Merge branch 'master' into cornu/clean_headers

.github/ISSUE_TEMPLATE/release-patch.md

@@ -13,8 +13,7 @@ Action items
 Pre-release
 ---
 - [ ] Create a cherrypicks branch where all commits go into new release and open a PR against `release/x.y` branch
-- [ ] Create CoreNEURON tag on the `release/x.y` branch after cherrypicking required commits, update semantic version in its `CMakeLists.txt`, tag it & update submodule in cherrypicks PR
-- [ ] Look out for ModelDB regressions by manually submitting and analyzing [nrn-modeldb-ci](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++) for the cherrypicks branch vs previous version
+- [ ] Make sure to look out for ModelDB regressions by manually submitting and analyzing [nrn-modeldb-ci](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++) for the cherrypicks branch vs previous version
 - [ ] Update cherrypicks PR:
   - [ ] Update semantic version in `CMakeLists.txt`
   - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` in the cherrypicks PR (copy structure as-is)
@@ -25,20 +24,20 @@ Sanity checks
 - [ ] After cherrypicks PR is merged, make sure GitHub, Azure and CircleCI builds pass for `release/x.y` branch
 - [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the `release/x.y` branch; see [nrn-build-ci guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
-- [ ] Run BBP Simulation Stack, CoreNEURON CI & other relevant tests
+- [ ] Run BBP Simulation Stack & other relevant tests
 - [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
 Releasing
 ---
-- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release.
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
 - [ ] Create, test and upload manual artifacts 
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
   - [ ] aarch64 wheels (use existing `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
 - [ ] Publish the `x.y.z` wheels on PyPI; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
 - [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`)
 - [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox) 
 
 

.github/ISSUE_TEMPLATE/release.md

@@ -12,15 +12,14 @@ Action items
 
 Pre-release
 ---
-- [ ] Look out for ModelDB regressions by analyzing [nrn-modeldb-ci last version vs nightly reports](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++)
-- [ ] Create CoreNEURON release branch, update semantic version in `CMakeLists.txt`, tag it & update submodule in NEURON
+- [ ] Make sur to look out for ModelDB regressions by launching analyzing [nrn-modeldb-ci last version vs nightly reports](https://github.com/neuronsimulator/nrn-modeldb-ci/actions/workflows/nrn-modeldb-ci.yaml?query=event%3Aschedule++)
 
 Sanity checks
 ---
 - [ ] Create `release/x.y` branch and make sure GitHub, Azure and CircleCI builds pass
 - [ ] Run [nrn-build-ci](https://github.com/neuronsimulator/nrn-build-ci/actions/workflows/build-neuron.yml) for the respective Azure build; see [Azure drop guide](https://github.com/neuronsimulator/nrn-build-ci#azure-wheels-testing---manual-workflow) 
 - [ ] Activate ReadTheDocs build for `release/x.y` & make it hidden. Check docs are fine after build is done.
-- [ ] Run BBP Simulation Stack, CoreNEURON CI & other relevant tests
+- [ ] Run BBP Simulation Stack & other relevant tests
 - [ ] Build release wheels but WITHOUT upload ([see details](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure))
 
 
@@ -30,14 +29,15 @@ Releasing
 - [ ] Update changelog below and agree on it with everyone; then commit it to `docs/changelog` (copy structure as-is)
 - [ ] Update `docs/index.rst` accordingly with the new `.pkg` and `.exe` links for `PKG installer` and `Windows Installer`
 - [ ] Run the ReadTheDocs build again for `release-x.y`, make sure the build passes and inspect the Changelog page.
-- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release.
-- [ ] Create, test and upload manual artifacts 
+- [ ] Create new release+tag on GitHub via [release workflow](https://github.com/neuronsimulator/nrn/actions/workflows/release.yml?query=workflow%3A%22NEURON+Release%22). Note that the GitHub release will be marked as pre-release and  will contain the full-src-package and the Windows installer at the end of the release workflow.
+- [ ] Create, test and upload manual artifacts
   - [ ] MacOS package installer (manual task, ask Michael)
   - [ ] arm64 wheels (manual task, check with Alex or Pramod)
   - [ ] aarch64 wheels (create a `release/x.y-aarch64` branch for this, see [guide](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-circleci))
 - [ ] Publish the `x.y.z` wheels on Pypi; see [wheel publishing instructions](https://nrn.readthedocs.io/en/latest/install/python_wheels.html#publishing-the-wheels-on-pypi-via-azure)
 - [ ] Once wheels are published, activate the `x.y.z` tag on ReadTheDocs
-- [ ] Upload Windows installer from the wheels publishing Azure run (to get correct tag)
+- [ ] Rename the Windows installer in the GitHub release to match the new version and the supported python versions (i.e. `nrn-8.2.2.w64-mingw-py-37-38-39-310-311-setup.exe`
+)
 - [ ] Publish release on GitHub (edit https://github.com/neuronsimulator/nrn/releases/tag/x.y.z and un-tick the pre-release checkbox)
 
 

