Installing PyFRAP via setup.py

PyFRAP can conveniently be installed via:

python setup.py install

Since PyFRAP requires on I/O of data files that come with it we recommend using:

python setup.py install --user

setuptools comes with multiple installation options, to check them out, type:

python setup.py install --help

PyFRAP has some additional installation options:

Option Effect
--fiji Download and install Fiji during PyFRAP installation. Link Fiji with PyFRAP
--gmsh Download and install Gmsh during PyFRAP installation. Link Gmsh with PyFRAP
--silent Print out less log messages.

For --fiji and --gmsh to work, you need to install wget. To install wget, type:

pip install wget

or if you use the Ananconda distribution:

conda install pywget

PyFRAP setup.py API

getOptions()

Checks options given to script:

  • If --fiji is in sys.argv, will set dFiji=1. n
  • If --gmsh is in sys.argv, will set dGmsh=1.
  • If --silent is in sys.argv, will set silent=1.

Note

Makes dGmsh and dFiji global: Not nice but seems easiest way to get options into OverrideInstall.

getOpt(optStr)

Checks if optStr is in sys.argv. If this is the case, returns 1 and removes it form sys.argv so setup.py will not crash, otherwise returns 0.

class OverrideInstall(install)

Override class subclassing install class from setuptools.

The Main purpose of this class is to give more possibilities when installing PyFRAP, such as:

  • Download Gmsh and enter it automatically into path spec file
  • Download Fiji and enter it automatically into path spec file
  • Set ownership of data files so that even PyFRAP gets installed as superuser, users will be able to use its full capacities.

Idea taken from here (thanks a bunch!)

initOptions()

Parses options into override class.

run()

Runs install.

addData()

Adds Datafiles to PyFRAP installation.

Makes sure that $USER has proper read/write/execute rights. Note that for Windows it will change rights, since it is not necesary. n Also makes sure that gmsh/Fiji bin ins properly linked.

cleanUpExe(fnDL,folderFn,filesBefore,exePath):

Moves it to executables directory and cleans up afterwards.

Parameters:
  • fnDL (str) – Filename of downloaded file.
  • folderFn (str) – Filename of folder containing extracted files.
  • filesBefore (list) – Snapshot of cwd.
  • exePath (str) – Path where executables go.
downloadGmsh()

Downloads Gmsh, moves it to executables directory and cleans up afterwards.

Note

Only works if wget is installed.

downloadGmshWin(arch, gmshVersion)

Downloads Gmsh from Gmsh website for Windows

Parameters:
  • arch (str) – System architecture, e.g. 64/32.
  • gmshVersion (str) – gmshVersion String, e.g. 2.12.0 .
Returns:

(Donwload filename, Filename of extracted download files)
Return type:

(str ,str)
downloadGmshOSX(arch, gmshVersion)

Downloads Gmsh from Gmsh website for OSX.

Parameters:
  • arch (str) – System architecture, e.g. 64/32.
  • gmshVersion (str) – gmshVersion String, e.g. 2.12.0 .
Returns:

(Donwload filename, Filename of extracted download files)
Return type:

(str ,str)
downloadGmshLinux(arch, gmshVersion)

Downloads Gmsh from Gmsh website for Linux.

Parameters:
  • arch (str) – System architecture, e.g. 64/32.
  • gmshVersion (str) – gmshVersion String, e.g. 2.12.0 .
Returns:

(Donwload filename, Filename of extracted download files)
Return type:

(str ,str)
makeExeFolder()

Make executables folder if it doesn’t exist yet

downloadFiji()

Downloads Gmsh, moves it to executables directory and cleans up afterwards.

Note

Only works if wget is installed.

downloadFijiLinux(arch)

Downloads Fiji from Fiji website for Linux.

Parameters:arch (str) – System architecture, e.g. 64/32.
Returns:(Donwload filename, Filename of extracted download files)
Return type:(str ,str)
downloadFijiWin(arch)

Downloads Fiji from Fiji website for Windows.

Parameters:arch (str) – System architecture, e.g. 64/32.
Returns:(Donwload filename, Filename of extracted download files)
Return type:(str ,str)
downloadFijiOSX()

Downloads Fiji from Fiji website for OSX.

Returns:(Donwload filename, Filename of extracted download files)
Return type:(str ,str)
setExePath(fn, identifier, exePath)

Enters executable path into path spec file.

Parameters:
  • fn (str) – Path to gmsh executable.
  • identifier (str) – Identifier in spec file.
  • exePath (str) – Path to exe file
setGmshPath(fn)

Enters gmsh executable path into path spec file.

Parameters:fn (str) – Path to gmsh executable.
setFijiPath(fn)

Enters fiji executable path into path spec file.

Parameters:fn (str) – Path to fiji executable.
changePermissions(filepath, uid, gid, mode)

Sets File Permissions.

Parameters:
  • filepath (str) – Path to file.
  • uid (int) – user ID.
  • gid (int) – group ID.
  • mode (int) – Permission mode.
Returns:

True if success
Return type:

bool
makeAdditionalDataFolders(folder, fn, uid, gid, mode)

Tries to generate additional data folders.

Parameters:
  • folder (str) – Path to containing folder.
  • fn (str) – New folder name
  • uid (int) – user ID.
  • gid (int) – group ID.
  • mode (int) – Permission mode.
Returns:

True if success
Return type:

bool