Mailman 3 - SfePy - python.org

system-wide install with 2010.1
by Robert Cimrman 12 Mar '10

12 Mar '10

Hi all, the version 2010.1, when installed system-wide, has wrong paths to meshes and other data files. It is still usable, but the tests fail so if you do not want to use sfepy in-place and you want all tests ok, get the latest git snapshot at [1]. r. [1] http://code.google.com/p/sfepy/wiki/Downloads?tm=2

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Some help about postproc.py
by Sylvain Arreckx 05 Mar '10

05 Mar '10

Hello, I installed your sfepy software yesterday without any trouble. I'm on ubuntu 9.10 Karmic and I have mayavi2 installed and working properly I followed the installation process. I ran ./runTests.py and got : << directory: tests, test files: 37 37 test file(s) executed in 86.85 s, 0 failure(s) of 50 test(s) So up to now everything is fine. Today, I tried ./simple.py input/poisson.py and then visualized the solution : ./postproc.py simple.vtk and got that : Traceback (most recent call last): File "./postproc.py", line 288, in <module> main() File "./postproc.py", line 281, in main view = view_file(filenames, filter_names, options) File "./postproc.py", line 147, in view_file step=options.step, anti_aliasing=options.anti_aliasing) File "/home/syarra/Programmes/sfepy/sfepy-release-2009.4/sfepy/ postprocess/viewer.py", line 557, in call_mlab scene = gui.scene.mayavi_scene AttributeError: 'MlabSceneModel' object has no attribute 'mayavi_scene' Could you please help me to solve this problem Thanks Sylvain

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ANN: SfePy 2010.1
by Robert Cimrman 01 Mar '10

01 Mar '10

I am pleased to announce release 2010.1 of SfePy. Description ----------- SfePy (simple finite elements in Python) is a software for solving systems of coupled partial differential equations by the finite element method. The code is based on NumPy and SciPy packages. It is distributed under the new BSD license. Mailing lists, issue tracking, git repository: http://sfepy.org Home page: http://sfepy.kme.zcu.cz Documentation: http://docs.sfepy.org/doc Contributors to this release: Vladimír Lukeš, Logan Sorenson. Highlights of this release -------------------------- - new sphinx-based documentation - refactoring of base functions (polynomial spaces) and element geometry description - interpolation between different meshes - terms for describing perfusion and active fibres in the total Lagrangian formulation (applicable, for example, to active muscle tissue models) Major improvements ------------------ Apart from many bug-fixes, let us mention: - data probing: - automatic refinement of probe points, speed-up - postprocessing and visualization: - VTK source construction for any format supported by MeshIO classes: - this means displaying meshes in formats Mayavi knows nothing about - graphical logging: - support logging to a text file, vertical line plot, allow several Log instances - new examples: - application of the theory of homogenization to elasticity - perfusion, active fibres - new tests and many new terms For more information on this release, see http://sfepy.googlecode.com/svn/web/releases/2010.1_RELEASE_NOTES.txt (full release notes, rather long). Best regards, Robert Cimrman

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pdf version of the docs
by Robert Cimrman 26 Feb '10

26 Feb '10

Hi, thanks to Logan's effort, there is now a PDF version of the docs, see [1]. The term table is still a bit bloated though. To fix that, we can either shorten some very long class names and the formal term argument names, and/or include less information into the PDF version of the table (e.g. just name, link and definition). Is there a way in sphinx for selective docs generation based on the target format (html vs. latex vs....)? r. [1] http://docs.sfepy.org/doc-devel/

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overview of terms in sphinx docs
by Robert Cimrman 22 Feb '10

22 Feb '10

Hi, I have added a basic autogenerated table of all available terms to the sphinx docs, see [1]. The sphinx docs now contain everything that was in the good old sfepy_manual.pdf (except the tables of notation - any volunteer for an easy job?), so I am going to remove the old documentation stuff soon. It would be good to release 2010.1 this month, so try the git version and report bugs, please, if you can find some spare time. r. [1] http://rc.github.com/sfepy/term_table.html

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Problem in fem_wrapper: TypeError: unknown array type
by Niels L Ellegaard 11 Feb '10

