v0.8 (#2028)

- Correct `.gitmodules` - Update all git submodules to latest released versions, except google-benchmark - Have CHANGELOG - Breaking changes since v0.7: - A change in API: `arbor.cable_cell` has the labels and decor arguments swapped. I.e.: `(tree, labels, decor)` -> `(tree, decor, label)`. Labels are now optional. - Mechanism ABI version is bumped to 0.3.1. #1884 - Remove the `generate-catalogue` script. `modcc` accepts now a list of NMODL files and is able to spit out a catalogue.cpp file - Rename spike detector -> threshold detector - Remove access to time `t` in NMODL. - Major dependency version bumps: - GCC: 9 and up - CUDA: 11 and up - Clang: 10 and up
arbor-sim · Nov 15, 2022 · 8e82ec1 · 8e82ec1
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diff --git a/.gitmodules b/.gitmodules
@@ -1,14 +1,14 @@
 [submodule "google-benchmark"]
 	path = ext/google-benchmark
-	url = https://github.com/google/benchmark
+	url = https://github.com/google/benchmark.git
 	branch = main
 [submodule "ext/fmt"]
 	path = ext/fmt
 	url = https://github.com/fmtlib/fmt.git
 	branch = master
 [submodule "ext/random123"]
 	path = ext/random123
-	url = https://github.com/DEShawResearch/random123
+	url = https://github.com/DEShawResearch/random123.git
 	branch = main
 [submodule "ext/json"]
 	path = ext/json
@@ -17,8 +17,9 @@
 [submodule "ext/pybind11"]
 	path = ext/pybind11
 	url = https://github.com/pybind/pybind11.git
+	branch = master
 [submodule "ext/googletest"]
 	path = ext/googletest
 	url = https://github.com/google/googletest.git	
-	branch = release-1.12.1
+	branch = main
 
diff --git a/ATTRIBUTIONS.md b/ATTRIBUTIONS.md
@@ -1,12 +1,42 @@
 Arbor includes code from the open source community. Thank you!
 
+## fmt
+
+{fmt} is an open-source formatting library providing a fast and safe alternative to C stdio and C++ iostreams.
+
+https://github.com/fmtlib/fmt
+
+## google-benchmark
+
+A library to benchmark code snippets, similar to unit tests.
+
+https://github.com/google/benchmark
+
+## GoogleTest
+
+GoogleTest is Google’s C++ testing and mocking framework.
+
+https://github.com/google/googletest
+
 ## JSON for Modern C++
 
 A header only C++11 json library, written by Niels Lohmann (GitHub user nlohmann).
 MIT license.
 
 https://github.com/nlohmann/json
 
+## pybind11
+
+pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
+
+https://github.com/pybind/pybind11
+
+## random123
+
+The Random123 library is a collection of counter-based random number generators ("CBRNGs") for CPUs (C and C++) and GPUs (CUDA and OpenCL).
+
+https://github.com/DEShawResearch/random123
+
 ## tinyopt
 
 A header only C++ library for command line argument parsing, written by Stuart Yates.

diff --git a/CHANGELOG.md b/CHANGELOG.md
diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-0.7.1-dev
+0.8.0
diff --git a/doc/contrib/pr.rst b/doc/contrib/pr.rst
@@ -33,16 +33,18 @@ the workflow is as follows:
 3. Make a pull request (PR) and refer to the issue(s) that the PR
    addresses. Some tips on how to write a good PR description:
 
-   -  You can use labels to categorize your PR. For very large PRs, it
-      is likely the reviewer will have many questions and comments. It
-      can be helpful to reach out on Gitter, Github Discussions or by email
-      beforehand if you’ve big things planned for Arbor!
-   -  Commit logical units with clear commit messages.
-   -  Add a change summary to the PR message. If you remembered to commit
-      logical units, this could simply be a bulleted list of all commit
-      messages in the PR. If during the review process you make changes
-      to the features in the PR, keep the PR description updated.
-   -  Use text like `fixes #123` in the description to refer to an issue.
+   - You can use labels to categorize your PR. For very large PRs, it
+     is likely the reviewer will have many questions and comments. It
+     can be helpful to reach out on Gitter, Github Discussions or by email
+     beforehand if you’ve big things planned for Arbor!
+   - Commit logical units with clear commit messages.
+   - Add a change summary to the PR message. If you remembered to commit
+     logical units, this could simply be a bulleted list of all commit
+     messages in the PR. If during the review process you make changes
+     to the features in the PR, keep the PR description updated.
+   - Use text like `fixes #123` in the description to refer to an issue.
+   - Prefix your PR title with BUGFIX, BREAKING, FEATURE if it fixes a bug, introduces
+     a breaking change or introduces a (major) new feature respectively.
 
 4. We will accept contributions licensed with the same
    `BSD 3-Clause "New" or "Revised" License <https://github.com/arbor-sim/arbor/blob/master/LICENSE>`_,

diff --git a/doc/contrib/release.rst b/doc/contrib/release.rst
@@ -40,7 +40,7 @@ Update tags/versions and test
 
 #. Check if some files are up to date
 
-   - README.md, ATTRIBUTIONS.md, CONTRIBUTING.md, RELEASE_NOTES.md
+   - README.md, ATTRIBUTIONS.md, CONTRIBUTING.md, CHANGELOG.md
    - Verify MANIFEST.in (required for PyPI sdist)
    - Double check that all examples/tutorials/etc are covered by CI
    - Check Python/pip/PyPi metadata and scripts, e.g. ``setup.py``, ``pyproject.toml``
@@ -51,9 +51,16 @@ Update tags/versions and test
    - See also :ref:`dev-version`
    - Append ``-rc``. (Make sure there's no ``-dev``)
 
-#. Run all tests.
+#. Create a draft PR. Tag and push with ``-rc``. E.g. ``v0.6-rc``
 
-   - ``ciwheel.yml`` triggers when you push a branch called ``ciwheel``, and on new Git tags. Since we've not tagged the release yet, run ``git push origin HEAD:ciwheel``. Make sure the tests pass.
+   - on cmdline: ``git tag -a TAGNAME``
+   - ``git push upstream refs/tags/TAGNAME``
+   - Githubs autogenerated release notes can only be generated on a tag. Use this ``-rc`` tag to do so, and add the commit to the draft PR. Ensure Github takes the previous release as base.
+
+#. Run and pass all tests.
+
+   - They should run automatically based on the draft PR. Pushing the tag kicks of ``ciwheel``.
+   - In case you want to test ``ciwheel.yml`` manually on your local repo ``origin``, push to a branch called ``ciwheel``, e.g. ``git push origin HEAD:ciwheel``.
 
       - ``ciwheel.yml`` pushes automatically to `Test.PyPI.org <https://test.pypi.org/project/arbor/>`_. This only passes if ran as branch of the main ``arbor-sim`` repo (as that's where the PyPI secret lives). On your own repo, the upload will fail (the rest should pass). If you want to test uploading, then force push to the _upstream_ ``ciwheel`` branch, e.g. ``git push upstream HEAD:ciwheel --force``.
 
@@ -63,7 +70,7 @@ Update tags/versions and test
 
         python -m venv env && source env/bin/activate
         pip install numpy
-        pip install -i https://test.pypi.org/simple/ arbor #should select the latest build, but doublecheck
+        pip install -i https://test.pypi.org/simple/ arbor #should select the latest build, otherwise e.g. arbor==0.8rc0
         python -c 'import arbor; print(arbor.__config__)'
 
    - Use build flags to test the source package: :ref:`in_python_adv`
@@ -79,9 +86,11 @@ Release
 
 #. Tag
 
-   - commit and open a PR for the above changes.
-   - on cmdline: ``git tag -a TAGNAME``
-   - ``git push upstream TAGNAME``
+   - commit and either reuse the draft PR for the RC, or open a new one.
+   - once merged, make and push tag.
+
+      - on cmdline: ``git tag -a TAGNAME``
+      - ``git push upstream TAGNAME``
 
 #. Upload to pypi & verify
 

diff --git a/ext/fmt b/ext/fmt
diff --git a/ext/json b/ext/json
diff --git a/ext/pybind11 b/ext/pybind11
diff --git a/spack/package.py b/spack/package.py
@@ -53,8 +53,8 @@ class Arbor(CMakePackage, CudaPackage):
     )
 
     # https://docs.arbor-sim.org/en/latest/install/build_install.html#compilers
-    conflicts("%gcc@:8.3")
-    conflicts("%clang@:7")
+    conflicts("%gcc@:8")
+    conflicts("%clang@:9")
     # Cray compiler v9.2 and later is Clang-based.
     conflicts("%cce@:9.1")
     conflicts("%intel")
@@ -63,10 +63,13 @@ class Arbor(CMakePackage, CudaPackage):
 
     # misc dependencies
     depends_on("[email protected]:", when="@0.5.3:")  # required by the modcc compiler
+    depends_on("[email protected]:", when="@0.7.1:")
     depends_on("nlohmann-json")
     depends_on("random123")
-    depends_on("cuda@10:", when="+cuda")
     depends_on("libxml2", when="+neuroml")
+    with when("+cuda"):
+        depends_on("cuda@10:")
+        depends_on("cuda@11:", when="@0.7.1:")
 
     # mpi
     depends_on("mpi", when="+mpi")
@@ -79,7 +82,7 @@ class Arbor(CMakePackage, CudaPackage):
     with when("+python"):
         depends_on("[email protected]:", type=("build"))
         depends_on("[email protected]:", when="@0.5.3:", type=("build"))
-        depends_on("[email protected].0:", when="@0.7.1:", type=("build"))
+        depends_on("[email protected].1:", when="@0.7.1:", type=("build"))
 
     # sphinx based documentation
     depends_on("[email protected]:", when="+doc", type="build")