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699 |
DM-3698
|
09/03/2015 09:42:03
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Replace --trace with --loglevel in pipe_base ArgumentParser
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Replace the --trace argument with an enhanced version of --loglevel that supports named values and numeric log levels (which are the negative of trace levels). This simplifies the interface for users and potentially reduces the log level/trace level confusion, though that won't fully happen until we finish replacing use of pex_logging Trace and Debug with Log. This work was already done as part of DM-3532; it just needs to be copied with minor changes (since there are no named trace levels in pex_logging).
| 1 |
700 |
DM-3702
|
09/03/2015 12:13:57
|
Assemble the report on DCR
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Everything learned through the literature search and project wide meeting should be synthesized into a single readable report that details the expected effects of DCR on difference imaging as well as possible mitigation techniques. This may involve some preliminary analysis work to measure effectiveness of various techniques. Note that I expect this to be two weeks of work for two people, thus the 40 story points. I don't know how to assign a story to two people.
| 40 |
701 |
DM-3705
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09/03/2015 14:58:49
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Update ndarray to use current numpy API
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When we build software that uses SWIG and ndarray we get {{warning "Using deprecated NumPy API}}. Please update ndarray so we are using the current API. If in the interim you want to suppress the warnings, I suggest issuing a separate ticket for that. I have mixed feelings about suppressing the warnings. On the one hand false warnings do make it harder to spot real problems. On the other hand these warnings are not very numerous (building afw only results in 8 of them) and so are fairly easy to ignore.
| 1 |
702 |
DM-3707
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09/03/2015 19:43:59
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qserv scons - do not copy files to variant_dir
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Some people are not happy with our current scons setup which copies source files from source directories to variant_dir, it makes it harder to trace errors using tools like eclipse or debug code. Would be nice to get rid of the extra copy, but we still want to have separate build directory (variant_dir). It should be simple enough, I think, but will need some testing of course.
| 2 |
703 |
DM-3749
|
09/04/2015 07:51:03
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Scons build of lapack_functions in PSFex fails if SCONSFLAGS are set
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The scons build system is unaware of extra flags which may be set in SCONSFLAGS environment variable, which are used from scons utils. This will cause the build to fail. The package needs to behave properly and build in the presence of these flags
| 2 |
704 |
DM-3763
|
09/04/2015 13:37:23
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Be friendlier to New Users on Discourse
|
Please adjust New Users thresholds so that the following common use case on Discourse will work: 1. I have a question/thread I'm really interested in so I join. 2. I post answers, questions, and links. I'm probably going to be heavily involved in this thread (it's why I bothered to create an account, after all). The current defaults allow me only 3 replies, posting of 2 URLs, and no attachments. I don't know what the exact values should be, but the current defaults don't seem to work for what would seem to me to be a pretty common use case.
| 0 |
705 |
DM-3768
|
09/04/2015 18:17:16
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Resolve the issues found in the S15 end-to-end system exercise
|
There are a few items we need to take care to finish the end-to-end system for S15.
| 8 |
706 |
DM-3769
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09/04/2015 18:22:26
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access the database created and populated for Bremerton end-to-end system
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Collect the information for the tables populated for Bremerton end-to-end exercise. Use them in SUI/T so we can access them using the DAX API.
| 2 |
707 |
DM-3770
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09/04/2015 18:24:23
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build the SUI system on NCSA to use the right database and tables
|
Due to the changes of the database and tables, the system has to be rebuilt.
| 1 |
708 |
DM-3771
|
09/04/2015 18:28:05
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Resolve the issues accessing the newly populated tables
|
There are several issues need to be resolved for the system to work properly.
| 5 |
709 |
DM-3772
|
09/07/2015 02:27:31
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Fix compiler detection for non-default gcc/g++ compiler
|
{{scons CXX=g+\+-4.4}} launches {{g\+\+-4.4 --version}} which returns {{g++-4.4 (Debian 4.4.7-2) 4.4.7}}. Nevertheless the {{-4.4}} is not supported by Qserv compiler detection tool. Support will be added here
| 0.5 |
710 |
DM-3773
|
09/08/2015 08:20:04
|
add RUNID option to EventAppender
|
A RUNID needs to be added as an option to EventAppender to allow event logging selectors to receive only events for a particular run.
| 3 |
711 |
DM-3774
|
09/08/2015 12:21:47
|
lsst_build's default ref from repos.yaml support is broken when building multiple packages
|
A problem with the default ref in {{repos.yaml}} support implemented in DM-3679 was discovered last Friday, shortly after deploying this feature to the production CI systems. The default ref for {{xrootd}} was changed/overridden in {{repos.yaml}} to {{legacy/master}}. This worked as expected (and as was tested) when setting {{xrootd}} as the sole {{lsstswBuild.sh}} product or when running {{rebuild}} by hand. However, when building any package that pulled in {{xrootd}} as a recursive dependency, the {{master}} branch was being used (this case had not been manually tested).
| 1 |
712 |
DM-3775
|
09/08/2015 13:09:19
|
HSC backport: updates to tract and patch finding
|
This is a port of the following HSC updates to how tracts and patches are found and listed given a set of coordinates. These are all standalone commits (i.e. not associated with a ticket): [Add findTract() and findTractPatchList() in ringsSkyMap.|https://github.com/HyperSuprime-Cam/skymap/commit/761e915dde25ce8ed5622c2d84b83793e9580fd7] [move RingsSkyMap.findTractPatchList to BaseSkyMap.findClosestTractPatchlist|https://github.com/HyperSuprime-Cam/skymap/commit/56476142060bdb7d8c7fb59eacc383f0e0d5c85b] [Small bug fix for RingsSkyMap.findTract().|https://github.com/HyperSuprime-Cam/skymap/commit/f202a7780ebb89166f03479d7447ace1555027c1] [Add fast findTractPatchList() in RingsSkyMap.|https://github.com/HyperSuprime-Cam/skymap/commit/7e49c358501f95ce4c0e1aa8f48103a24391fc22] [Fixed the problems regarding poles and RA wrap.|https://github.com/HyperSuprime-Cam/skymap/commit/841b0c9eda7462a7a4f182b7971d5e8e81478bfe] [Add spaces around '+' and '-' to match LSST standard coding style.|https://github.com/HyperSuprime-Cam/skymap/commit/f7e2f036494afe382e653194c82bb15728c60fc3]
| 1 |
713 |
DM-3778
|
09/08/2015 16:51:37
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Fix compiler warns in protobuf clients
|
Google protobufs 2.6.1 includes a few unnecessary semicolons in some of its supplied header files; these generate a lot of compiler warnings when compiling client packages. Proposed fix is to add a patch to our eups t&p protobufs package to remove the offending semicolons.
| 1 |
714 |
DM-3779
|
09/08/2015 17:04:34
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clean up gcc and eclipse code analyzer warns
|
We've been ignoring some accumulating warns in the qserv build for some time now. Now that it is possible to develop qserv in eclipse, it would be useful to address warns and analyzer issues so that we can start to notice when new ones pop up.
