Merge branch 'main' into feature/devices_metadata

.github/workflows/black.yml

@@ -1,10 +1,9 @@
 name: Black
 
-on: [push, pull_request]
+on: [workflow_call]
 
 jobs:
   black:
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     runs-on: ubuntu-latest
 
     steps:

.github/workflows/branch.yml

@@ -0,0 +1,15 @@
+name: Check branch commit
+
+on:
+  push:
+    branches:
+      - '**'  # matches every branch ...
+      - '!main'  # ... that is not main
+
+jobs:
+  isort:
+    uses: ./.github/workflows/isort.yml
+  black:
+    uses: ./.github/workflows/black.yml
+  build:
+    uses: ./.github/workflows/build.yml

.github/workflows/main.yaml → .github/workflows/build.yml

@@ -1,10 +1,9 @@
 name: Test BSB NEURON adapter
 
-on: [push, pull_request]
+on: [workflow_call]
 
 jobs:
   build:
-    if: github.event_name == 'push' || github.event.pull_request.head.repo.full_name != github.repository
     runs-on: ubuntu-latest
     strategy:
       matrix:
@@ -26,8 +25,9 @@ jobs:
       run: |
         pip install --upgrade pip
         # Install self, with test dependencies
-        pip install .[test,parallel]
+        pip install .[test]
+
     - name: Run tests & coverage
       run: |
         coverage run -p -m unittest discover -v -s ./tests
-        mpiexec -n 2 coverage run -p -m unittest discover -v -s ./tests
+        mpiexec -n 2 coverage run -p -m unittest discover -v -s ./tests

.github/workflows/external_pr.yml

@@ -0,0 +1,33 @@
+name: Validate external Pull Request
+
+on:
+  pull_request:
+    types: [opened, synchronize, reopened]
+
+env:
+  LOCAL_PR: ${{ github.event.pull_request.head.repo.full_name == github.repository }}
+
+jobs:
+  variables: # env variables are not accessible through job.if (https://stackoverflow.com/q/73558652)
+    runs-on: ubuntu-latest
+    outputs:
+      LOCAL_PR: ${{ steps.init.outputs.LOCAL_PR }}
+    steps:
+      - name: Make environment variables global
+        id: init
+        run: |
+          echo "LOCAL_PR=${{ env.LOCAL_PR }}" >> $GITHUB_OUTPUT
+
+  isort:
+    needs: variables
+    # if PR is external, trigger the tests on push or new PR
+    if: ${{ needs.variables.outputs.LOCAL_PR == 'false'}}
+    uses: ./.github/workflows/isort.yml
+  black:
+    needs: variables
+    if: ${{ needs.variables.outputs.LOCAL_PR == 'false' }}
+    uses: ./.github/workflows/black.yml
+  build:
+    needs: variables
+    if: ${{ needs.variables.outputs.LOCAL_PR == 'false' }}
+    uses: ./.github/workflows/build.yml

.github/workflows/isort.yml

@@ -1,6 +1,6 @@
 name: Run isort
-on:
-  - push
+
+on: [workflow_call]
 
 jobs:
   isort:
@@ -17,4 +17,4 @@ jobs:
           sudo apt install openmpi-bin libopenmpi-dev
       # Install dependencies for proper 1st/2nd/3rd party import sorting
       - run: pip install -e .[parallel]
-      - uses: isort/isort-action@master
+      - uses: isort/isort-action@v1.1.0

