Release Notes¶

v3.0.1 August 2020¶

Requirement changes:
- OpenEye-drconvert==1.1.1
  - Minor documentation fix for OEDUConverter

v3.0.0 August 2020¶

Support for Python versions that are less than or equal to 3.6 is being deprecated in the next Orion release.
Design Unit support has been added to FileToRecordConverter and RecordsToFileConverter
Requirement changes:
- OpenEye-floe==0.11.0
  
  Changes since 0.9.6
  - CubeTestRunner.set_parameters has been modified to trigger parameter validation and conversion on the underlying cube in order to support testing parameters which override get_runtime_value.
  - An issue that resulted in errors running a floe due to very slow Python imports has been resolved.
  - Issues with Cube inheritance and constructor parameters are now more thoroughly validated.
  - An issue related to memory overflows has been fixed.
  - floe detect now enables the Python fault handler.
  - Cube parameters and parameter groups are copied as cube instance attributes.
  - cube.modify_parameter(cube.param, **fields) checks if param belongs to cube.
  - When promoting parameter it is sufficient to provide promoted_name only.
  - The documentation of the disk_space and memory_mb parameters has been fixed to reflect the backend implementation. The units of both parameters are mebibytes (MiB == 1048576 B) rather than megabytes (MB). Also, notes regarding taking into account overheads by requesting a couple hundred MiB more than is required have been added.
  - The instance_tags parameter is deprecated and will be removed in the future.
  - Issue where running floes outside of Orion would not honor item_count has been resolved.
  - An issue causing local parallel cubes in a cycle to hang has been fixed.
  - An issue preventing large cube groups from passing validation has been fixed.
  - floe.api.ordering.cube_precedents now correctly returns upstream cubes.
  - An issue where the max value of Parallel Cube parameter item_count would allow overflows has been resolved and reduced from 100000 to 65535.
  - An issue where sink Cubes would hang when using an initializer has been resolved.
  - An issue where parameters with many and required set would allow no input to be set has been resolved.
  - An issue related to the default validation of parameters with many=False has been resolved.
  - An issue where the required attribute of promoted parameters would be ignored has been fixed.
  Breaking Changes
  - cube.parameters() and cube.parameter_groups() methods now list parameters that are attributes of cube instance, not attributes of cube class.
  - A ValidationError is now raised when the name of a Parameter or Port is the same as the name of one of the cube attributes, which previously caused this cube attribute to be shadowed unintentionally.
- OpenEye-datarecord==3.0.0
  - Changed type string for field type DesignUnit from “DesignUnit” to “Chem.DesignUnit”
  - datarecord.utils.TemporaryPath has been deprecated. orionclient.utils.TemporaryPath should be used instead.
  - A field type DesignUnit for storing OEDesignUnits has been added.
  Breaking Changes
  - The implementation of datarecord has mostly moved to C++ in the toolkits.
- OpenEye-drconvert==1.1.0
  - Support for OEDesignUnit has been added
  - The dependency on structlog has been removed
  - The log level of INFO statements has been decreased to DEBUG
- OpenEye-orionclient==3.0.0
  - Added OEDesignUnit support for dataset upload and download
  - Support for uploading OEDU files to datarecords has been added to upload()
  - Orion server API version has been increased to require 5.0 or later.
  - A new type, Balance, has been added.
  - Support for retrieving cost information on a WorkFloeJob has been added. Cube cost will show automatically when using the --wait flag on jobs in the command line.
  - get_current_workfloe_job() has been added to help cubes running in Orion get the WorkFloeJob that the cube is running in.
  - A flag with-token has been added to ocli config profile to optionally create a profile using a token value.
  - datarecord.utils.TemporaryPath has been deprecated. TemporaryPath should be used instead.
  - The dependency on Click has been updated to >=6.7,<8.0.
  - To improve debugging capabilities, an additional request header has been added.
  - An issue where providing an organization id when sharing with Organizations would not make the data available globally.
  - orionclient.types.Datarecord.records now yields OEMolRecord
  - orionclient.session.in_orion() now correctly returns a boolean.
  Breaking Changes
  - Datetimes on Orion Client objects now contain seconds, format %Y-%m-%d %H:%M:%S