| 1 |
715 |
DM-3780
|
09/08/2015 17:13:13
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Rationalize lsst/xrootd repo and maintenance procedures
|
The procedure for pulling/pushing xrootd changes from/to the upstream official xrootd repo is cumbersome, confusing, and error-prone. Buildbot now has support for releasing packages from branches other than master. Given this, we can now reasonably replace our lsst/xrootd repo with a fresh genuine fork (shared history) of upstream, then carry our lsst-specific work forward on a dev-branch. This will make it much easier to track and contribute to the xrootd project moving forward. Existing legacy branches and tags are to be migrated to the fresh fork, so historical builds will not be broken.
| 1 |
716 |
DM-3790
|
09/09/2015 11:20:18
|
Top level product for obs_decam
|
We have an action to allow people to pull obs_decam and a working stack without including obs_decam in lsst_distrib. And we want to CI it. The strawman plan is to make a new TLP for decam. SQuaRE will discuss.
| 0 |
717 |
DM-3792
|
09/09/2015 13:06:13
|
obs_test data mis-assembled
|
obs_test images are mis-assembled and need to be regenerated. This may affect some existing unit tests that rely on the data.
| 2 |
718 |
DM-3797
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09/10/2015 11:56:38
|
Enable SSL to community.lsst.org
|
Enable SSL (https) for the Discourse site at community.lsst.org
| 1 |
719 |
DM-3798
|
09/10/2015 12:22:06
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Update flag names and config override files to current conventions
|
The {{deblend.masked}} and {{deblend.blendedness}} flag names in {{meas_deblender}} need to be updated to use underscores instead of periods. Various flag names in the {{examples}} scripts also need updating to the underscore and camelCase format. A search for these flags throughout the database revealed a number of config files that need updating to current conventions. These are also included here.
| 0.5 |
720 |
DM-3800
|
09/10/2015 15:31:45
|
testProcessCcd.py computes values that are too different between MacOS and linux
|
tests/testProcessCcd.py runs processCcd on visit 1 of obs_test's data repository. The result on MacOS is surprisingly different than on linux in at least one case: psfShape.getIxx() computes 2.71 on MacOS X and 2.65 on linux. Iyy and Ixy are likely different. It's worth checking all other computed values, as well. These differences likely indicate that something is wrong, e.g. in obs_test, processCcd, or the way the test runs processCcd. This showed up as part of fixing DM-3792, but it is not clear if the changes on DM-3792 actually caused or increased the difference between MacOS and linux, or if the difference was always too large, but was masked by an intentionally generous tolerance in the unit test.
| 2 |
721 |
DM-3803
|
09/10/2015 15:55:51
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Fix Qserv compiler warnings with clang
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Qserv triggers numerous warnings with clang on OS X. Full details are in the attached ticket, here we summarize the distinct warnings classes: h5. Protobuf {code} /Users/timj/work/lsstsw/stack/DarwinX86/protobuf/2.6.1+fbf04ba888/include/google/protobuf/unknown_field_set.h:214:13: warning: anonymous types declared in an anonymous union are an extension [-Wnested-anon-types] mutable union { ^ {code} h5. Qserv {code} In file included from core/modules/sql/statement.cc:32: core/modules/sql/Schema.h:74:1: warning: 'Schema' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Schema { ^ core/modules/sql/statement.h:35:1: note: did you mean struct here? class Schema; // Forward ^~~~~ struct {code} {code} core/modules/proto/WorkerResponse.h:34:1: warning: 'WorkerResponse' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct WorkerResponse { ^ core/modules/ccontrol/MergingRequester.h:38:3: note: did you mean struct here? class WorkerResponse; ^~~~~ struct {code} {code} In file included from core/modules/qana/QueryMapping.cc:46: core/modules/qproc/ChunkSpec.h:51:1: warning: 'ChunkSpec' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct ChunkSpec { ^ core/modules/qana/QueryMapping.h:44:5: note: did you mean struct here? class ChunkSpec; ^~~~~ struct {code} {code} core/modules/qana/TableInfo.h:186:1: warning: 'DirTableInfo' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct DirTableInfo : TableInfo { ^ core/modules/qana/TableInfo.h:86:1: note: did you mean struct here? class DirTableInfo; ^~~~~ struct core/modules/qana/TableInfo.h:221:1: warning: 'ChildTableInfo' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct ChildTableInfo : TableInfo { ^ core/modules/qana/TableInfo.h:87:1: note: did you mean struct here? class ChildTableInfo; ^~~~~ struct core/modules/qana/TableInfo.h:260:1: warning: 'MatchTableInfo' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct MatchTableInfo : TableInfo { ^ core/modules/qana/TableInfo.h:88:1: note: did you mean struct here? class MatchTableInfo; ^~~~~ struct In file included from core/modules/qana/ColumnVertexMap.cc:36: core/modules/qana/RelationGraph.h:513:1: warning: struct 'Vertex' was previously declared as a class [-Wmismatched-tags] struct Vertex; ^ core/modules/qana/ColumnVertexMap.h:44:7: note: previous use is here class Vertex; ^ In file included from core/modules/qana/ColumnVertexMap.cc:36: core/modules/qana/RelationGraph.h:547:1: warning: 'Vertex' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct Vertex { ^ core/modules/qana/ColumnVertexMap.h:44:1: note: did you mean struct here? class Vertex; ^~~~~ struct {code} {code} core/modules/wbase/Base.h:72:1: warning: 'ScriptMeta' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct ScriptMeta { ^ core/modules/wbase/Task.h:41:5: note: did you mean struct here? class ScriptMeta; ^~~~~ struct {code} {code} In file included from core/modules/parser/BoolTermFactory.cc:46: core/modules/query/Predicate.h:86:27: warning: 'lsst::qserv::query::GenericPredicate::putStream' hides overloaded virtual function [-Woverloaded-virtual] virtual std::ostream& putStream(std::ostream& os) = 0; ^ core/modules/query/Predicate.h:71:27: note: hidden overloaded virtual function 'lsst::qserv::query::Predicate::putStream' declared here: different qualifiers (const vs none) virtual std::ostream& putStream(std::ostream& os) const = 0; ^ {code} {code} core/modules/parser/FromFactory.cc:62:15: warning: unused function 'walkToSiblingBefore' [-Wunused-function] inline RefAST walkToSiblingBefore(RefAST node, int typeId) { ^ core/modules/parser/FromFactory.cc:72:1: warning: unused function 'getSiblingStringBounded' [-Wunused-function] getSiblingStringBounded(RefAST left, RefAST right) { ^ {code} {code} In file included from core/modules/wsched/ChunkDisk.cc:25: core/modules/wsched/ChunkDisk.h:130:10: warning: private field '_completed' is not used [-Wunused-private-field] bool _completed; ^ {code} {code} In file included from core/modules/parser/PredicateFactory.cc:45: core/modules/query/Predicate.h:86:27: warning: 'lsst::qserv::query::GenericPredicate::putStream' hides overloaded virtual function [-Woverloaded-virtual] virtual std::ostream& putStream(std::ostream& os) = 0; ^ core/modules/query/Predicate.h:71:27: note: hidden overloaded virtual function 'lsst::qserv::query::Predicate::putStream' declared here: different qualifiers (const vs none) virtual std::ostream& putStream(std::ostream& os) const = 0; ^ {code} {code} core/modules/parser/WhereFactory.cc:265:31: warning: binding reference member 'c' to stack