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-rw-r--r--.github/how_to_use_github_to_contribute_to_gudhi.md15
-rw-r--r--.github/next_release.md3
-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
8 files changed, 65 insertions, 22 deletions
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 d5fcef1c..929a7ce6 100644
--- a/.github/next_release.md
+++ b/.github/next_release.md
@@ -9,6 +9,9 @@ Below is a list of changes made since GUDHI 3.6.0:
- [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`.
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 2024-05-29 00:39:39 +0000