From 293b34a0274d299ac3da0af8786913066ea01c32 Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 15:18:30 +0200 Subject: [PATCH 1/7] BlueBrain -> openbraininstitute --- .github/workflows/mirror-ebrains.yml | 8 ++++---- .gitmodules | 2 +- README.rst | 10 +++++----- docs/source/conf.py | 4 ++-- setup.py | 2 +- 5 files changed, 13 insertions(+), 13 deletions(-) diff --git a/.github/workflows/mirror-ebrains.yml b/.github/workflows/mirror-ebrains.yml index ef738f0..691753e 100644 --- a/.github/workflows/mirror-ebrains.yml +++ b/.github/workflows/mirror-ebrains.yml @@ -11,14 +11,14 @@ jobs: - name: syncmaster uses: wei/git-sync@v3 with: - source_repo: "BlueBrain/libsonata" + source_repo: "openbraininstitute/libsonata" source_branch: "master" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/BlueBrain/libsonata.git" + destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/openbraininstitute/libsonata.git" destination_branch: "main" - name: synctags uses: wei/git-sync@v3 with: - source_repo: "BlueBrain/libsonata" + source_repo: "openbraininstitute/libsonata" source_branch: "refs/tags/*" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/BlueBrain/libsonata.git" + destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/openbraininstitute/libsonata.git" destination_branch: "refs/tags/*" diff --git a/.gitmodules b/.gitmodules index e7002a3..87b0f1f 100644 --- a/.gitmodules +++ b/.gitmodules @@ -3,7 +3,7 @@ url = https://github.com/fmtlib/fmt.git [submodule "extlib/HighFive"] path = extlib/HighFive - url = https://github.com/BlueBrain/HighFive.git + url = https://github.com/openbraininstitute/HighFive.git [submodule "python/pybind11"] path = python/pybind11 url = https://github.com/pybind/pybind11.git diff --git a/README.rst b/README.rst index 03a8f79..7fef5b3 100644 --- a/README.rst +++ b/README.rst @@ -23,14 +23,14 @@ Installing as a Python package, directly from GitHub .. code-block:: shell - pip install git+https://github.com/BlueBrain/libsonata + pip install git+https://github.com/openbraininstitute/libsonata Building the C++ library ~~~~~~~~~~~~~~~~~~~~~~~~ .. code-block:: shell - git clone git@github.com:BlueBrain/libsonata.git --recursive + git clone git@github.com:openbraininstitute/libsonata.git --recursive cd libsonata mkdir build && cd build cmake -DCMAKE_BUILD_TYPE=Release -DEXTLIB_FROM_SUBMODULES=ON .. @@ -419,10 +419,10 @@ along with libsonata. If not, see . .. |license| image:: https://img.shields.io/pypi/l/libsonata - :target: https://github.com/BlueBrain/libsonata/blob/master/COPYING.LESSER + :target: https://github.com/openbraininstitute/libsonata/blob/master/COPYING.LESSER -.. |coverage| image:: https://coveralls.io/repos/github/BlueBrain/libsonata/badge.svg - :target: https://coveralls.io/github/BlueBrain/libsonata +.. |coverage| image:: https://coveralls.io/repos/github/openbraininstitute/libsonata/badge.svg + :target: https://coveralls.io/github/openbraininstitute/libsonata .. |docs| image:: https://readthedocs.org/projects/libsonata/badge/?version=latest :target: https://libsonata.readthedocs.io/ diff --git a/docs/source/conf.py b/docs/source/conf.py index b547a00..3b193e8 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -56,8 +56,8 @@ html_show_sourcelink = False html_extra_path = ["doxygen"] html_theme_options = { - "repo_url": "https://github.com/BlueBrain/libsonata/", - "repo_name": "BlueBrain/libsonata", + "repo_url": "https://github.com/openbraininstitute/libsonata/", + "repo_name": "openbraininstitute/libsonata", } autodoc_default_options = {"members": True, "imported-members": True} diff --git a/setup.py b/setup.py index 7c275a6..a662ed4 100644 --- a/setup.py +++ b/setup.py @@ -113,7 +113,7 @@ def build_extension(self, ext): long_description=README, long_description_content_type='text/x-rst', license="LGPLv3", - url='https://github.com/BlueBrain/libsonata', + url='https://github.com/openbraininstitute/libsonata', classifiers=[ "License :: OSI Approved :: GNU Lesser General Public License v3 (LGPLv3)", ], From cdd8abb1bc52ecc6ab3749c9fe811d1b3dacad0a Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 15:53:02 +0200 Subject: [PATCH 2/7] better highfive --- .gitmodules | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.gitmodules b/.gitmodules index 87b0f1f..4a0b054 100644 --- a/.gitmodules +++ b/.gitmodules @@ -3,7 +3,7 @@ url = https://github.com/fmtlib/fmt.git [submodule "extlib/HighFive"] path = extlib/HighFive - url = https://github.com/openbraininstitute/HighFive.git + url = https://github.com/highfive-devs/highfive.git [submodule "python/pybind11"] path = python/pybind11 url = https://github.com/pybind/pybind11.git From 80faeba7a2780f3f4c82366c474af5bfc6ed157d Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 15:55:20 +0200 Subject: [PATCH 3/7] ebrains file was obsolete --- .github/workflows/mirror-ebrains.yml | 24 ------------------------ 1 file changed, 24 deletions(-) delete mode 100644 .github/workflows/mirror-ebrains.yml diff --git a/.github/workflows/mirror-ebrains.yml b/.github/workflows/mirror-ebrains.yml deleted file mode 100644 index 691753e..0000000 --- a/.github/workflows/mirror-ebrains.yml +++ /dev/null @@ -1,24 +0,0 @@ -name: Mirror to Ebrains - -on: - push: - branches: [ master ] - -jobs: - to_ebrains: - runs-on: ubuntu-latest - steps: - - name: syncmaster - uses: wei/git-sync@v3 - with: - source_repo: "openbraininstitute/libsonata" - source_branch: "master" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/openbraininstitute/libsonata.git" - destination_branch: "main" - - name: synctags - uses: wei/git-sync@v3 - with: - source_repo: "openbraininstitute/libsonata" - source_branch: "refs/tags/*" - destination_repo: "https://ghpusher:${{ secrets.EBRAINS_GITLAB_ACCESS_TOKEN }}@gitlab.ebrains.eu/openbraininstitute/libsonata.git" - destination_branch: "refs/tags/*" From 0337cc5a68595ea851f29f0daa383287eaa41db4 Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 16:02:42 +0200 Subject: [PATCH 4/7] test CI --- .github/workflows/clang_format_check.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/.github/workflows/clang_format_check.yaml b/.github/workflows/clang_format_check.yaml index 7617624..b309e6e 100644 --- a/.github/workflows/clang_format_check.yaml +++ b/.github/workflows/clang_format_check.yaml @@ -5,8 +5,7 @@ jobs: build: name: clang-format-check runs-on: ubuntu-20.04 - # Run on external PRs, but not internal PRs as they'll be run by the push - if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository + if: github.event_name == 'pull_request' steps: - name: Fetch repository From d7bc7b0092f68f42f0ff19402d50e9d05f4db818 Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 16:11:25 +0200 Subject: [PATCH 5/7] test ubuntu 22.04 --- .github/workflows/clang_format_check.yaml | 5 +++-- .github/workflows/coverage_test.yaml | 2 +- .github/workflows/docstring_check.yaml | 2 +- .github/workflows/publish-sdist-wheels.yml | 2 +- .readthedocs.yaml | 2 +- 5 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.github/workflows/clang_format_check.yaml b/.github/workflows/clang_format_check.yaml index b309e6e..fc68c09 100644 --- a/.github/workflows/clang_format_check.yaml +++ b/.github/workflows/clang_format_check.yaml @@ -4,8 +4,9 @@ on: [pull_request, push] jobs: build: name: clang-format-check - runs-on: ubuntu-20.04 - if: github.event_name == 'pull_request' + runs-on: ubuntu-22.04 + # Run on external PRs, but not internal PRs as they'll be run by the push + if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository steps: - name: Fetch repository diff --git a/.github/workflows/coverage_test.yaml b/.github/workflows/coverage_test.yaml index 54ee654..8857371 100644 --- a/.github/workflows/coverage_test.yaml +++ b/.github/workflows/coverage_test.yaml @@ -4,7 +4,7 @@ on: [pull_request, push] jobs: build: name: coverage-test - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 # Run on external PRs, but not internal PRs as they'll be run by the push if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository diff --git a/.github/workflows/docstring_check.yaml b/.github/workflows/docstring_check.yaml index 9baba06..59cdb99 100644 --- a/.github/workflows/docstring_check.yaml +++ b/.github/workflows/docstring_check.yaml @@ -4,7 +4,7 @@ on: [pull_request, push] jobs: build: name: docstring-check - runs-on: ubuntu-20.04 + runs-on: ubuntu-22.04 # Run on external PRs, but not internal PRs as they'll be run by the push if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository diff --git a/.github/workflows/publish-sdist-wheels.yml b/.github/workflows/publish-sdist-wheels.yml index e6ad6ec..35a1a50 100644 --- a/.github/workflows/publish-sdist-wheels.yml +++ b/.github/workflows/publish-sdist-wheels.yml @@ -20,7 +20,7 @@ jobs: strategy: matrix: # macos-13 is an intel runner, macos-14 is apple silicon - os: [ubuntu-20.04, macos-13, macos-14] + os: [ubuntu-22.04, macos-13, macos-14] steps: - uses: actions/checkout@v4 diff --git a/.readthedocs.yaml b/.readthedocs.yaml index 05fc916..6a9734b 100644 --- a/.readthedocs.yaml +++ b/.readthedocs.yaml @@ -10,7 +10,7 @@ submodules: recursive: true build: - os: "ubuntu-20.04" + os: "ubuntu-22.04" apt_packages: - libhdf5-dev tools: From cd5d45bea9b36f83682115969cdb55c21388f1cf Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 16:16:04 +0200 Subject: [PATCH 6/7] testing more --- .github/workflows/docstring_check.yaml | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/.github/workflows/docstring_check.yaml b/.github/workflows/docstring_check.yaml index 59cdb99..1e5fb1f 100644 --- a/.github/workflows/docstring_check.yaml +++ b/.github/workflows/docstring_check.yaml @@ -17,13 +17,13 @@ jobs: - name: Install packages run: | sudo apt-get update - sudo apt-get install build-essential libhdf5-dev python3-venv libclang1-9 + sudo apt-get install build-essential libhdf5-dev python3-venv libclang-14-dev clang-14 # debug - dpkg -L libclang1-9 - ls -al /usr/lib/x86_64-linux-gnu/libclang* + dpkg -L libclang-14-dev + ls -al /usr/lib/llvm-14/lib/libclang* - name: Check docstrings run: | - export LIBCLANG_PATH=/usr/lib/x86_64-linux-gnu/libclang-9.so.1 - ci/check_generated_docstrings.sh || true + export LIBCLANG_PATH=/usr/lib/llvm-14/lib/libclang.so + ci/check_generated_docstrings.sh || true \ No newline at end of file From 9c4434a7ca7666c0e8bb417bf8c5849cefa6f014 Mon Sep 17 00:00:00 2001 From: Alessandro Cattabiani Date: Fri, 23 May 2025 16:20:40 +0200 Subject: [PATCH 7/7] more changes --- .github/workflows/run-tests.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml index d1f9457..17d7bf2 100644 --- a/.github/workflows/run-tests.yml +++ b/.github/workflows/run-tests.yml @@ -12,8 +12,8 @@ env: jobs: build-linux-cpp: - name: Run tests on ubuntu-20.04 - runs-on: ubuntu-20.04 + name: Run tests on ubuntu-22.04 + runs-on: ubuntu-22.04 strategy: matrix: compiler: @@ -66,8 +66,8 @@ jobs: ./ci/cpp_test.sh build-linux-python: - name: Run python tests on ubuntu-20.04 - runs-on: ubuntu-20.04 + name: Run python tests on ubuntu-22.04 + runs-on: ubuntu-22.04 strategy: matrix: