[SCM] The Molecular Modelling Toolkit packaging branch, master, updated. 9d95748f3a0f4388cf8500fbae12ed425b4ad459
Frédéric-Emmanuel P?==?UTF-8?Q?ICCA
picca at synchrotron-soleil.fr
Tue Sep 20 15:51:20 UTC 2011
The following commit has been merged in the master branch:
commit e3ed056e86bb5537f704ef0693b0b1e0a979b9c6
Author: Frédéric-Emmanuel PICCA <picca at synchrotron-soleil.fr>
Date: Tue Sep 20 16:56:51 2011 +0200
update the todo list
diff --git a/debian/todo b/debian/todo
index 946af74..77ac6dc 100644
--- a/debian/todo
+++ b/debian/todo
@@ -1,198 +1,16 @@
-licences de dpmta ??? faut-il faire un paquer pour cette librairie
-sachant qu'il ne semble plus tellement maintenu ???
-
-http://www.debian.org/doc/packaging-manuals/python-policy/ch-programs.html
-
-il faudrait utiliser #!/usr/bin/env python dans tviewer
-
-que faire avec le code cython ?
-
-comment installer les exemples ?
-
-picca at mordor:~/Debian/mmtk/mmtk/Examples/DNA$ python construction.py
-Warning: No PDB or VRML viewer defined.
-
-
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ python2.7 additional_objects.py
-Traceback (most recent call last):
- File "additional_objects.py", line 30, in <module>
- color = 'blue')
- File "/usr/lib/python2.7/dist-packages/MMTK/Visualization.py", line 178, in graphicsObjects
- return self._graphics(conf, distance_fn, model, module, options)
- File "/usr/lib/python2.7/dist-packages/MMTK/Collections.py", line 855, in _graphics
- return sum(lists)
-TypeError: unsupported operand type(s) for +: 'int' and 'list'
-
-
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ ls
-additional_objects.py graphics_data.py vector_field_chimera.py vector_field_vmd.py vrml2_cameras_vdw.py
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ python vector_field_chimera.py
-Traceback (most recent call last):
- File "vector_field_chimera.py", line 17, in <module>
- from Scientific.Visualization import Chimera
-ImportError: cannot import name Chimera
-
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ python vector_field_vmd.py
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ ???
-
-picca at mordor:~/Debian/mmtk/mmtk/Examples/Visualization$ python vrml2_cameras_vdw.py
-Loading protein file
-Finding centre of mass and moment of inertia
-Creating view points
-Creating vdw graphic of Protein
-Creating arrows below protein
-Creating arrows above protein
-Viewing vdw model with all four cameras...
-No VRML2 viewer defined
-Done
-
-visiblement lorsque je teste l'installation avec test_pi.py
-
-picca at mordor:~/Debian/mmtk/mmtk/test$ python test_pi.py
-Traceback (most recent call last):
- File "test_pi.py", line 4, in <module>
- from MMTK_PINormalModeIntegrator import PINormalModeIntegrator, PILangevinNormalModeIntegrator
-ImportError: No module named MMTK_PINormalModeIntegrator
-
-Effectivementil n'y a aucune trace de ce module
-MMTK_PINormalModeIntegrator dans le paquet ??? ni dans le setup.py.
-
-si je regarde dans le directory Test il y a d'autres tests qui eux fonctionnent.
-avec neanmoins deux failures dur une architecture i386 pentium.
-
-test_energy (pickle_tests.WaterTest) ... ok
-test_parent (pickle_tests.WaterTest) ... ok
-test_type (pickle_tests.WaterTest) ... ok
-test_dihedral (energy_tests.DihedralTest) ... ok
-test_nonbondedList (energy_tests.InfiniteUniverseNonbondedListTest) ... ok
-test_nonbondedList (energy_tests.OrthorhombicUniverseNonbondedListTest) ... ok
-test_nonbondedList (energy_tests.ParallelepipedicUniverseNonbondedListTest) ... ok
-test_singleSubset (energy_tests.LennardJonesSubsetTest) ... ok
-test_twoSubsets (energy_tests.LennardJonesSubsetTest) ... ok
-test_energeticModes (normal_mode_tests.WaterTest) ... ok
-test_vibrationalModes (normal_mode_tests.WaterTest) ... ok
-test_subspaceModes (normal_mode_tests.PeptideTest) ... ok
-test_subspaceModesWithExclusion (normal_mode_tests.PeptideTest) ... ok
-test_subspaceModesWithNumericalDifferentiation (normal_mode_tests.PeptideTest) ... ok
-test_lrb (subspace_tests.RigidBodyTest) ... ok
-test_projections (subspace_tests.RigidBodyTest) ... ok
-test_pdProjections (subspace_tests.PeptideNormalModeTest) ... ok
-test_rmProjections (subspace_tests.PeptideNormalModeTest) ... ok
-test_snapshot (trajectory_tests.InfiniteUniverseTestSP) ... ok
-test_snapshot (trajectory_tests.InfiniteUniverseTestDP) ... ok
-test_snapshot (trajectory_tests.OrthorhombicUniverseTestSP) ... ok
-test_snapshot (trajectory_tests.OrthorhombicUniverseTestDP) ... ok
-test_snapshot (trajectory_tests.ParallelepipedicUniverseTestSP) ... ok
-test_snapshot (trajectory_tests.ParallelepipedicUniverseTestDP) ... ok
-test_singleSubset (enm_tests.CalphaFFSubsetTest) ... ok
-test_twoSubsets (enm_tests.CalphaFFSubsetTest) ... FAIL
-test_singleSubset (enm_tests.DeformationFFSubsetTest) ... ok
-test_twoSubsets (enm_tests.DeformationFFSubsetTest) ... FAIL
-test_singleSubset (enm_tests.ANMFFSubsetTest) ... ok
