Python wrapper (the tests and examples specific to the Python wrapper
+# are pure Python scripts, thus no compilation is needed for them).
+if(HIPOP_WITH_PYTHON)
+    message(STATUS "Building HiPOP Python wrapper")
+    add_subdirectory(python)
+endif()

scisoftdev_tmp_hipop-1.0.2/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

scisoftdev_tmp_hipop-1.0.2/PKG-INFO

@@ -0,0 +1,64 @@
+Metadata-Version: 2.4
+Name: scisoftdev-tmp-HiPOP
+Version: 1.0.2
+Summary: High Performance Optimal Path module
+License-Expression: LGPL-3.0-only
+License-File: LICENSE
+Project-URL: Repository, https://github.com/EMob-Lab/HiPOP
+Project-URL: Issues, https://github.com/EMob-Lab/HiPOP/issues
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+
+# HiPOP
+High Performance Optimal Path module
+
+## Install Hipop
+
+HiPOP is the C++ graph library used by [MnMS](https://github.com/EMob-Lab/MnMS.git). 
+You must have `CMake` and `make` installed on your computer.
+
+## WARNING
+If you are using MacOS ARM64, install the openmp library using Homebrew:
+```shell
+brew install libomp
+```
+
+### C++ only
+
+Inside your conda environment go to the cpp folder, and install the code using cmake:
+
+```shell
+cd cpp
+mkdir build
+cd build
+cmake .. -DCMAKE_PREFIX_PATH=<PREFIX>\
+         -DCMAKE_INSTALL_PREFIX=<PREFIX>\
+         -DCMAKE_BUILD_TYPE=Release\
+         -DBUILD_TESTS=ON
+cmake --build . --target install --config Release
+```
+Where `<PREFIX>` is the path to your prefix.
+
+If you used conda to install the dependencies, replace it by `$CONDA_PREFIX`.
+
+If you used venv to install the dependencies, replace it by the path to your venv.
+
+You can then lauch the tests in the `build` directory:
+
+```shell
+ctest --output-on-failure
+```
+
+
+### Python
+
+To install C++ code use the script `install_cpp.py`:
+
+```shell
+python python/install_cpp.py   
+```
+
+Then install the python lib:
+```shell
+python -m pip install python/
+```

scisoftdev_tmp_hipop-1.0.2/README.md

@@ -0,0 +1,53 @@
+# HiPOP
+High Performance Optimal Path module
+
+## Install Hipop
+
+HiPOP is the C++ graph library used by [MnMS](https://github.com/EMob-Lab/MnMS.git). 
+You must have `CMake` and `make` installed on your computer.
+
+## WARNING
+If you are using MacOS ARM64, install the openmp library using Homebrew:
+```shell
+brew install libomp
+```
+
+### C++ only
+
+Inside your conda environment go to the cpp folder, and install the code using cmake:
+
+```shell
+cd cpp
+mkdir build
+cd build
+cmake .. -DCMAKE_PREFIX_PATH=<PREFIX>\
+         -DCMAKE_INSTALL_PREFIX=<PREFIX>\
+         -DCMAKE_BUILD_TYPE=Release\
+         -DBUILD_TESTS=ON
+cmake --build . --target install --config Release
+```
+Where `<PREFIX>` is the path to your prefix.
+
+If you used conda to install the dependencies, replace it by `$CONDA_PREFIX`.
+
+If you used venv to install the dependencies, replace it by the path to your venv.
+
+You can then lauch the tests in the `build` directory:
+
+```shell
+ctest --output-on-failure
+```
+
+
+### Python
+
+To install C++ code use the script `install_cpp.py`:
+
+```shell
+python python/install_cpp.py   
+```
+
+Then install the python lib:
+```shell
+python -m pip install python/
+```

