summaryrefslogtreecommitdiff
path: root/.github
diff options
context:
space:
mode:
Diffstat (limited to '.github')
-rw-r--r--.github/build-requirements.txt5
-rw-r--r--.github/for_maintainers/new_gudhi_version_creation.md71
-rw-r--r--.github/for_maintainers/next_release_template.md10
-rw-r--r--.github/for_maintainers/tests_strategy.md97
-rw-r--r--.github/how_to_compile_gudhi_in_a_conda_env.md93
-rw-r--r--.github/how_to_use_github_to_contribute_to_gudhi.md14
-rw-r--r--.github/next_release.md28
-rw-r--r--.github/test-requirements.txt15
-rw-r--r--.github/workflows/pip-build-linux.yml29
-rw-r--r--.github/workflows/pip-build-osx.yml34
-rw-r--r--.github/workflows/pip-build-windows.yml45
-rw-r--r--.github/workflows/pip-packaging-linux.yml86
-rw-r--r--.github/workflows/pip-packaging-osx.yml34
-rw-r--r--.github/workflows/pip-packaging-windows.yml38
14 files changed, 446 insertions, 153 deletions
diff --git a/.github/build-requirements.txt b/.github/build-requirements.txt
deleted file mode 100644
index 7de60d23..00000000
--- a/.github/build-requirements.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-setuptools
-wheel
-numpy
-Cython
-pybind11 \ No newline at end of file
diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md
index 4de81b8a..de8d0aa5 100644
--- a/.github/for_maintainers/new_gudhi_version_creation.md
+++ b/.github/for_maintainers/new_gudhi_version_creation.md
@@ -18,15 +18,14 @@ Checkin the modifications, build and test the version:
```bash
git submodule update --init
rm -rf build; mkdir build; cd build
-cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ -DPython_ADDITIONAL_VERSIONS=3 ..
+cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_REMOTE_TEST=ON -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON -DUSER_VERSION_DIR=gudhi.@GUDHI_VERSION@ -DPython_ADDITIONAL_VERSIONS=3 ..
make user_version
date +"%d-%m-%Y-%T" > gudhi.@GUDHI_VERSION@/timestamp.txt
tar -czvf gudhi.@GUDHI_VERSION@.tar.gz gudhi.@GUDHI_VERSION@
-md5sum gudhi.@GUDHI_VERSION@.tar.gz > md5sum.txt
sha256sum gudhi.@GUDHI_VERSION@.tar.gz > sha256sum.txt
sha512sum gudhi.@GUDHI_VERSION@.tar.gz > sha512sum.txt
-make -j 4 all && ctest -j 4 --output-on-failure
+make && ctest --output-on-failure
```
***[Check there are no error]***
@@ -34,16 +33,21 @@ make -j 4 all && ctest -j 4 --output-on-failure
## Create the documentation
```bash
mkdir gudhi.doc.@GUDHI_VERSION@
-make doxygen 2>&1 | tee dox.log && grep warning dox.log
```
***[Check there are no error and the warnings]***
```bash
-cp -R gudhi.@GUDHI_VERSION@/doc/html gudhi.doc.@GUDHI_VERSION@/cpp
cd gudhi.@GUDHI_VERSION@
rm -rf build; mkdir build; cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAMPLE=ON -DPython_ADDITIONAL_VERSIONS=3 ..
+make doxygen 2>&1 | tee dox.log && grep warning dox.log
+```
+
+***[Check there are no error and the warnings]***
+
+```bash
+cp -R html ../../gudhi.doc.@GUDHI_VERSION@/cpp
export LC_ALL=en_US.UTF-8 # cf. bug https://github.com/GUDHI/gudhi-devel/issues/111
make sphinx
```
@@ -56,27 +60,25 @@ cd ../..
tar -czvf gudhi.doc.@GUDHI_VERSION@.tar.gz gudhi.doc.@GUDHI_VERSION@
cd gudhi.@GUDHI_VERSION@/build
-make -j 4 all && ctest -j 4 --output-on-failure
+make && ctest --output-on-failure
```
***[Check there are no error]***
## Upload the documentation
-Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/cpp in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/doc/@GUDHI_VERSION@
+[GUDHI GitHub pages](https://gudhi.github.io/) is only used as a _"qualification"_ web hosting service.
+The _"production"_ web hosting service is https://files.inria.fr (cf. [this doc](https://doc-si.inria.fr/display/SU/Espace+web)
+or [this one](https://www.nextinpact.com/article/30325/109058-se-connecter-a-serveur-webdav-sous-linux-macos-ou-windows)).