.github/workflows/main.yml

@@ -0,0 +1,155 @@
+name: Bump version, create release and deploy
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  isort:
+    uses: ./.github/workflows/isort.yml
+  black:
+    uses: ./.github/workflows/black.yml
+  build:
+    uses: ./.github/workflows/build.yml
+
+  tag_release:
+    needs: [isort, black, build]
+    runs-on: ubuntu-latest
+    outputs:
+      tag: ${{ steps.semver.outputs.next }}
+      old_tag: ${{ steps.semver.outputs.current }}
+
+    steps:
+      - name: Create Github token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.DBBS_APP_ID }}
+          private-key: ${{ secrets.DBBS_APP_PRIVATE_KEY }}
+
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ steps.app-token.outputs.token }}
+
+      - name: Get Next Version
+        id: semver
+        uses: ietf-tools/semver-action@v1
+        with:
+          token: ${{ steps.app-token.outputs.token }}
+          branch: main
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Bump version in Python project
+        run: |
+          pip install --upgrade pip bump-my-version
+          oldv="${{ steps.semver.outputs.current }}"
+          newv="${{steps.semver.outputs.next}}"
+          # Bump the version, dropping the leading `v` with `${x:1}`
+          bump-my-version replace --current-version=${oldv:1} --new-version=${newv:1} pyproject.toml
+
+      - name: Commit & Push version change
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: main
+          commit_message: 'docs: bump version: ${{ steps.semver.outputs.current }} → ${{ steps.semver.outputs.next }} [skip ci]'
+
+      - name: Create tag
+        uses: rickstaa/action-create-tag@v1
+        with:
+          tag: ${{ steps.semver.outputs.next }}
+          github_token: ${{ steps.app-token.outputs.token }}
+
+  release:
+    runs-on: ubuntu-latest
+    needs: tag_release
+
+    steps:
+      - name: Create Github token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.DBBS_APP_ID }}
+          private-key: ${{ secrets.DBBS_APP_PRIVATE_KEY }}
+
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ steps.app-token.outputs.token }}
+
+      - name: Pull commit of version change
+        run: |
+          git pull origin main 
+
+      - name: Update CHANGELOG
+        id: changelog
+        uses: requarks/changelog-action@v1
+        with:
+          token: ${{ steps.app-token.outputs.token }}
+          fromTag: ${{ needs.tag_release.outputs.tag }}
+          toTag: ${{ needs.tag_release.outputs.old_tag }}
+
+      - name: Create Release
+        uses: ncipollo/[email protected]
+        with:
+          allowUpdates: true
+          draft: false
+          makeLatest: true
+          tag: ${{ needs.tag_release.outputs.tag }}
+          name: ${{ needs.tag_release.outputs.tag }}
+          body: ${{ steps.changelog.outputs.changes }}
+          token: ${{ steps.app-token.outputs.token }}
+
+      - name: Commit CHANGELOG.md
+        uses: stefanzweifel/git-auto-commit-action@v5
+        with:
+          branch: main
+          commit_message: 'docs: update CHANGELOG.md for ${{ github.ref_name }} [skip ci]'
+          file_pattern: CHANGELOG.md
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs: release
+    environment:
+      name: pypi
+      url: https://pypi.org/p/bsb-neuron
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - name: Create Github token
+        uses: actions/create-github-app-token@v1
+        id: app-token
+        with:
+          app-id: ${{ vars.DBBS_APP_ID }}
+          private-key: ${{ secrets.DBBS_APP_PRIVATE_KEY }}
+
+      - name: Checkout Code
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+          token: ${{ steps.app-token.outputs.token }}
+
+      - name: Pull commits of version bump
+        run: |
+          git pull origin main
+
+      - name: Set up Python 3.11
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependencies and build dist
+        run: |
+          python -m pip install --upgrade pip
+          pip install build
+          python -m build
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/pull_request.yml

@@ -0,0 +1,16 @@
+name: Validate Pull Request Name
+
+on:
+  pull_request:
+    types: [edited, opened, reopened]
+
+jobs:
+  validate-pr-title:
+    # Trigger only for local PR when PR is edited (title, description, etc.)
+    if: ${{ github.event.pull_request.head.repo.full_name == github.repository }}
+    runs-on: ubuntu-latest
+    steps:
+      - name: PR Conventional Commit Validation
+        uses:  ytanikin/[email protected]
+        with:
+          task_types: '["feat","fix","docs","test","ci","refactor","perf","revert"]'