Bugfixes:¶

An issue with too frequent flushing in DatasetUpdaterCube has been fixed.
The DatasetAppenderCube now finalizes datasets.

v2.4.6 May 2020¶

Requirement changes:
- OpenEye-floe==0.9.6
  - An issue causing memory overflows has been fixed

v2.4.5 April 2020¶

Requirement changes:
- OpenEye-orionclient==2.6.3
  - The efficiency and reliability of ShardCollection.list_shards has been improved.

v2.4.4 March 2020¶

Requirement changes:
- OpenEye-OrionClient==2.6.2
  - The dependency on OpenEye-Datarecord has been updated to >=0.13.0,<0.15.0.
  - An issue that broke python 3.5 support has been resolved.
  - An issue with the encoding of credentials has been fixed.
  - An issue in which uploading shards would not correctly retry has been fixed.
- OpenEye-Floe==0.9.5
  - An issue that resulted in errors running a floe due to very slow Python imports has been resolved.
  - Issues with Cube inheritance and constructor parameters are now more thoroughly validated.

v2.4.3 March 2020¶

Issues with finding the primary molecule field and logging in RecordsToCollectionCube have been fixed.
The max parallelism of ParallelCloseShardsCube is now limited to 10.
Requirement changes:
- OpenEye-floe==0.9.3
  - floe detect now has a flag --no-json to not inspect JSON files as Workfloes.
  - Validation of ports has been improved.
- OpenEye-Datarecord==0.14.0
  - Infinite bounds in Range fields produce valid JSON.
- OpenEye-Drconvert==0.7.3
  - The datarecord dependency has been updated to >=0.13.0,<0.15.0.

v2.4.2 February 2020¶

Requirement changes:
- OpenEye-orionclient==2.6.1
  - Supports the OpenEye-floe 0.9.* series.
- OpenEye-Drconvert==0.7.2
  - Support added for Float and Int vectors
  - Drconvert CLI now supports going from records to mols
- OpenEye-floe==0.9.2
  - floe lint now incorporates errors and returns a non-zero exit code if it encounters an error.
  - floe.api.parameter has been deprecated in favor of floe.api.parameters. floe.api.parameter will be removed in the next major release of the OpenEye-floe package.
  - An issue that resulted in the loss of parameter groups at package ingestion has been resolved.
  - An issue that resulted in Cubes and Workfloes not being detected if the same UUID was used has been resolved.

v2.4.1 January 2020¶

Requirement changes:
- OpenEye-floe==0.9.1
  - Internal Floe code, which was deprecated in previous Orion releases, and is no longer used, was removed.

v2.4.0 December 2019¶

Support for the OEZ format has been added to the following cubes:
- CollectionResizeCube
- CollectionToRecordsCube
- RecordsToCollectionCube
orionplatform.cubes.files.RecordsToRecordFileConverter now uploads its files in parts reducing the disk usage
Requirement changes:
- OpenEye-floe==0.9.0
  - New parameters, which optionally enable metric collection for cubes have been added.
- OpenEye-OrionClient==2.6.0
  - A new field owner has been added to ShardCollection.
  - Support for sharing and unsharing with organizations without ``ID``s have been added.

v2.3.0: November 2019¶

Requirement changes:
- OpenEye-floe==0.8.11
  - A new method WorkFloe.check_arguments(), which performs basic validation of runtime arguments without actually running a floe has been added.
  - ImportError for floe parameters when calling WorkFloe.from_json(no_imports=True) is no longer raised.
  - Parameter defaults are now validated when calling WorkFloe.validate(), unless the parameter requires a value to be given.
  - Validation of command line arguments for floes created with no_imports=True has been improved.
  - A ValidationError is now raised for unknown command line arguments.
  - The WorkFloe UUID in a specification is now included in the WorkFloe object upon instantiation.
- OpenEye-Datarecord==0.13.0
  - Sets lower bound on OpenEye-toolkits>=2019.10.2
- OpenEye-Drconvert==0.7.0
  - Sets lower bound on OpenEye-toolkits>=2019.10.2
- OpenEye-orionclient==2.5.0
  - Sets lower bound on OpenEye-toolkits>=2019.10.2

v2.2.1 November 2019¶

Bugfixes:¶

The constructors of FieldParameter and its subclasses have been made compatible with floe.api.parameters.BaseParameter

v2.2.0 November 2019¶

Requirement changes:
- OpenEye-floe==0.8.9
  - Raises error when attempting to emit more than the maximum allowed bytes onto a port.
  - An issue where re-use of a cube having an UUID assigned is incorrectly detected more than once has been fixed.

