Leginon

Python and Support Packages (Note that python 2.7 must be used to match window installers of myami modules):¶

You should generally be able to use the most recent versions of these packages that are available from their respective web sites. Just be sure to always get the version that is compatible with Python 2.7. However, you must use the exact version for numpy. If you are having trouble with the most recent version, try to use the specific versions we include in http://emg.nysbc.org/projects/leginon/files

Program	package web site	local copy of win32 installer	local copy of amd64 installer
Python > 2.7.10	http://www.python.org	python-2.7.16.msi	python-2.7.18.amd64.msi
wxPython 2.8 or newer	http://www.wxpython.org	wxPython2.8-win32-unicode-2.8.12.1-py27.exe	wxPython2.8-win64-unicode-2.8.12.1-py27.exe
MySQL Python client 1.2 or newer	http://sourceforge.net/projects/mysql-python	MySQL-python-1.2.4b4.win32-py2.7.exe	MySQL-python-1.2.3.win-amd64-py2.7.exe
Python Imaging Library (PIL) 1.1.4 or newer	http://www.pythonware.com/products/pil/	PIL-1.1.7.win32-py2.7.exe	PIL-fork-1.1.7.win-amd64-py2.7.exe
NumPy	(use only from our file to match compiled numextension	numpy-1.7.0-win32-python2.7.exe	numpy-MKL-1.6.2.win-amd64-py2.7.exe
SciPy 0.5.1 or newer	http://www.scipy.org	scipy-0.11.0-win32-superpack-python2.7.exe	scipy-0.11.0.win-amd64-py2.7.exe

Use pyMySQL for leginon 3.6 and above instead of MySQL Python client for both win32 and 64.

pyMySQL 0.10.1 (not higher)

https://pypi.org/project/PyMySQL/

pyMySQL-0.10.1-py2.py3-none-any.whl

(3.2 and earlier) SVN client used for check out from our repository¶

This is required for following this instruction. We have used Tortois SVN client. Alternatively, you may copy the required NRAMM source files from another computer.

Name:	Download site:
Tortoise SVN client	http://tortoisesvn.tigris.org

(trunk) GIT client used for check out from our repository¶

We have switched to git revision control recently. If you want to install the newest changes, you need to use the files from git repository.

You can clone our repository with

Name:	Download site:
git for Windows	https://git-for-windows.github.io

• During the installation, select "Checkout as-is, commit as-is" option at the step regarding automated translation of CRLF and LF line endings if you are a developer and may commit changes.
• Default is fine with the rest of the options.

Packages from NRAMM¶

Most of the subpackages from NRAMM are obtained through our svn repository.

Check out SVN Source Files from the repository¶

Use your mouse to do the following

• Create a folder at your convenience to gather all download files. Let's call it myami-VERSION where VERSION would corresponds to your check version. For example, myami-3.1 for 3.1 release

• Change directory into myami-VERSION

• Right-click the mouse botton in this directory window and select Tortoise svn
  Checkout in the menu:
  

• Set up svn checkout window like this but change shaded area according to the version you want and the destination.
• We recommend that you put the destination to myami-VERSION\myami so that it is easy to recognize in the future.

Note: the URL has changed to http://emg.nysbc.org/svn/myami/branches/myami-3.2

See Acquiring NRAMM SVN Repository files for different examples and match the repository with what you do on the Linux side.

Cloning git repository after version 3.2.¶

We recommend using git bash to do so which gives most freedom in configuration and so that you can use unix syntax.

• Right Click at the folder where it will contain your clone and choose "Git Bash Here" to start the shell window.

• With Windows XP "Git Bash Here" does not appear with right-click. In this case, you can start git bash from Start menu/Programs/Git/Git Bash and move the folder created to where you want it to be.

To checkout (called clone in git) the package from NRAMM:
See Acquiring NRAMM SVN Repository files for different examples and match the repository with what you do on the Linux side.¶

numextension windows installer¶

Because numextension and would require extra compilers if you build them yourself, we have created Windows installers for them for python 2.7 and made them available at /redmine/projects/leginon/files.

These are the current Leginon python 2.7 compiled packages you should install by opening them on Windows.¶

Package	win32	amd64
numextension	numextension-svn.win32-py2.7-numpy1.7.0.exe	numextension-svn.win-amd64-py2.7-numpy1.6.2.exe