Merge pull request #447 from VincentRouvreau/cgal_5_2_for_ci

CGAL 5.2 for pip and CI

.appveyor.yml

@@ -60,7 +60,7 @@ build_script:
       cd src/python &
       type setup.py &
       MSBuild Cython.sln /m /p:Configuration=Release /p:Platform=x64 &
-      ctest -j 1 --output-on-failure -C Release -E sphinx
+      ctest -j 1 --output-on-failure -C Release
     ) else (
       MSBuild GUDHIdev.sln /m /p:Configuration=Release /p:Platform=x64 &
       ctest -j 1 --output-on-failure -C Release -E diff_files

.github/for_maintainers/tests_strategy.md

@@ -0,0 +1,90 @@
+# Tests strategy
+
+This document tries to sum up the tests strategy that has been put in place for gudhi continuous integration.
+
+The aim is to help maintainers to anticipate third parties modifications, updates.
+
+## Builds
+
+### Linux
+
+As all the third parties are already installed (thanks to docker), the compilations has been seperated by categories to be parallelized:
+
+* examples (C++)
+* tests (C++)
+* utils (C++)
+* doxygen (C++ documentation that is available in the artefacts)
+* python (including documentation and code coverage that are available in the artefacts)
+
+(cf. `.circleci/config.yml`)
+
+These build categories are done with and without CGAL, and, with and without Eigen to be sure the users won't be annoyed if a third party is missing.
+
+With CGAL and with Eigen builds are performed inside the docker image `gudhi/ci_for_gudhi` based on `Dockerfile_for_circleci_image` file.
+Without CGAL, and, with or without Eigen builds are performed inside the docker image `gudhi/ci_for_gudhi_wo_cgal` based on `Dockerfile_for_circleci_image_without_cgal` file.
+
+#### Update docker images
+
+C++ third parties installation are done thanks to apt on Ubuntu latest LTS.
+
+Docker images need to be rebuild and push each time `.github/build-requirements`, `.github/test-requirements`, when a new third party is added, when a new CGAL version improves gudhi performances, ...
+
+```bash
+docker build -f Dockerfile_for_circleci_image -t gudhi/ci_for_gudhi:latest .
+docker build -f Dockerfile_for_circleci_image_without_cgal -t gudhi/ci_for_gudhi_wo_cgal:latest .
+docker login # requires some specific rights on https://hub.docker.com/u/gudhi/repository/docker/gudhi
+docker push gudhi/ci_for_gudhi:latest
+docker push gudhi/ci_for_gudhi_wo_cgal:latest
+```
+
+### Windows
+
+The compilations has been seperated by categories to be parallelized, but I don't know why builds are not run in parallel:
+
+* examples (C++)
+* tests (C++)
+* utils (C++)
+* python
+
+Doxygen (C++) is not tested.
+(cf. `.appveyor.yml`)
+
+C++ third parties installation are done thanks to [vcpkg](https://github.com/microsoft/vcpkg/).
+In case of installation issue, check in [vcpkg issues](https://github.com/microsoft/vcpkg/issues).
+
+### OSx
+
+The compilations has been seperated by categories to be parallelized:
+
+* examples (C++)
+* tests (C++)
+* utils (C++)
+* python
+* Doxygen (C++)
+
+(cf. `azure-pipelines.yml`)
+
+C++ third parties installation are done thanks to [brew](https://formulae.brew.sh/formula/).
+In case of installation issue, check in formula issues.
+
+## Pip packaging
+
+Pip packaging is done in 2 parts:
+
+* on push and pull requests, the wheels are built (pip package dry-run)
+* on releases, the wheels are built and sent to pypi.org (package)
+
+Only the Linux pip package is based on a docker image (`gudhi/pip_for_gudhi` based on `Dockerfile_for_pip` file) to make it faster.
+
+### Update docker image
+
+C++ third parties installation are done thanks to yum on an image based on `quay.io/pypa/manylinux2014_x86_64`.
+
+Docker image need to be rebuild and push each time `.github/build-requirements`, when a new third party is added, when a new CGAL version improves gudhi performances, ...
+As `.github/test-requirements` is not installed, no need to rebuild image when this file is modified.
+
+```bash
+docker build -f Dockerfile_for_pip -t gudhi/pip_for_gudhi:latest .
+docker login # requires some specific rights on https://hub.docker.com/u/gudhi/repository/docker/gudhi
+docker push gudhi/pip_for_gudhi:latest
+```

.github/test-requirements.txt

@@ -1,7 +1,7 @@
 pytest
 pytest-cov
 sphinx
-sphinxcontrib-bibtex
+sphinxcontrib-bibtex==1.0.0
 sphinx-paramlinks
 matplotlib
 scipy

