[h5md-commit] [SCM] UNNAMED PROJECT annotated tag, v1.0_rc3, created. v1.0_rc3

[Pierre de Buyl]

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The annotated tag, v1.0_rc3 has been created
        at  c27ff0d86d35225842e43fe7fa495bffd582097e (tag)
   tagging  d491e2ab4cbf027bd6162997fc8bcbefcac41c82 (commit)
  replaces  v1.0_rc2
 tagged by  Pierre de Buyl
        on  Tue Jan 14 21:45:04 2014 +0100

- Log -----------------------------------------------------------------
Tag v1.0_rc3

Felix Höfling (53):
      slightly rephrase objective and notation
      move spec of root groups after time-dependent data
      Reword general organization and data layout
      revise spec of root level
      reword spec of h5md group
      fix level of subsection headlines
      move note on storage order to general section
      revise particles group
      cleanup observables group
      box spec: minor rewording
      add a bit more explanation to the parameters group
      replace content by contents
      fix spelling
      parameters: fix notation in tree graph
      put the definition of "data group" in italics
      replace "like" by "as"
      box: drop geometry attribute, change "nonperiodic" to "none"
      particles: Mention that some identifiers are part of the specification
      box: define boundary conditions 'periodic' and 'none'
      tree graph for particles group: make all data optional
      replace "H5MD file" by "H5MD structure"
      fix missing vertical bars in tree graphs
      discussions: clean up section on particle number
      discussions: add time-dependent data with constant increments
      thermodynamics: add 'volume'
      thermodynamics: drop per particle quantities, add enthalpy
      be more precise about the types
      draft: some clean-up and reformatting
      draft: revise section on modules slightly
      draft: drop "time series" for observables
      modules: add a draft for the units module
      draft: drop `unit` attribute, refer to 'units' module
      refine thermodynamics module
      2nd revision of thermodynamics module
      version: clarify that the patch number is not stored
      thermodynamics: make volume optional, replace it by density
      units modules: drop UTF8 encoding
      unit modules: fix table entries spanning two lines
      draft: typeset H5MD element in normal font or with emphasis
      draft: explain semantic versioning only once
      draft: omit examples from description of fields
      particles: mention that subgroups are independent
      particles/species: make meaning of 'species' more precise
      minor editing to improve text flow
      units module: rearrange subsections, move all text before the tables
      box/offset: replace "lower" by "minimal (lower left)"
      box: say that other shapes may be transformed to the triclinic one
      add explicit references next to most inline links
      particles/id: state more precise what unique means
      clarify interpretation of position data (folded/unfolded)
      box: remove 'offset' from box specification
      particle/position: specify optional bounding box
      bounding_box: reformat and shorten specification

Olaf Lenz (3):
      explain the interpretation of "particles/id"
      Small fixes.
      h5md: make paragraph on particles/…/image more precise

Peter Colberg (75):
      Remove Draft from title
      Update summary of parameters group.
      Typeset HDF5 names and string values in typewriter font.
      Reflow overlong lines.
      Place semantic links to project page and mailing list.
      Mention a few computational methods.
      Reorder sections.
      Consistently order group diagrams and descriptions.
      Consistently use [variable] for dimension.
      Avoid repeated definitions of box group.
      Split author attribute into ``author`` and ``author_email``.
      Revise grammar and formatting.
      State full license.
      Include H5MD version.
      Use unabbreviated observable group names.
      Avoid overlong line with ``..., temperature``.
      Remove verbatim escape sequences.
      Use definition lists in place of bullet lists.
      Use “must” to emphasize mandatory presences of box specification.
      Avoid overlong line for ``author_email``.
      Non-specified elements include attributes.
      Use definition of group, dataset and attribute from HDF5.
      Explicitly define and use the term "data-group".
      Describe optional root groups as optional.
      Define <identifier> to distinguish between unspecified and specified 
names.
      Spell out attribute.
      Revert to “data group” instead of “data-group”.
      Organize meta-data of author and creator into subgroups.
      Move attribute “unit” to discussion section.
      Avoid duplicate specification of particles data groups.
      Format data_group as unspecified identifier.
      Consistently use “metadata”.
      Link to VMD-h5mdplugin repository.
      Move Language-independent before language-specific hints
      Store time-independent data as compact datasets
      Revert "Move attribute “unit” to discussion section."
      Add optional unit attribute to dimensional data
      Use single number for H5MD file format version.
      Specify variable-length string datatype for specified attributes.
      Define H5MD modules
      Fix verbatim block
      Specify monotonically increasing order of step and time
      Move modules to H5MD metadata
      Switch source format to Pandoc's Markdown
      Revise markdown following automatic conversion
      Deduplicate README and index
      Remove symbolic link from repository
      Remove box from observables group
      Hard-link step/time datasets of position and box
      Add draft of thermodynamics module
      Use x.y.z version for specification and modules
      Fix description of module version
      Work around broken reStructuredText code directive.
      Generate citations using pandoc-citeproc
      Consider subsystems with varying number of particles
      Add Enumeration datatype for particle species
      Clarify varying particle number
      Rename index document
      Split modules into separate documents
      Title
      Link to H5MD website
      Use sphinx-bootstrap theme
      Link to git repository and mailing list archive
      Move python extensions to subdirectory
      Render math as MathML in HTML output
      Silence MathJax rendering
      Shorten section label
      Rename H5MD specification document
      Fix spelling misakes in units module
      Build PDF file using pandoc
      Link to PDF file
      Fix Unicode exponents of SI prefixes in PDF
      Define "SI" unit system
      Avoid Unicode in bibliography
      Fix capitalization of SI

Pierre de Buyl (28):
      Remove dataset confusion in definition of h5md version attribute.
      Add hint on the use of the enum datatype for the species. Idea taken from 
http://article.gmane.org/gmane.science.simulation.h5md.user/244 with additional 
info from http://article.gmane.org/gmane.science.simulation.h5md.user/248
      Allow to omit edges and offset when all elements of boundary are none.
      Remove the word 'element' wherever possible.
      Introduce H5MD elements.
      Explicit type and dimension added in the notation, according to Olaf 
Lenz's suggestion.
      Update settings for latex generation:
      Update settings for manpages generation.
      Minor edit to clarify version scheme according to
      Add meaning of VL type.
      Minor style edit.
      Revert bug removing the table of contents.
      Precise dataspace for box dimension.
      Wording was not clear. H5MD elements are for both time-dependent and 
time-independent data.
      Consistent use of 'dimensions'.
      Add illustration of time-independent observable.
      Clarify inferring box type from shape of edges.
      Correct table formatting.
      Add table captions.
      Use markdown notation for subscript.
      Move authorship to "The H5MD Developers"
      typo
      Inclusion of AUTHORS.mdwn in the document.
      Addition of 'system' attributes to the 'units' module.
      Revert "bounding_box: reformat and shorten specification"
      Revert "particle/position: specify optional bounding box"
      Get Felix's style correction back.
      Add information on udunits2 in implementation.

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