.github/workflows/coverage.yml

@@ -30,7 +30,7 @@ jobs:
 
     name: Code Coverage
 
-    timeout-minutes: 45
+    timeout-minutes: 60
 
     env:
       DISPLAY: ${{ ':0' }}
@@ -153,7 +153,7 @@ jobs:
           # By default we get a modern version of CMake that understands --parallel.
           cmake --build . --parallel 2
           cmake --build . --target cover_baseline
-          xvfb-run ctest -VV --output-on-failure;
+          xvfb-run ctest --rerun-failed --output-on-failure;
           for python in "${PYTHON_MIN}" "${PYTHON_MAX}"
           do
             echo "Using ${python}"

.github/workflows/release.yml

@@ -23,6 +23,7 @@ jobs:
     name: tag-n-release ${{ github.event.inputs.rel_tag }} (${{ github.event.inputs.rel_branch }})
     outputs:
       release_url: ${{ steps.create_release.outputs.upload_url }}
+      rel_tag: ${{ env.REL_TAG }}
     steps:
       - uses: actions/checkout@v3
         name: Checkout branch ${{ env.REL_BRANCH }}
@@ -74,15 +75,17 @@ jobs:
     - name: Create full-src-package
       id: tar
       run: |
-        tar -czvf ${REL_TAG}.tar.gz nrn
-        echo "asset_file=${REL_TAG}.tar.gz" >> $GITHUB_OUTPUT
+        tar -czvf full-src-package-${REL_TAG}.tar.gz nrn
+        echo "asset_file=full-src-package-${REL_TAG}.tar.gz" >> $GITHUB_OUTPUT
 
     - name: Upload full-src-package to release
-      uses: actions/upload-release-asset@v1
-      with:
-        upload_url: ${{ needs.tag-n-release.outputs.release_url }}
-        asset_name: ${{ github.job }}-${{ steps.tar.outputs.asset_file }}
-        asset_content_type: application/gzip
-        asset_path: ${{ steps.tar.outputs.asset_file }}
+      run: |
+        gh release upload ${{ needs.tag-n-release.outputs.rel_tag }} ${{ steps.tar.outputs.asset_file }}
       env:
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+
+  windows-installer:
+    needs: tag-n-release
+    uses: neuronsimulator/nrn/.github/workflows/windows.yml@master
+    with:
+      tag: ${{ needs.tag-n-release.outputs.rel_tag }}

.github/workflows/windows.yml

@@ -5,8 +5,16 @@ concurrency:
   cancel-in-progress: true  
 
 on:
+  workflow_call:
+    inputs:
+      tag:
+        description: 'Release version (tag name)'
+        default: ''
+        required: true
+        type: string
   push:
     branches: 
+      - master
       - release/**
   pull_request:
     branches:
@@ -28,7 +36,7 @@ jobs:
     steps:
     - uses: actions/checkout@v3
       with:
-        fetch-depth: 0
+        ref: ${{ inputs.tag }}
 
     - name: Retrieve rxd test data
       run: |
@@ -84,3 +92,11 @@ jobs:
       run: .\ci\win_test_installer.cmd
       shell: cmd
       working-directory: ${{runner.workspace}}\nrn
+
+    - name: Publish Release Installer
+      working-directory: ${{runner.workspace}}\nrn
+      if: inputs.tag != ''
+      run: |
+        gh release upload ${{ inputs.tag }} nrn-nightly-AMD64.exe
+      env:
+        GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

CMakeLists.txt

@@ -494,7 +494,6 @@ if(NRN_ENABLE_CORENEURON)
   list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake/coreneuron
        ${PROJECT_SOURCE_DIR}/cmake/coreneuron/packages)
 
-  set(nrn_using_ext_corenrn FALSE)
   # If NEURON tests are enabled then enable CoreNEURON tests too
   set(CORENRN_ENABLE_UNIT_TESTS
       ${NRN_ENABLE_TESTS}
@@ -567,6 +566,7 @@ endif()
 # =============================================================================
 # Add project directories AFTER CMake modules
 # =============================================================================
+add_subdirectory(src/gnu)
 add_subdirectory(src/nrniv)
 
 # Collect the environment variables that are needed to execute NEURON from the build directory. This

azure-pipelines.yml

@@ -150,42 +150,6 @@ stages:
       - template: ci/azure-wheel-test-upload.yml
 
 
-    # Jobs to build NEURON installer natively
-    - job: 'WindowsInstaller'
-      timeoutInMinutes: 45
-      pool:
-        vmImage: windows-latest
-      variables:
-        MSYS2_ROOT: C:\msys64
-
-      steps:
-      - checkout: self
-        submodules: 'true'
-        clean: 'true'
-
-      - task: BatchScript@1
-        inputs:
-          filename: ci/win_download_deps.cmd
-        displayName: "Download Dependencies"
-        condition: succeeded()
-
-      - task: BatchScript@1
-        inputs:
-          filename: ci/win_install_deps.cmd
-        displayName: "Install Dependencies"
-        condition: succeeded()
-
-      # WSL is enabled by default in the image, with no installed linux distribution.
-      # WSL creates an unusable `bash.EXE` that can be resolved first from the environment.
-      # This is why we remove that file.
-      - script: |
-          rm.exe "C:/WINDOWS/system32/bash.EXE"
-          %MSYS2_ROOT%\usr\bin\bash -lc "$BUILD_SOURCESDIRECTORY/ci/win_build_cmake.sh"
-        displayName: "Build and Create Installer"
-        condition: succeeded()
-
-      - template: ci/azure-win-installer-upload.yml
-
   - stage: Final
     jobs:
       - job: AzureDropURL