allocated parameter 'c_' [-Wdangling-field] PrintExcept(Check c_) : c(c_) {} ^~ core/modules/parser/WhereFactory.cc:291:28: note: in instantiation of member function 'lsst::qserv::parser::PrintExcept<lsst::qserv::parser::MetaCheck>::PrintExcept' requested here PrintExcept<MetaCheck> p(mc); ^ core/modules/parser/WhereFactory.cc:269:12: note: reference member declared here Check& c; ^ {code} {code} core/modules/rproc/ProtoRowBuffer.cc:44:11: warning: unused variable 'largeRowThreshold' [-Wunused-const-variable] int const largeRowThreshold = 500*1024; ^ {code} {code} core/modules/util/testIterableFormatter.cc:85:43: warning: suggest braces around initialization of subobject [-Wmissing-braces] std::array<std::string, 6> iterable { "1", "2", "3", "4", "5", "6"}; ^~~~~~~~~~~~~~~~~~~~~~~~~~~~ { } {code} {code} In file included from core/modules/qdisp/XrdSsiMocks.cc:37: core/modules/qdisp/XrdSsiMocks.h:64:16: warning: private field '_executive' is not used [-Wunused-private-field] Executive *_executive; ^ {code} {code} core/modules/xrdoss/QservOss.cc:77:1: warning: unused function 'print' [-Wunused-function] print(std::ostream& os, lsst::qserv::xrdoss::QservOss::StringSet const& h) { ^ {code} h5. OS X {code} core/modules/qdisp/QueryRequest.h:54:25: warning: 'lsst::qserv::qdisp::BadResponseError::what' hides overloaded virtual function [-Woverloaded-virtual] virtual char const* what() throw() { ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/exception:95:25: note: hidden overloaded virtual function 'std::exception::what' declared here: different qualifiers (const vs none) virtual const char* what() const _NOEXCEPT; ^ In file included from core/modules/qdisp/Executive.cc:64: In file included from core/modules/qdisp/XrdSsiMocks.h:37: core/modules/qdisp/QueryRequest.h:67:25: warning: 'lsst::qserv::qdisp::RequestError::what' hides overloaded virtual function [-Woverloaded-virtual] virtual char const* what() throw() { ^ /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1/exception:95:25: note: hidden overloaded virtual function 'std::exception::what' declared here: different qualifiers (const vs none) virtual const char* what() const _NOEXCEPT; ^ {code} {code} core/modules/proto/TaskMsgDigest.cc:55:5: warning: 'MD5' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations] MD5(reinterpret_cast<unsigned char const*>(str.data()), ^ /usr/include/openssl/md5.h:116:16: note: 'MD5' has been explicitly marked deprecated here unsigned char *MD5(const unsigned char *d, size_t n, unsigned char *md) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER; ^ {code} {code} core/modules/util/StringHash.cc:78:24: warning: 'SHA1' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations] return wrapHashHex<SHA1, SHA_DIGEST_LENGTH>(buffer, bufferSize); ^ /usr/include/openssl/sha.h:124:16: note: 'SHA1' has been explicitly marked deprecated here unsigned char *SHA1(const unsigned char *d, size_t n, unsigned char *md) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER; ^ core/modules/util/StringHash.cc:83:24: warning: 'SHA256' is deprecated: first deprecated in OS X 10.7 [-Wdeprecated-declarations] return wrapHashHex<SHA256, SHA256_DIGEST_LENGTH>(buffer, bufferSize); ^ /usr/include/openssl/sha.h:150:16: note: 'SHA256' has been explicitly marked deprecated here unsigned char *SHA256(const unsigned char *d, size_t n,unsigned char *md) DEPRECATED_IN_MAC_OS_X_VERSION_10_7_AND_LATER; ^ {code} h5. Xrootd {code} In file included from core/modules/qdisp/Executive.cc:64: In file included from core/modules/qdisp/XrdSsiMocks.h:33: In file included from /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiRequest.hh:37: /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiRespInfo.hh:43:1: warning: 'XrdSsiRespInfo' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct XrdSsiRespInfo ^ /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiSession.hh:45:1: note: did you mean struct here? class XrdSsiRespInfo; ^~~~~ struct {code} {code} core/modules/xrdoss/QservOss.h:64:17: warning: 'lsst::qserv::xrdoss::FakeOssDf::Opendir' hides overloaded virtual function [-Woverloaded-virtual] virtual int Opendir(const char *) { return XrdOssOK; } ^ /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdOss/XrdOss.hh:63:17: note: hidden overloaded virtual function 'XrdOssDF::Opendir' declared here: different number of parameters (2 vs 1) virtual int Opendir(const char *, XrdOucEnv &) {return -ENOTDIR;} ^ {code} {code} In file included from core/modules/xrdsvc/SsiSession.h:32: /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiResponder.hh:177:27: warning: control may reach end of non-void function [-Wreturn-type] } ^ {code} h5. boost {code} /Users/timj/work/lsstsw/stack/DarwinX86/boost/1.55.0.1.lsst2+fbf04ba888/include/boost/regex/v4/regex_raw_buffer.hpp:132:7: warning: 'register' storage class specifier is deprecated [-Wdeprecated-register] register pointer result = end; ^~~~~~~~~ {code}
| 0.5 |
722 |
DM-3804
|
09/10/2015 16:44:05
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Fix order of arguments - run method of meas_base SingleFrameMeasurementTask
|
In sfm.py on line 271, a comment indicates that some code is a temporary work around until the switch from meas_algorithms to meas_base is complete. This work is complete, so this temporary workaround should be removed, or if it is decided it should be kept, the comment should be removed. See https://github.com/lsst/meas_base/blob/tickets/DM-2915/python/lsst/meas/base/sfm.py#L271
| 2 |
723 |
DM-3808
|
09/10/2015 20:11:13
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Setup lsst_sphinx_kit package structure
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Setup the lsst_sphinx_kit package, including * setup.py * unit tests, tox and Travis CI * README stub * Sphinx stub and readthedocs
| 0.5 |
724 |
DM-3816
|
09/13/2015 10:11:24
|
levels in DecamMapper.paf is not quite right
|
When ccdnum is not given as part of the dataId, instead of iterating over it, an error like this happens {code:java} RuntimeError: No unique lookup for ['ccdnum'] from {'visit': 205344}: 61 matches {code} Likely a problem in policy/DecamMapper.paf
| 1 |
725 |
DM-3821
|
09/14/2015 08:15:37
|
Recent CModel bugfixes from HSC
|
I've just fixed two rather critical bugs in the CModel code on the HSC side (they would have been introduced on the LSST side in the last transfer, DM-2977): - The {{minInitialRadius}} configuration parameter had a default that is too small, causing many galaxies to be fit with point source models, leading to bad star/galaxy classifications. This is HSC-1306. - There was a simple but important algebra error in the uncertainty calculation, making the uncertainty a strong function of magnitude. This is HSC-1313. On the LSST side, the transfer should be quite simple; we'll have to rewrite a bit of code due to the difference in measurement frameworks, but there was very little to begin with (most of the effort in the HSC issues was in debugging).
| 1 |
726 |
DM-3836
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09/14/2015 12:41:42
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Migrate LDM-129 to new design docs platform
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Convert LDM-129 from Word to restructuredText and deploy onto readthedocs.org
| 2 |
727 |
DM-3840
|
09/14/2015 13:58:21
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LSE-72: Phase 3 in X16
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Advance Phase 3 details as needed to eliminate obstacles to OCS and DM development during F16.