-test_twoSubsets (enm_tests.ANMFFSubsetTest) ... ok
-test_changeangle (internal_coordinate_tests.ICTest) ... ok
-test_changebond (internal_coordinate_tests.ICTest) ... ok
-test_changephi (internal_coordinate_tests.ICTest) ... ok
-test_cyclic (internal_coordinate_tests.ICTest) ... ok
-test_phipsi (internal_coordinate_tests.ICTest) ... ok
-
-======================================================================
-FAIL: test_twoSubsets (enm_tests.CalphaFFSubsetTest)
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/home/picca/Debian/mmtk/mmtk/Tests/subsets.py", line 27, in test_twoSubsets
- self.assert_((N.fabs(fc[a1,a2].array) < 1.e-14).all())
-AssertionError
-
-======================================================================
-FAIL: test_twoSubsets (enm_tests.DeformationFFSubsetTest)
-----------------------------------------------------------------------
-Traceback (most recent call last):
- File "/home/picca/Debian/mmtk/mmtk/Tests/subsets.py", line 27, in test_twoSubsets
- self.assert_((N.fabs(fc[a1,a2].array) < 1.e-14).all())
-AssertionError
-
-----------------------------------------------------------------------
-Ran 51 tests in 114.494s
-
-FAILED (failures=2)
-
-que faut-il faire avec tout cela ?
-
-Il faudrait intégrer les test lors du build de fançon à avoir les
-tests sur les differentes architectures.
-
-
-
-lintian (outil qualité de Debian)
-
-W: python-mmtk: extended-description-line-too-long
-N:
-N: One or more lines in the extended part of the "Description:" field have
-N: been found to contain more than 80 characters. For the benefit of users
-N: of 80x25 terminals, it is recommended that the lines do not exceed 80
-N: characters.
-N:
-N: Refer to Debian Policy Manual section 3.4.1 (The single line synopsis)
-N: for details.
-N:
-N: Severity: normal, Certainty: certain
-N:
-N: Check: description, Type: binary, udeb
-N:
-W: python-mmtk: extended-description-line-too-long
-W: python-mmtk: extended-description-line-too-long
-
-il faudrait que tu me donnes une description courte et une longue de mmtk
-regarde dans le fichier debian/control ou cela doit se trouver :)
-
-W: python-mmtk: binary-without-manpage usr/bin/tviewer
-N:
-N: Each binary in /usr/bin, /usr/sbin, /bin, /sbin or /usr/games should
-N: have a manual page
-N:
-N: Note that though the man program has the capability to check for several
-N: program names in the NAMES section, each of these programs should have
-N: its own manual page (a symbolic link to the appropriate manual page is
-N: sufficient) because other manual page viewers such as xman or tkman
-N: don't support this.
-N:
-N: If the name of the man page differs from the binary by case, man may be
-N: able to find it anyway; however, it is still best practice to make the
-N: case of the man page match the case of the binary.
-N:
-N: If the man pages are provided by another package on which this package
-N: depends, lintian may not be able to determine that man pages are
-N: available. In this case, after confirming that all binaries do have man
-N: pages after this package and its dependencies are installed, please add
-N: a lintian override.
-N:
-N: Refer to Debian Policy Manual section 12.1 (Manual pages) for details.
-N:
-N: Severity: normal, Certainty: possible
-N:
-N: Check: manpages, Type: binary
-N:
-
-La je crois que c'est limpide ;)
-
-W: python-mmtk: executable-not-elf-or-script usr/share/pyshared/MMTK/Database/Atoms/ca
-N:
-N: This executable file is not an ELF format binary, and does not start
-N: with the #! sequence that marks interpreted scripts. It might be a sh
-N: script that fails to name /bin/sh as its shell, or it may be incorrectly
-N: marked as executable. Sometimes upstream files developed on Windows are
-N: marked unnecessarily as executable on other systems.
-N:
-N: If you are using debhelper to build your package, running dh_fixperms
-N: will often correct this problem for you.
-N:
-N: Refer to Debian Policy Manual section 10.4 (Scripts) for details.
-N:
-N: Severity: normal, Certainty: certain
-N:
-N: Check: scripts, Type: binary
-N:
-N: Removing /tmp/jjJjrzVQ3u ...
-
-visiblement un fichier n'a pas le bon 644, il faudrait corriger cela dans la distribution.
\ No newline at end of file
+dpmta licences:
+ faut-il faire un paquer pour cette librairie
+ sachant qu'il ne semble plus tellement maintenu ???
+
+python-policy:
+ http://www.debian.org/doc/packaging-manuals/python-policy/ch-programs.html
+ .
+ il faudrait utiliser #!/usr/bin/env python dans tviewer
+
+cython:
+ what do we do with cython.
+
+test integration:
+ Test in the Tests directory should be executed during the build process.
+ maybe asking for a MMTK.test() method that can be run to check the library in place.
+ add a python setup.py test method for the build.
\ No newline at end of file
--
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