Activity

From 13 Nov 2016 to 12 Dec 2016

12 Dec 2016

17:23 Refactoring #1732: Optimization in innermost loop in RT computation: Solved in 2baf9d, pull request 122. wuttke
15:15 Refactoring #1732: Optimization in innermost loop in RT computation: Implemented in branch bisectRT+test. wuttke
08:48 Refactoring #1732 (Rejected): Optimization in innermost loop in RT computation: SpecularMatrix::calculateUpFromLayer contains an innermost loop.
For thick multilayer system with few scattering lay... wuttke
17:19 Refactoring #1735 (Resolved): remove include guards from unit tests: Resolved in 38845bca. wuttke
13:08 Refactoring #1735: remove include guards from unit tests: -> pull request 121 wuttke
09:43 Refactoring #1735 (Resolved): remove include guards from unit tests: There is no reason why a unit test h file should be included twice, therefore there is no reason to have include guar... wuttke
16:40 Feature #1738 (Rejected): Rename files and classes in Multilayer to resolve ambiguity about "Matrix": Currently:... wuttke
13:08 Bug #1734 (Resolved): Investigate numerical stability of multilayer RT computation: Cannot confirm.
Tests supplied in pull request 121. wuttke
09:12 Bug #1734 (Resolved): Investigate numerical stability of multilayer RT computation: Details will follow. I'm investigating. wuttke
09:15 Feature #1103: extend simulation to transmission geometry (detector images with z<0): Probably this requires a renaming of variables or functions at some places: R and T will become Up and Down. wuttke
09:06 Feature #1706 (Resolved): Profile simulation with multilayers containing large amount of layers: For proposed solution see #1732 and #1733. wuttke
09:02 Refactoring #1733 (Resolved): Avoid multiple calculations of same RT coefficients: Currently, SpecularMatrix::calculateUpFromLayer is called within loops... wuttke
08:44 Refactoring #1673 (Resolved): Design proposal for all subtasks under #1645: No comments received, so proposal is accepted. wuttke

09 Dec 2016

14:05 Feature #31: Core: beam propagation: Implement x-ray polarization factor: For a multilayer, it's not just one polarization factor.
Rather, polarization must be taken into account at each int... wuttke

07 Dec 2016

15:50 Feature #1670 (Sprint): Provide interface for adding particle shapes in different layers that are...: herck
14:54 Refactoring #1731 (Rejected): Reduce number of TODOs in code: Currently counting 105. herck
14:01 Configuration #1496 (Rejected): Switch Windows10 buildslave from virtual box to vagrant box: Currently, the VM is always on (thanks to Jan). This should resolve many of the problems we experience with the Windo... herck
12:33 Refactoring #1730 (Sprint): Refactor ICompositeSample hierarchy: Then I start slowly via focused pull requests to have only few changes at a time. pospelov
10:39 Refactoring #1730 (Rfc): Refactor ICompositeSample hierarchy: pospelov
12:13 Configuration #1729 (Resolved): Fix centos7 CI build on buildbot: herck
10:52 Bug #1641 (Resolved): histogram2d test fails under certain configurations: Test was fixed by requiring numpy array to be of type dtype=float64.
Also we've discovered, that there is no 'a... pospelov
10:35 Bug #1674 (Resolved): Possible bug introduced in Polygon in Python context: pospelov

06 Dec 2016

17:44 Refactoring #1730 (Resolved): Refactor ICompositeSample hierarchy: To implement #1624 (#1562 is also related), we might have to provide the following
* Turn lots of ISample into ICo... pospelov
17:21 Feature #1667 (Resolved): Read DESY/dpdak tiff files to BornAgain GUI: TiffHandler now reads TIFF files with IEEE float sample format. Anonymous
16:54 Configuration #1729 (Resolved): Fix centos7 CI build on buildbot: herck
15:04 Configuration #1544: require libcerf instead of providing ThirdParty/Fadeeva: It might be advantageous to first provide a C++ version of the library (using C++ std::complex instead of C complex t... herck
12:39 Refactoring #1659 (Resolved): rename PixelMap -> Pixel: herck
10:49 Refactoring #1407 (Rejected): rotate the sample, not Q: Not worth a separate refactoring, but will be done when implementing graded layers, as explained in design proposal. wuttke