scisoftdev_tmp_hipop-1.0.2/bump_version.py

@@ -0,0 +1,48 @@
+import re
+from pathlib import Path
+import argparse
+
+PATTERN_VERSION = r"\d+\.\d+\.\d+"
+
+files = [("cpp/CMakeLists.txt", re.compile(rf"(project\(HiPOP VERSION )({PATTERN_VERSION})(\))")),
+         ("python/hipop/__init__.py", re.compile(rf'(__version__ = ")({PATTERN_VERSION})(")')),
+         ("conda/recipe/meta.yaml", re.compile(r'({% set version = ")('+PATTERN_VERSION+r')(" %})'))]
+
+
+def read(file):
+    with open(file, "r") as f:
+        contents = f.read()
+    return contents
+
+
+def write(file, new_contents):
+    with open(file, "w") as f:
+        f.write(new_contents)
+
+
+cwd = Path(__file__).parent.resolve()
+
+
+def show_diff(contents, new_contents):
+    for i, (lc, lnc) in enumerate(zip(contents.split("\n"), new_contents.split("\n"))):
+        if lc != lnc:
+            print(f"\tline {i}: {lc} -> {lnc}")
+
+
+if __name__ == "__main__":
+    import argparse
+    parser = argparse.ArgumentParser()
+    parser.add_argument('MAJOR', help='major version number', type=int)
+    parser.add_argument('MINOR', help='minor version number', type=int)
+    parser.add_argument('PATCH', help='patch version number', type=int)
+    args = parser.parse_args()
+
+    new_version = f"{args.MAJOR}.{args.MINOR}.{args.PATCH}"
+
+    for f, pattern in files:
+        print("Bumping version in file:", f)
+        f_path = cwd.joinpath(f)
+        contents = read(f_path)
+        new_contents = pattern.sub(f"\g<1>{new_version}\g<3>", contents, count=1)
+        show_diff(contents, new_contents)
+        write(f_path, new_contents)

scisoftdev_tmp_hipop-1.0.2/conda/env.yaml

@@ -0,0 +1,17 @@
+# Development / CI environment for HiPOP.
+#
+# Usage:
+#   conda create -f conda/env.yaml    # Only once, to create the environment.
+#   conda activate hipop-dev          # Each time you want to work on HiPOP.
+#
+name: hipop-dev
+channels:
+  - conda-forge
+  - nodefaults # Disable the default Anaconda channel. TODO still some warnings in CI logs...
+dependencies:
+  - cxx-compiler
+  - cmake
+  - ninja
+  - llvm-openmp
+  - pip
+  - python=3.10

scisoftdev_tmp_hipop-1.0.2/conda/recipe/README.md

@@ -0,0 +1,11 @@
+# Build conda pkgs
+
+You need to have the conda package `conda-build` installed in your `base` environment.
+
+At the root of `hipop` run the following command inside a terminal:
+
+```shell
+conda build . -c conda-forge --output-folder conda-bld
+```
+
+If it is a success, you will find the package inside the `conda-bld` folder.

scisoftdev_tmp_hipop-1.0.2/conda/recipe/build-hipoplib.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+set -ex
+
+cd cpp
+
+cmake \
+    -DCMAKE_PREFIX_PATH=$PREFIX\
+    -DCMAKE_INSTALL_PREFIX=$PREFIX\
+    -DBUILD_TESTS=ON\
+    -DCMAKE_BUILD_TYPE=Release\
+    -B build
+
+cmake --build build --parallel "${CPU_COUNT}"
+cmake --install build --config Release
+
+cd build && ctest

scisoftdev_tmp_hipop-1.0.2/conda/recipe/meta.yaml

@@ -0,0 +1,57 @@
+{% set version = "0.0.3" %}
+package:
+  name: hipop-pkgs
+  version: {{ version }}
+
+source:
+  path: ../..
+
+build:
+  number: 0
+  skip: true  # [win]
+
+outputs:
+  - name: hipoplib
+    version: {{ version }}
+    build:
+      script: ${RECIPE_DIR}/build-hipoplib.sh
+    requirements:
+      build:
+        - {{ compiler('cxx') }}
+        - make
+        - cmake
+        - openmp
+    test:
+      script: ${RECIPE_DIR}/test-hipoplib.sh
+
+  - name: hipop
+    version: {{ version }}
+    build:
+      script: $PYTHON -m pip install --no-deps ./python
+    requirements:
+      build:
+        - {{ compiler('cxx') }}
+        - make
+        - cmake
+        - python=3.10
+      host:
+        - python=3.10
+        - hipoplib
+        - pybind11
+      run:
+        - python=3.10
+        - hipoplib
+        - numpy
+        - matplotlib
+    test:
+      imports:
+        - hipop.cpp
+
+about:
+#  license: LGPL 3.0
+  # license_file:
+  summary: 'HiPOP is a graph implementation for traffic simulation in C++ with python bindings.'
+  description: |
+    HiPOP is a graph implementation for traffic simulation in C++ with python bindings.
+#  doc_url:
+  dev_url: https://github.com/licit-lab/HiPOP