| 8 |
728 |
DM-3841
|
09/14/2015 14:01:34
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LSE-75: Refine WCS and PSF requirements in W16
|
Clarify the data format and precision requirements of the TCS (or other Telescope and Site components) on the reporting of WCS and PSF information by DM on a per-image basis. Depends on the ability of the T&S group to engage with this subject. Current PMCS deadline for Phase 3 readiness of LSE-75 is 29-Sep-2015.
| 8 |
729 |
DM-3850
|
09/14/2015 19:06:16
|
Nebula metadata service is intermittent
|
Upon restarting one of my nebula instances (ktl-test), I noticed a failure in the logs: {quote} Sep 14 18:07:29 ktl-test cloud-init: 2015-09-14 18:07:29,157 - util.py[WARNING]: Failed fetching metadata from url http://169.254.169.254/latest/meta-data {quote} Attempting to retrieve that URL seems to randomly vary between succeeding, which returns: {quote} ami-id ami-launch-index ami-manifest-path [...] {quote} and failing, which returns: {quote} <html> <head> <title>500 Internal Server Error</title> </head> <body> <h1>500 Internal Server Error</h1> Remote metadata server experienced an internal server error.<br /><br /> </body> </html> {quote} These failures may be contributing to observed sporadic {{ssh}} key injection failures.
| 2 |
730 |
DM-3860
|
09/15/2015 13:38:38
|
Communication Toolchain support
|
This epic covers support of communication tools primarily used by DM and/or supported by DM on behalf of other parts of the project - JIRA, Discourse, Hipchat, etc The source of this work is primarily driven by short-term user requests, and so the outcome is timeboxed rather than planned. [JS 50% FE 50%]
| 20 |
731 |
DM-3863
|
09/15/2015 14:17:14
|
Web design fixes DM Design Documents on Sphinx/Read The Docs
|
Solve fit-and-finish issues with the stock readthedocs.org Sphinx template when rendering DM design documents. Issues include: * Sections need to be numbered and those numbers need to appear in TOC * RTD's TOC does not properly collapse sub-topics * Appropriate styling for document title and author list * Wrapping the changelog table * Adapt section references so that just the section number can be referenced, independently of the section number and title in combination * Section labels given explicitly in the reST markup are different from the anchors that Sphinx gives to the {{<hN>}}tags; the former are simply divs inserted in the HTML. The solutions may involve # reconfiguring the Sphinx installation of individual documents # forking the RTD HTML template, and/or # developing extensions for Sphinx in {{sphinxkit}}.
| 2 |
732 |
DM-3887
|
09/16/2015 09:28:05
|
Review ICD flowdown to DMSR and design documents
|
This epic will result in a plan for how DM will manage the ICD requirements and their relationship to LSE-61 (DMSR). This plan should make it easier for authors of design documents to understand which requirements are relevant.
| 8 |
733 |
DM-3892
|
09/16/2015 11:58:27
|
Review current version of LSE-78, prepare for LCR
|
Do a comprehensive read-through of the previous released version of LSE-78. Look for self-consistency and for consistency with the rest of the DM and overall system design. Report issues to appropriate people.
| 3 |
734 |
DM-3898
|
09/16/2015 12:44:10
|
Fix xrootd compiler warnings with clang
|
h5. Xrootd {code} In file included from core/modules/qdisp/Executive.cc:64: In file included from core/modules/qdisp/XrdSsiMocks.h:33: In file included from /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiRequest.hh:37: /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiRespInfo.hh:43:1: warning: 'XrdSsiRespInfo' defined as a struct here but previously declared as a class [-Wmismatched-tags] struct XrdSsiRespInfo ^ /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiSession.hh:45:1: note: did you mean struct here? class XrdSsiRespInfo; ^~~~~ struct {code} {code} core/modules/xrdoss/QservOss.h:64:17: warning: 'lsst::qserv::xrdoss::FakeOssDf::Opendir' hides overloaded virtual function [-Woverloaded-virtual] virtual int Opendir(const char *) { return XrdOssOK; } ^ /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdOss/XrdOss.hh:63:17: note: hidden overloaded virtual function 'XrdOssDF::Opendir' declared here: different number of parameters (2 vs 1) virtual int Opendir(const char *, XrdOucEnv &) {return -ENOTDIR;} ^ {code} {code} In file included from core/modules/xrdsvc/SsiSession.h:32: /Users/timj/work/lsstsw/stack/DarwinX86/xrootd/u.timj.DM-3584-ge22410fa7f+da39a3ee5e/include/xrootd/XrdSsi/XrdSsiResponder.hh:177:27: warning: control may reach end of non-void function [-Wreturn-type] } ^ {code}
| 0.5 |
735 |
DM-3910
|
09/18/2015 04:22:27
|
Run and document multi-node test with docker
|
In order to validate Docker setup on CC-IN2P3 cluster, it is required to launch some test on consistent data. S15 LargeScaleTest data doesn't seems to be compliant with latest Qserv version so running multi-node test would be interesting. Nevertheless the multi-node setup doesn't seems to be documented and, hence, is difficult to reproduce.
| 3 |
736 |
DM-3911
|
09/18/2015 11:27:19
|
HSC backport: avoid I/O race conditions config write out
|
This is a port of [HSC-1106|https://hsc-jira.astro.princeton.edu/jira/browse/HSC-1106] When running tasks that write out config settings files ({{processCcd.py}}, for example), if multiple processes start simultaneously, an I/O race condition can occur in writing these files. This is solved here by writing to temp files and then renaming them to the correct destination filename in a single operation. Also, to avoid similar race conditions in the backup file creation (e.g. config.py~1, config.py~2, ...), a {{--no-backup-config}} option (to be used with --clobber-config) is added here to prevent the backup copies being made. The outcome for this option is that the config that are still recorded are for the most recent run.
| 1 |
737 |
DM-3912
|
09/18/2015 14:16:30
|
some ctrl_events tests execute outside of execution domain
|
There are a couple of ctrl_events tests that attempt to execute outside of the valid domains acceptable by the tests, when they shouldn't be. There's a check in place for tests to find this, but a couple of the tests do not have this check.
| 0.5 |
738 |
DM-3922
|
09/21/2015 14:41:19
|
Update multi-node setup documentation
|
Workers in multi-node setup no longer require granting mysql permissions for test datasets since direct mysql connections are no longer used by the data loader.
| 1 |
739 |
DM-3926
|
09/22/2015 11:58:04
|
Implement iostream-style formatting in log package
|
Implement proposed in RFC-96 change to log macros. This ticket only covers defining new set of macros (LOGS() and friends) which use ostringstream for formatting messages. Migration of all clients and removal of LOGF macros will be done in separate ticket.
