h5rdmtoolbox - v2.2.0

• improved semantic serialization of HDF5 content
• housekeeping

- Python
Published by matthiasprobst 10 months ago

h5rdmtoolbox - v2.1.0

• upgrade setuptools due to cve and therefore limit minimum python version to 3.9

- Python
Published by matthiasprobst 12 months ago

h5rdmtoolbox - v2.0.0

• changed version number to 2.0.0
• housekeeping

- Python
Published by matthiasprobst about 1 year ago

h5rdmtoolbox - v2.0.0a0

• Major change: Removed code for standard names as it is outsourced to the ssnolib package
• fix and upgrade feature Convention so that user-defined validators work as expected

- Python
Published by matthiasprobst about 1 year ago

h5rdmtoolbox - v1.7.3

Changes

• hotfix serialization when multiple rdf:type values are set
• move jsonld sub-module from wrapper to ld module
• hotfix when instantiating File with fileobj, which is the case when working with hdf5 through streamlit, for instance

- Python
Published by matthiasprobst about 1 year ago

h5rdmtoolbox - v1.7.2

Changes

• remove skipND from being deprecated
• separation of "linked data" code into a separate repo
• update documentation

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.7.1

Changes

• fix documentation at readthedocs

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.7.0

Changes

• chunks=None as default for create_dataset to mimic behavior of h5py
• improved formalized representation of the HDF5 file structure based on the Allotrope Foundation's ontology
• removed unclear parameter resolve_keys from dump_jsonld() and serialize()
• HDF.File is not automatically returned if h5.frdf.type is called
• update to ontolutils v0.13.3
• improve semantic structural description of HDF5 file content

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.6.2

Changes

• hotfix rdf_find
• using ontolutils v0.13.2 and its HDF5 namespace definition
• update/improve CLI interface

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.6.1

• hotfix skipND when calling dump_jsonld(). Option was not passed correctly to underlying function.

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.6.0

v1.6.0

• rootgroup as alias for rootparent
• ZenodoRecord has new property env_name_for_token to define the environment variable name to be used for the Zenodo token
• bugfix downloading zenodo files
• allowing higher versions of pymongo

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - Updated dependency versions

This release puts more script versions to dependencies. Especially enabling to use newer versions of pydantic, now.

- Python
Published by matthiasprobst over 1 year ago

h5rdmtoolbox - v1.4.1

Hotfix release resolving an issue when deleting cache directory after 6 days.

- Python
Published by matthiasprobst almost 2 years ago

h5rdmtoolbox - v1.4.0

Version corresponding to the paper published in the ing.grid journal. - update package dependency versions - minor bugfixes and updates in documentation

- Python
Published by matthiasprobst almost 2 years ago

h5rdmtoolbox - v1.4.0rc2

• using suffix .jsonld instead of .json for JSON-LD files, as it is recommended (see https://www.w3.org/TR/json-ld/#iana-considerations)
• bugfixes in documentation (links, figures, ...)
• enhancing zenodo interfaces:
  • removed depr methods, e.g. get() from AbstractZenodoInterface
  • using cached json dict for zenodo records. call refresh() to update the json
  • minor bugfixes
  • introduced property files, which is Dict[str, RepositoryFile]
  • improve url handling by using properties instead of class variables

- Python
Published by matthiasprobst almost 2 years ago

h5rdmtoolbox - v1.4.0rc1

• The repository interface to Zenodo has one single upload method upload_file with the parameter metamapper. It is a callable which extracts meta information from the actual file to be uploaded. This is especially useful and specifically intended for HDF5 files. Unless the value for metamapper is None, the upload_file method will use the built-in hdf5 extraction function automatically on HDF5 files.
• Clarify abstraction for HDF5 database interfaces. HDF5DBInterface is the top abstraction from which ExtHDF5Interface inherits. ExtHDF5Interface makes use of external databases such as mongoDB.
• fix issue in online documentation: mongomock is used to run the mongodb jupyter notebook in the documentation
• codemeta.json file is updated with author and institution ROR ID

- Python
Published by matthiasprobst almost 2 years ago

h5rdmtoolbox - v1.3.0

• important changes:
  • improved and consequent support of RDF/JSON-LD. This means, an HDF5 can be created from a JSON-LD file and vice versa. The JSON-LD file contains the structural and contextual metadata of the HDF5 file.
  • namespaces are outsourced to ontolutils
• minor changes:
  • When a file is opened with a filename which does not exist and mode is None, the file will NOT be created. This was the case in the past, but this may lead to unwanted empty files.
  • Bugfix namespace creation
  • some method renaming and refactoring
  • accessors are refactored and improved (especially shifted away from xarray and fully integrated in hdf)

- Python
Published by matthiasprobst about 2 years ago

h5rdmtoolbox - v1.0.0

The version v1.0.0 introduced major changes:

• zenodo is not a dependency anymore but is implemented as a new subpackage of the toolbox
• zenodo is part or repository which is designed to provide interfaces to different data repositories (however, only zenodo is implemented at the moment)
• the database architecture is changed similarly, such that it has a more logic structure
• both above changes follow a more or less strict inheritance structure from abstract classes defining the interface to repositories or databases (databases are meant to be local, like mongoDB, SQL, etc., repositories are online data storage, like zenodo, which allows searching for metadata but not within the raw files.)
• python 3.8 until 3.12 inclusive are supported
• IRI as persistent identifier is now supported, which fulfills the F3 requirement of the FAIR principles ("Metadata clearly and explicitly include the identifier of the data they describe", https://www.go-fair.org/fair-principles/)
• package renaming and reorganization: conventions is now convention, layout is now a module, new is repository
• usage of IRI (persistent identifier) is now supported

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.12.2

v0.12.2

• bugfix requirements
• add $exist find()-methods inside of HDF files
• bugfix 0D time data as dimension
• module query functions (find, ...) can guess the filename from objects that have with hasattr(hdf_filename, 'hdf_filename')
• bugfix in zenodo search (did Zenodo change their API?)
• 0D data is written to MongoDB
• new utils like computing filesize
• update to new zenodo_search package due to change in backend at Zenodo.org
• find, find_one and distinct can be called on HDF files
• small bugfixes

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.11.1

v0.11.1

• bugfixes. See changelog

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.11.0

v0.11.0

• working with time data is now possible:
  • time data can be created using the high-level method create_time_dataset
  • slicing the above "time datasets" will return xarray data
  • See docs/wrapper/Misc.ipynb
• fixed issue with user-defined & nested standard attributes

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.10.0

Initial version. A publication is submitted to the journal ing.grid.

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.9.0

v0.9.0

New concept for defining conventions. They are still defined in YAML files but validators can be defined in the same file, too, e.g. a list of values associated to a standard attribute.

What's Changed

- Using `pydantic` to validate the standard attributes
- Giving a better error message about what exactly is wrong about the attribute
- Much convention code is gone thanks to the restructure. Convention code is generated and stored in the local user directory

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.8.3

v0.8.3

Small improvementsand fixes

What's Changed

• h5py min. req. package updated to >3.7 still had a typo in requirements.txt
• h5tbx.conventions.core._use(<convention>) returns a Conventionobject
• dump and dumps can handle inputs that are strings or have attribute hdf_filename
• bugfix __repr__ of contacts

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.8.2

v0.8.2

Mainly fixes small issues.

What's Changed

• h5py min. req. package updated to >3.7 (in 3.7 h5py.Dataset.is_scale is not available)
• bugfix touching HDF5 file
• updated doc strings
• bugfix reopen file with r+ when a convention is in place but standard attributes are already existing. Existing attributes should not be expected again when the file is opened like this. This is fixed now.
• bugfix dumping files in notebook looked not nice in dark-mode. removed background color

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - v0.8.1

v0.8.1

This release brings only corrections of typo. Also, the classifier Topic is added.

- Python
Published by matthiasprobst over 2 years ago

h5rdmtoolbox - Release v0.8.0

This is the first official release. All current features of the toolbox can be found in the documentation.

- Python
Published by matthiasprobst over 2 years ago