CHANGELOG.md

Change Log

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v?.?.? (Unreleased)

• Improvements
  • Adds User-Agent headers to outgoing calls to BossDB (#110)
  • Adds the ability to toggle the public status of a Boss Resource (#109)
• Fixes
  • Fixes single-index cutouts in the CloudVolume convenience volume provider (#108)

v1.4.1 (March 2023)

• Improvements
  • Removes the mock library (thanks @musicinmybrain!)
  • Confirms that incoming upload data are C-contiguous prior to upload
  • Extracts the normalize_key function to make slicing into convenience arrays more robust and reports voxel size relative to the requested resolution (thanks @CBroz1!)

v1.4.0 (November 2022)

• Features
  • A new convenience function array.from_images uploads an entire directory as a new BossDB dataset

v1.3.3 (October 2022)

• Fixes
  • Resolves a TypeError when warning in the non-cloudvolume case.

v1.3.2 (October 2022)

• Fixes
  • Resolves an issue with cloudvolume imports on non-cloudvolume-dependent resources.

v1.3.1 (July 2022)

• Fixes
  • Resolves an issue with accessing cloudvolume-backed public data in BossDB with ZYX/XYZ axis-ordering

v1.3.0 (June 2022)

• Convenience API
  • Adds support for channel-level metadata using the array().metadata dict-like API (#87)
  • Adds a array().downsampled property on the convenience API (#84)
  • Fixes voxel_unit getters and setters to be more consistent with convenience API constructor (#83)
  • Adds data-source inference to redirect requests to the correct Remote (#91)
  • Adds a metadata interface Metadata() for general metadata read/write access (#92)
• Improvements
  • Adds a BossResource.public boolean flag to mirror if a resource is publicly accessible (#89)
• Fixes
  • Closes the multiprocessing Pool to avoid too many open files when parallelizing requests (#86)

v1.2.0 (April 15, 2021)

Updates to the cloudvolume adapters, and parallelism fixes.

• Convenience API
  • Adds support for uint16 image channel creation with the convenience API (#71)
  • Now, the array class reports voxel size as a float[3] and voxel_units as a string (e.g. "nanometers") to match the input arguments to the array constructor (#83)
• Parallelism
  • Fixes parallelism defaulting to n=1 (#70)
• CloudVolume
  • Removes cloudvolume core dependency, and makes it an optional extra-install (#68)
• Fixes and Improvements
  • Adds support for the new "queued" downsample channel status (#78)
  • Adds support for z-index slicing in the convenience array API (#77)

v1.1.1 — September 2, 2020

Pip-installability fix (#67).

v1.1.0 — July 27, 2020

Updates to the convenience API.

• Convenience API
  • New arguments to specify the source channel for annotation channels
  • Specify BossDB config inline without special imports with array(..., boss_config: dict) argument
  • Specify descriptions for newly created resources when calling array(..., create_new=True).

v1.0.0 — June 1, 2020

This version introduces the convenience API which uses numpy-like indexing.

This build switches intern CI to GitHub actions, and now tests both 3.6 as well as 3.7. Python 2.7 testing is no longer supported.

Features

• Convenience API (#48)
  • This adds support for the simple intern.array interface which mocks the numpy array API for getters and setters.
• Add support for DVID and cloud-volume hosted data with DVIDRemote and CloudVolumeRemote. (#46)
• Add parallelism to BossRemote#get_cutout calls by passing parallel=True or parallel=<int # of jobs> as an argument. (#52)
• Addition of a MeshService for local meshing of 3D segmentation data.

v0.10.0 — April 16, 2020

v0.10.0 is the last version of intern that support Python 2.x. If you need Python 2 support, you must run pip install intern==0.10.0. The development team does not anticipate further development for Python 2, and support for Python 2 environments will be discontinued. In future versions of intern, it will be assumed that the user is on Python 3 (3.6 or above).