| 1 |
740 |
DM-3940
|
09/24/2015 06:02:33
|
NaiveDipoleCentroid/NaiveDipoleFlux algorithms should not require centroid slot
|
The {{NaiveDipoleCentroid}} and {{NaiveDipoleFlux}} algorithms in {{ip_diffim}} have members which are instances of {{meas::base::SafeCentroidExtractor}}. Due to the prerequisites that imposes, it is impossible to initialize these algorithms without first defining a {{centroid}} slot. However, there is nothing in these algorithms which actually uses the {{SafeCentroidExtractor}} or any of the information stored in the slot; this seems to be an entirely arbitrary restriction which is likely a legacy of the port to the {{meas_base}} framework. We should remove the use of {{SafeCentroidExtractor}} to simply the code and make it easier to run the test suite (since it will no longer be necessary to run a centroider).
| 0.5 |
741 |
DM-3943
|
09/24/2015 16:13:58
|
QMeta thread safety
|
Initial QMeta implementation is not thread safe, it uses sql/mysql modules which also do not have any protection (there are some mutexes there but not used). Need an urgent fix to avoid crashes due to concurrent queries in czar.
| 1 |
742 |
DM-3947
|
09/25/2015 17:55:18
|
Remove dependency on mysqldb in wmgr
|
Move remaining code that depends on mysqldb to db module
| 0.5 |
743 |
DM-3949
|
09/25/2015 21:27:30
|
Remove dependency on mysqldb in qserv
|
Remove remaining dependencies on mysqldb in qserv.: {code} ./core/modules/tests/MySqlUdf.py ./core/modules/wmgr/python/config.py {code} and use the sqlalchemy from db module instead.
| 2 |
744 |
DM-3951
|
09/28/2015 03:04:19
|
Remove qserv_objectId restrictor
|
qserv_objectId restrictor can be replaced by the IN restrictor. This story involves checking if performance is acceptable if we use IN restrictor instead of qserv_objectId restictor, and if it is, doing the switch and removing the qserv_objectId restictor code.
| 3 |
745 |
DM-3957
|
09/28/2015 13:01:39
|
Enable CModel in CalibrateTask prior to PhotoCal
|
CModel needs to run in CalibrateTask before PhotoCal in order to compute aperture corrections, but it also needs a Calib objects as input, and that isn't available until after PhotoCal is run. On the HSC side, we dealt with this by adding preliminary PhotoCal run before CModel is run, but we could also deal with it by removing the need for a Calib as input, at least in some situations.
| 1 |
746 |
DM-3971
|
09/29/2015 02:34:48
|
Package sqlalchemy in eups
|
Db module is expected to be used by science pipelines, and (per K-T, see qserv hipchat room) we have to package it through eups.
| 1 |
747 |
DM-3980
|
09/30/2015 10:07:32
|
Post SQLAlchemy-migration tweaks
|
Implement some minor tweaks take came in late through PR comments, mostly related to sqlalchemy related migration
| 0.5 |
748 |
DM-3981
|
09/30/2015 11:42:58
|
Improve the performance for making the image plot
|
Make FitsRead work better for multi-threads
| 1 |
749 |
DM-3982
|
09/30/2015 16:40:45
|
CalibrateTask is incompatible with older astrometry tasks
|
[~lauren] and I recently discovered an incompatibility between {{CalibrateTask}}'s schema-handling and the older astrometry tasks, such as {{ANetAstrometryTask}} (the problem affects any astrometry task that utilizes its {{schema}} constructor argument). The problem is that astrometry is called twice in {{CalibrateTask}}: - Just before PSF estimation, in order to get matches to support {{CatalogStarSelector}}. This call is passed {{sources1}}, a catalog containing only the initial, pre-PSF measurements. - After the second measurement stage, to determine the {{Wcs}} and get matches to feed {{PhotoCal}}. This call is passed {{sources}}. The problem is that {{sources.schema != sources1.schema}}, and the astrometry subtask is initialized with {{schema1 == sources1.schema}}. So if the astrometry task needs to fields it added to the schema (the default {{AstrometryTask}} does not), it will likely fail in the second run, as it's being given a catalog that doesn't correspond to the schema it was initialized with. Comments in the code indicate that there's a desire that future {{AstrometryTask}} s will not take a schema argument, and that would mean that they could be called repeatedly with different schemas (as we are doing). I'm not sure that's viable; I think it'd probably be appropriate for {{AstrometryTask}} to set flags indicated the sources it's using (or considered using), as the other calibrate subtasks do. Instead, I think we're probably best off creating two separate astrometry subtasks, each with a different schema, and using the appropriate subtask for each input/output catalog. Clearly we need to come up with a better solution when in the upcoming {{CalibrateTask}} redesign; two subtasks is obviously clunky. Whether this is high-priority before then depends on how much we're dependent on {{ANetAstrometryTask}} as a fallback option, and I haven't been following that conversation closely.
| 0 |
750 |
DM-3987
|
10/01/2015 10:25:19
|
remove unnecessary 'psf' arg to SourceDeblendTask.run()
|
{{SourceDeblendTask.run}} takes both an {{Exposure}} and a {{Psf}}, even though it can get the latter from the former and always should.
| 1 |
751 |
DM-3993
|
10/01/2015 11:07:10
|
Display.dot origin swaps x and y
|
Correcting for xy0 in {{dot}} currently does: {code:hide-linenum} r -= x0 c -= y0 {code} which is backwards.
| 0.5 |
752 |
DM-4002
|
10/01/2015 14:02:55
|
Add doc dir and main.dox to obs_test
|
No obs_* packages have a doc dir. I suggest starting with obs_test since it is perhaps less obvious what it is used for than the others and in some ways acts as a template.
| 0 |
753 |
DM-4003
|
10/01/2015 14:20:04
|
Replace zookeeper CSS with mysql
|
To switch from QservAdmin to CssAccess interface in our Python tools we will need to replace zookeeper with mysql implementation because we do not have C++ KvInterface implementation for zookeeper.
| 2 |
754 |
DM-4009
|
10/02/2015 13:04:33
|
Allow FlagHandler to be used from Python
|
The {{FlagHandler}} utility class makes it easier to manage the flags for a measurement algorithm, and using it also makes it possible to use the {{SafeCentroidExtractor}} and {{SafeShapeExtractor}} classes. Unfortunately, its constructor requires arguments that can only be provided in C++. A little extra Swig wrapper code should make it usable in Python as well.
| 3 |
755 |
DM-4014
|
10/05/2015 17:56:47
|
Replace boost::tuple with <tuple>
|
Replace boost::tuple with <tuple> This ticket will be completed as part of the DM bootcamp at UW.
| 1 |
756 |
DM-4020
|
10/06/2015 10:00:18
|
Remove #!/usr/bin/env from pipe_tasks library code
|
Many tasks in pipe_tasks start with #!/usr/bin/env..., yet are not executable.
| 0 |
757 |
DM-4021
|
10/06/2015 16:00:25
|
Replace boost::unordered_map with std::unordered_map
|
DM boot camp tutorial.
