BlueBrain -> openbraininstitute

.github/workflows/clang_format_check.yaml

@@ -4,7 +4,7 @@ on: [pull_request, push]
 jobs:
   build:
     name: clang-format-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
 

.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
 

.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
 
@@ -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

.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

.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:

.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/highfive-devs/highfive.git
 [submodule "python/pybind11"]
 	path = python/pybind11
 	url = https://github.com/pybind/pybind11.git

.readthedocs.yaml

@@ -10,7 +10,7 @@ submodules:
   recursive: true
 
 build:
-  os: "ubuntu-20.04"
+  os: "ubuntu-22.04"
   apt_packages:
     - libhdf5-dev
   tools:

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 <https://www.gnu.org/licenses/>.
 
 
 .. |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/

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}

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)",
     ],