Bugfixes:¶

A duplicate of output_tags in the DatasetWriterCube Options parameter group has been removed.

v2.1.0 October 2019¶

BooleanSwitch and ParallelBooleanSwitch have been added.
FieldSelectorParameter which allows selecting fields by name has been added.
RecordBinaryOutPort allowing emitting records as bytes without having to deserialize them has been added.
limit parameter added to ShardReaderCube to allow streaming only some shards from a collection.
Requirement changes:
- OpenEye-orionclient==2.4.0
  - Support for uploading files by parts added.
  - orionclient.types.Token added.
  - Closing shards in the same cube as it was created now logs a warning.
- OpenEye-Datarecord==0.12.12
  - Support for reading records from stdin added.
- OpenEye-floe==0.8.8
  - A new command floe html path/to/file to generate a simple HTML representation of a floe has been added.
  - Avoid importing code from cubes outside a cube group.
  - A bug related to exporting cycle information to JSON when ProxyCubes are involved has been fixed.
  - from_json() has new arguments to optionally remove rank and cycle details when reading a spec so that it can be resorted.

v2.0.1 September 2019¶

Bugfixes:¶

RecordsToCollectionCube now recovers from rare write errors.
Shard upload attempts have been increased to 10.

v2.0.0 August 2019¶

Requirement changes:
- OpenEye-orionclient==2.2.0
  - Support for uploading packages via url has been added.
  - Support for Floe package deprecation and un-deprecation has been added. (Requires 3.0 API version)
  - A new command ocli packages download to download packages has been added.
  - A new command ocli config delete to delete profiles has been added.
  - Arguments --limit and --offset to listing commands for the CLI have been added.
  - Various bugfixes have been made.

v1.1.4 August 2019¶

Requirement changes:
- OpenEye-floe==0.8.7
  - Promoted parameters can now be given a default name by using modify_parameter.

v1.1.2 August 2019¶

Requirement changes:
- OpenEye-drconvert==0.6.19
  - The handling of conformer data on OEMolRecords and OEMols has been improved.

v1.1.0 August 2019¶

LinkFieldParameter has been added.
Requirement changes:
- OpenEye-Floe==0.8.5
  - Minor bugfixes have been made.
- OpenEye-OrionClient==1.2.0
  - The ability to untag resources has been added.
  - Additional fields have been added to ShardCollection and Shard objects

Bugfixes:¶

Occasional traceback in RecordsToCollectionCube has been fixed.
The name argument to orionplatform.parameters.FieldParameter and its derived classes is now optional, to match the defaults in Floe.
Input parameters can now be None if they are not required.

v1.0.2 July 2019¶

The verbosity of RecordsToCollectionCube has been decreased.
Documentation about using collections and batching work has been added.
Requirement changes:
- OpenEye-Floe==0.8.4
  - The argument validation to the main thread has been moved and now delivers a cleaner error message.
  - Parsing parameters without any imports to enable Orion Client validation has been enabled.
- OpenEye-Floe==0.8.3
  - Command line parameter messages to facilitate determining which parameters are unsatisfied has been improved.

v1.0.1 July 2019¶

Constants for DatasetInputParameter, CollectionInputParameter, CollectionOutputParameter, and SecretInputParameter parameter types have been added.
Requirement changes:
- OpenEye-Floe==0.8.2
  - A debug mode to troubleshoot issues in cubes and keeps connections alive has been added.
  - A bug related to detecting cycles in Cube Groups has been fixed.

v1.0.0 June 2019¶

Requirement changes:
- OpenEye-datarecord==0.12.11
  - The OEField names that are non-empty strings are now validated.
- OpenEye-orionclient==1.0.0
  - The latest available HTTP endpoints can now be used.
  - API version validation is now performed upon communication with the server.
  - The --verify-ssl flag has been removed for ocli config profile
  - Prompts for Secrets values on CLI have been added.
- OpenEye-Floe==0.8.0
  - New simplified syntax for ports, parameters and Cubes have been added that allow for their names to be omitted.