Dockerfile_for_circleci_image

@@ -50,14 +50,14 @@ RUN apt-get install -y make \
     pkg-config \
     curl
 
-RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz" \
-    && tar xf CGAL-5.1.tar.xz \
+RUN curl -LO "https://github.com/CGAL/cgal/releases/download/v5.2/CGAL-5.2.tar.xz" \
+    && tar xf CGAL-5.2.tar.xz \
     && mkdir build \
     && cd build \
-    && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \
+    && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.2/ \
     && make install \
     && cd .. \
-    && rm -rf build CGAL-5.1
+    && rm -rf build CGAL-5.2
 
 ADD .github/build-requirements.txt /
 ADD .github/test-requirements.txt /
@@ -66,4 +66,4 @@ RUN pip3 install -r build-requirements.txt
 RUN pip3 --no-cache-dir install -r test-requirements.txt
 
 # apt clean up
-RUN apt autoremove && rm -rf /var/lib/apt/lists/*
+RUN apt-get autoremove && rm -rf /var/lib/apt/lists/*

Dockerfile_for_circleci_image_without_cgal

@@ -0,0 +1,55 @@
+FROM ubuntu:20.04
+
+# Update and upgrade distribution
+RUN apt update && \
+    apt upgrade -y
+
+# Tools necessary for installing and configuring Ubuntu
+RUN apt install -y \
+    apt-utils \
+    locales \
+    tzdata
+
+# Timezone
+RUN echo "Europe/Paris" | tee /etc/timezone && \
+    ln -fs /usr/share/zoneinfo/Europe/Paris /etc/localtime && \
+    dpkg-reconfigure -f noninteractive tzdata
+
+# Locale with UTF-8 support
+RUN echo en_US.UTF-8 UTF-8 >> /etc/locale.gen && \
+    locale-gen && \
+    update-locale LC_ALL=en_US.UTF-8 LANG=en_US.UTF-8
+ENV LANG en_US.UTF-8
+ENV LANGUAGE en_US:en
+ENV LC_ALL en_US.UTF-8
+
+# Update again
+RUN apt update
+
+# Required for Gudhi compilation
+RUN apt install -y make \
+    git \
+    g++ \
+    cmake \
+    perl \
+    libboost-all-dev \
+    locales \
+    python3 \
+    python3-pip \
+    python3-tk \
+    python3-grpcio \
+    libfreetype6-dev \
+    pkg-config \
+    curl
+
+RUN curl -LO "https://gitlab.com/libeigen/eigen/-/archive/3.3.9/eigen-3.3.9.tar.gz" \
+    && tar xf eigen-3.3.9.tar.gz
+
+ADD .github/build-requirements.txt /
+ADD .github/test-requirements.txt /
+
+RUN pip3 install -r build-requirements.txt
+RUN pip3 --no-cache-dir install -r test-requirements.txt
+
+# apt clean up
+RUN apt-get autoremove && rm -rf /var/lib/apt/lists/*

Dockerfile_for_pip

@@ -24,14 +24,14 @@ RUN wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.
     && cd .. \
     && rm -rf boost
 
-RUN wget https://github.com/CGAL/cgal/releases/download/v5.1/CGAL-5.1.tar.xz \
-    && tar xf CGAL-5.1.tar.xz \
+RUN wget https://github.com/CGAL/cgal/releases/download/v5.2/CGAL-5.2.tar.xz \
+    && tar xf CGAL-5.2.tar.xz \
     && mkdir build \
     && cd build \
-    && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \
+    && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.2/ \
     && make install \
     && cd .. \
-    && rm -rf build CGAL-5.1
+    && rm -rf build CGAL-5.2
 
 ADD .github/build-requirements.txt /
 

Dockerfile_gudhi_installation

@@ -68,7 +68,7 @@ RUN pip3 install \
     scikit-learn
 
 # apt clean up
-RUN apt autoremove && rm -rf /var/lib/apt/lists/*
+RUN apt-get autoremove && rm -rf /var/lib/apt/lists/*
 
 RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-3.3.0/gudhi.3.3.0.tar.gz" \
 && tar xf gudhi.3.3.0.tar.gz \

azure-pipelines.yml

@@ -33,5 +33,5 @@ jobs:
         cmake -DCMAKE_BUILD_TYPE:STRING=$(cmakeBuildType) -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
         make -j 4
         make doxygen
-        ctest -j 4 --output-on-failure -E sphinx # remove sphinx build as it fails
+        ctest -j 4 --output-on-failure # -E sphinx remove sphinx build as it fails
       displayName: 'Build, test and documentation generation'

src/Alpha_complex/test/CMakeLists.txt

@@ -59,4 +59,18 @@ if (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)
   endif()
   gudhi_add_boost_test(Weighted_alpha_complex_test_unit)
 
