https://github.com/mcellteam/mcell_tools
Package build repository
https://github.com/mcellteam/mcell_tools
Last synced: 4 months ago
JSON representation
Package build repository
- Host: GitHub
- URL: https://github.com/mcellteam/mcell_tools
- Owner: mcellteam
- License: other
- Created: 2019-08-12T17:28:54.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2025-05-07T18:12:03.000Z (about 1 year ago)
- Last Synced: 2025-05-18T01:36:33.182Z (about 1 year ago)
- Language: Python
- Size: 182 KB
- Stars: 2
- Watchers: 17
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# mcell_tools
This repository contains all tools to clone MCell repositories and build them.
Required system packages (on Debian 9) are:
```
sudo apt install git cmake build-essential bison flex swig python3 python3-dev libboost-dev zip
```
To checkout all the repositories and build mcell along with other tools, run the following commands:
```
mkdir mcell
git clone https://github.com/mcellteam/mcell_tools.git
cd mcell_tools
python3 run.py # optional argument -b BRANCH_NAME selects branch, mcell4_dev is the default branch
```
The resulting build directory of mcell is then located in work/build_mcell.
To run tests afterwards, these packages need to be installed (on Debian 9):
```
sudo apt install python3-pip python3-tk
pip3 install toml pyparsing lxml pyyaml psutil matplotlib pathlib pandas
```
And this is how the test are run:
```
cd ../mcell_tests
python3 run-tests.py # optional argument -c TEST_CONFIG selects test configuration, test_configs/default.tomp is the default config
```
## Windows System Setup
These sections desribe how to setup a Windows build&test system.
### 1) Downloads
https://visualstudio.microsoft.com/vs/features/cplusplus/
- install C++ compiler, might need recent windows upgrades
https://repo.msys2.org/distrib/x86_64/msys2-x86_64-20210105.exe
https://github.com/cmderdev/cmder/releases/download/v1.3.17/cmder.zip
https://www.eclipse.org/downloads/packages/
https://www.python.org/ftp/python/3.5.0/python-3.5.0-amd64.exe
https://github.com/Kitware/CMake/releases/download/v3.15.5/cmake-3.15.5-win64-x64.msi
https://sourceforge.net/projects/mingw-w64/files/Toolchains%20targetting%20Win32/Personal%20Builds/mingw-builds/installer/mingw-w64-install.exe/download
### 2) Add Python, visual studio, mingw, msys, and cmake to PATH
Example PATH value for tools under c:\mcell\tools and user name tester:
C:\mcell\tools\mingw-w64\x86_64-8.1.0-posix-seh-rt_v6-rev0\mingw64\bin;C:\Program Files (x86)\Microsoft Visual Studio\2019\Community\VC\Tools\MSVC\14.28.29333\bin\Hostx64\x64;C:\mcell\tools\Python35;C:\mcell\tools\msys64\usr\bin;C:\Users\tester\AppData\Local\Microsoft\WindowsApps;C:\mcell\tools\cmder\vendor\git-for-windows\mingw64\bin;C:\mcell\tools\cmder\vendor\git-for-windows\usr\bin;C:\mcell\tools\cmder
### 3) Make a python3.exe copy
cp /c/mcell/tools/Python35/python.exe /c/mcell/tools/Python35/python3.exe
### 4) Install python libs
Old versions of pip cannot install the dependencies and newer version e.g. 20.x is not compatible with 3.5
so we must use 10.0.
python.exe -m pip install pip==10.0.1
python -m pip install toml pyparsing lxml pyyaml psutil
### 5) Install zip and gcc
pacman -S zip unzip flex bison make swig
### 6) Fix python installation according to notes in cellblender/windows_build_readme.txt
### 7) Remove unzip from git installation
which unzip
-> make sure that unzip comes from msys
### 8) Update python.py according to notes in cellblender