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commit b38b6af
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 12:29:49 2024 +0530

    Reverted windows build attempts.

commit 4c60035
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:52:46 2024 +0530

    Updated workflow

commit 95febb9
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:51:56 2024 +0530

    Updated wortkflow

commit 5042502
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:34:03 2024 +0530

    Updated workflow file.

commit ac6ba27
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:27:33 2024 +0530

    Update workflow

commit 5ae39a9
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:25:11 2024 +0530

    Updated workflow

commit b62cf5d
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:15:22 2024 +0530

    Update workflow

commit be7132e
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:13:35 2024 +0530

    Updated build

commit e7e2925
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:08:39 2024 +0530

    Update pymoose.yml

commit cc6bce8
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:07:10 2024 +0530

    Update pymoose.yml

commit 28eadbf
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:05:46 2024 +0530

    Update pymoose.yml

commit e9ae785
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:00:15 2024 +0530

    github workflow msvc/gsl

commit 6aba825
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:58:51 2024 +0530

    github workflow: msvc/gsl build

commit 31617f5
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:52:46 2024 +0530

    github workflow: windows GSL build test

commit 8ac5de1
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:48:32 2024 +0530

    github workflow: windows build of GSL

commit 96b9583
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:46:55 2024 +0530

    github workflow: Testing GSL build for windows

commit 60363ec
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 00:17:23 2024 +0530

    Bumped up cmake version to 3.20

    - Also trying to install GSL via vcpkg for WIN32

commit e475389
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 00:00:53 2024 +0530

    Fixed github workflow file

commit 7169d23
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:59:36 2024 +0530

    Trying to fix win build

commit a80fd8e
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:56:49 2024 +0530

    Fixing github workflow for WIN/MSVC build

commit a9909bf
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:41:53 2024 +0530

    Switched from C++11 to C++14

    - MSVC 2015 and later do not support c++11 - causing build to fail

commit ae43694
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:25:34 2024 +0530

    Github workflow update for windows build

    - C++11 support check does not work for MSVC cl. Trying a fix.

commit a3fe008
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:08:16 2024 +0530

    Github workflow for windows build: fixing micromamba options

commit b22e200
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:04:26 2024 +0530

    Fixing windows build workflow: micromamba path

commit f68e4b0
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:01:09 2024 +0530

    Attempt fixing micromamba for windows build

commit fd99794
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:58:19 2024 +0530

    Added windows build action to guthub workflow

commit 5b458d8
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:43:01 2024 +0530

    Fix to github workflow for build

commit 401bd27
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:40:32 2024 +0530

    Further fix to build

commit 0d7d2aa
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:25:34 2024 +0530

    Further fix to micromamba

commit b88d231
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:23:14 2024 +0530

    Further fix to micromamba command

commit 1401e35
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:21:03 2024 +0530

    Fixed micromamba commands

commit 7cc0289
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:16:23 2024 +0530

    Fix for github action

commit 2c4c4ed
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:07:29 2024 +0530

    Attempting github action to build for both Ubuntu and MacOSX M1

commit d91ca02
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 21:20:26 2024 +0530

    Build updated

    - Removed deprecated CMake version setting
    - Removed python2: out of life. Only supporting Python>=3.8
    - Removed pybind11: should be installed directly with pip
    - Added MacOSX build workflow: to be tested

* Modified test script for Granule98 to take model dir arg

* Fixed github workflow to build on Ubuntu and MacOSX

Squashed commit of the following:

commit b38b6af
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 12:29:49 2024 +0530

    Reverted windows build attempts.

commit 4c60035
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:52:46 2024 +0530

    Updated workflow

commit 95febb9
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:51:56 2024 +0530

    Updated wortkflow

commit 5042502
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:34:03 2024 +0530

    Updated workflow file.

commit ac6ba27
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:27:33 2024 +0530

    Update workflow

commit 5ae39a9
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:25:11 2024 +0530

    Updated workflow

commit b62cf5d
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:15:22 2024 +0530

    Update workflow

commit be7132e
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:13:35 2024 +0530

    Updated build

commit e7e2925
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:08:39 2024 +0530

    Update pymoose.yml

commit cc6bce8
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:07:10 2024 +0530

    Update pymoose.yml

commit 28eadbf
Author: subhacom <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:05:46 2024 +0530

    Update pymoose.yml

commit e9ae785
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 11:00:15 2024 +0530

    github workflow msvc/gsl

commit 6aba825
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:58:51 2024 +0530

    github workflow: msvc/gsl build

commit 31617f5
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:52:46 2024 +0530

    github workflow: windows GSL build test

commit 8ac5de1
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:48:32 2024 +0530

    github workflow: windows build of GSL

commit 96b9583
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 10:46:55 2024 +0530

    github workflow: Testing GSL build for windows

commit 60363ec
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 00:17:23 2024 +0530

    Bumped up cmake version to 3.20

    - Also trying to install GSL via vcpkg for WIN32

commit e475389
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Tue Apr 23 00:00:53 2024 +0530

    Fixed github workflow file

commit 7169d23
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:59:36 2024 +0530

    Trying to fix win build

commit a80fd8e
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:56:49 2024 +0530

    Fixing github workflow for WIN/MSVC build

commit a9909bf
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:41:53 2024 +0530

    Switched from C++11 to C++14

    - MSVC 2015 and later do not support c++11 - causing build to fail

commit ae43694
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:25:34 2024 +0530

    Github workflow update for windows build

    - C++11 support check does not work for MSVC cl. Trying a fix.

commit a3fe008
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:08:16 2024 +0530

    Github workflow for windows build: fixing micromamba options

commit b22e200
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:04:26 2024 +0530

    Fixing windows build workflow: micromamba path

commit f68e4b0
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 23:01:09 2024 +0530

    Attempt fixing micromamba for windows build

commit fd99794
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:58:19 2024 +0530

    Added windows build action to guthub workflow

commit 5b458d8
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:43:01 2024 +0530

    Fix to github workflow for build

commit 401bd27
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:40:32 2024 +0530

    Further fix to build

commit 0d7d2aa
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:25:34 2024 +0530

    Further fix to micromamba

commit b88d231
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:23:14 2024 +0530

    Further fix to micromamba command

commit 1401e35
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:21:03 2024 +0530

    Fixed micromamba commands

commit 7cc0289
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:16:23 2024 +0530

    Fix for github action

commit 2c4c4ed
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 22:07:29 2024 +0530

    Attempting github action to build for both Ubuntu and MacOSX M1

commit d91ca02
Author: Subhasis Ray <ray.subhasis@gmail.com>
Date:   Mon Apr 22 21:20:26 2024 +0530

    Build updated

    - Removed deprecated CMake version setting
    - Removed python2: out of life. Only supporting Python>=3.8
    - Removed pybind11: should be installed directly with pip
    - Added MacOSX build workflow: to be tested

---------

Co-authored-by: HarshaRani <ranishashi@gmail.com>
  • Loading branch information
subhacom and hrani authored May 7, 2024
1 parent 8939ede commit 94fe3d6
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Showing 291 changed files with 155 additions and 64,900 deletions.
3 changes: 1 addition & 2 deletions .ci/build_wheels_osx.sh
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,6 @@ export PATH=/usr/local/bin:$PATH
brew update || echo "Failed to update brew"
brew install gsl || brew upgrade gsl
brew upgrade python3 || echo "Failed to upgrade python3"
brew upgrade python2 || echo "Failed to upgrade python2"
brew upgrade python || echo "Failed to upgrade python"

# Following are to remove numpy; It is breaking the build on Xcode9.4.
Expand Down Expand Up @@ -48,7 +47,7 @@ for _py in 3 2; do
$PYTHON -m pip install numpy --upgrade --user
$PYTHON -m pip install twine --upgrade --user

PLATFORM=$($PYTHON -c "import distutils.util; print(distutils.util.get_platform())")
PLATFORM=$($PYTHON -c "import sysconfig; print(sysconfig.get_platform())")

(
cd $MOOSE_SOURCE_DIR
Expand Down
13 changes: 0 additions & 13 deletions .ci/travis_build_linux.sh
Original file line number Diff line number Diff line change
Expand Up @@ -12,12 +12,8 @@ set -x
BUILDDIR=_build_travis
mkdir -p $BUILDDIR

PYTHON2="/usr/bin/python2"
PYTHON3="/usr/bin/python3"

$PYTHON2 -m pip install pip --upgrade --user
$PYTHON2 -m pip install libNeuroML numpy==1.14 scipy==1.2 \
pyNeuroML python-libsbml --upgrade --user

$PYTHON3 -m pip install pip --upgrade --user
$PYTHON3 -m pip install libNeuroML pyNeuroML python-libsbml --upgrade --user
Expand All @@ -37,7 +33,6 @@ unset PYTHONPATH
# many not be available. Therefore, it is neccessary to use fixed path for
# python executable.

$PYTHON2 -m compileall -q .
$PYTHON3 -m compileall -q .

# Python3 with GSL in debug more.
Expand Down Expand Up @@ -68,13 +63,5 @@ $PYTHON3 -m compileall -q .
make coverage
)

# GSL and python2, failure is allowed
set +e
(
mkdir -p $BUILDDIR && cd $BUILDDIR && \
cmake -DPYTHON_EXECUTABLE=$PYTHON2 -DCMAKE_INSTALL_PREFIX=/usr ..
$MAKE && MOOSE_NUM_THREADS=$NPROC ctest -j$NPROC --output-on-failure
)
set -e

echo "All done"
45 changes: 27 additions & 18 deletions .github/workflows/pymoose.yml
Original file line number Diff line number Diff line change
Expand Up @@ -4,28 +4,37 @@ on: [push]

jobs:
build:
name : Python Package

runs-on: ubuntu-latest
strategy:
runs-on: ${{ matrix.os }}
strategy:
matrix:
python-version: [3.8, 3.9, '3.10',3.11,3.12]

os: [ubuntu-latest, macos-14]
build_type: [Release]
c_compiler: [clang]
python-version: ["3.12"]
include:
- os: ubuntu-latest
apt: 10
- os: macos-14
brew: 20
steps:
- uses: actions/checkout@v2
- if: ${{ matrix.apt }}
run: sudo apt-get install libhdf5-dev libgsl0-dev
- if: ${{ matrix.brew }}
run: |
brew install gsl
brew install hdf5
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
shell: bash
run: |
export DEBIAN_FRONTEND=noninteractive
sudo -E apt clean
sudo -E apt update
sudo -E apt install -y cmake libgsl-dev g++ gcc git
sudo -E apt install python3-tk
sudo -E apt install -y libhdf5-dev doxygen
python -m pip install numpy matplotlib vpython --user
"${SHELL}" <(curl -L micro.mamba.pm/install.sh)
micromamba self-update
micromamba create -n moose python=${{ matrix.python-version }} graphviz lxml cmake numpy matplotlib vpython hdf5 pytables doxygen -c conda-forge
eval "$(micromamba shell hook --shell bash)"
micromamba activate moose
pip install python-libsbml
pip install pyneuroml
- name: Build
run: |
pip install .
pip install .
21 changes: 13 additions & 8 deletions CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 3.2.3 FATAL_ERROR)
cmake_minimum_required(VERSION 3.20 FATAL_ERROR)

# Project to build MOOSE's python module.
project(PyMOOSE)
Expand Down Expand Up @@ -317,13 +317,18 @@ endif( WITH_BOOST )

######################### BUILD PYMOOSE ########################################

if(NOT WITH_LEGACY_BINDING)
add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
add_subdirectory(pybind11)
else()
message(STATUS "Building legacy python binding.")
add_subdirectory(pymoose)
endif()
# pybind11 should be installed as a dependency.
# It can be easily done with `pip install pybind11`
# See: https://pybind11.readthedocs.io/en/stable/installing.html
# - Subha, Mon Apr 22 14:26:58 IST 2024

# if(NOT WITH_LEGACY_BINDING)
# add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/external/pybind11)
# add_subdirectory(pybind11)
# else()
# message(STATUS "Building legacy python binding.")
# add_subdirectory(pymoose)
# endif()


# always override debian default installation directory. It will be installed in
Expand Down
13 changes: 9 additions & 4 deletions CONTRIBUTING.md
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
To contribute, fork this repo and submit your changes via a pull-request.
Before sending pull-request, check the following:
We use the `fork-and-pull` workflow for moose development.

- [ ] Software builds locally
- [ ] `ctest --output-on-failure` passes all tests.
To contribute:
1. Fork this repo on github
2. Make the changes you want to contribute
3. Check that moose builds locally on your version
4. Check all tests pass `ctest --output-on-failure` passes all tests (TODO: cleanup/fix/update the tests)
5. Submit your changes via a pull-request.

After this the repository admin will check your pull request and merge it to the main branch.
22 changes: 15 additions & 7 deletions CheckCXXCompiler.cmake
Original file line number Diff line number Diff line change
Expand Up @@ -7,8 +7,12 @@ endif()

########################### COMPILER MACROS #####################################
include(CheckCXXCompilerFlag)
CHECK_CXX_COMPILER_FLAG("-std=c++11" COMPILER_SUPPORTS_CXX11 )
CHECK_CXX_COMPILER_FLAG("-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
if(WIN32)
CHECK_CXX_COMPILER_FLAG("/std:c++14" COMPILER_SUPPORTS_CXX14 )
else(WIN32)
CHECK_CXX_COMPILER_FLAG("-std=c++14" COMPILER_SUPPORTS_CXX14 )
CHECK_CXX_COMPILER_FLAG("-Wno-strict-aliasing" COMPILER_WARNS_STRICT_ALIASING )
endif(WIN32)

# Turn warning to error: Not all of the options may be supported on all
# versions of compilers. be careful here.
Expand Down Expand Up @@ -42,15 +46,19 @@ if(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)
add_definitions( "-Wno-unused-but-set-variable" )
endif(COMPILER_SUPPORT_UNUSED_BUT_SET_VARIABLE_NO_WARN)

if(COMPILER_SUPPORTS_CXX11)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++11")
if(COMPILER_SUPPORTS_CXX14)
if(WIN32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /std:c++14")
else(WIN32)
set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -std=c++14")
endif(WIN32)
if(APPLE)
add_definitions( -mllvm -inline-threshold=1000 )
endif(APPLE)
else(COMPILER_SUPPORTS_CXX11)
else(COMPILER_SUPPORTS_CXX14)
message(FATAL_ERROR "The compiler ${CMAKE_CXX_COMPILER} is too old. \n"
"Please use a compiler which has full c++11 support."
"Please use a compiler which has full c++14 support."
)
endif(COMPILER_SUPPORTS_CXX11)
endif(COMPILER_SUPPORTS_CXX14)

set(COMPILER_IS_TESTED ON)
10 changes: 8 additions & 2 deletions INSTALL.md
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Building MOOSE

To build `MOOSE` from source, you need `cmake` and `python-setuptools`. We
recommend to use Python 3.5 or higher. Python 2.7 is also supported.
recommend to use Python 3.8 or higher.

Before running the following command to build and install, make sure that
followings are installed.
Expand All @@ -15,7 +15,7 @@ On Ubuntu-16.04 or higher, these dependencies can be installed with:
sudo apt-get install python-pip python-numpy cmake libgsl-dev g++
```

Now use `pip` to download and install the `pymoose`.
Now use `pip` to download and install `pymoose` from the [github repository](https://github.com/BhallaLab/moose-core).

```
$ pip install git+https://github.com/BhallaLab/moose-core --user
Expand All @@ -41,6 +41,12 @@ from github.
This will build moose, `ctest` will run few tests to check if build process was
successful.

To rebuild, delete the `_build` directory and the generated `_temp__build/` directory and recreate the `_build` directory:

$ cd ..; rm -rf _build; rm -rf _temp__build

and continue the steps following that described above.

To make in debug mode use:
$ cmake -DCMAKE_BUILD_TYPE=Debug ..

Expand Down
2 changes: 1 addition & 1 deletion basecode/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )
add_library(basecode
Element.cpp
Expand Down
2 changes: 1 addition & 1 deletion basecode/global.cpp
Original file line number Diff line number Diff line change
Expand Up @@ -226,7 +226,7 @@ string moosePathToColumnName(const string& path, char delim, size_t maxParents)
string toString(double x)
{
char buffer[50];
sprintf(buffer, "%.17g", x);
snprintf(buffer, sizeof buffer, "%.17g", x);
return string(buffer);
}

Expand Down
2 changes: 1 addition & 1 deletion biophysics/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include(${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)

if(WITH_GSL)
Expand Down
2 changes: 1 addition & 1 deletion builtins/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake )

# NSDF5 support. Disabled by default.
Expand Down
1 change: 0 additions & 1 deletion devel/docker/travis/Dockerfile
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,6 @@ RUN apt update && apt install -y cmake gcc g++ make valgrind \
python-dev python3-dev \
&& rm -rf /var/lib/apt/lists/*

RUN python2 -m pip --no-cache-dir install pyneuroml python-libsbml
RUN python3 -m pip --no-cache-dir install pyneuroml python-libsbml
WORKDIR /root
RUN ls -ltrah
Expand Down
2 changes: 1 addition & 1 deletion device/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
add_library(device
PulseGen.cpp
Expand Down
2 changes: 1 addition & 1 deletion diffusion/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)

if(WITH_GSL)
Expand Down
2 changes: 1 addition & 1 deletion examples/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)
include( ${CMAKE_CURRENT_SOURCE_DIR}/../CheckCXXCompiler.cmake)
ADD_LIBRARY(examples
Example.cpp
Expand Down
2 changes: 1 addition & 1 deletion external/fmt/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8 FATAL_ERROR)
cmake_minimum_required(VERSION 3.20 FATAL_ERROR)

add_library(fmt STATIC src/format.cc src/os.cc)
target_include_directories(fmt PRIVATE include)
2 changes: 1 addition & 1 deletion external/libsoda/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
cmake_minimum_required(VERSION 2.8)
cmake_minimum_required(VERSION 3.20)

find_package(Threads REQUIRED)

Expand Down
35 changes: 0 additions & 35 deletions external/pybind11/.appveyor.yml

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38 changes: 0 additions & 38 deletions external/pybind11/.clang-format

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