| 2 |
758 |
DM-4022
|
10/07/2015 08:31:57
|
forcedPhotCoadd.py fails on HSC data
|
When trying to run {{forcedPhotCoadd.py}} on HSC data, I see the following error: {code} $ forcedPhotCoadd.py /raid/swinbank/rerun/LSST/bootcamp --id filter='HSC-I' tract=0 patch=7,7 : Loading config overrride file '/nfs/home/swinbank/obs_subaru/config/forcedPhotCoadd.py' Cannot import lsst.meas.extensions.photometryKron: disabling Kron measurements Traceback (most recent call last): File "/home/lsstsw/stack/Linux64/meas_base/11.0+2/bin/forcedPhotCoadd.py", line 24, in <module> ForcedPhotCoaddTask.parseAndRun() File "/home/lsstsw/stack/Linux64/pipe_base/11.0+2/python/lsst/pipe/base/cmdLineTask.py", line 433, in parseAndRun parsedCmd = argumentParser.parse_args(config=config, args=args, log=log, override=cls.applyOverrides) File "/home/lsstsw/stack/Linux64/pipe_base/11.0+2/python/lsst/pipe/base/argumentParser.py", line 360, in parse_args self._applyInitialOverrides(namespace) File "/home/lsstsw/stack/Linux64/pipe_base/11.0+2/python/lsst/pipe/base/argumentParser.py", line 475, in _applyInitialOverrides namespace.config.load(filePath) File "/home/lsstsw/stack/Linux64/pex_config/11.0/python/lsst/pex/config/config.py", line 529, in load self.loadFromStream(stream=code, root=root) File "/home/lsstsw/stack/Linux64/pex_config/11.0/python/lsst/pex/config/config.py", line 549, in loadFromStream exec stream in {}, local File "/nfs/home/swinbank/obs_subaru/config/forcedPhotCoadd.py", line 10, in <module> config.deblend.load(os.path.join(os.environ["OBS_SUBARU_DIR"], "config", "deblend.py")) AttributeError: 'ForcedPhotCoaddConfig' object has no attribute 'deblend' {code} This is with the stack version 11.0+3 and {{obs_subaru}} 5.0.0.1-676-g4ae362c.
| 0.5 |
759 |
DM-4036
|
10/09/2015 16:12:52
|
Change from boost::math
|
Most boost::math contents (not including pi) are now available in standard C++. Please convert the code accordingly. In addition to the packages listed above, boost/math is used in "partition" a package I don't recognize and not a component JIRA accepts.
| 5 |
760 |
DM-4043
|
10/09/2015 23:19:01
|
update memory management in jointcal
|
jointcal currently uses a combination of raw pointers and a custom reference-counted smart pointer class, {{CountedRef}} (similar to {{boost::intrusive_ptr}}). The code needs to be modified to use a combination of {{shared_ptr}} (most code), {{unique_ptr}} local-scope variables and factory functions, and {{weak_ptr}} (at least some will be necessary to avoid cycles in some of the more complex data structures). As part of this work, we'll also have to remove a lot of inheritance from {{RefCounted}}, which is part of the {{CountedRef}} implementation. This ticket looks like it will require a lot of work, because we'll have to be careful about every conversion to avoid cycles and memory leaks. Nevertheless, I think it will be necessary to do this conversion before attempting any other major refactoring, as I'm worried that having a newcomer make changes to the codebase without first making the memory management less fragile could be very dangerous.
| 8 |
761 |
DM-4063
|
10/12/2015 11:02:15
|
Support new casting requirements in NumPy 1.10
|
The function imagesDiffer() in testUtils attempts to OR an array of unit16s (LHS) against an array of bools(RHS) {{valSkipMaskArr |= skipMaskArr}} and errors with message {code} TypeError: ufunc 'bitwise_or' output (typecode 'H') could not be coerced to provided output parameter (typecode '?') according to the casting rule ''same_kind'' {code} preventing afw from building correctly.
| 1 |
762 |
DM-4065
|
10/12/2015 11:26:11
|
Discuss with MySQL team
|
This story captures issues/topics that we want to bring up with mysql team.
| 2 |
763 |
DM-4071
|
10/12/2015 12:12:33
|
testPsfDetermination broken due to NumPy behaviour change
|
Old NumPy behaviour (tested on 1.6.2): {code} In [1]: import numpy In [2]: a = numpy.array([]) In [3]: numpy.median(a) /usr/lib64/python2.6/site-packages/numpy/core/fromnumeric.py:2374: RuntimeWarning: invalid value encountered in double_scalars return mean(axis, dtype, out) Out[3]: nan {code} New NumPy behaviour (1.10.0): {code} In [1]: import numpy In [2]: a = numpy.array([]) In [3]: numpy.median(a) [...] IndexError: index -1 is out of bounds for axis 0 with size 0 {code} This breaks {{testPsfDeterminer}} and {{testPsfDeterminerSubimage}}, e.g.: {code} ERROR: testPsfDeterminerSubimage (__main__.SpatialModelPsfTestCase) Test the (PCA) psfDeterminer on subImages ---------------------------------------------------------------------- Traceback (most recent call last): File "./testPsfDetermination.py", line 342, in testPsfDeterminerSubimage trimCatalogToImage(subExp, self.catalog)) File "/Users/jds/Projects/Astronomy/LSST/src/meas_algorithms/python/lsst/meas/algorithms/objectSizeStarSelector.py", line 377, in selectStars widthStdAllowed=self._widthStdAllowed) File "/Users/jds/Projects/Astronomy/LSST/src/meas_algorithms/python/lsst/meas/algorithms/objectSizeStarSelector.py", line 195, in _kcenters centers[i] = func(yvec[clusterId == i]) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3084, in median overwrite_input=overwrite_input) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/function_base.py", line 2997, in _ureduce r = func(a, **kwargs) File "/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/numpy/lib/function_base.py", line 3138, in _median n = np.isnan(part[..., -1]) IndexError: index -1 is out of bounds for axis 0 with size 0 {code}
| 0.5 |
764 |
DM-4075
|
10/13/2015 17:19:47
|
Assemble eslint rules for JavaScript code quality control
|
Review and assemble eslint rules, which enforce clean JavaScript and JSX code. Code cleanup to avoid too many rule violations.
| 8 |
765 |
DM-4076
|
10/13/2015 17:26:41
|
JavaScript code cleanup - remove unused packages
|
Remove es6-promise, react-modal, other cleanup
| 2 |
766 |
DM-4078
|
10/13/2015 21:44:57
|
convert underscore to lodash
|
lodash has become a superset of underscore, providing more consistent API behavior, more features, and more thorough documentation. We'd like to convert our underscore package dependencies to lodash while we have only ~20 calls to underscore functions
| 2 |
767 |
DM-4080
|
10/14/2015 10:19:18
|
Shutdown mechanism doesn't work when logging process is disabled.
|
If the logging mechanism is turned off in ctrl_execute, the ctrl_orca Logger doesn't get launched. The current shutdown mechanism waits for the last logging message to be transmitted before shutting down so it doesn't kill off that process. If the logger.launch config file option is set to false, this process never get launched and ctrl_orca hangs after the shutdown waiting for the message to arrive.
| 8 |
768 |
DM-4085
|
10/14/2015 11:29:08
|
Attend DM boot camp
|
Attend DM boot camp to learn more about DM stack, butler, and task.
| 2 |
769 |
DM-4086
|
10/14/2015 11:30:13
|
Attend DM boot camp
|
Attend DM boot camp to learn more about DM stack, butler, and task. Most of the presentations are located at URL https://community.lsst.org/t/dm-boot-camp-announcement/249. Presentations like afw, eups, tasks, and butler are necessary to participate in LSST, so everyone on LSST must understand these concepts. Look at the list of presentations covering these topics and make sure your understand them. Some of the remaining talks go into more detail or cover more specialized topics. Those talks should be scanned to see if they are of interestß to you.
