neuronsimulator · alexsavulescu · Feb 2, 2022 · Feb 1, 2022 · Feb 1, 2022 · Feb 2, 2022
diff --git a/.github/workflows/coverage.yml b/.github/workflows/coverage.yml
@@ -1,5 +1,9 @@
 name: NEURON Code Coverage
 
+concurrency:
+  group: ${{ github.workflow }}#${{ github.ref }}
+  cancel-in-progress: true
+
 on:
   push:
     branches:
@@ -9,14 +13,15 @@ on:
     branches:
       - master
       - release/**
-    paths-ignore:
-      - '**.md'
-      - '**.rst'
-      - 'docs/**'
+# TODO : https://github.com/neuronsimulator/nrn/issues/1063
+#    paths-ignore:
+#      - '**.md'
+#      - '**.rst'
+#      - 'docs/**'
 
 env:
-  PY_MIN_VERSION: 2.7
-  PY_MAX_VERSION: 3.8
+  PY_MIN_VERSION: '3.6'
+  PY_MAX_VERSION: '3.10'
 
 jobs:
   coverage:
@@ -30,9 +35,17 @@ jobs:
 
       - name: Install apt packages
         run: |
-          sudo apt-get install  build-essential doxygen autoconf automake libtool lcov autotools-dev libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf python-pip python-tk python-numpy python3-numpy python3-pip g++-5 g++-6 g++-8 g++-9
+          sudo apt-get install  build-essential doxygen lcov libopenmpi-dev libmpich-dev libx11-dev libxcomposite-dev mpich openmpi-bin patchelf gpg
         shell: bash
 
+      - name: Setup Caliper profiler
+        run: |
+          git clone https://github.com/LLNL/Caliper.git
+          cd Caliper
+          mkdir build && cd build
+          cmake ..
+          make && sudo make install
+
       - name: Set up Python@${{ env.PY_MIN_VERSION }}
         uses: actions/setup-python@v2
         with:
@@ -71,7 +84,7 @@ jobs:
 
           # CMake options & flags
           export COVERAGE_FLAGS="--coverage -O0 -fno-inline -g";
-          export CMAKE_OPTION="-DNRN_ENABLE_BINARY_SPECIAL=ON -DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON";
+          export CMAKE_OPTION="-DNRN_ENABLE_MPI=ON -DNRN_ENABLE_INTERVIEWS=ON -DNRN_ENABLE_PYTHON=ON -DNRN_ENABLE_PYTHON_DYNAMIC=ON -DNRN_PYTHON_DYNAMIC=${PYTHON_MIN};${PYTHON_MAX} -DNRN_ENABLE_CORENEURON=ON -DNRN_ENABLE_PROFILING=ON";
           cmake $CMAKE_OPTION -DCMAKE_C_COMPILER=$CC -DCMAKE_CXX_COMPILER=$CXX -DNRN_ENABLE_TESTS=ON -DCMAKE_C_FLAGS="${COVERAGE_FLAGS}" -DCMAKE_CXX_FLAGS="${COVERAGE_FLAGS}" ..;
 
           # Coverage
@@ -84,15 +97,27 @@ jobs:
           ctest -VV;
           (cd ..; lcov --capture  --directory . --no-external --output-file build/coverage-run.info)
           lcov --add-tracefile coverage-base.info --add-tracefile coverage-run.info --output-file coverage-combined.info
+
+          # Download codecov script and perform integrity checks
+          curl https://keybase.io/codecovsecurity/pgp_keys.asc | gpg --import # One-time step 
+          curl -Os https://uploader.codecov.io/latest/linux/codecov 
+          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM 
+          curl -Os https://uploader.codecov.io/latest/linux/codecov.SHA256SUM.sig 
+          gpg --verify codecov.SHA256SUM.sig codecov.SHA256SUM 
+          shasum -a 256 -c codecov.SHA256SUM 
+          chmod +x codecov 
+
           # Prefer auto-discovery for now. Specify reports once all python testing is unified under single report (-f option).
-          bash <(curl -s https://codecov.io/bash)
+          ./codecov
         env:
           MATRIX_EVAL: "CC=gcc CXX=g++"
           PYTHON_MIN_NAME: "python${{ env.PY_MIN_VERSION }}"
           PYTHON_MAX_NAME: "python${{ env.PY_MAX_VERSION }}"
 
       # This step will set up an SSH connection on tmate.io for live debugging.
-      # To trigger it, simply add 'live-debug-coverage' to your last pushed commit message.
-      - name: live debug session on failure
-        if: failure() && contains(github.event.head_commit.message, 'live-debug-coverage')
+      # To enable it, you have to:
+      #   * add 'live-debug-coverage' to your PR title
+      #   * push something to your PR branch (note that just re-running the pipeline disregards the title update)
+      - name: live debug session on failure (manual steps required, check `.github/coverage.yml`)
+        if: failure() && contains(github.event.pull_request.title, 'live-debug-coverage')
         uses: mxschmitt/action-tmate@v3
diff --git a/.github/workflows/docs.yml b/.github/workflows/docs.yml
@@ -11,7 +11,9 @@ on:
       - release/**
 
 env:
-  DEFAULT_PY_VERSION: 3.8
+  # Python 3.10 fails executing jupyter notebooks. Don't need 3.10 for building docs anyway.
+  # see https://github.com/neuronsimulator/nrn/issues/1612
+  DEFAULT_PY_VERSION: '3.8'
 
 jobs:
   documentation:

diff --git a/.github/workflows/windows.yml b/.github/workflows/windows.yml
@@ -1,5 +1,9 @@
 name: Windows Installer
 