-Upload by ftp the content of the directory gudhi.doc.@GUDHI_VERSION@/python in a new directory on ForgeLogin@scm.gforge.inria.fr:/home/groups/gudhi/htdocs/python/@GUDHI_VERSION@
+Upload the content of the directory gudhi.doc.@GUDHI_VERSION@/cpp in a new directory on gudhi WebDAV in doc/@GUDHI_VERSION@
+Delete the directory doc/latest on gudhi WebDAV.
+Copy gudhi WebDAV doc/@GUDHI_VERSION@ as doc/latest (no symbolic link with WebDAV).
+
+Upload the content of the directory gudhi.doc.@GUDHI_VERSION@/python in a new directory on gudhi WebDAV in python/@GUDHI_VERSION@
+Delete the directory python/latest on gudhi WebDAV.
+Copy gudhi WebDAV python/@GUDHI_VERSION@ as python/latest (no symbolic link with WebDAV).
-Through ssh, make the **latest** link to your new version of the documentation:
-```bash
-ssh ForgeLogin@scm.gforge.inria.fr
-cd /home/groups/gudhi/htdocs/doc
-rm latest
-ln -s @GUDHI_VERSION@ latest
-cd /home/groups/gudhi/htdocs/python
-rm latest
-ln -s @GUDHI_VERSION@ latest
-```
## Put a version label on files
@@ -84,13 +86,14 @@ ln -s @GUDHI_VERSION@ latest
* Name the tag: tags/gudhi-release-@GUDHI_VERSION@
* Name the release GUDHI @GUDHI_VERSION@ release
* Write the release note
-* Drag'n drop *gudhi.@GUDHI_VERSION@.tar.gz*, *md5sum.txt*, *sha256sum.txt*, *sha512sum.txt* files
+* Drag'n drop *gudhi.@GUDHI_VERSION@.tar.gz*, *sha256sum.txt*, *sha512sum.txt* files
* Tick the *This is a pre-release* check button if this is a release candidate (untick if this is an official version)
* Click the *Publish the release* button
## Pip package
-The pip package construction shall be started on release creation, you just have to check [gudhi github actions](https://github.com/GUDHI/gudhi-devel/actions) results.
+The pip package construction shall be started on release creation, you just have to check
+[gudhi github actions](https://github.com/GUDHI/gudhi-devel/actions) results.
The version number must be conform to [pep440](https://www.python.org/dev/peps/pep-0440/#pre-releases)
## Conda package
@@ -105,30 +108,22 @@ If you need to update conda tools (conda-build, conda-smithy, ...), add a commen
## Docker image
-You have to modify the `Dockerfile_gudhi_installation` at the root of this repository in order to use the last release, cf. lines:
+You have to modify the
+[Dockerfile_gudhi_installation](https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_gudhi_installation)
+in gudhi-deploy repository in order to use the last release, cf. lines:
```
...
-RUN curl -LO "https://github.com/GUDHI/gudhi-devel/releases/download/tags%2Fgudhi-release-@GUDHI_VERSION@/gudhi.@GUDHI_VERSION@.tar.gz" \
-&& tar xf gudhi.@GUDHI_VERSION@.tar.gz \
-&& cd gudhi.@GUDHI_VERSION@ \
+ARG GUDHI_VERSION="3.X.X"
...
```
-Build and push images to docker hub:
-```
-docker build -f Dockerfile_gudhi_installation -t gudhi/latest_gudhi_version:@GUDHI_VERSION@ .
-docker run --rm -it gudhi/latest_gudhi_version:@GUDHI_VERSION@
-```
-
-***[Check there are no error with utils and python version]***
+After pushing the changes the docker image build will be automatically performed for
+[latest_gudhi_version](https://hub.docker.com/repository/docker/gudhi/latest_gudhi_version)
+docker image on docker hub.
-```
-docker tag gudhi/latest_gudhi_version:@GUDHI_VERSION@ gudhi/latest_gudhi_version:latest
-docker push gudhi/latest_gudhi_version:latest
-docker push gudhi/latest_gudhi_version:@GUDHI_VERSION@
-```
+***[Check there are no error]***
## Mail sending
Send version mail to the following lists :
-* gudhi-devel@lists.gforge.inria.fr
-* gudhi-users@lists.gforge.inria.fr (not for release candidate)
+* gudhi-devel@inria.fr
+* gudhi-users@inria.fr (not for release candidate)
diff --git a/.github/for_maintainers/next_release_template.md b/.github/for_maintainers/next_release_template.md
index a2805a55..c57ae4eb 100644
--- a/.github/for_maintainers/next_release_template.md
+++ b/.github/for_maintainers/next_release_template.md
@@ -1,16 +1,16 @@
We are pleased to announce the release 3.X.X of the GUDHI library.
