Use gudhi-deploy external submodules and removes former files

11 files changed, 12 insertions, 210 deletions

diff --git a/.appveyor.yml b/.appveyor.yml
index 06de5b14..c2b140e9 100644
--- a/.appveyor.yml
+++ b/.appveyor.yml
@@ -48,9 +48,9 @@ install:
   - python --version
   - pip --version
   - python -m pip install --user --upgrade pip
-  - python -m pip install --user -r .github/build-requirements.txt
+  - python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
   # No PyKeOps on windows, let's workaround this one.
-  - for /F "tokens=*" %%A in (.github/test-requirements.txt) do python -m pip install --user  %%A
+  - for /F "tokens=*" %%A in (ext/gudhi-deploy/test-requirements.txt) do python -m pip install --user  %%A
 
 build_script:
   - mkdir build
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
index 50b8b09c..732e26af 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -22,7 +22,7 @@ jobs:
         run: |
           brew update || true
           brew install boost eigen gmp mpfr cgal || true
-          python -m pip install --user -r .github/build-requirements.txt
+          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine delocate
       - name: Build python wheel
         run: |
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index aacbbc52..d07e8c46 100644
--- a/.github/workflows/pip-build-windows.yml
+++ b/.github/workflows/pip-build-windows.yml
@@ -24,7 +24,7 @@ jobs:
           vcpkg upgrade --no-dry-run
           type c:/vcpkg/ports/cgal/portfile.cmake
           vcpkg install eigen3 cgal --triplet x64-windows
-          python -m pip install --user -r .github/build-requirements.txt
+          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip list
       - name: Build python wheel
         run: |
diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
index 46441e65..56309b88 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -24,7 +24,7 @@ jobs:
         run: |
           brew update || true
           brew install boost eigen gmp mpfr cgal || true
-          python -m pip install --user -r .github/build-requirements.txt
+          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine delocate
       - name: Build python wheel
         run: |
diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index 3a751486..a428eaba 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -26,7 +26,7 @@ jobs:
           vcpkg upgrade --no-dry-run
           type c:/vcpkg/ports/cgal/portfile.cmake
           vcpkg install eigen3 cgal --triplet x64-windows
-          python -m pip install --user -r .github/build-requirements.txt
+          python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
           python -m pip install --user twine
           python -m pip list
       - name: Build python wheel
diff --git a/.gitmodules b/.gitmodules
index f70c570d..2aa8ad96 100644
--- a/.gitmodules
+++ b/.gitmodules
@@ -1,3 +1,6 @@
 [submodule "ext/hera"]
 	path = ext/hera
 	url = https://github.com/grey-narn/hera.git
+[submodule "ext/gudhi-deploy"]
+	path = ext/gudhi-deploy
+	url = https://github.com/GUDHI/gudhi-deploy
diff --git a/Dockerfile_for_circleci_image b/Dockerfile_for_circleci_image
deleted file mode 100644
index ec1b8ff8..00000000
--- a/Dockerfile_for_circleci_image
+++ /dev/null
@@ -1,69 +0,0 @@
-FROM ubuntu:20.04
-
-# Update and upgrade distribution
-RUN apt-get update && \
-    apt-get upgrade -y
-
-# Tools necessary for installing and configuring Ubuntu
-RUN apt-get 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-get update
-
-# Required for Gudhi compilation
-RUN apt-get install -y make \
-    git \
-    g++ \
-    cmake \
-    graphviz \
-    perl \
-    texlive-full \
-    biber \
-    doxygen \
-    libboost-all-dev \
-    libeigen3-dev \
-    libgmp3-dev \
-    libmpfr-dev \
-    libtbb-dev \
-    locales \
-    python3 \
-    python3-pip \
-    python3-tk \
-    python3-grpcio \
-    libfreetype6-dev \
-    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 \
-    && mkdir build \
-    && cd build \
-    && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \
-    && make install \
-    && cd .. \
-    && rm -rf build CGAL-5.1
-
-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 autoremove && rm -rf /var/lib/apt/lists/*
diff --git a/Dockerfile_for_pip b/Dockerfile_for_pip
deleted file mode 100644
index d5ae6417..00000000
--- a/Dockerfile_for_pip
+++ /dev/null
@@ -1,52 +0,0 @@
-FROM quay.io/pypa/manylinux2014_x86_64
-