cmake/NeuronFileLists.cmake

@@ -444,24 +444,6 @@ set(SCOPMATH_FILES_LIST
 
 set(NRNMPI_FILES_LIST nrnmpi.cpp bbsmpipack.cpp mpispike.cpp)
 
-set(NRNGNU_FILES_LIST
-    ACG.cpp
-    Binomial.cpp
-    DiscUnif.cpp
-    Erlang.cpp
-    Geom.cpp
-    HypGeom.cpp
-    LogNorm.cpp
-    MLCG.cpp
-    NegExp.cpp
-    Normal.cpp
-    Poisson.cpp
-    RNG.cpp
-    Random.cpp
-    RndInt.cpp
-    Uniform.cpp
-    Weibull.cpp)
-
 # nrnpython sources (only if ${NRN_ENABLE_PYTHON_DYNAMIC} is OFF}
 set(NRNPYTHON_FILES_LIST
     nrnpython.cpp
@@ -570,7 +552,6 @@ nrn_create_file_list(NRN_SPARSE13_SRC_FILES ${PROJECT_SOURCE_DIR}/src/sparse13
 nrn_create_file_list(NRN_SCOPMATH_SRC_FILES ${PROJECT_SOURCE_DIR}/src/scopmath
                      ${SCOPMATH_FILES_LIST})
 nrn_create_file_list(NRN_NRNMPI_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnmpi ${NRNMPI_FILES_LIST})
-nrn_create_file_list(NRN_NRNGNU_SRC_FILES ${PROJECT_SOURCE_DIR}/src/gnu ${NRNGNU_FILES_LIST})
 nrn_create_file_list(NRN_NRNPYTHON_SRC_FILES ${PROJECT_SOURCE_DIR}/src/nrnpython
                      ${NRNPYTHON_FILES_LIST})
 nrn_create_file_list(NRN_MODFILE_BASE_NAMES src/nrnoc ${MODFILE_BASE_NAMES})

docs/courses/intro_to_gui.rst

@@ -222,7 +222,7 @@ Halve the duration and double the amplitude.
     Change the number of Points plotted/ms to 100 and dt to 0.01 ms and run again.
 
 5. 
-    **Increase the amplitude to 1e4 nA, cut the duration to 1e-5 ms, inrease Points plotted/ms to 1e5, and start a simulation...**
+    **Increase the amplitude to 1e4 nA, cut the duration to 1e-5 ms, increase Points plotted/ms to 1e5, and start a simulation...**
 
     After a few seconds of eternity, stop the simulation by clicking on RunControl / stop
 
@@ -242,7 +242,7 @@ Halve the duration and double the amplitude.
 
     :download:`bilayer.hoc <code/bilayer.hoc>` contains a properly configured CellBuilder, plus a custom interface for running simulations. The one item it doesn't have is a VariableStepControl. 
 
-    :download:`bilayer.hoc <code/bilayer.hoc>` is actually a session file that was given the "hoc" extension so that MSWin users could launch it by double clickin on the file name. For didactic reasons we prefer that you load it from Python instead.
+    :download:`bilayer.hoc <code/bilayer.hoc>` is actually a session file that was given the "hoc" extension so that MSWin users could launch it by double clicking on the file name. For didactic reasons we prefer that you load it from Python instead.
 
     1. 
         Save :download:`bilayer.hoc <code/bilayer.hoc>` to your machine, open up in a terminal, then cd to the directory that contains bilayer.hoc

docs/courses/multithread_parallelization.rst

@@ -1,6 +1,6 @@
 .. _multithread_parallelization:
 
-Multithreaded paralellization
+Multithreaded parallelization
 =============================
 
 If a model has more than a few thousand states, it may run faster with multiple threads.

docs/dealing_simulations_generate_lot.rst

@@ -12,4 +12,4 @@ The answer to your problem is to break the simulation into shorter segments, eac
 Comments and suggestions
 -------------
 
-As always, these examples illustrate modular code organization, and iterative refinement and testing of code, both of which are useful strategies for productive programming. If you run into keywords that are new to you, or unfamilar usage of familiar keywords, be sure to look them up in the :ref:`programmer's reference <python_prog_ref>`.
+As always, these examples illustrate modular code organization, and iterative refinement and testing of code, both of which are useful strategies for productive programming. If you run into keywords that are new to you, or unfamiliar usage of familiar keywords, be sure to look them up in the :ref:`programmer's reference <python_prog_ref>`.