-As a major new feature, the GUDHI library now offers ...
+As a major new feature, the GUDHI library now offers **...**
We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
Below is a list of changes made since GUDHI 3.X-1.X-1:
- [Module](link)
- - ...
+ - **...**
- [Module](link)
- - ...
+ - **...**
- Miscellaneous
- The [list of bugs that were solved since GUDHI-3.X-1.X-1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.1.1+is%3Aclosed) is available on GitHub.
@@ -26,3 +26,7 @@ Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any
For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/latest/installation.html) or [Python](https://gudhi.inria.fr/python/latest/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+## Contributors
+
+- **...**
+- **...** \ No newline at end of file
diff --git a/.github/for_maintainers/tests_strategy.md b/.github/for_maintainers/tests_strategy.md
new file mode 100644
index 00000000..d0ae76ef
--- /dev/null
+++ b/.github/for_maintainers/tests_strategy.md
@@ -0,0 +1,97 @@
+# 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.
+
+## CMake options
+
+[CMake GUDHI options](../../src/cmake/modules/GUDHI_options.cmake) allows to activate/deactivate what should be built and tested.
+Note the special option `WITH_GUDHI_THIRD_PARTY` that, when set to `OFF`, accelerates doxygen documentation generation or `user_version` for instance.
+
+## Builds
+
+### Linux
+
+As all the third parties are already installed (thanks to docker), the compilations have been separated in 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; here the WITH_GUDHI_REMOTE_TEST option is enabled which adds datasets fetching test)
+
+(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 is done thanks to apt on Ubuntu latest LTS.
+
+Docker images need to be rebuilt and pushed 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 are not parallelized, as installation time (about 30 minutes) is too much compared to
+build and tests timings (about 30 minutes). Builds and tests include:
+
+* examples (C++)
+* tests (C++)
+* utils (C++)
+* python (here the WITH_GUDHI_REMOTE_TEST option is enabled which adds datasets fetching test)
+
+Doxygen (C++) is not generated.
+(cf. `azure-pipelines.yml`)
+
+C++ third parties installation is done thanks to [vcpkg](https://github.com/microsoft/vcpkg/).
+In case of an installation issue, check in [vcpkg issues](https://github.com/microsoft/vcpkg/issues).
+
+### OSx
+
+The compilations are not parallelized, but they should, as installation time (about 4 minutes) is
+negligible compared to build and tests timings (about 30 minutes). Builds and tests include:
+
+* examples (C++)
+* tests (C++)
+* utils (C++)
+* python (here the WITH_GUDHI_REMOTE_TEST option is enabled which adds datasets fetching test)
+* Doxygen (C++)
+
+(cf. `azure-pipelines.yml`)
+
+C++ third parties installation is done thanks to [brew](https://formulae.brew.sh/formula/).
+In case of an 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 is done thanks to yum on an image based on `quay.io/pypa/manylinux2014_x86_64`.
+
+Docker image needs to be rebuilt and pushed 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
+```
diff --git a/.github/how_to_compile_gudhi_in_a_conda_env.md b/.github/how_to_compile_gudhi_in_a_conda_env.md
new file mode 100644
index 00000000..4acfca2e
--- /dev/null
+++ b/.github/how_to_compile_gudhi_in_a_conda_env.md
@@ -0,0 +1,93 @@
+# Install a conda development environment to compile GUDHI
+
+## Install miniconda
+
+Download the [installer](https://docs.conda.io/en/latest/miniconda.html) required by your system and follow the [instructions](https://conda.io/projects/conda/en/latest/user-guide/install/index.html).
+
+## Create a dedicated environment
+
+```bash
+conda install -c conda-forge mamba # installation with mamba is faster
+conda create --name gudhi
+conda activate gudhi
+mamba install -c conda-forge python cmake doxygen eigen cgal-cpp
+```
+
+Some of the requirements are in the gudhi-devel repository (please refer to
+[how to use github to contribute to gudhi](how_to_use_github_to_contribute_to_gudhi.md)).
