week June 5 -- June 11

On Sunday I moved to Livermore.

On Monday I rebased my patches for Euler Equations, DG and FVM for hermes2d, sent for review. Unfortunately it took till Friday until they got reviewed, but they are now in.
I couldn't sleep, so at around midnight I turned on my computer and rewrote the build system for femhub, it took me about 1.5h. Then I could finally sleep well.

On Tuesday I had my new hire orientation. During it I wrote couple more patches for femhub.

On Wednesday I got my badge and spent the rest of the day with paperwork. They didn't manage to get my computer setup, so I studied a bit of Quantum Field Theory from a book that I found in our room and then spent the rest of the night figuring out the weak formulation for the radial Dirac equation. So far no luck, but at least I wrote it in many different forms in my hand written notes. Sometimes it's not bad to be cut off the internet and computers.

On Thursday I got my computer account setup and spent most of the day with paperwork.

On Friday I finally did some real work. Then we got to a pub, got home and drank the rest of my Budvars (Czechvar) and Plzeňs (Pilsner Urquell).

The FEMhub build system is really cool. It's written in Python and I totally got rid of the old Sage build system. Some features of the new one:

* dependencies
* automatically uses all your processors (unless told otherwise)
* simple Python script (414 lines) that handles everything, plus sage-env, sage-spkg and sage-make_relative scripts (the rest I simply deleted)
* allows you to install just some packages, for example "./femhub -i python" just installs python and it's dependencies
* allows you to unpack any package into the devel/ directory and then build it

I will not use it to develop hermes1d+schroedinger and dirac solvers over the summer, so it will likely get improved in the coming weeks. (I have to use it, because my computer is some old RHEL5, and I don't have a root access. With FEMhub, I have all the Python libraries plus cmake and similar stuff right there. It's really awesome.)

In total, I wrote 52 patches for FEMhub, 3 for hermes_common, 9 for hermes2d, 8 for hermes1d and 1 for sympy:

FEMHUB:
Ondrej Certik (52):
      scipy and python upgraded
      Remove the old buildsystem
      New Python based buildsystem implemented
      Install hermes2d by default
      Compile in parallel
      Let CmdException propagate
      Handle dependencies
      Fix the PYTHONPATH issue
      Add a check that IPython is installed
      Add Cython dependency to hermes2d
      Add matplotlib to hermes2d deps
      Keep track of installed packages
      Add the -j option
      Add the rest of the packages
      Disable sphinx for now
      Add a todo item
      Disable mayavi for now
      Add pysparse to fipy deps
      Change the banner
      Fix a typo
      Remove old .hg files
      setuptools added into fipy's deps
      lab() implemented
      Don't let other import errors to pass silently
      Build bzip2 before Python
      Simplify the makefile
      Add the jinja2 package
      Remove one forgotten " from a message
      --shell and -s/--script options implemented
      Fix cmake so that it builds if old cmake is present
      expandvars() added to cmd()
      Remove the rest of old buildsystem files
      Move spd imports to femhub imports
      Move download_packages into the femhub buildsystem
      Remove a forgotten file from the old buildsystem
      Create the standard directory if it doesn't exists
      Polish the banner appearance
      femhub-run: little refactoring
      Use proper ipythonrc and matplotlibrc
      Wrap lab(), add debugging statements
      Don't import lab() in the ipythonrc
      Fix the missing "-p" when creating the standard directory
      Fix the problem with ambiguous names
      cpu_count refactored
      hermes1d added
      -f/--force option added
      --unpack added
      --pack option implemented
      --devel-install option implemented
      Use MAKEFLAGS instead of MAKE env variable
      Improve the FEMhub shell prompt
      Print info when unpacking


hermes2d:
Ondrej Certik (9):
      Removing the old-code directory
      hermes_common update
      Reformat the documentation in the Geom class
      Python wrappers updated
      Regenerate the _hermes2d.cpp
      plot.py: ScalarView updated
      Element orientation exported
      Sanity checks and docs
      Add all shapefunctions to the space L2

hermes1d:
Ondrej Certik (8):
      spkg-install added
      "make install" implemented
      Make it build on the Mac
      Allow to turn off examples
      Use std::max(), fixed several warnings
      hermes_common updated
      Fix h1_polys.py to work with FEMhub's SymPy
      Fix the new line warning

hermes_common:
Ondrej Certik (3):
      Add numpy2c_double_inplace() to _hermes_common.pxd
      Update the generated cpp file
      Fix a small double -> int bug/warning

sympy:
Ondrej Certik (1):
      pyglet: fix string exceptions