Merge branch 'master' into old-fn

BlueBrain · Oct 18, 2023 · 5349862 · 5349862
2 parents bed0b9f + 8ce1476
commit 5349862
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diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml
@@ -14,7 +14,7 @@ jobs:
   tag:
     name: Bump version, push tag and make a release
     needs: call-test-workflow
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     permissions:
       contents: write
     steps:
@@ -54,13 +54,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-20.04, macos-latest, windows-latest]
+        os: [ubuntu-22.04, macos-latest, windows-latest]
         python: [cp38, cp39, cp310, cp311]
         arch: [x86_64, amd64]
         exclude:
           - os: macos-latest
             arch: amd64
-          - os: ubuntu-20.04
+          - os: ubuntu-22.04
             arch: amd64
           - os: windows-latest
             arch: x86_64
@@ -90,7 +90,7 @@ jobs:
 
   tarball:
     name: Build tarball
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: [call-test-workflow, tag]
     steps:
       - uses: actions/checkout@v3
@@ -111,7 +111,7 @@ jobs:
 
   publish:
     name: Release and Publish on PyPI
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     needs: [call-test-workflow, tag, wheels, tarball]
     steps:
       - uses: actions/checkout@v3

diff --git a/.github/workflows/keep-alive.yml b/.github/workflows/keep-alive.yml
@@ -11,7 +11,7 @@ jobs:
 
   keep-workflow-alive:
     name: Keep workflow alive
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
         with:

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -7,7 +7,7 @@ on:
 
 jobs:
   test:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ["3.8", "3.9", "3.10", "3.11"]
@@ -26,10 +26,11 @@ jobs:
         pip install tox tox-gh-actions
 
     - name: Run tox
-      run: tox  # this does not call docs
+      run: |
+        tox  # this does not call docs
 
   coverage:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     strategy:
       matrix:
         python-version: ["3.11"]
@@ -55,7 +56,7 @@ jobs:
       with:
         fail_ci_if_error: false
   docs:
-    runs-on: ubuntu-20.04
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v2
     - name: Set up Python 3.9

diff --git a/.readthedocs.yaml b/.readthedocs.yaml
@@ -7,7 +7,7 @@ version: 2
 
 # Set the version of Python and other tools you might need
 build:
-  os: ubuntu-20.04
+  os: ubuntu-22.04
   tools:
     python: "3.9"
 
@@ -16,6 +16,7 @@ python:
   install:
     - method: pip
       path: .
+    - requirements: requirements_docs.txt
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

diff --git a/efel/cppcore/CMakeLists.txt b/efel/cppcore/CMakeLists.txt
@@ -15,15 +15,22 @@
 # along with this library; if not, write to the Free Software Foundation, Inc., 
 # 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.                   
 
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.12)
+
+# Set C++ standard
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
 
 set(CMAKE_BUILD_TYPE Debug)
 
-set(FEATURESRCS Utils.cpp LibV1.cpp LibV2.cpp LibV3.cpp LibV4.cpp LibV5.cpp
+set(FEATURESRCS Utils.cpp LibV1.cpp LibV2.cpp LibV3.cpp LibV5.cpp
     FillFptrTable.cpp DependencyTree.cpp efel.cpp cfeature.cpp
     mapoperations.cpp)
 
 set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC")
+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra")
+
 
 add_library(efelStatic ${FEATURESRCS})
 set_target_properties(efelStatic PROPERTIES OUTPUT_NAME efel)
@@ -33,6 +40,6 @@ add_library(efel SHARED ${FEATURESRCS})
 install(TARGETS efel LIBRARY DESTINATION lib)
 