| 3 |
770 |
DM-4087
|
10/14/2015 11:32:24
|
Attend DM boot camp
|
Attend DM boot camp to learn more about DM stack, butler, and task.
| 3 |
771 |
DM-4092
|
10/14/2015 14:25:18
|
Update qserv for lastest xrootd
|
Small API change in latest xrootd, requires a parallel change to qserv. Paves the way for DM-2334
| 0.5 |
772 |
DM-4095
|
10/15/2015 14:05:04
|
Please port showVisitSkyMap.py from HSC
|
The HSC documentation at http://hsca.ipmu.jp/public/scripts/showVisitSkyMap.html includes a useful script for displaying the skymap and CCDs from a set of visits. It would be convenient if a version of this script was available in the LSST stack.
| 1 |
773 |
DM-4098
|
10/16/2015 00:45:17
|
Update Trust Level of all LSST DM Staff to Level 4 via the API
|
It seems safe to update the Discourse trust level of all members of the LSSTDM group on community.lsst.org to Level 4 (full permissions). See https://meta.discourse.org/t/consequences-of-using-or-bypassing-trust-levels-for-company-organization-staff/34564?u=jsick This should alleviate concerns that DM staff are being prevented from fully using the forum. This ticket implements a small notebook to exercise the Discourse API to make this trust level migration possible.
| 0.5 |
774 |
DM-4100
|
10/16/2015 14:18:50
|
Replace use of image <<= with [:] in python code
|
Replace all use of the afw image pixel copy operator {{<<=}} with {{\[:]}} in Python code. See DM-4102 for the C++ version. These can be done independently.
| 2 |
775 |
DM-4102
|
10/16/2015 16:21:44
|
Remove use of <<= from C++ code in our stack
|
Replace usage of deprecated Image operator {{<<=}} in C++ code with {{assign(rhs, bbox=Box2I(), origin=PARENT)}} as per RFC-102 Switch from [:] to assign pixels in Python code where an image view is created for the sole purpose of assigning pixels (thus turning 2-4 lines of code to one and eliminating the need to make a view).
| 3 |
776 |
DM-4104
|
10/16/2015 16:28:23
|
Document that <<= is deprecated
|
Update our documentation to replace Image {{<<=}} pixel copy operator with {{[:] =}} for Python code and {{set(rhs)}} for C++ code (or whatever RFC-102 decides), with a note that {{<<=}} exists but is deprecated.
| 0 |
777 |
DM-4105
|
10/16/2015 16:33:00
|
Update user documentation
|
{{ORDER BY}}, {{objectId IN}} and {{objectId BETWEEN}} predicates support have been improved, this should be documented.
| 1 |
778 |
DM-4117
|
10/16/2015 18:24:17
|
Clean up lsst_stack_docs for preview
|
Improve the presentation of the New docs overall: # Add a Creative Commons license # Remove stub documents from the presentation # Put READMEs in all doc directories to explain what content will go in them # Clean up and update the source installation guide to reflect 11_0
| 0.5 |
779 |
DM-4125
|
10/20/2015 09:37:29
|
pipe_tasks/examples/calibrateTask.py fails
|
The self contained example calibrateTask.py in pipe_tasks/examples/ fails when attempting to set field "coord" in refCat. Exact error message - {code} 11:04:19-vish~/lsst/pipe_tasks (u/lauren/DM-3693)$ examples/calibrateTask.py --ds9 calibrate: installInitialPsf fwhm=5.40540540548 pixels; size=15 pixels calibrate.repair: Identified 7 cosmic rays. calibrate.detection: Detected 4 positive sources to 5 sigma. calibrate.detection: Resubtracting the background after object detection calibrate.initialMeasurement: Measuring 4 sources (4 parents, 0 children) Traceback (most recent call last): File "examples/calibrateTask.py", line 150, in <module> run(display=args.ds9) File "examples/calibrateTask.py", line 119, in run result = calibrateTask.run(exposure) File "/home/vish/lsst/lsstsw/stack/Linux64/pipe_base/11.0-2-g8218aaa+5/python/lsst/pipe/base/timer.py", line 118, in wrapper res = func(self, *args, **keyArgs) File "/home/vish/lsst/pipe_tasks/python/lsst/pipe/tasks/calibrate.py", line 478, in run astromRet = self.astrometry.run(exposure, sources1) File "examples/calibrateTask.py", line 90, in run m.set("coord", wcs.pixelToSky(s.getCentroid())) File "/home/vish/lsst/lsstsw/stack/Linux64/afw/11.0-5-g97168e0+1/python/lsst/afw/table/tableLib.py", line 2372, in set self.set(self.schema.find(key).key, value) File "/home/vish/lsst/lsstsw/stack/Linux64/afw/11.0-5-g97168e0+1/python/lsst/afw/table/tableLib.py", line 1064, in find raise KeyError("Field '%s' not found in Schema." % k) KeyError: "Field 'coord' not found in Schema." {code} Note that {{wcs.pixelToSky(s.getCentroid())}} is set to {{Fk5Coord(15.007663073114244 * afwGeom.degrees, 1.0030133772819259 * afwGeom.degrees, 2000.0)}}
| 0.5 |
780 |
DM-4129
|
10/20/2015 15:09:29
|
Database connection problems in daf_ingest
|
The DbAuth connection fallback in ingestCatalogTask passes the "password" keyword argument to {{MySQLdb.connect}} instead of "passwd", which fails. Also, the "port" command line argument isn't marked as an integer, causing port strings to be passed down to MySQLdb. This results in a type error.
| 0.5 |
781 |
DM-4133
|
10/20/2015 23:00:57
|
Change type of LTV1/2 from int to float when writing afw images to FITS
|
The LTV1/2 problem is originally my bug. I used integer LTV1/2 in {code} afw/src/image/ExposureInfo.cc: data.imageMetadata->set("LTV1", -xy0.getX()); afw/src/image/ExposureInfo.cc: data.imageMetadata->set("LTV2", -xy0.getY()); {code} whereas a more careful reading of the NOAO page [http://iraf.noao.edu/projects/ccdmosaic/imagedef/imagedef.html] introducing them includes floating point examples. The fix is to cast the XY0 values to float. I'm not sure if there'll be any side effects of fixing this, but if so they'll be obvious and trivial.
| 1 |
782 |
DM-4137
|
10/21/2015 13:13:18
|
Update DECam CCDs gain, read noise, and saturation values
|
The values of DECam gain, read noise, and saturation value need to be updated. This ticket is to update them in the Detector amplifier information, which is used in IsrTask. Talked to Robert Gruendl. These values should take precedence over the values in the fits header. They seem stable and do not seem to vary with time.