30 Nov 2016

13:04 Bug #1689 (Resolved): memory leak in ParameterSample: ganeva
09:43 Bug #1689: memory leak in ParameterSample: I believe that due to API changes @wl_distr.generateSamples(nsamples, xmin, xmax)@ should instead be something like @... jmfisher
11:07 Feature #1691 (Resolved): Decrease number of warnings produced by Windows build: Currently number of Windows warnings is tremendous, makes it difficult to analyze logs.
* In Release 1.8 Appveyo... pospelov

29 Nov 2016

16:44 Bug #1689: memory leak in ParameterSample: It appears that the template @std::vector< ParameterSample > >@ is not being exported by swig. So it should be a simp... jmfisher
16:28 Bug #1689 (Sprint): memory leak in ParameterSample: ganeva
16:14 Bug #1689 (Resolved): memory leak in ParameterSample: The following simple script... ganeva
15:03 Documentation #1141: Manual: describe multi layers: will come back to it later wuttke
11:38 Bug #1658: add qt5-svg as a dependency: Resolved in f1de40e, pull request #93.f1de40e
Can be transfered to hotfix branch using git cherry-pick f1de40e. wuttke
11:22 Bug #1662: CMake: require Qt version 5.4: In hotfix branch, apply git cherry-pick b4f148 wuttke
11:20 Bug #1662: CMake: require Qt version 5.4: Solved in b4f14 (pull request #93). wuttke
10:40 Configuration #1615: Code organisation: in each third-party source directory, provide information...: The information file shall be called 00_PROVENANCE.
Work on this issue started with gtest-1.8.0.
wuttke
10:39 Configuration #1635: update to gtest-1.8: Done in 2ff998fba, pull request #92. wuttke
09:37 Refactoring #1660 (Resolved): remove global functions: Learned from Walter that not all global functions are bad. Unnecessary globals are mostly removed with pull request #88. wuttke
09:27 Refactoring #1479 (Rejected): presence of some boost components not checked by cmake: Rejected for two reasons:
* CMake and Boost are changing so quickly that there is no way for us to provide a lasting... wuttke
09:00 Feature #1688 (Rejected): == Roughness ==: wuttke

28 Nov 2016

17:06 Bug #1687 (Resolved): LMA is incorrectly normalized: Fixed in hotfix-1.7.1 branch herck
15:45 Bug #1687 (Resolved): LMA is incorrectly normalized: When two layouts are attached to one layer, relative abundances are scaled with respect to the sum of all particles, ... herck
17:05 Refactoring #1456 (Rejected): Automatize update of Py Examples: automatizing is not an aim in itself wuttke
14:51 Feature #1686 (Rejected): == Release procedures and pre-release actions ==: wuttke
14:32 Configuration #1665 (Rejected): Take swig-generated Python wrappers out of git repository: Agreed. Restriction of the Python API now requested by #1685. wuttke
14:07 Configuration #1665: Take swig-generated Python wrappers out of git repository: Another solution could be to severely limit the public API we export to Python. This would result in regeneration of ... herck
14:31 Refactoring #1685 (Backlog): PythonAPI: Only expose classes/functions that users might need: The user constructs models, runs simulation, and retrieves results. Nothing else needs to be supported by the Python ... wuttke
14:25 Feature #1684 (Resolved): nicer layout for newsletter@bornagainproject.org: #1238 was archived too early; the announcement of 1.7 still came with no left margin and a fat black top bar. wuttke
14:16 Feature #1683 (Resolved): GUI: provide persistence of plot settings (interpolation, color scale, ...: See the request on BornAgain forum:
http://www.bornagainproject.org/node/161 herck
14:13 Refactoring #1604 (Resolved): move expected inaccuracy (m_variability) out of class OutputData: Resolved in 5baab.
For standard simulations, the expected inaccuracy is hard-coded in StandardSimulationsRegistry.cp... wuttke
09:22 Feature #1667: Read DESY/dpdak tiff files to BornAgain GUI: I've got a user permission to upload the data file to redmine. ganeva

