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-rw-r--r--.github/for_maintainers/new_gudhi_version_creation.md3
-rw-r--r--.github/how_to_use_github_to_contribute_to_gudhi.md15
-rw-r--r--.github/next_release.md19
-rw-r--r--.github/workflows/pip-build-linux.yml18
-rw-r--r--.github/workflows/pip-build-osx.yml14
-rw-r--r--.github/workflows/pip-build-windows.yml2
-rw-r--r--.github/workflows/pip-packaging-linux.yml14
-rw-r--r--.github/workflows/pip-packaging-osx.yml19
-rw-r--r--.github/workflows/pip-packaging-windows.yml2
9 files changed, 72 insertions, 34 deletions
diff --git a/.github/for_maintainers/new_gudhi_version_creation.md b/.github/for_maintainers/new_gudhi_version_creation.md
index 19ef168e..9634adae 100644
--- a/.github/for_maintainers/new_gudhi_version_creation.md
+++ b/.github/for_maintainers/new_gudhi_version_creation.md
@@ -22,7 +22,6 @@ cmake -DCMAKE_BUILD_TYPE=Release -DCGAL_DIR=/your/path/to/CGAL -DWITH_GUDHI_EXAM
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
@@ -87,7 +86,7 @@ Copy gudhi WebDAV python/@GUDHI_VERSION@ as python/latest (no symbolic link with
* 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
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 738c1ce9..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:
@@ -25,16 +25,14 @@ 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
```
-[gudhi-deploy](https://github.com/GUDHI/gudhi-deploy) is used for Continuous Integration python
-requirements and will also be downloaded by the above command.
+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
@@ -68,6 +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 929a7ce6..937fc557 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -1,25 +1,20 @@
-We are pleased to announce the release 3.7.0 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 ...
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 3.6.0:
+Below is a list of changes made since GUDHI 3.7.0:
- [Module](link)
- ...
-- [Simplex tree](https://gudhi.inria.fr/python/latest/simplex_tree_ref.html)
- - New functions to initialize from a matrix or insert batches of simplices of the same dimension.
-
-- [Rips complex](https://gudhi.inria.fr/python/latest/rips_complex_user.html)
- - Construction now rejects positional arguments, you need to specify `points=X`.
+- [Module](link)
+ - ...
-- Installation
- - c++17 is the new minimal standard to compile the library. This implies Visual Studio minimal version is now 2017.
- Miscellaneous
- - The [list of bugs that were solved since GUDHI-3.6.0](https://github.com/GUDHI/gudhi-devel/issues?q=label%3A3.7.0+is%3Aclosed) is available on GitHub.
+ - The [list of bugs that were solved since GUDHI-3.7.0](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.
@@ -32,3 +27,7 @@ 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/workflows/pip-build-linux.yml b/.github/workflows/pip-build-linux.yml
index 11b6271d..bc4f999e 100644
--- a/.github/workflows/pip-build-linux.yml
+++ b/.github/workflows/pip-build-linux.yml
@@ -12,16 +12,16 @@ jobs:
- uses: actions/checkout@v3
with:
submodules: true
- - name: Build wheel for Python 3.10
+ - name: Build wheel for Python 3.11
run: |
- mkdir build_310
- cd build_310
- cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON310/bin/python ..
+ mkdir build_311
+ cd build_311
+ cmake -DCMAKE_BUILD_TYPE=Release -DPYTHON_EXECUTABLE=$PYTHON311/bin/python ..
cd src/python
- $PYTHON310/bin/python setup.py bdist_wheel
+ $PYTHON311/bin/python setup.py bdist_wheel
auditwheel repair dist/*.whl
- - name: Install and test wheel for Python 3.10
+ - name: Install and test wheel for Python 3.11
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
+ $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
diff --git a/.github/workflows/pip-build-osx.yml b/.github/workflows/pip-build-osx.yml
index 59e94ca5..a438124a 100644
--- a/.github/workflows/pip-build-osx.yml
+++ b/.github/workflows/pip-build-osx.yml
@@ -2,13 +2,18 @@ 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: ['3.10']
+ python-version: ['3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- uses: actions/checkout@v3
@@ -24,14 +29,21 @@ jobs:
brew install boost eigen gmp mpfr cgal || true
python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
python -m pip install --user 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
+ 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
diff --git a/.github/workflows/pip-build-windows.yml b/.github/workflows/pip-build-windows.yml
index b3d75706..50bdfe2c 100644
--- a/.github/workflows/pip-build-windows.yml
+++ b/.github/workflows/pip-build-windows.yml
@@ -8,7 +8,7 @@ jobs:
strategy:
max-parallel: 4
matrix:
- python-version: ['3.10']
+ python-version: ['3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- uses: actions/checkout@v3
diff --git a/.github/workflows/pip-packaging-linux.yml b/.github/workflows/pip-packaging-linux.yml
index 285cfa00..14b1cf7a 100644
--- a/.github/workflows/pip-packaging-linux.yml
+++ b/.github/workflows/pip-packaging-linux.yml
@@ -79,6 +79,19 @@ jobs:
$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 setup.py bdist_wheel
+ 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__
@@ -89,3 +102,4 @@ jobs:
$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 3ae840c6..9ddbcfce 100644
--- a/.github/workflows/pip-packaging-osx.yml
+++ b/.github/workflows/pip-packaging-osx.yml
@@ -4,13 +4,18 @@ 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: ['3.7', '3.8', '3.9', '3.10']
+ python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- uses: actions/checkout@v3
@@ -26,8 +31,13 @@ jobs:
brew install boost eigen gmp mpfr cgal || true
python -m pip install --user -r ext/gudhi-deploy/build-requirements.txt
python -m pip install --user 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
@@ -45,6 +55,7 @@ jobs:
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 6f544499..df0db9a5 100644
--- a/.github/workflows/pip-packaging-windows.yml
+++ b/.github/workflows/pip-packaging-windows.yml
@@ -10,7 +10,7 @@ jobs:
strategy:
max-parallel: 4
matrix:
- python-version: ['3.7', '3.8', '3.9', '3.10']
+ python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
name: Build wheels for Python ${{ matrix.python-version }}
steps:
- uses: actions/checkout@v3
generated by cgit v1.2.3 (git 2.39.1) at 2024-06-26 13:24:08 +0000