coding-conventions: use new formatting helpers (#1982)

* coding-conventions: use new formatting helpers.
* coreneuron: update submodule.
* docs CI: fix by banning the new matplotlib version.

.bbp-project.yaml

@@ -0,0 +1,14 @@
+tools:
+  Black:
+    enable: True
+    include:
+      match:
+      - '.*\.(py|ipynb)$'
+    option: [--color, --diff, --target-version, py37]
+    version: '[jupyter] ~=22.3'
+  ClangFormat:
+    enable: True
+    version: == 12.0.1
+  CMakeFormat:
+    enable: True
+    version: == 0.6.13

.github/workflows/docs.yml

@@ -35,7 +35,7 @@ jobs:
         shell: bash
 
       - name: Set up Python@${{ env.DEFAULT_PY_VERSION }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
           python-version: ${{ env.DEFAULT_PY_VERSION }}
 
@@ -50,6 +50,7 @@ jobs:
         working-directory: ${{runner.workspace}}/nrn
         run: |
           python -m pip install --upgrade -r docs/docs_requirements.txt
+          python -c 'import plotnine; print(plotnine.__version__); print(plotnine)'
 
       - name: Documentation
         id: documentation

.github/workflows/formatting.yml

@@ -15,102 +15,15 @@ on:
       - release/**
 
 jobs:
-  black:
-    name: Python
-    runs-on: ubuntu-20.04
+  all:
+    name: C/C++, CMake and Python
+    runs-on: ubuntu-22.04
     timeout-minutes: 5
     steps:
-      - name: Set up Python@3.7
-        uses: actions/setup-python@v3
-        with:
-          python-version: 3.7
-
-      - name: Install Black
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade black[jupyter]
-
       - uses: actions/checkout@v3
-
-      - name: Check Python formatting
+      - name: Update submodule
         working-directory: ${{runner.workspace}}/nrn
-        run: |
-          git ls-tree -z -r HEAD --name-only \
-          | grep -z '\.\(py\|ipynb\)$' \
-          | xargs -0 black --check --color --diff --target-version py37
-
-  cmake:
-    name: CMake
-    runs-on: ubuntu-20.04
-    timeout-minutes: 5
-    steps:
-      - name: Set up Python@3.7
-        uses: actions/setup-python@v3
-        with:
-          python-version: 3.7
-
-      - name: Install cmake-format
-        run: |
-          python -m pip install --upgrade pip
-          python -m pip install --upgrade cmake-format pyyaml
-
-      - name: Install Ninja
-        run: |
-          sudo apt-get update
-          sudo apt-get install ninja-build
-
-      - uses: actions/checkout@v3
-
-      - name: Configure
+        run: git submodule update --init external/coding-conventions
+      - name: Check formatting
         working-directory: ${{runner.workspace}}/nrn
-        run: |
-          mkdir build
-          cd build/
-          # Need to configure the build to trigger the hpc-coding-conventions
-          # YAML magic
-          cmake -G Ninja .. \
-            -DNRN_CMAKE_FORMAT=ON \
-            -DNRN_ENABLE_RX3D=OFF \
-            -DNRN_ENABLE_PYTHON=OFF \
-            -DNRN_ENABLE_INTERVIEWS=OFF \
-            -DNRN_ENABLE_MPI=OFF
-
-      - name: Check CMake formatting
-        working-directory: ${{runner.workspace}}/nrn/build
-        run: ninja check-cmake-format
-
-  cpp:
-    name: C/C++
-    runs-on: ubuntu-20.04
-    timeout-minutes: 5
-    steps:
-      - name: Install dependencies
-        run: |
-          sudo apt-get update
-          sudo apt-get install ninja-build
-          # The last .1 refers to ssciwr/clang-format-wheel#23.
-          sudo pip install clang-format==12.0.1.1
-          command -v clang-format
-          clang-format --version
-
-      - uses: actions/checkout@v3
-
-      - name: Configure
-        working-directory: ${{runner.workspace}}/nrn
-        run: |
-          mkdir build
-          cd build/
-          # Need to configure the build to trigger the hpc-coding-conventions
-          # YAML magic. Disable as much as possible now that the list of files
-          # to format is based on git ls-tree.
-          cmake -G Ninja .. \
-            -DClangFormat_EXECUTABLE=$(command -v clang-format) \
-            -DNRN_CLANG_FORMAT=ON \
-            -DNRN_ENABLE_INTERVIEWS=OFF \
-            -DNRN_ENABLE_MPI=OFF \
-            -DNRN_ENABLE_PYTHON=OFF \
-            -DNRN_ENABLE_RX3D=OFF
-
-      - name: Check C/C++ formatting
-        working-directory: ${{runner.workspace}}/nrn/build
-        run: ninja check-clang-format
+        run: external/coding-conventions/bin/format -v --dry-run

.gitignore

@@ -1,3 +1,4 @@
+.bbp-project-venv/
 .clang-format
 .cmake-format.yaml
 external/tests/

CMakeLists.txt

@@ -230,8 +230,6 @@ configure_file(src/nrnoc/nrnsemanticversion.h.in src/nrnoc/nrnsemanticversion.h
 # =============================================================================
 set(CODING_CONV_PREFIX "NRN")
 set(${CODING_CONV_PREFIX}_3RDPARTY_DIR "external")
-set(${CODING_CONV_PREFIX}_ClangFormat_REQUIRED_VERSION 12.0.1)
-set(${CODING_CONV_PREFIX}_ClangFormat_EXCLUDES_RE CACHE STRING "") # None needed
 set(CODING_CONV_CMAKE "${PROJECT_SOURCE_DIR}/${NRN_3RDPARTY_DIR}/coding-conventions/cpp/cmake")
 if(NOT EXISTS "${CODING_CONV_CMAKE}/3rdparty.cmake")
   # Abort with a helpful message if the current source tree lacks .git information, as in that case

docs/docs_requirements.txt

@@ -3,7 +3,8 @@ sphinx_rtd_theme
 jupyter
 nbconvert
 recommonmark
-matplotlib
+# 3.6.0 clashes with plotnine 0.9.0
+matplotlib == 3.5.3
 bokeh
 # do not check import of next line
 ipython