25 Nov 2016

13:32 Bug #1661: FitSuite doesn't know about TestMinimizer: yes, it was requested and it is easy to fix pospelov
13:30 Bug #1661: FitSuite doesn't know about TestMinimizer: hope I understand correctly that this is to go into the hotfix? wuttke
13:31 Bug #1682 (Resolved): hotfix: rm local version of FindBoost.cmake: wuttke
13:24 Bug #1682 (Resolved): hotfix: rm local version of FindBoost.cmake: cmake/generic/modules/FindBoost.cmake was created because cmake-3.6 did not recognize boost >= 1.62.
This problem is... wuttke
13:31 Bug #1679 (Resolved): Remove leading U+FEFF from FindYamlCpp05.cmake => needs hotfix: wuttke
12:10 Bug #1679 (Resolved): Remove leading U+FEFF from FindYamlCpp05.cmake => needs hotfix: Somehow, a leading unicode mark has slipped into FindYamlCpp05.cmake.
For at least two users, this caused CMake to a... wuttke
12:32 Bug #1681 (Resolved): Fitting GUI: free parameter error: Setting fitting parameter as 'free' causes an error (see also the attached screenshot):... ganeva
12:19 Feature #1680 (Resolved): Provide 1.7.1 hotfix: See subtasks.
Also it is absolutely necessary to run some Windows simulations next days and try to find the reason... pospelov
11:33 Feature #1677 (Backlog): Core: roughness: Independent roughness cross-correlation for disjoint se...: To support Henrich, it is required to simulate resonator on top of the lipid bilayer system. Both, resonator and set ... ganeva

24 Nov 2016

18:02 Feature #1562: Provide ISample with possibility to export parameter tree in Python dictionary: * std output generated by IParameterized::printParameters doesn't appear in ipython notebook
* all std::cout usage i... pospelov
18:00 Feature #1562 (Sprint): Provide ISample with possibility to export parameter tree in Python dicti...: pospelov
17:57 Feature #1675 (Rejected): Get rid of ctypes.addressof in PySampleBuilder: As Jonathan suggested, we can get rid from ctype's dependency in Python by replacing it with its numpy alternative.... pospelov
17:47 Refactoring #1623 (Sprint): Parameter name translation (GUI -> domain): pospelov
17:46 Feature #1624 (Sprint): Make all reasonable parameter values into fittable parameter: pospelov
17:36 Refactoring #1673 (Sprint): Design proposal for all subtasks under #1645: well, let's see whether and when we write up how the API will change ... wuttke
11:40 Refactoring #1673 (Resolved): Design proposal for all subtasks under #1645: wuttke
17:33 Feature #1631 (Rejected): No impact of abundance optional argument in ParticleLayout addParticle ...: Seems we agreed with Artur that it is a feature, not bug. Rejecting pospelov
17:32 Feature #1667 (Sprint): Read DESY/dpdak tiff files to BornAgain GUI: pospelov
10:06 Feature #1667 (Resolved): Read DESY/dpdak tiff files to BornAgain GUI: Some DESY tiff files are not loaded correctly in BornAgain GUI. File is loaded, but instead of the GISAXS pattern, us... ganeva
17:32 Refactoring #1604 (Sprint): move expected inaccuracy (m_variability) out of class OutputData: pospelov
17:31 Feature #1617 (Sprint): Implement rotation of 2D OutputData on 90 deg: pospelov
14:35 Bug #1658 (Sprint): add qt5-svg as a dependency: pospelov
14:34 Bug #1674 (Resolved): Possible bug introduced in Polygon in Python context: Earlier version of Polygon had copying of input arrays instead of const reference.
This was because of crash if on... pospelov
14:21 Bug #1641 (Sprint): histogram2d test fails under certain configurations: From the discussion with Jonathan and my wage remembering, it will be enough to use... pospelov
14:09 Testing #1609: Clarify relation between PyPersistence tests and tutorial examples: May I also add that this refactoring could also be used to get rid of massive extra data in our repository and tarbal... herck
14:04 Testing #1609: Clarify relation between PyPersistence tests and tutorial examples: Then I will summarize my proposal here.
* Move persistence check from "make check" to "make stresscheck"
> 'stres... pospelov
11:31 Feature #1670 (Rfc): Provide interface for adding particle shapes in different layers that are to...: wuttke
11:31 Feature #1670: Provide interface for adding particle shapes in different layers that are to be tr...: Add one particle to several layers? Or add particles at Sample=Multilayer level, and let the internal machinery figur... wuttke
11:28 Feature #1670 (Resolved): Provide interface for adding particle shapes in different layers that a...: herck
11:30 Feature #1672 (Resolved): Implement subdivision of a layer into multiple layers for graded interf...: herck
11:29 Feature #1671 (Resolved): Provide automatic splitting of particle shapes when they cross a layer ...: herck
11:27 Feature #1669 (Resolved): Allow for multiple form factors (dwba or not) in FromFactorWrapper and ...: Since the dwba form factors contain the respective layer Fresnel coefficients, this would allow for a coherent treatm... herck
10:24 Bug #1664 (Resolved): FitSuite.runFit() crashes with unclear error message: herck
09:57 Feature #1666 (Backlog): PythonAPI: Constructor of Histogram2D should accept also numpy arrays wi...: For the moment, constructor ... ganeva