-RUN yum -y update && yum -y install \
-    wget \
-    zlib-devel \
-    eigen3-devel \
-    mpfr-devel \
-    gmp-devel \
-    devtoolset-8 \
-    && yum clean all
-
-RUN mkdir -p /opt/cmake \
-    && wget https://github.com/Kitware/CMake/releases/download/v3.16.2/cmake-3.16.2-Linux-x86_64.sh \
-    && sh cmake-3.16.2-Linux-x86_64.sh  --skip-license --prefix=/opt/cmake \
-    && rm -f cmake-3.16.2-Linux-x86_64.sh
-
-# yum install boost-devel installs boost 1.53 and copy is the only way to install headers only boost
-RUN wget https://dl.bintray.com/boostorg/release/1.73.0/source/boost_1_73_0.tar.gz \
-    && tar xf boost_1_73_0.tar.gz \
-    && cd boost_1_73_0 \
-    && ./bootstrap.sh \
-    && ls \
-    && cp -r boost /usr/local/include/ \
-    && 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 \
-    && mkdir build \
-    && cd build \
-    && /opt/cmake/bin/cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \
-    && make install \
-    && cd .. \
-    && rm -rf build CGAL-5.1
-
-ADD .github/build-requirements.txt /
-
-RUN /opt/python/cp35-cp35m/bin/pip install -r build-requirements.txt \
-    && /opt/python/cp36-cp36m/bin/pip install -r build-requirements.txt\
-    && /opt/python/cp37-cp37m/bin/pip install -r build-requirements.txt\
-    && /opt/python/cp38-cp38/bin/pip install -r build-requirements.txt\
-    && /opt/python/cp39-cp39/bin/pip install -r build-requirements.txt\
-    && /opt/python/cp39-cp39/bin/pip install twine
-
-ENV PYTHON35="/opt/python/cp35-cp35m/"
-ENV PYTHON36="/opt/python/cp36-cp36m/"
-ENV PYTHON37="/opt/python/cp37-cp37m/"
-ENV PYTHON38="/opt/python/cp38-cp38/"
-ENV PYTHON39="/opt/python/cp39-cp39/"
-
-ENV PATH="/opt/cmake/bin:${PATH}"
-ENV PATH="/opt/rh/devtoolset-8/root/usr/bin:${PATH}"
diff --git a/Dockerfile_gudhi_installation b/Dockerfile_gudhi_installation
deleted file mode 100644
index ebd21f8d..00000000
--- a/Dockerfile_gudhi_installation
+++ /dev/null
@@ -1,80 +0,0 @@
-FROM ubuntu:20.04
-
-# Update and upgrade distribution
-RUN apt-get update && \
-    apt-get upgrade -y
-
-# Tools necessary for installing and configuring Ubuntu
-RUN apt-get 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-get update
-
-# Required for Gudhi compilation
-RUN apt-get install -y make \
-    g++ \
-    cmake \
-    graphviz \
-    perl \
-    texlive-bibtex-extra \
-    biber \
-    libboost-all-dev \
-    libeigen3-dev \
-    libgmp3-dev \
-    libmpfr-dev \
-    libtbb-dev \
-    libcgal-dev \
-    locales \
-    python3 \
-    python3-pip \
-    python3-pytest \
-    python3-tk \
-    python3-pybind11 \
-    libfreetype6-dev \
-    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 \
-    && mkdir build \
-    && cd build \
-    && cmake -DCMAKE_BUILD_TYPE=Release ../CGAL-5.1/ \
-    && make install \
-    && cd .. \
-    && rm -rf build CGAL-5.1
-
-RUN pip3 install \
-    numpy \
-    matplotlib \
-    scipy \
-    Cython \
-    POT \
-    scikit-learn
-
-# apt clean up
-RUN apt 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 \
-&& cd gudhi.3.3.0 \
-&& mkdir build && cd build && cmake -DCMAKE_BUILD_TYPE=Release -DWITH_GUDHI_PYTHON=OFF -DPython_ADDITIONAL_VERSIONS=3 ..  \
-&& make all test install \
-&& cmake -DWITH_GUDHI_PYTHON=ON . \
-&& cd python \
-&& python3 setup.py install
diff --git a/azure-pipelines.yml b/azure-pipelines.yml
index 64f3d141..14e195d2 100644
--- a/azure-pipelines.yml
+++ b/azure-pipelines.yml
@@ -19,15 +19,15 @@ jobs:
   
     - bash: |
         source activate gudhi_build_env
+        git submodule update --init
         sudo conda install --yes --quiet --name gudhi_build_env python=$(pythonVersion)
-        python -m pip install --user -r .github/build-requirements.txt
-        python -m pip install --user -r .github/test-requirements.txt
+        python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+        python -m pip install --user -r ext/gudhi-deploy/test-requirements.txt
         brew update || true
         brew install graphviz doxygen boost eigen gmp mpfr tbb cgal || true
       displayName: 'Install build dependencies'
     - bash: |
         source activate gudhi_build_env
-        git submodule update --init
         mkdir build
         cd build
         cmake -DCMAKE_BUILD_TYPE:STRING=$(cmakeBuildType) -DWITH_GUDHI_TEST=ON -DWITH_GUDHI_UTILITIES=ON -DWITH_GUDHI_PYTHON=ON -DPython_ADDITIONAL_VERSIONS=3 ..
diff --git a/ext/gudhi-deploy b/ext/gudhi-deploy
new file mode 160000
+Subproject f71c3749c4d57afcb9747fe99a8cfbb8aa960b6