11 Feb '10

I did a fres install of the newest sfepy from git (on debian sid), and I have trouble running ./runTests.py. Can you see if I am doing something wrong? cd /home/niels/local/src/ && git clone git://git.sympy.org/sfepy.git && cd sfepy && make && ./runTests.py --debug ./runTests.py --debug<<< directory: tests, test files: 40 <<< tests/test_lcbc_2d.py sfepy: left over: ['__builtins__', '__file__', '__name__', 'wy', 'wx', 'TestLCBC', 'top_dir', '_filename', 'output_name', '__doc__'] >>> test instance prepared (1 test(s)) sfepy: reading mesh (/home/niels/local/src/sfepy/meshes/2d/special/ circle_in_square.mesh)... sfepy: ...done in 0.02 s sfepy: setting up domain edges... sfepy: ...done in 0.01 s sfepy: creating regions... sfepy: Bottom sfepy: Top sfepy: Y1 sfepy: Y sfepy: Y3 sfepy: Y2 sfepy: ...done in 0.02 s >>> <type 'exceptions.TypeError'> Traceback (most recent call last): File "./runTests.py", line 226, in <module> main() File "./runTests.py", line 220, in main op.walk( options.test_dir, run_tests, stats ) File "/usr/lib/python2.5/posixpath.py", line 290, in walk func(arg, top, names) File "./runTests.py", line 148, in run_tests n_fail, n_total, test_time = run_test( conf_name, options ) File "./runTests.py", line 111, in run_test ok, n_fail, n_total = test.run( options.debug ) File "/home/niels/local/src/sfepy/sfepy/base/testing.py", line 38, in run ret = test_method() File "tests/testsBasic.py", line 107, in test_linear_rigid_body_bc nls_status = status ) File "/home/niels/local/src/sfepy/sfepy/solvers/generic.py", line 58, in solve_stationary problem = ProblemDefinition.from_conf( conf ) File "/home/niels/local/src/sfepy/sfepy/fem/problemDef.py", line 84, in from_conf obj.set_fields( conf.fields ) File "/home/niels/local/src/sfepy/sfepy/fem/problemDef.py", line 132, in set_fields self.fields = Fields.from_conf(conf_fields, self.domain.regions) File "/home/niels/local/src/sfepy/sfepy/fem/fields.py", line 19, in from_conf objs.append(Field.from_conf(val, regions)) File "/home/niels/local/src/sfepy/sfepy/fem/fields.py", line 88, in from_conf bases = conf.bases) File "/home/niels/local/src/sfepy/sfepy/fem/fields.py", line 137, in __init__ self.setup_coors() File "/home/niels/local/src/sfepy/sfepy/fem/fields.py", line 210, in setup_coors self.aps.setup_coors( self.domain.mesh, self.cnt_vn ) File "/home/niels/local/src/sfepy/sfepy/fem/fea.py", line 852, in setup_coors ap.eval_extra_coor( self.coors, mesh ) File "/home/niels/local/src/sfepy/sfepy/fem/fea.py", line 239, in eval_extra_coor bf = ginterp.poly_spaces['v'].eval_base(qp_coors) File "/home/niels/local/src/sfepy/sfepy/fem/poly_spaces.py", line 207, in eval_base eps=eps) File "/home/niels/local/src/sfepy/sfepy/fem/poly_spaces.py", line 325, in _eval_base self.mtx_i, bc, suppress_errors, eps) File "/home/niels/local/src/sfepy/sfepy/fem/extmods/fem.py", line 159, in eval_lagrange_simplex return _fem.eval_lagrange_simplex(*args) TypeError: unknown array type

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basic term documentation
by Robert Cimrman 01 Feb '10

01 Feb '10

Hi, At [1] you can see the basic sphinx documentation of the terms (scroll down). It took me some time to convert the docstrings, but the result is not bad. The new sources are for the moment at [2], I will push it to the master repo after I get some feedback. I do not know yet how to hide the common methods of the terms, i.e. do the following split: 1. The Term class documentation with all the common methods 2. The Term subclass documentation with only Description, Definition, and possibly the extra methods not already defined by Term. After this is done, we could happily abandon the old way of generating the sfepy_manual.pdf (which is broken now anyway, as the docstrings changed). r. [1] http://rc.github.com/sfepy/developer_guide.html [2] http://github.com/rc/sfepy

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reorganizing examples (issue 103)
by Robert Cimrman 28 Jan '10

28 Jan '10

Hi, at [1] you can find a first version of my attempt to clean up a bit the directory structure and naming of the example problems. I did not fix the file contents yet, so the tests do not pass, nevertheless I would appreciate comments on the used naming scheme and structure. At the top level, database/ -> meshes/, input/ -> examples and examples/ -> examples/standalone. Note that a single mesh is often reused in several examples, therefore I did not put the meshes directly to the same directories as the corresponding examples. r. [1] http://github.com/rc/sfepy/tree/examples

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emacs, sphinx & LaTeX
by Robert Cimrman 25 Jan '10

25 Jan '10

FYI: when writing the sphinx docs, I use the following regular expression in Emacs's query replace regexp command: from \$$[^$]+$\$ to :math:`\1` That way I can write the inline math (on a single line!) using the usual $ signs and replace them just before making the docs. Simple, but helps. r.

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docs again
by Robert Cimrman 22 Jan '10

22 Jan '10

Hello in 2010! I have finally resolved the segfault problem with sphinx (btw. completely unrelated to sphinx). Logan, the documentation version at your github site (= what is at docs.sfepy.org) is the most recent, right? I will put the docs of the git version to [1], and convert the term docstrings soon. r. [1] http://docs.sfepy.org/doc-devel

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