23 Nov 2016

15:00 Configuration #1665 (Rejected): Take swig-generated Python wrappers out of git repository: Little API changes cause huge changes of the swig-generated wrappers.
This bloats the git file system, and in partic... wuttke
11:02 Bug #1664 (Resolved): FitSuite.runFit() crashes with unclear error message: When no fit parameters are added, runFit() crashes. On Windows, it does this without printing a clear message indicat... herck

22 Nov 2016

17:58 Refactoring #1650 (Resolved): Designation "ROOT" (or "Root" or "BA_ROOT") should not be used for ...: Gennady's comments used to extend class header comments in b0e128d0c. wuttke
14:36 Refactoring #1650: Designation "ROOT" (or "Root" or "BA_ROOT") should not be used for code other ...: > Why are other minimizers wrapped by code in a directory "RootAdapter", and enclosed in a namespace "BA_ROOT"?
... pospelov
15:53 Bug #1662 (Resolved): CMake: require Qt version 5.4: Triggered by Qt 5.3.1 which is the system one on Ubuntu 14.04.4 and doesn't compile on BornAgain because of QMargin... pospelov
15:48 Refactoring #1660 (Sprint): remove global functions: wuttke
10:59 Refactoring #1660: remove global functions: Moving global functions to scope-limited functions is a good refactoring. Moving them to class methods increases the ... herck
10:33 Refactoring #1660 (Resolved): remove global functions: Now listed under Doxygen tab "Globals".
Some global functions are actually used in one file only => enclose them in ... wuttke
15:16 Bug #1661 (Resolved): FitSuite doesn't know about TestMinimizer: During last minimizer refactoring I've lost TestMinimizer, which is the favorite of Dominique.
Following lines a... pospelov
10:01 Refactoring #1659 (Resolved): rename PixelMap -> Pixel: It's not only about the mapping [0,1]x[0,1] -> K.
It also contains a function solidAngle(), which is a global proper... wuttke
09:59 Refactoring #1651 (Resolved): remove last occurences of "using namespace BornAgain": resolved in 2d3c4 wuttke
09:31 Bug #1658 (Resolved): add qt5-svg as a dependency: The qt5 svg libraries are a runtime dependency of BornAgain GUI, but not a compile-time dependency. On Arch linux for... jmfisher

21 Nov 2016

11:01 Refactoring #1652 (Resolved): Sort namespaces, and provide Doxygen comments: wuttke
11:01 Refactoring #1652: Sort namespaces, and provide Doxygen comments: Resolved in 6979a3c35e wuttke

20 Nov 2016

14:50 Documentation #1654 (Resolved): Update "Working with Python scripts" to new style "import bornaga...: http://bornagainproject.org/documentation/usage/scripting/basic_simulation_tutorial and the other pages under http://... wuttke
13:55 Feature #1653 (Resolved): Outcome of BornAgain user meetings in November: Given issue contains a collection of user requests, observations discovered during Hamburg/Munich BornAgain tutoria... pospelov
10:43 Refactoring #1652 (Sprint): Sort namespaces, and provide Doxygen comments: * No need for namespace "Geometry"
* Namespace "Materials" contains only one function, which should be converted int... wuttke
10:41 Refactoring #1652 (Resolved): Sort namespaces, and provide Doxygen comments: wuttke
10:40 Refactoring #1651 (Resolved): remove last occurences of "using namespace BornAgain": Use of "using namespace" should be restricted to cases where a namespace is heavily used in a specific source file. T... wuttke
10:20 Configuration #1175: Installer: Linux: Provide official debian package: For acceptance in Debian, the source tree must be patched by deleting the third-party code, which instead will be pro... wuttke
10:14 Configuration #1615: Code organisation: in each third-party source directory, provide information...: ROOT code is patched by substituting the namespace name "BA_ROOT" for "ROOT".
Are there other patches in the ThirdPa... wuttke
10:11 Refactoring #1650 (Resolved): Designation "ROOT" (or "Root" or "BA_ROOT") should not be used for ...: To avoid confusion, ROOT should stand for CERN ROOT, and nothing else.
Why are other minimizers wrapped by code in a... wuttke