| 1 |
783 |
DM-4141
|
10/21/2015 20:47:59
|
cmdLineTasks should provide proper unix return codes
|
When a cmdLineTask fails it doesn't appear to return a non-0 exit code to the shell, making it hard to write shell scripts that chain commands together. Please fix this. E.g. {code} $ bin/assembleCoadd.py /lustre/Subaru/SSP --rerun yasuda/SSP3.8.5_20150810_cosmos:rhl/brightObjectMasks --id tract=9813 patch=5,5 filter=HSC-I --selectId ccd=0..103 visit=1238..1246:2 -c doMaskBrightObjects=True && echo "Success" ... 2015-10-22T02:44:13: assembleCoadd FATAL: Failed in task initialization: Your Eups versions have changed. The difference is: --- +++ @@ -48 +48 @@ -obs_subaru HSC-3.11.0a_hsc /data1a/ana/products2014/Linux64/obs_subaru/HSC-3.11.0a_hsc +obs_subaru LOCAL:/home/rhl/LSST/obs/subaru rev:ef3c892f clean-working-copy @@ -55 +55 @@ -pipe_tasks LOCAL:/home/rhl/LSST/pipe/tasks-HSC-1342 rev:84b0f3c4 2 files changed, 5 insertions(+), 6 deletions(-) +pipe_tasks LOCAL:/home/rhl/LSST/pipe/tasks-HSC-1342 rev:9e8ed18b 2 files changed, 47 insertions(+), 42 deletions(-) @@ -60 +59,0 @@ -pyflakes git /home/rhl/Src/pyflakes Please run with --clobber-config to override Success {code}
| 1 |
784 |
DM-4143
|
10/21/2015 23:52:51
|
Demonstrate using Breathe for Python & C++ API reference in New Docs
|
Demonstrate use of breathe for utilizing the existing Doxygen API documentation in the new Sphinx-based doc platform.
| 3 |
785 |
DM-4145
|
10/22/2015 09:42:56
|
Reduce scons output in qserv
|
Yesterday AndyH expressed a valid concern that qserv prints too much info which makes it hard to find errors. By default scons prints whole command line for C++ compilation and linking which are quite long (~half screen depending on your screen size). Most of the time we don't need to see that, so it would be better to replace that with shorter messages like "Compiling Something.cxx" and have an option to print full command with --verbose option.
| 0.5 |
786 |
DM-4151
|
10/22/2015 16:36:03
|
Search for uses of current afw.wcs in the stack
|
Search through the stack for all the uses of our Wcs implementation (Wcs, TanWcs, makeWcs, and any other hidden objects) and make a list of all of those uses (on Community for example). This list should note whether the usage is in C++ or python.
| 2 |
787 |
DM-4158
|
10/23/2015 06:23:07
|
Allow configuring more statistical options for assembleCoadds.py
|
The assembleCoadd.py task has a configuration option doSigmaClip which chooses between MEAN and MEANCLIP. Please replace this with an option to specify the algorithm to be used. Note that afwMath.stringToStatisticsProperty can be used to convert a string to an enum value. In particular, this would allow me to specify a MEDIAN stack if desired (e.g. to make pretty RGB images)
| 3 |
788 |
DM-4160
|
10/23/2015 06:38:36
|
Unused variables in meas.algorithms.utils
|
Pyflakes 1.0.0 reports: {code} $ pyflakes-2.7 utils.py utils.py:232: local variable 'chi2' is assigned to but never used utils.py:481: local variable 'numCandidates' is assigned to but never used utils.py:482: local variable 'numBasisFuncs' is assigned to but never used utils.py:487: local variable 'ampGood' is assigned to but never used utils.py:492: local variable 'ampBad' is assigned to but never used {code} In the best case, those variables are simply unnecessary, and they should be removed to simplify the code and avoid wasting time. Alternatively, it's possible that they ought to be used elsewhere in the calculation but have been omitted accidentally. Please establish this for each one, then either remove them or fix the rest of the code.
| 1 |
789 |
DM-4165
|
10/23/2015 11:22:06
|
Take upstream boost 1.59 patch to squelch warnings for gcc 5.2.1
|
Under gcc 5.2.1, use of boost 1.59.0 produces a torrent of compiler warns from within boost headers about use of deprecated std::auto_ptr (see https://svn.boost.org/trac/boost/ticket/11622). A patch for this is already committed upstream in boost. It is proposed that we take this patch into the lsst t&p in interim until the next official boost release.
| 0.5 |
790 |
DM-4194
|
10/26/2015 16:59:15
|
Python LogHandler does not pass logger name to log4cxx
|
Not sure how or why it happened, but presently Python LogHandler for lsst.log does not pass logger name to log4cxx layer and all messages from Python logging end in root logger.
| 1 |
791 |
DM-4202
|
10/27/2015 14:14:49
|
Revert temporary disabling of CModel in config override files
|
Revert the temporary disabling of CModel that relates to a bug noted in DM-4033 that was causing too many failures to test that processCcd (etc.) would run all the way to completion (most of the other fixes/updates related to the initial disabling in the multiband tasks have now been completed in DM-2977 & DM-3821). Relevant files: {code} config/processCcd.py config/forcedPhotCcd.py config/forcedPhotCoadd.py config/measureCoaddSources.py {code}
| 1 |
792 |
DM-4206
|
10/28/2015 10:13:52
|
wmgr should delete database from inventory when dropping it
|
When wmgr drops database it should also cleanup chunk inventory for that database.
| 2 |
793 |
DM-4219
|
10/29/2015 15:12:53
|
Package capnproto for eups
|
Prototype is now getting to the point where a wire-protocol package like capnproto or protobuf is needed. capnproto is the new hotness, and we're probably going to want to migrate qserv from protobuf->capnproto at some point. This task is to go ahead and get capnproto packaged and published for use in the replication prototype.
| 2 |
794 |
DM-4223
|
10/30/2015 07:15:26
|
IsrTask calls removeFringe in FringeTask but the method does not exist
|
The method {{removeFringe}} of {{FringeTask}} is called in {{IsrTask}} but there is no {{removeFringe}}. Not sure if {{removeFringe}} was meant to be a place holder
| 1 |
795 |
DM-4225
|
10/30/2015 11:07:43
|
Collect single-host performance data for secondary index
|
Run production-scale (billions of entries) tests on different index options, collect performance statistics for allocation (CPU, memory) and for queries.
| 3 |
796 |
DM-4229
|
10/30/2015 11:31:52
|
Identify candidate technology for secondary index
|
Evaluate results of production-scale performance tests, both single and multiple host. Identify the technology most likely to meet requirements, and estimate performance capability with respect to those requirements
| 3 |
797 |
DM-4230
|
10/30/2015 12:30:38
|
Port HSC-1355: Improved fringe subtraction
|
[HSC-1355|https://hsc-jira.astro.princeton.edu/jira/browse/HSC-1355]: "with this fix, we get much better fringe subtraction".
| 2 |
798 |
DM-4232
|
11/02/2015 10:54:08
|
Variance is set after dark subtraction
|
In the default {{IsrTask}}, the variance is currently set after dark subtraction. This means that photon noise from the dark is not included in the variance plane, which is incorrect. The variance should be set after bias subtraction and before dark subtraction. [~hchiang2] also points out (DM-4191) that the {{AssembleCcdTask}} with default parameters requires amplifier images with variance planes, even though the variance cannot be set properly until after full-frame bias subtraction. I believe that {{AssembleCcdTask}} only requires a variance plane in the amp images because it does an "effective gain" calculation, but I suggest that this isn't very useful (an approximation of an approximation, and you're never going to use that information anyway because it's embedded in the variance plane with better fidelity). I therefore suggest that this effective gain calculation be stripped out and that {{AssembleCcdTask}} not require variance planes.
| 5 |
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