Flexiznam v0.4

Main changes

• New SequencingData class to handle sequencing data
• GUI can now be used to add data to flexilims with flexiznam gui
• Add a conda_envs field in the config file to use in conjuction with znamutils
• get_children can work with name or id (instead of id only)
• check_flexilims_issues can now add missing paths
• Dataset.from_origin has a new extra_attributes argument to match online datasets with specific attributes only.
• delete_recursively can delete all children of an entity
• Offline mode using downloaded copy of the database

Minor

• add_mouse uploads birth and death dates in a human readable format instead.
• Add conflicts argument to add_mouse to overwrite existing mice
• get_entities does not raise warnings anymore if name is specified and datatype is not. This is now supported upstream by flexilims
• Clearer error message when mouse info cannot be found in MCMS
• load_param can print the file used to read config with the verbose flag.

Bugfixes

• update_config actually adds the new fields (i.e. fields that are in the default config but not the local config) to the config file

Flexiznam v0.3.11

Minor bugfix

Flexilims v0.3.10

Change log

v0.3.10

Main changes

• Make update_entity safer by crashing if reserved fields are used as attributes.

Flexilims 0.3.9

v0.3.9

Main changes

• Replace crash for conflicting attributes by a warning

v0.3.8

Main changes

• Add get_data_root function to get raw or processed root for a project
• get_children can filter children by attributes before returning results
• refactor get_datasets to be non recursive and add filtering options. Also add
  multiple options to filter datasets and format output
• add get_datasets_recursively to get all datasets below a given entity

### Bugfixes

• return empty dataframe if filter in get_children filters out everything (instead
  of crashing)
• update_flexilims correctly uploads tuples parameters
• update_flexilims correctly uploads floats and np.float/np.int parameters
• update_flexilims can overwrite existing datasets (if conflicts='overwrite')
• Add filelock for token creation to avoid concurrent access and move token to their own
  file

Minor

• harp_dataset.from_folder will now match csv even if there is nothing before or after
  harpmessage in the file name (i.e. the file is harpmessage.bin, and all csvs in
  the folder will be matched)
• private function config_tools._find_files has now a create_if_missing argument to
  create the file if it does not exist

v0.3.7

Main changes

• Separate Dataset.from_dataseries and Dataset.from_flexilims to avoid confusion

Minor

• get_children output is filtered to contain only relevant columns when children_datatype is not None

Flexiznam v0.3.6

v0.3.6

Main changes

• New SequencingData class to handle sequencing data
• Add a conda_envs field in the config file to use in conjuction with znamutils
• get_children can work with name or id (instead of id only)

Minor

• add_mouse uploads birth and death dates in a human readable format instead.
• get_entities does not raise warnings anymore if name is specified and datatype
  is not. This is now supported upstream by flexilims

## Bugfixes

• update_config actually adds the new fields (i.e. fields that are in the default
  config but not the local config) to the config file

Flexiznam v0.3.5

v0.3.5

Main changes

• flz.get_datasets can return Dataset objects instead of path strings if
  return_paths=False
• New OnixData class to handle Onix data
• get_flexilims_session can now re-use token from a previous session

Minor

• More generic clean_recursively replaces the clean_dictionary_recursively. It
  handle more complex nesting and replaces non finite float by their string repr.
• CameraDataset metadata can also be .yml, not only .txt.
• Dataset.format(mode='yaml') ensure yaml compatibility. (path to str, tuple to list,
  etc...)
• add_experimental_session can be done with parent_id (or parent_name).
• add_dataset can add a dataset to a mouse.
• get_password syntax changed to match the add_password syntax.

Bugfixes

• Fix #68. Dataset.format returns
  always the path in posix format.
• Fix #88. Now make attributes JSON
  compatible before uploading to flexilims. This will replace special characters in
  attribute names by _ in the database.

Flexiznam v0.3.4

Merge pull request #98 from znamlab/dev

Dev

Flexiznam v0.3.3

Merge pull request #96 from znamlab/dev

v0.3.3

Flexiznam v0.3.2

Merge pull request #94 from znamlab/dev

v0.3.2

Flexiznam v0.3.1

Merge pull request #90 from znamlab/dev

Update to v0.3.1