19 Nov 2016

19:41 Bug #1641: histogram2d test fails under certain configurations: On a fresh Arch installation I re-encountered this problem with gcc+Python3 so it may not be limited to clang. jmfisher
17:28 Refactoring #1649 (Resolved): Ensure consistent use of ambientMaterial: Is ambientMaterial==nullptr allowed?
If no, prevent it from ever occuring.
If yes, make sure we don't call *ambient... wuttke

17 Nov 2016

19:59 Bug #1646 (Rejected): Reversed order numpy array: Since version 1.6 (I think) the returned array from the simulation result using .getArray() is reversed in the first ... a.glavic

16 Nov 2016

18:51 Feature #720 (Rejected): Provide OpenMPI support in FitSuite: Since our model evaluation is parallelized, there is no case for parallelizing the enveloping fit routine. wuttke
18:45 Documentation #1638 (Backlog): Manual: Improve / restore side bar navigation: Actually, the side bar navigation is there in the online manual.
Nice to have: by default, expand to section level... wuttke
18:42 Feature #1004: GUI: revise tooltips in all GUI elements: Nice to have, even important, but not high priority wuttke
18:27 Refactoring #1582 (Sprint): Correct model for dense particles on surface: wuttke
18:18 Feature #1645 (Rejected): == Graded layer and cross-layer particles ==: Urgently requested by E13, and promised to them. wuttke
18:09 Feature #300 (Long Term Idea): Investigate alternatives to Monte-Carlo computation of non-analyti...: wuttke
18:04 Documentation #1451 (Rejected): update to Drupal 8: Not clear whether Drupal 8 is mature enough and worth the move.
Anyway, this upgrade is not an aim in itself, but ... wuttke
18:01 Envelope task #1606 (Archived): === Manual and Examples ===: merged with #966 Theory & Manual wuttke
17:40 Documentation #1644 (Rejected): "User Login" block on homepage should explain _why_ to create acc...: ... namely, to be able to post to the forum and to subscribe to our newletter (low traffic).
Question: what sounds... wuttke
17:29 Support #852 (Rejected): Make GUI available at JCNS servers: I added one step to our release procedures: submit installation request to the IT issue tracker. This is all we shoul... wuttke
15:19 Documentation #976 (In Progress): Derive scalar and polarized wave equation for both X-rays and n...: wuttke
15:18 Feature #163 (Sprint): implement IsGISAXS Example 14 (graded layer): Urgently needed by E13. I promised them we will deliver soon. wuttke
12:33 Testing #1609: Clarify relation between PyPersistence tests and tutorial examples: I'll try to work out a solution along Gennady's proposal of writing test wrappers around old-style tutorial examples. wuttke
12:27 Documentation #1628 (Resolved): Can't clone git repositiory: Web docs now clearly refer to the new repository location. Hopefully this solves the issue. wuttke
10:54 Bug #1641: histogram2d test fails under certain configurations: I have just tested clang+Python2 on Yakkety and there seems to be no problem. So the issue is restricted clang+Python3. jmfisher
10:32 Bug #1641 (Resolved): histogram2d test fails under certain configurations: The test histogram2d.py fails under certain configurations (see buildbot). On my Arch setup it fails for clang+Python... jmfisher

15 Nov 2016

12:19 Configuration #1640 (Rejected): Doxygen generation on apps server not compatible anymore with lin...: Doxygen now generates all html in ./html/std, while all the links on our website refer to ./html
herck

14 Nov 2016

18:04 Bug #1639 (Sprint): GUI: crash if fitting parameter removed: Removal of parameter link from fit parameter, while keeping fit parameter alive for following re-use, is intended beh... pospelov
17:56 Bug #1639 (Resolved): GUI: crash if fitting parameter removed: To reproduce:
create a project, load the experimental data. Add fit parameter, then remove it (see screenshot). Run ... ganeva
16:57 Documentation #1638 (Rejected): Manual: Improve / restore side bar navigation: Side bar in HTML version does not show contents below Part level. Side bar navigation in PDF reader is also broken (r... wuttke
16:56 Bug #1637 (Rejected): GUI: just loaded fitting project appears as already changed: Just loaded project appears as changed - i.e. project name is "*Untitled" instead of "Untitled". Attempt to quit fr... pospelov
16:52 Bug #1634 (Resolved): MacOS dmg 1.7 installation is partly broken: pospelov
13:40 Bug #1636 (Rejected): Unexpected wavelength depent intensity Roughness vs. ParticleLayout: When implementing a DWBA model I would expect the intensities of the structure factors to mostly depend (in first ord... a.glavic

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