+Once the gudhi-devel repository is cloned on your machine (`git clone...`) - let's call it `/workdir/gudhi-devel` i.e. -
+and once the submodules are initialised (`git submodule update --init`):
+
+```bash
+pip install -r ext/gudhi-deploy/build-requirements.txt
+pip install -r ext/gudhi-deploy/test-requirements.txt # pytorch can be painful to install - not mandatory
+```
+
+## Compilation
+
+In order to compile all c++ utilities, examples, benchmarks, unitary tests, and python module:
+```bash
+cd /workdir/gudhi-devel
+rm -rf build; mkdir build # /!\ any existing build folder will be removed
+cd build
+# To build all even examples and benchmarks
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_EXAMPLE=ON -DWITH_GUDHI_BENCHMARK=ON ..
+```
+
+### Specific python compilation
+
+In order to compile only python module
+```bash
+cd /workdir/gudhi-devel
+rm -rf build; mkdir build # /!\ any existing build folder will be removed
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX ..
+cd src/python
+# To build python module in parallel
+python setup.py build_ext -j 16 --inplace # 16 is the number of CPU that are used to compile the python module. Can be any other value.
+# to clean the build
+# python setup.py clean --all
+```
+
+In order to use freshly compiled gudhi python module:
+```bash
+PYTHONPATH=/workdir/gudhi-devel/build/src/python python # or ipython, jupyter, ...
+```
+
+### Specific C++ documentation generation
+
+```bash
+cd /workdir/gudhi-devel
+rm -rf build; mkdir build # /!\ any existing build folder will be removed
+cd build
+# python OFF to prevent python modules search makes cmake faster
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..
+make user_version;
+cd version
+mkdir build
+cd build
+# python OFF to prevent python modules search makes cmake faster
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_PYTHON=OFF ..
+make doxygen 2>&1 | tee dox.log
+grep warning dox.log # Warnings can be lost with parallel doxygen
+firefox html/index.html # [optional] To display the c++ documentation. Anything else than firefox can be used.
+```
+
+### Specific python documentation generation
+
+```bash
+cd /workdir/gudhi-devel
+rm -rf build; mkdir build # /!\ any existing build folder will be removed
+cd build
+# python OFF to prevent python modules search makes cmake faster - it is the next cmake call in user version that matters
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX -DWITH_GUDHI_PYTHON=OFF -DUSER_VERSION_DIR=version ..
+make user_version;
+cd version
+mkdir build
+cd build
+cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH=$CONDA_PREFIX ..
+cd python
+# To build python module in parallel
+python setup.py build_ext -j 16 --inplace # 16 is the number of CPU that are used to compile the python module. Can be any other value.
+firefox sphinx/index.html # [optional] To display the python documentation. Anything else than firefox can be used.
+``` \ No newline at end of file
diff --git a/.github/how_to_use_github_to_contribute_to_gudhi.md b/.github/how_to_use_github_to_contribute_to_gudhi.md
index 747ca39b..f72bb9d6 100644
--- a/.github/how_to_use_github_to_contribute_to_gudhi.md
+++ b/.github/how_to_use_github_to_contribute_to_gudhi.md
@@ -17,7 +17,7 @@ You can see your fork at https://github.com/LOGIN/gudhi-devel
## Create a local clone on your computer
```bash
-git clone https://github.com/LOGIN/gudhi-devel.git
+git clone --recurse-submodules https://github.com/LOGIN/gudhi-devel.git
```
This creates a directory gudhi-devel, which you are free to move around or rename. For the following, change to that directory:
@@ -25,14 +25,15 @@ This creates a directory gudhi-devel, which you are free to move around or renam
cd gudhi-devel
```
-When you clone the repository, you also need to download the *submodules*.
-
## Submodules
-Hera, used for Wasserstein distance, is available on an external git repository. To download it:
+When you clone the repository, you also need to download the *submodules*. This is done automatically thanks to `--recurse-submodules`.
+If you forgot this option, you can still download them with
```bash
git submodule update --init
```
+The submodules appear in the `ext/` subdirectory. There are currently 2, [Hera](https://github.com/anigmetov/hera) for distances between persistence diagrams, and [gudhi-deploy](https://github.com/GUDHI/gudhi-deploy) for Continuous Integration.
+
## Configuring a remote for a fork
```bash
git remote add upstream https://github.com/GUDHI/gudhi-devel.git
@@ -65,6 +66,11 @@ It is safe, it will not mess with your files.
git submodule sync
git submodule update --init
```
+You can configure `git` to do this automatically with
+```bash
+git config submodule.recurse true
+```
+(add `--global` if you want it to apply to other projects as well)
## Create a branch, based on the current master
```bash
diff --git a/.github/next_release.md b/.github/next_release.md
index 5a74966d..f27af825 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -1,23 +1,22 @@
-We are pleased to announce the release 3.4.0 of the GUDHI library.
+We are pleased to announce the release 3.8.0 of the GUDHI library.
-As a major new feature, the GUDHI library now offers dD weighted alpha complex, pip and conda packages for Python 3.9.
+As a major new feature, the GUDHI library now offers Perslay, a Tensorflow model for the representations module.
-We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.4.0.tar.gz).
+We are now using GitHub to develop the GUDHI library, do not hesitate to [fork the GUDHI project on GitHub](https://github.com/GUDHI/gudhi-devel). From a user point of view, we recommend to download GUDHI user version (gudhi.3.X.X.tar.gz).
-Below is a list of changes made since GUDHI 3.3.0:
+Below is a list of changes made since GUDHI 3.7.1:
-- [Alpha complex](https://gudhi.inria.fr/doc/latest/group__alpha__complex.html)
- - the C++ weighted version for alpha complex is now available in any dimension D.
+- [Perslay](https://gudhi.inria.fr/python/latest/representations_tflow_itf_ref.html)
+ - Tensorflow model for the representations module
-- Simplex tree [C++](https://gudhi.inria.fr/doc/latest/class_gudhi_1_1_simplex__tree.html) [Python](http://gudhi.gforge.inria.fr/python/latest/simplex_tree_ref.html)
- - A new method to reset the filtrations
- - A new method to get the boundaries of a simplex
+- [Hera version of Wasserstein distance](https://gudhi.inria.fr/python/latest/wasserstein_distance_user.html#hera)
+ - now provides matching in its interface
-- [Subsampling](https://gudhi.inria.fr/doc/latest/group__subsampling.html)
- - The C++ function `choose_n_farthest_points()` now takes a distance function instead of a kernel as first argument, users can replace `k` with `k.squared_distance_d_object()` in each call in their code.
+- [Module](link)
+ - **...**
- Miscellaneous
- - The [list of bugs that were solved since GUDHI-3.3.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.4.0+is%3Aclosed) is available on GitHub.
+ - The [list of bugs that were solved since GUDHI-3.7.1](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.8.0+is%3Aclosed) is available on GitHub.
All modules are distributed under the terms of the MIT license.
However, there are still GPL dependencies for many modules. We invite you to check our [license dedicated web page](https://gudhi.inria.fr/licensing/) for further details.
@@ -29,3 +28,8 @@ We provide [bibtex entries](https://gudhi.inria.fr/doc/latest/_citation.html) fo
Feel free to [contact us](https://gudhi.inria.fr/contact/) in case you have any questions or remarks.
For further information about downloading and installing the library ([C++](https://gudhi.inria.fr/doc/latest/installation.html) or [Python](https://gudhi.inria.fr/python/latest/installation.html)), please visit the [GUDHI web site](https://gudhi.inria.fr/).
+
+## Contributors
+
+- **...**
+- **...**
diff --git a/.github/test-requirements.txt b/.github/test-requirements.txt
deleted file mode 100644
index 688a2a11..00000000
--- a/.github/test-requirements.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-pytest
-pytest-cov
-sphinx
-sphinxcontrib-bibtex
-sphinx-paramlinks
-matplotlib
-scipy
-scikit-learn
-POT
-tensorflow
-tensorflow-addons
-torch<1.5
-pykeops
-hnswlib
-eagerpy
diff --git a/.github/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
index cf8ddadf..88ca7db3 100644
--- a/.github/workflows/pip-build-linux.yml
+++ b/.github/workflows/pip-build-linux.yml
@@ -4,18 +4,31 @@ on: [push, pull_request]
jobs:
build:
- name: build pip wheels
+ name: build pip wheel
runs-on: ubuntu-latest
+ # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
container: gudhi/pip_for_gudhi
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - name: Build wheels for Python 3.9
+ - name: Build wheel for Python 3.11
run: |
- mkdir build_39
- cd build_39
- cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
+ mkdir build_311
+ cd build_311
+ cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
cd src/python
- $PYTHON39/bin/python setup.py bdist_wheel
- auditwheel repair dist/*.whl \ No newline at end of file
+ $PYTHON311/bin/python -m build -n
+ auditwheel show dist/*.whl
+ auditwheel repair dist/*.whl
+ ls wheelhouse/*.whl
+ - name: Install and test wheel for Python 3.11
+ run: |
+ $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/wheelhouse/*.whl