.gitignore

@@ -124,3 +124,4 @@ dmypy.json
 .pyre/
 
 .idea/
+*.hdf5

.pre-commit-config.yaml

@@ -1,3 +1,6 @@
+default_install_hook_types:
+  - pre-commit
+  - commit-msg
 repos:
   - repo: https://github.com/psf/black-pre-commit-mirror
     rev: 24.1.1
@@ -7,4 +10,11 @@ repos:
     rev: 5.12.0
     hooks:
       - id: isort
-        name: isort (python)
+        name: isort (python)
+  - repo: https://github.com/compilerla/conventional-pre-commit
+    rev: v3.3.0
+    hooks:
+      - id: conventional-pre-commit
+        name: conventional-commit
+        stages: [ commit-msg ]
+        args: [ ]

CHANGELOG.md

@@ -0,0 +1,12 @@
+## [v4.1.0] - 2024-10-07
+### :sparkles: New Features
+- [`9857e54`](https://github.com/dbbs-lab/bsb-neuron/commit/9857e54ab65826afd75f46eae059df39c5a6cb80) - add auto release pipeline *(PR [#20](https://github.com/dbbs-lab/bsb-neuron/pull/20) by [@drodarie](https://github.com/drodarie))*
+
+
+## [v4.0.3] - 2024-09-26
+
+### What's Changed
+* Fix NeuronPopulation class issue by @filimarc in https://github.com/dbbs-lab/bsb-neuron/pull/14
+* Let NeuronAdapter adjust simdata.placement to chunks by @filimarc in https://github.com/dbbs-lab/bsb-neuron/pull/19
+* Fixed GID assignment to transmitters involved in multiple connectivity sets by @danilobenozzo in https://github.com/dbbs-lab/bsb-neuron/pull/15
+[v4.1.0]: https://github.com/dbbs-lab/bsb-neuron/compare/v4.0.3...v4.1.0

README.md

@@ -1 +1,9 @@
+[![Build Status](https://github.com/dbbs-lab/bsb-neuron/actions/workflows/main.yml/badge.svg)](https://github.com/dbbs-lab/bsb-neuron/actions/workflows/main.yml)
+[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
+
 # bsb-neuron
+
+bsb-neuron is a pluggin of [BSB](https://github.com/dbbs-lab/bsb) (see also 
+[bsb-core](https://github.com/dbbs-lab/bsb-core)). 
+It contains the interfaces and tools to simulate BSB circuit with the 
+[neuron simulator](https://www.neuron.yale.edu/neuron/).

bsb_neuron/__init__.py

@@ -8,5 +8,5 @@
 from .adapter import NeuronAdapter
 from .simulation import NeuronSimulation
 
-__version__ = "4.0.2"
+__version__ = "4.1.0"
 __plugin__ = SimulationBackendPlugin(Simulation=NeuronSimulation, Adapter=NeuronAdapter)

pyproject.toml

@@ -23,12 +23,21 @@ neuron = "bsb_neuron"
 
 [project.optional-dependencies]
 parallel = ["bsb-core[parallel]"]
-test = ["bsb-test~=4.0", "coverage~=7.0", "bsb-hdf5~=4.0"]
+test = [
+    "bsb-core[parallel]",
+    "bsb-test~=4.0",
+    "coverage~=7.0",
+    "bsb-hdf5~=4.0"
+]
 dev = [
+    "bsb-neuron[test]",
+    "build~=1.0",
+    "twine~=4.0",
     "pre-commit~=3.5",
-    "black~=24.0",
+    "black~=24.1.1",
     "isort~=5.12",
-    "bump-my-version~=0.18"
+    "snakeviz~=2.1",
+    "bump-my-version~=0.24"
 ]
 
 [tool.black]
@@ -38,7 +47,7 @@ line-length = 90
 profile = "black"
 
 [tool.bumpversion]
-current_version = "4.0.2"
+current_version = "4.1.0"
 parse = "(?P<major>\\d+)\\.(?P<minor>\\d+)\\.(?P<patch>\\d+)"
 serialize = ["{major}.{minor}.{patch}"]
 search = "{current_version}"