+  add_executable ( Weighted_alpha_complex_non_visible_points_test_unit Weighted_alpha_complex_non_visible_points_unit_test.cpp )
+  target_link_libraries(Weighted_alpha_complex_non_visible_points_test_unit ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Weighted_alpha_complex_non_visible_points_test_unit ${TBB_LIBRARIES})
+  endif()
+  gudhi_add_boost_test(Weighted_alpha_complex_non_visible_points_test_unit)
+
+  add_executable ( Zero_weighted_alpha_complex_test_unit Zero_weighted_alpha_complex_unit_test.cpp )
+  target_link_libraries(Zero_weighted_alpha_complex_test_unit ${CGAL_LIBRARY})
+  if (TBB_FOUND)
+    target_link_libraries(Zero_weighted_alpha_complex_test_unit ${TBB_LIBRARIES})
+  endif()
+  gudhi_add_boost_test(Zero_weighted_alpha_complex_test_unit)
+
 endif (NOT CGAL_WITH_EIGEN3_VERSION VERSION_LESS 5.1.0)

src/Alpha_complex/test/Weighted_alpha_complex_non_visible_points_unit_test.cpp

@@ -0,0 +1,60 @@
+/*    This file is part of the Gudhi Library - https://gudhi.inria.fr/ - which is released under MIT.
+ *    See file LICENSE or go to https://gudhi.inria.fr/licensing/ for full license details.
+ *    Author(s):       Vincent Rouvreau
+ *
+ *    Copyright (C) 2020 Inria
+ *
+ *    Modification(s):
+ *      - YYYY/MM Author: Description of the modification
+ */
+
+#define BOOST_TEST_DYN_LINK
+#define BOOST_TEST_MODULE "weighted_alpha_complex_non_visible_points"
+#include <boost/test/unit_test.hpp>
+#include <boost/mpl/list.hpp>
+
+#include <CGAL/Epick_d.h>
+#include <CGAL/Epeck_d.h>
+
+#include <vector>
+
+#include <gudhi/Alpha_complex.h>
+#include <gudhi/Simplex_tree.h>
+
+
+using list_of_1d_kernel_variants = boost::mpl::list<CGAL::Epeck_d< CGAL::Dynamic_dimension_tag >,
+                                                    CGAL::Epeck_d< CGAL::Dimension_tag<1>>,
+                                                    CGAL::Epick_d< CGAL::Dynamic_dimension_tag >,
+                                                    CGAL::Epick_d< CGAL::Dimension_tag<1>>
+                                                    >;
+
+BOOST_AUTO_TEST_CASE_TEMPLATE(Weighted_alpha_complex_non_visible_points, Kernel, list_of_1d_kernel_variants) {
+  // check that for 2 closed weighted 1-d points, one with a high weight to hide the second one with a small weight,
+  // that the point with a small weight has the same high filtration value than the edge formed by the 2 points
+  using Point_d = typename Kernel::Point_d;
+  std::vector<Point_d> points;
+  std::vector<double> p1 {0.};
+  points.emplace_back(p1.begin(), p1.end());
+  // closed enough points
+  std::vector<double> p2 {0.1};
+  points.emplace_back(p2.begin(), p2.end());
+  std::vector<typename Kernel::FT> weights {100., 0.01};
+
+  Gudhi::alpha_complex::Alpha_complex<Kernel, true> alpha_complex(points, weights);
+  Gudhi::Simplex_tree<> stree;
+  BOOST_CHECK(alpha_complex.create_complex(stree));
+
+  std::clog << "Iterator on weighted alpha complex simplices in the filtration order, with [filtration value]:"
+            << std::endl;
+  for (auto f_simplex : stree.filtration_simplex_range()) {
+    std::clog << "   ( ";
+    for (auto vertex : stree.simplex_vertex_range(f_simplex)) {
+      std::clog << vertex << " ";
+    }
+    std::clog << ") -> " << "[" << stree.filtration(f_simplex) << "] " << std::endl;
+  }
+
+  BOOST_CHECK(stree.filtration(stree.find({0})) == -100.);
+  BOOST_CHECK(stree.filtration(stree.find({1})) == stree.filtration(stree.find({0, 1})));
+  BOOST_CHECK(stree.filtration(stree.find({1})) > 100000);
+}