+ $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON311/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Upload linux python wheel
+ uses: actions/upload-artifact@v3
+ with:
+ name: linux python wheel
+ path: build_311/src/python/wheelhouse/*.whl
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
index 50b8b09c..81f516cd 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -2,19 +2,24 @@ name: pip build osx
on: [push, pull_request]
+env:
+ MACOSX_DEPLOYMENT_TARGET: 10.14
+ _PYTHON_HOST_PLATFORM: macosx-10.14-universal2
+ ARCHFLAGS: "-arch arm64 -arch x86_64"
+
jobs:
build:
runs-on: macos-latest
strategy:
max-parallel: 4
matrix:
- python-version: ['3.9']
+ python-version: ['3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
@@ -22,13 +27,30 @@ 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 twine delocate
+ python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+ python -m pip install --user build twine delocate
+ ./scripts/build_osx_universal_gmpfr.sh
+ # Now the universal libraries are in $PWD/deps-uni/lib
- name: Build python wheel
run: |
+ export GMP_LIB_DIR=$PWD/deps-uni/lib
+ export GMPXX_LIB_DIR=$PWD/deps-uni/lib
+ export MPFR_LIB_DIR=$PWD/deps-uni/lib
python --version
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
cd src/python
- python setup.py bdist_wheel
+ python -m build -n
+ export PATH="$PATH:`python -m site --user-base`/bin"
+ delocate-wheel --require-archs universal2 -v dist/*.whl
+ - name: Install and test python wheel
+ run: |
+ python -m pip install --user pytest build/src/python/dist/*.whl
+ python -c "import gudhi; print(gudhi.__version__)"
+ python -m pytest src/python/test/test_alpha_complex.py
+ - name: Upload OSx python wheel
+ uses: actions/upload-artifact@v3
+ with:
+ name: osx python wheel
+ path: build/src/python/dist/*.whl
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index aacbbc52..02617e31 100644
--- a/.github/workflows/pip-build-windows.yml
+++ b/.github/workflows/pip-build-windows.yml
@@ -8,30 +8,45 @@ jobs:
strategy:
max-parallel: 4
matrix:
- python-version: ['3.9']
+ python-version: ['3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install dependencies
run: |
- vcpkg update
- vcpkg upgrade --no-dry-run
- type c:/vcpkg/ports/cgal/portfile.cmake
+ set VCPKG_BUILD_TYPE=release
vcpkg install eigen3 cgal --triplet x64-windows
- python -m pip install --user -r .github/build-requirements.txt
- python -m pip list
- - name: Build python wheel
+ vcpkg version
+ ls "C:\vcpkg\installed\x64-windows\bin\"
+ python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
+ python -m pip install --user build
+ - name: Build python wheel and install it
run: |
mkdir build
- cd build
- cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DPython_ADDITIONAL_VERSIONS=3 ..
- cd src/python
- cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
- cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
- python setup.py bdist_wheel \ No newline at end of file
+ cd ".\build\"
+ cmake -DCMAKE_BUILD_TYPE=Release -DFORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT=ON -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows ..
+ cd ".\src\python\"
+ cp "C:\vcpkg\installed\x64-windows\bin\mpfr*.dll" ".\gudhi\"
+ cp "C:\vcpkg\installed\x64-windows\bin\gmp*.dll" ".\gudhi\"
+ python -m build -n
+ ls ".\dist\"
+ cd ".\dist\"
+ Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
+ - name: Test python wheel
+ run: |
+ Get-Location
+ dir
+ python -m pip install --user pytest
+ python -c "import gudhi; print(gudhi.__version__)"
+ python -m pytest ".\src\python\test\test_alpha_complex.py"
+ - name: Upload Windows python wheel
+ uses: actions/upload-artifact@v3
+ with:
+ name: windows python wheel
+ path: build/src/python/dist/*.whl
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 469c3b3b..866f4335 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -6,60 +6,100 @@ on:
jobs:
build:
- name: build pip wheels
+ name: build pip wheel
runs-on: ubuntu-latest
+ # cf. https://github.com/GUDHI/gudhi-deploy/blob/main/Dockerfile_for_pip
container: gudhi/pip_for_gudhi
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - name: Build wheels for Python 3.5
- run: |
- mkdir build_35
- cd build_35
- cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON35/bin/python ..
