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  1. Data Management
  2. DM-22389

verify fails with Astropy 4

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    Details

    • Type: Bug
    • Status: Done
    • Resolution: Done
    • Fix Version/s: None
    • Component/s: verify
    • Labels:
      None
    • Story Points:
      2
    • Epic Link:
    • Sprint:
      AP F19-6 (November)
    • Team:
      Alert Production

      Description

      Doing a build with Astropy4 I now get failures from verify package relating to YAML serialization.

      This works fine with the same version of YAML on Astropy 3 but fails on Astropy 4.

      self = <yaml.loader.SafeLoader object at 0x7fbb0063aba8>
      		 
      node = SequenceNode(tag='tag:yaml.org,2002:python/object/apply:numpy.core.multiarray.scalar', value=[MappingNode(tag='tag:yam...Node(tag='tag:yaml.org,2002:int', value='0')]))]), ScalarNode(tag='tag:yaml.org,2002:binary', value='AAAAAAAAFEA=\n')])
      		 
       
      		 
          def construct_undefined(self, node):
      		 
              raise ConstructorError(None, None,
      		 
                      "could not determine a constructor for the tag %r" % node.tag,
      		 
      >               node.start_mark)
      		 
      E       yaml.constructor.ConstructorError: could not determine a constructor for the tag 'tag:yaml.org,2002:python/object/apply:numpy.core.multiarray.scalar'
      		 
      E         in "<unicode string>", line 9, column 14:
      		 
      E                 value: !!python/object/apply:numpy.core ... 
      E                        ^
      		 
       
      		 
      ../../stack/DarwinX86/pyyaml/5.1+2/lib/python/yaml/constructor.py:420: ConstructorError

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          Issue Links

          is triggered by

          Story - Created by Jira Software - do not edit or delete. Issue type for a user story. DM-22388 Investigate Astropy 4

          • Done
          relates to

          Story - Created by Jira Software - do not edit or delete. Issue type for a user story. DM-21875 Add StorageClass and Formatter support necessary to persist lsst.verify.Measurement in Gen3 repos

          • Done
          links to

          Web Link GitHub issue

            Activity

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            tjenness Tim Jenness added a comment -

            On Astropy 4 for the blob test:

            !<lsst.verify.Blob>
            		 
            data:
            		 
              mag1: !<lsst.verify.Datum>
            		 
                description: Magnitude
            		 
                label: mag1
            		 
                unit: mag
            		 
                value: !!python/object/apply:numpy.core.multiarray.scalar
            		 
                - &id001 !!python/object/apply:numpy.dtype
            		 
                  args:
            		 
                  - f8
            		 
                  - 0
            		 
                  - 1
            		 
                  state: !!python/tuple
            		 
                  - 3
            		 
                  - <
            		 
                  - null
            		 
                  - null
            		 
                  - null
            		 
                  - -1
            		 
                  - -1
            		 
                  - 0
            		 
                - !!binary |
            		 
                  AAAAAAAAFEA=
            		 
              mag2: !<lsst.verify.Datum>
            		 
                description: Magnitude
            		 
                label: mag2
            		 
                unit: mag
            		 
                value: !!python/object/apply:numpy.core.multiarray.scalar
            		 
                - *id001
            		 
                - !!binary |
            		 
                  AAAAAAAAJEA=
            		 
            identifier: 81b88b52a20b47bda3a11cb74db9f41b
            		 
            name: demo

            For the working test with astropy 3:

            !<lsst.verify.Blob>
            		 
            data:
            		 
              mag1: !<lsst.verify.Datum>
            		 
                description: Magnitude
            		 
                label: mag1
            		 
                unit: mag
            		 
                value: 5.0
            		 
              mag2: !<lsst.verify.Datum>
            		 
                description: Magnitude
            		 
                label: mag2
            		 
                unit: mag
            		 
                value: 10.0
            		 
            identifier: 78dfeee927cf4962bc2b1143b0e75184
            		 
            name: demo

            Show
            tjenness Tim Jenness added a comment - On Astropy 4 for the blob test: !<lsst.verify.Blob> data: mag1: !<lsst.verify.Datum> description: Magnitude label: mag1 unit: mag value: !!python/object/apply:numpy.core.multiarray.scalar - &id001 !!python/object/apply:numpy.dtype args: - f8 - 0 - 1 state: !!python/tuple - 3 - < - null - null - null - -1 - -1 - 0 - !!binary | AAAAAAAAFEA= mag2: !<lsst.verify.Datum> description: Magnitude label: mag2 unit: mag value: !!python/object/apply:numpy.core.multiarray.scalar - *id001 - !!binary | AAAAAAAAJEA= identifier: 81b88b52a20b47bda3a11cb74db9f41b name: demo For the working test with astropy 3: !<lsst.verify.Blob> data: mag1: !<lsst.verify.Datum> description: Magnitude label: mag1 unit: mag value: 5.0 mag2: !<lsst.verify.Datum> description: Magnitude label: mag2 unit: mag value: 10.0 identifier: 78dfeee927cf4962bc2b1143b0e75184 name: demo
            Hide
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            tjenness Tim Jenness added a comment - - edited

            The difference seems to be in datum_representer where .value returns a float in astropy3 but numpy.float64 in astropy4.

            Show
            tjenness Tim Jenness added a comment - - edited The difference seems to be in datum_representer where .value returns a float in astropy3 but numpy.float64 in astropy4.
            Hide
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            tjenness Tim Jenness added a comment -

            Astropy 4:

            >>> import astropy.units as u
            		 
            >>> import numpy
            		 
            >>> a = 5 * u.s
            		 
            >>> type(a.value)
            		 
            <class 'numpy.float64'>

            Astropy 3:

            >>> import astropy.units as u
            		 
            >>> import numpy
            		 
            >>> a = 5 * u.s
            		 
            >>> type(a.value)
            		 
            <class 'float'>

            Show
            tjenness Tim Jenness added a comment - Astropy 4: >>> import astropy.units as u >>> import numpy >>> a = 5 * u.s >>> type(a.value) <class 'numpy.float64'> Astropy 3: >>> import astropy.units as u >>> import numpy >>> a = 5 * u.s >>> type(a.value) <class 'float'>
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            krzys Krzysztof Findeisen added a comment -

            Tim Jenness, can you test this on your system? I don't have Astropy 4 myself.

            Show
            krzys Krzysztof Findeisen added a comment - Tim Jenness , can you test this on your system? I don't have Astropy 4 myself.
            Hide
            Permalink
            tjenness Tim Jenness added a comment -

            Tests pass with this. Thank you for the quick fix.

            Show
            tjenness Tim Jenness added a comment - Tests pass with this. Thank you for the quick fix.

              People

              Assignee:
              krzys Krzysztof Findeisen
              Reporter:
              tjenness Tim Jenness
              Reviewers:
              Tim Jenness
              Watchers:
              John Swinbank, Krzysztof Findeisen, Tim Jenness
              Votes:
              0 Vote for this issue
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: