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Steps to setup environment for development

1. Make sure you have anaconda installed and working. Clone the repository from github

git clone https://github.com/neoceph/FAME

2. Create appropriate python environment by issuing the following command

conda env create -f environment_linux.yaml

If there are errors, try

conda env create -f environment_linux.yaml --force

If environment is created and needs updating the packages list after dependancy install (i.e. petsc4py) try

conda env update --name FAME --file environment_linux.yaml

If PETSc installation is failing make sure you have BLAS and LAPACK available

conda install -c conda-forge blas lapack

3. You are ready to contribute code under .\src or .\tests.

When its time to push changes read the instructions from here

Download and installation of vtk from source if needed (Windows)

1. Make sure you have cmake installed and the path is added to environment variable.

git clone https://gitlab.kitware.com/vtk/vtk.git
cd vtk

2. Create a directory titled build

mkdir build
cd build

3. Configure the project using CMake. Make note of the appropriate 'Visual Studio' version specification. You also need to have write access to the D:/destination/to/installation/of/VTK directory. You might need to open command prompt or powershell as an administrator. Make sure you have hdf5=YES. set for installation setup.

cmake .. -G "Visual Studio 17 2022" -A x64 `
  -DBUILD_SHARED_LIBS=ON `
  -DVTK_WRAP_PYTHON=ON `
  -DVTK_GROUP_ENABLE_Qt=NO `
  -DVTK_USE_SYSTEM_HDF5=OFF `
  -DVTK_MODULE_ENABLE_VTK_hdf5=YES `
  -DVTK_PYTHON_VERSION=3 `
  -DVTK_INSTALL_PYTHON_MODULE_DIR="$env:CONDA_PREFIX\Lib\site-packages" `
  -DPYTHON_EXECUTABLE="$env:CONDA_PREFIX\python.exe" `
  -DCMAKE_INSTALL_PREFIX="D:/destination/to/installation/of/VTK"

4. Install with multiple cpus. If you are using single cpu, it will take days.

cmake --build . --config Release --target INSTALL --parallel

5. Once installation complete, create a set_pythonpath.ps1 file for powershell or set_pythonpath.bat for CMD under directory anaconda\installation\directory\etc\conda\activate.dand set the VTK installation path.

If specific environment other than the base environment is of interest, the files need to be placed under %CONDA_PREFIX%\etc\conda\deactivate.d and %CONDA_PREFIX%\etc\conda\activate.d

powershell

$env:PYTHONPATH = "D:/destination/to/installation/of/VTK/Lib/site-packages;" + $env:PYTHONPATH

CMD

set PYTHONPATH=D:\ProgramFiles\VTK\Lib\site-packages;%PYTHONPATH%

6. You can check the PYTHONPATH variable with powershell

echo $env:PYTHONPATH

CMD

echo %PYTHONPATH%

7. Setup clearing of PYTHONPATH for conda environment deactivation by creating unset_pythonpath.ps1 or unset_pythonpath.bat with the following content

powershell

$env:PYTHONPATH = ""

CMD

@echo off
set PYTHONPATH=

8. Check appropriate version of vtk is installed and hdf5 is activated with

import vtk

print(vtk.VTK_VERSION)
try:
    vtk.vtkHDFReader
    vtk.vtkHDFWriter
    print("HDF5 support is available in your VTK build.")
except AttributeError:
    print("HDF5 support is NOT available in your VTK build.")

You can issue these lines of code on the terminal window by running python with command python or paste them into a python.py file and running the file with appropriate environment activated.

Generating Sphinx documentation

From the root directory run the following commands [Powershell in windows]

  • ./docs/make clean
  • sphinx-apidoc -o ./docs/source/ ./src
  • ./docs/make html
  • ./docs/make latexpdf to generate pdf. The appropriate latex compiler must be installed and available..

Or bash in linux

  • make -C ./docs clean
  • sphinx-apidoc -o ./docs/source/ ./src
  • make -C ./docs html
  • make -C ./docs latexpdf The appropriate latex compiler must be installed and available..

Generating Docstring using VSCode extension

If you are using VS code, the Python Docstring extension can be used to auto-generate a docstring snippet once a function/class has been written. If you want the extension to generate docstrings in Sphinx format, you must set the "autoDocstring.docstringFormat": "sphinx" setting, under File > Preferences > Settings.

Note that it is best to write the docstrings once you have fully defined the function/class, as then the extension will generate the full dosctring. If you make any changes to the code once a docstring is generated, you will have to manually go and update the affected docstrings.

FAME: FVM Based Laser Powder Bed Fusion Additive Manufacturing Process Simulation

restructred text live preview on vscode

  • need the extension pip install esbonio and 'esbonio'. After that make sure python path is manually setup if esbonio is having difficulty finding the python interpreter. You can do that by going to File->Preference->Settings and finding Esbonio>Server:Python Path For example: C:\\msys64\\ucrt64\\bin\\python.exe

restructured text cheatsheet

Details of rST is found here

building the package

python -m build

uploading the package to the test package host using "twine"

twine upload --repository-url https://test.pypi.org/legacy/ dist/* --verbose