- cd src/python
- $PYTHON35/bin/python setup.py bdist_wheel
- auditwheel repair dist/*.whl
- - name: Build wheels for Python 3.6
+ - name: Build wheel for Python 3.6
run: |
mkdir build_36
cd build_36
cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON36/bin/python ..
cd src/python
- $PYTHON36/bin/python setup.py bdist_wheel
+ $PYTHON36/bin/python -m build -n
auditwheel repair dist/*.whl
- - name: Build wheels for Python 3.7
+ - name: Install and test wheel for Python 3.6
+ run: |
+ $PYTHON36/bin/python -m pip install --user pytest build_36/src/python/dist/*.whl
+ $PYTHON36/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON36/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.7
run: |
mkdir build_37
cd build_37
cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON37/bin/python ..
cd src/python
- $PYTHON37/bin/python setup.py bdist_wheel
+ $PYTHON37/bin/python -m build -n
auditwheel repair dist/*.whl
- - name: Build wheels for Python 3.8
+ - name: Install and test wheel for Python 3.7
+ run: |
+ $PYTHON37/bin/python -m pip install --user pytest build_37/src/python/dist/*.whl
+ $PYTHON37/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON37/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.8
run: |
mkdir build_38
cd build_38
cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON38/bin/python ..
cd src/python
- $PYTHON38/bin/python setup.py bdist_wheel
+ $PYTHON38/bin/python -m build -n
auditwheel repair dist/*.whl
- - name: Build wheels for Python 3.9
+ - name: Install and test wheel for Python 3.8
+ run: |
+ $PYTHON38/bin/python -m pip install --user pytest build_38/src/python/dist/*.whl
+ $PYTHON38/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON38/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.9
run: |
mkdir build_39
cd build_39
cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON39/bin/python ..
cd src/python
- $PYTHON39/bin/python setup.py bdist_wheel
+ $PYTHON39/bin/python -m build -n
auditwheel repair dist/*.whl
+ - name: Install and test wheel for Python 3.9
+ run: |
+ $PYTHON39/bin/python -m pip install --user pytest build_39/src/python/dist/*.whl
+ $PYTHON39/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON39/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.10
+ run: |
+ mkdir build_310
+ cd build_310
+ cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
+ cd src/python
+ $PYTHON310/bin/python -m build -n
+ auditwheel repair dist/*.whl
+ - name: Install and test wheel for Python 3.10
+ run: |
+ $PYTHON310/bin/python -m pip install --user pytest build_310/src/python/dist/*.whl
+ $PYTHON310/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON310/bin/python -m pytest src/python/test/test_alpha_complex.py
+ - name: Build wheel for Python 3.11
+ run: |
+ mkdir build_311
+ cd build_311
+ cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
+ cd src/python
+ $PYTHON311/bin/python -m build -n
+ auditwheel repair dist/*.whl
+ - name: Install and test wheel for Python 3.11
+ run: |
+ $PYTHON311/bin/python -m pip install --user pytest build_311/src/python/dist/*.whl
+ $PYTHON311/bin/python -c "import gudhi; print(gudhi.__version__)"
+ $PYTHON311/bin/python -m pytest src/python/test/test_alpha_complex.py
- name: Publish on PyPi
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
run: |
- $PYTHON39/bin/python -m twine upload build_35/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_36/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_37/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_38/src/python/wheelhouse/*
- $PYTHON39/bin/python -m twine upload build_39/src/python/wheelhouse/* \ No newline at end of file
+ $PYTHON36/bin/python -m twine upload build_36/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_37/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_38/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_39/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_310/src/python/wheelhouse/*
+ $PYTHON36/bin/python -m twine upload build_311/src/python/wheelhouse/*
diff --git a/.github/workflows/pip-packaging-osx.yml b/.github/workflows/pip-packaging-osx.yml
index 46441e65..15840c9a 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -4,19 +4,24 @@ on:
release:
types: [published]
+env:
+ MACOSX_DEPLOYMENT_TARGET: 10.15
+ _PYTHON_HOST_PLATFORM: macosx-10.15-universal2
+ ARCHFLAGS: "-arch arm64 -arch x86_64"
+
jobs:
build:
runs-on: macos-latest
strategy:
max-parallel: 4
matrix:
- python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+ python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
@@ -24,22 +29,33 @@ 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 twine delocate
+ python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
+ python -m pip install --user build twine delocate
+ ./scripts/build_osx_universal_gmpfr.sh
+ # Now the universal libs are in $PWD/deps-uni/lib
- name: Build python wheel
run: |
+ export GMP_LIB_DIR=$PWD/deps-uni/lib
+ export GMPXX_LIB_DIR=$PWD/deps-uni/lib
+ export MPFR_LIB_DIR=$PWD/deps-uni/lib
python --version
mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DPython_ADDITIONAL_VERSIONS=3 ..