 install(FILES efel.h cfeature.h FillFptrTable.h LibV1.h LibV2.h LibV3.h
-    LibV4.h LibV5.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h
+    LibV5.h mapoperations.h Utils.h DependencyTree.h eFELLogger.h
     types.h
     DESTINATION include)
diff --git a/efel/cppcore/FillFptrTable.cpp b/efel/cppcore/FillFptrTable.cpp
@@ -20,23 +20,17 @@
 int FillFptrTable() {
   //****************** for FptrTableV1 *****************************
   FptrTableV1["interpolate"] = &LibV1::interpolate;
-  FptrTableV1["peak_indices"] = &LibV1::peak_indices;
   FptrTableV1["ISI_values"] = &LibV1::ISI_values;
   FptrTableV1["peak_voltage"] = &LibV1::peak_voltage;
   FptrTableV1["mean_frequency"] = &LibV1::firing_rate;
   FptrTableV1["peak_time"] = &LibV1::peak_time;
   FptrTableV1["time_to_first_spike"] = &LibV1::first_spike_time;
-  FptrTableV1["min_AHP_indices"] = &LibV1::min_AHP_indices;
-  FptrTableV1["min_AHP_values"] = &LibV1::min_AHP_values;
-  FptrTableV1["voltage_base"] = &LibV1::rest_voltage_value;
   FptrTableV1["burst_ISI_indices"] = &LibV1::burst_ISI_indices;
   FptrTableV1["adaptation_index"] = &LibV1::adaptation_index;
   FptrTableV1["trace_check"] = &LibV1::trace_check;
-  FptrTableV1["spike_half_width"] = &LibV1::spike_width1;
   FptrTableV1["spike_width2"] = &LibV1::spike_width2;
   FptrTableV1["burst_mean_freq"] = &LibV1::burst_mean_freq;
   FptrTableV1["interburst_voltage"] = &LibV1::interburst_voltage;
-  FptrTableV1["AHP_depth_abs"] = &LibV1::AHP_depth_abs;
   // passive properties
   FptrTableV1["time_constant"] = &LibV1::time_constant;
   FptrTableV1["voltage_deflection"] = &LibV1::voltage_deflection;
@@ -65,17 +59,9 @@ int FillFptrTable() {
 
   //****************** for FptrTableV2 *****************************
   /*
-  FptrTableV2["peak_indices"]         = &LibV2::peak_indices;
-  FptrTableV2["ISI_values"]           = &LibV2::ISI_values;
-  FptrTableV2["peak_voltage"]         = &LibV2::peak_voltage;
-  FptrTableV2["firing_rate"]          = &LibV2::firing_rate;
-  FptrTableV2["peak_time"]    = &LibV2::peak_time;
-  FptrTableV2["first_spike_time"]     = &LibV2::first_spike_time;
   FptrTableV2["AHP_min_indices"]      = &LibV2::AHP_min_indices;
   FptrTableV2["AHP_values"]           = &LibV2::AHP_values;
-  FptrTableV2["rest_voltage_value"]   = &LibV2::rest_voltage_value;
   FptrTableV2["burst_vector"]         = &LibV2::burst_vector;
-  FptrTableV2["adaptation_index"]     = &LibV2::adaptation_index;
   */
 
   // AP parameter
@@ -137,18 +123,11 @@ int FillFptrTable() {
   //****************** end of FptrTableV2 *****************************
 
   //******************  FptrTableV3 *****************************
-  FptrTableV3["AP_amplitude"] = &LibV3::AP_amplitude;
-  FptrTableV3["AP_width"] = &LibV3::AP_width;
-
-  FptrTableV3["AP_begin_indices"] = &LibV3::AP_begin_indices;
-  FptrTableV3["AP_end_indices"] = &LibV3::AP_end_indices;
   // eFeatures
   FptrTableV3["depolarized_base"] = &LibV3::depolarized_base;
 
   //****************** end of FptrTableV3 *****************************
 
-  FptrTableV4["peak_indices"] = &LibV4::peak_indices;
-
   //******************  FptrTableV5 *****************************
 
   FptrTableV5["ISI_log_slope"] = &LibV5::ISI_log_slope;

diff --git a/efel/cppcore/FillFptrTable.h b/efel/cppcore/FillFptrTable.h
@@ -24,13 +24,11 @@
 #include "LibV1.h"
 #include "LibV2.h"
 #include "LibV3.h"
-#include "LibV4.h"
 #include "LibV5.h"
 
 extern feature2function FptrTableV1;
 extern feature2function FptrTableV2;
 extern feature2function FptrTableV3;
-extern feature2function FptrTableV4;
 extern feature2function FptrTableV5;
 
 int FillFptrTable();