• Allow the "~" character in config-file path pointers when creating a new BossRemote
• BossRemote#get_channel now supports a single string argument of the form bossdb://[collection]/[experiment]/[channel]. Likewise, you can pass this string directly to, e.g., BossRemote#get_cutout as the first argument.
• Chunked downloads and uploads enable arbitrarily large cutouts from BossRemote.

v0.9.12

intern incorporates the access_mode parameter when grabbing cutouts of small AND large sizes. Backwards compatibility with previous versions that make use of the no_cache boolean parameter. Whenever a user makes use of the no_cache param intern will return a deprecation warning. The translation occurs in intern/remote/boss/remote.py and should be removed in future major version upgrades. intern now uses an enum class to limit the possibility of cache modes.

• access_mode = CacheMode.cache - Utilizes the cache and checks for dirty keys
• access_mode = CacheMode.no_cache - Does not check the cache but does check for dirty keys
• access_mode = CacheMode.raw - Does not check the cache and DOES NOT check for dirty keys

This is for functions:

• intern.remote.boss.remote.py: BossRemote.get_cutout()
• intern.serivce.boss.baseversion.py: BaseVersion.get_cutout_request()

v0.9.11

Convenience functions added:

• BossRemote#get_experiment()
• BossRemote#get_coordinate_frame()
• BossRemote#get_neuroglancer_link() get a neuroglancer URL from cutout arguments
• create_cutout will now chunk large cutouts into smaller components to eliminate HTTP size limitation and timeout errors.

v0.9.10

• Intern now forwards no_cache option when breaking apart large cutouts.

v0.9.9

• Modified the intern get_cutout() no_cache option to default to true instead of false

v0.9.8

• BugFix: Removed extra slash after no-cache option on URL that was causing issues.

v0.9.7

• Added new no-cache option to the get_cutout(... no_cache=True) This option will pull directly from the S3. It should be used when reading large amounts of data at once. Using this option can also increase throughput as the cache can become a bottleneck if a large amount of data is cycled through the cache

v0.9.6

• Merged PR #14 from ben_dev - correctly populate downsample_status of ChannelResource.
• Relaxed requests dependency to >= 2.11.1.

v0.9.5

• Added BossRemote.get_channel() to ensure users use a fully specified channel with the cutout service.
• Allow experiment time units to be unspecified.

v0.9.4

• API v1
• Fix recursion loop when breaking cutout into chunks.
• Fix x-y mistake in chunking.
• Coordinate frame hierarchy methods now anisotropic and isotropic.
• Channels now have downsample_status.

Sprint 7

Rebranded as intern.

General changes:

• Made Python 2 compatible.
• Version no longer controlled by resources. Now passed into BossRemote constructor.
• Imports simplified.
• Older Boss API support removed.
• Config dictionary can be used instead of a config file.
• Cutout range args now passed as a list of ints instead of a string.
• Separate list methods for each resource type provided for convenience.
• JHU ndio dependencies removed from requirements.txt.
• Additional legacy code removed
• Can provide config for each service or globally under the [Default] section of the config file
• Can provide config via environment variables
• Changed from a noun_verb convention to a verb_noun convention for function names

v0.7 changes:

• User management now done through entirely through SSO (Keycloak) server.
• Resource, group, and permission API updates reflected in intern

Sprint 4

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v0.5 changes:

• New ndio.remote.boss.remote.Remote methods that support user and access management:
• group_create()
• group_delete()
• group_get()
• group_add_user()
• permissions_add()
• permissions_get()
• permissions_delete()
• user_get_roles()
• user_add_role()
• user_delete_role()
• user_get()
• user_get_groups()
• user_add()
• user_delete()
• Only the name and description of a coordinate frame, can be changed, after creation.

General changes:

• ndio.remote.boss.remote.Remote method changes:
• Exceptions are raised when any non-2xx response received from the Boss.
• Methods that previously returned True to indicate success no longer return a value. Instead, an exception indicates failure (see above).
• project_create() returns an ndio.resource.boss.resource.Resource instead of a dictionary.
• project_get() returns an ndio.resource.boss.resource.Resource instead of a dictionary.
• project_update() returns an ndio.resource.boss.resource.Resource instead of a bool.
• ndio.resource.boss.resource.ChannelResource no longer allows the uint64 data type.

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Sprint 3

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Initial release.

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