cd src/python
- python setup.py bdist_wheel
+ python -m build -n
+ - name: Install and test python wheel
+ run: |
+ python -m pip install --user pytest build/src/python/dist/*.whl
+ python -c "import gudhi; print(gudhi.__version__)"
+ python -m pytest src/python/test/test_alpha_complex.py
- name: Publish on PyPi
env:
TWINE_USERNAME: __token__
TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
run: |
mkdir wheelhouse
- /Users/runner/.local/bin/delocate-listdeps build/src/python/dist/*
- /Users/runner/.local/bin/delocate-wheel --require-archs x86_64 -w wheelhouse build/src/python/dist/*
- python -m twine upload wheelhouse/* \ No newline at end of file
+ export PATH="$PATH:`python -m site --user-base`/bin"
+ delocate-listdeps build/src/python/dist/*
+ delocate-wheel --require-archs universal2 -w wheelhouse build/src/python/dist/*
+ python -m twine upload wheelhouse/*
diff --git a/.github/workflows/pip-packaging-windows.yml b/.github/workflows/pip-packaging-windows.yml
index 3a751486..e5a7d817 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -10,34 +10,42 @@ jobs:
strategy:
max-parallel: 4
matrix:
- python-version: ['3.5', '3.6', '3.7', '3.8', '3.9']
+ python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- - uses: actions/checkout@v1
+ - uses: actions/checkout@v3
with:
submodules: true
- - uses: actions/setup-python@v1
+ - uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python-version }}
architecture: x64
- name: Install dependencies
run: |
- vcpkg update
- vcpkg upgrade --no-dry-run
- type c:/vcpkg/ports/cgal/portfile.cmake
+ set VCPKG_BUILD_TYPE=release
vcpkg install eigen3 cgal --triplet x64-windows
- python -m pip install --user -r .github/build-requirements.txt
- python -m pip install --user twine
+ vcpkg version
+ ls "C:\vcpkg\installed\x64-windows\bin\"
+ python -m pip install --user -r .\ext\gudhi-deploy\build-requirements.txt
+ python -m pip install --user build twine
python -m pip list
- - name: Build python wheel
+ - name: Build python wheel and install it
run: |
mkdir build
- cd build
- cmake -DCMAKE_BUILD_TYPE=Release -DGMP_INCLUDE_DIR="c:/vcpkg/installed/x64-windows/include" -DGMP_LIBRARIES="c:/vcpkg/installed/x64-windows/lib/mpir.lib" -DGMP_LIBRARIES_DIR="c:/vcpkg/installed/x64-windows/lib" -DCMAKE_TOOLCHAIN_FILE=C:/vcpkg/scripts/buildsystems/vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows -DPython_ADDITIONAL_VERSIONS=3 ..
- cd src/python
- cp c:/vcpkg/installed/x64-windows/bin/mpfr.dll gudhi/
- cp c:/vcpkg/installed/x64-windows/bin/mpir.dll gudhi/
- python setup.py bdist_wheel
+ cd ".\build\"
+ cmake -DCMAKE_BUILD_TYPE=Release -DFORCE_EIGEN_DEFAULT_DENSE_INDEX_TYPE_TO_INT=ON -DCMAKE_TOOLCHAIN_FILE=c:\vcpkg\scripts\buildsystems\vcpkg.cmake -DVCPKG_TARGET_TRIPLET=x64-windows ..
+ cd ".\src\python\"
+ cp "C:\vcpkg\installed\x64-windows\bin\mpfr*.dll" ".\gudhi\"
+ cp "C:\vcpkg\installed\x64-windows\bin\gmp*.dll" ".\gudhi\"
+ python -m build -n
+ ls ".\dist\"
+ cd ".\dist\"
+ Get-ChildItem *.whl | ForEach-Object{python -m pip install --user $_.Name}
+ - name: Test python wheel
+ run: |
+ python -m pip install --user pytest
+ python -c "import gudhi; print(gudhi.__version__)"
+ python -m pytest ".\src\python\test\test_alpha_complex.py"
- name: Publish on PyPi
env:
TWINE_USERNAME: __token__
generated by cgit v1.2.3 (git 2.39.1) at 2024-05-19 04:34:12 +0000