+concurrency: 
+  group: ${{ github.workflow }}#${{ github.ref }}
+  cancel-in-progress: true  
+
 on:
   push:
     branches: 
@@ -26,7 +30,12 @@ jobs:
     - uses: actions/checkout@v2
       with:
         fetch-depth: 0
-
+
+    - name: Set up Python3
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.10'
+
     - name: Download Dependencies
       run: |
         .\nrn\ci\win_download_deps.cmd
@@ -48,9 +57,11 @@ jobs:
         BUILD_SOURCESDIRECTORY: ${{runner.workspace}}\nrn
 
     # This step will set up an SSH connection on tmate.io for live debugging.
-    # To trigger it, simply add 'live-debug-win' to your last pushed commit message.
-    - name: live debug session on failure
-      if: failure() && contains(github.event.head_commit.message, 'live-debug-win')
+    # To enable it, you have to:
+    #   * add 'live-debug-win' to your PR title
+    #   * push something to your PR branch (note that just re-running the pipeline disregards the title update)
+    - name: live debug session on failure (manual steps required, check `.github/windows.yml`)
+      if: failure() && contains(github.event.pull_request.title, 'live-debug-win')
       uses: mxschmitt/action-tmate@v3
 
     - name: Upload build artifact

diff --git a/docs/changelog.md b/docs/changelog.md
@@ -1,5 +1,14 @@
 # NEURON 8.0
 
+## 8.0.2
+_Release Date_ : 02-02-2022
+
+
+### Bug Fixes
+
+Python 3.10 bugfixes for RXD and Windows, more details in [GitHub PR #1614](https://github.com/neuronsimulator/nrn/pull/1614)
+
+
 ## 8.0.1
 _Release Date_ : 28-01-2022
 

diff --git a/share/lib/python/neuron/rxd/node.py b/share/lib/python/neuron/rxd/node.py
@@ -7,7 +7,13 @@
 from .rxdException import RxDException
 import warnings
 import ctypes
-import collections
+
+# For 8.0.x release, keep backward compat with older python versions
+try:
+    from collections.abc import Callable
+except ImportError:
+    from collections import Callable
+
 
 # function to change extracellular diffusion
 set_diffusion = nrn_dll_sym("set_diffusion")
@@ -313,7 +319,7 @@ def include_flux(self, *args, **kwargs):
                 source[0]
             except:
                 raise RxDException("HocObject must be a pointer")
-        elif len(args) == 1 and isinstance(args[0], collections.Callable):
+        elif len(args) == 1 and isinstance(args[0], Callable):
             flux_type = 2
             source = args[0]
             warnings.warn(

diff --git a/src/nrniv/nrnpy.cpp b/src/nrniv/nrnpy.cpp
@@ -12,6 +12,9 @@
 #include "classreg.h"
 #include "nonvintblock.h"
 #include "nrnmpi.h"
+#include <algorithm>
+#include <cctype>
+
 
 extern "C" {
 extern int nrn_nopython;
@@ -371,41 +374,24 @@ static void* load_nrnpython_helper(const char* npylib) {
 	return handle;
 }
 
-int digit_to_int(char ch) {
-  int d = ch - '0';
-  if ((unsigned) d < 10) {
-    return d;
-  }
-  d = ch - 'a';
-  if ((unsigned) d < 6) {
-    return d + 10;
-  }
-  d = ch - 'A';
-  if ((unsigned) d < 6) {
-    return d + 10;
-  }
-  return -1;
-}
-
-static int pylib2pyver10(const char* pylib) {
-  // check backwards for N.N or NN // obvious limitations
-  int n1 = -1; int n2 = -1;
-  for (const char* cp = pylib + strlen(pylib) -1 ; cp > pylib; --cp) {
-    if (isdigit(*cp)) {
-      if (n2 < 0) {
-        n2 = digit_to_int(*cp);
-      } else {
-        n1 = digit_to_int(*cp);
-        return n1*10 + n2;
-      }
-    }else if (*cp == '.') {
-      // skip
-    }else{ //
-      // start over
-      n2 = -1;
-    }
-  }
-  return 0;
+// Get python version as integer from pythonlib path
+static int pylib2pyver10(std::string pylib) {
+	//skip past last \ or /
+	const auto pos = pylib.find_last_of("/\\");
+	if (pos != std::string::npos) {
+		pylib = pylib.substr(pos + 1);
+	}
+
+	// erase nondigits
+	pylib.erase(
+	  std::remove_if(pylib.begin(),
+	    pylib.end(),
+	    [](char c) {
+	      return !std::isdigit(c);
+	    }), pylib.end());
+
+	// parse number. 0 is fine to return as error (no need for stoi)
+	return std::atoi(pylib.c_str());
 }
 
 static void load_nrnpython(int pyver10, const char* pylib) {