Bugfixes:¶

An issue that prevented using files named with special characters (e.g., |, /, and >) has been fixed.

v0.3.2 June 2019¶

Requirement changes:
- OpenEye-Floe==0.7.1
  - An issue with initializers that caused upstream cubes to hang indefinitely has been fixed.

v0.3.1 May 2019¶

Bugfixes:¶

An issue that caused orionplatform.parameters.FileStream to fail on local files if not authenticated in Orion has been fixed.

v0.3.0 May 2019¶

Requirement changes:
- OpenEye-Floe==0.7.0
  - Handling of parameter validation has been improved.
  - The validate_default() method has been removed.

v0.2.3 May 2019¶

Requirement changes:
- OpenEye-Floe==0.6.27
  - An issue that caused messages to be duplicated when sent from a Cube group to multiple downstream Cubes has been fixed.
- OpenEye-Drconvert==0.6.18
  - An issue that caused an isomeric conf test to be enabled by default for SDF and MOL2 files, resulting in fewer records than expected, has been fixed.
  - Blob data is no longer written into CSV files.
  - An option to add the title of molecules to a field on the record has been added.

Bugfixes:¶

A default value of a FieldParameter no longer becomes the title if no title is provided.
FileInputParameter now correctly supports a dictionary with a single key file.

v0.2.2 May 2019¶

Requirement changes:
- OpenEye-datarecord==0.12.10
  - A bug in datarecord.types.IntVec that stored certain values incorrectly has been fixed. All previous records that have such a field may be corrupt.
    - An datarecord.types.IntVec that is known to only contain positive numbers is safe.
- OpenEye-Floe==0.6.26
  - Floe detection has been improved to catch more issues before runtime and show the path where issues occurred in all cases.
  - Multiple cubes in a WorkFloe ca no longer have the same name.
  - All required ports now must be used at runtime.
  - The min_parallel default value has been reduced from of 1 to 0 to avoid running allocations when there is no work to be done.

Bugfixes:¶

ORION_CPU, ORION_GPU, ORION_MEM, ORION_DISK, ORION_TAGS, ORION_JOB_ID, and ORION_PROJECT, ORION_INSTANCE constants for Orion environment variables have been added.
DatasetAppenderCube, FileInputParameter, FileOutputParameter, BinaryFileReaderCube, CloseShardsCube, and ParallelCloseShardsCube have been added.
Types have been added to FieldParameters.
Optional validation has been added to CollectionResizeCube.
Requirement changes:
- Requirements are now fully pinned
- OpenEye-Floe==0.6.25
  - An issue where a required parameter with choices would require that the default is in the choices has been fixed. None is now a valid choice.
  - An issue where validate_default() for StringParameters to handle None defaults incorrectly has been fixed.
  - An issue that caused min_parallel and max_parallel parameters to not have a description field has been fixed.
- OpenEye-orionclient==0.6.14
  - Collection commands on the CLI have been improved.
- OpenEye-orionclient==0.6.13
  - orionclient.helpers.try_hard_to_create_shard() and orionclient.helpers.try_hard_to_download_shard() have been added.
  - Log messages for failures and retries have been clarified.
  - Logs now display retry statistics if total time of request exceeds 60 seconds.
  Bugfixes:
  - Silent failure of uploading datasets with files that aren’t supported has been fixed.
  - An internal server error that caused an issue with requests has been fixed. All requests are now retried.
  - Shard uploads on 400s are now retried.

Bugfixes¶

Shards are now emitted in the “ready” state only, by default, from CollectionStream and CollectionReaderCube.
The ParallelCollectionToRecordsCube item and prefetch counts are now set to 1.
orionclient.helpers.collections.try_hard_to_create_shard() and orionclient.helpers.collections.try_hard_to_download_shard() can now be used to improve reliability of large scale floes.
All errors that occur when processing shards are now caught and logged as failures.
Shard-related retry logging has been clarified.
Collections from orionplatform.cubes.collections.CollectionReaderCube are now emitted.

v0.2.1 March 2019¶

Requirement changes:
- OpenEye-Floe>=0.6.24,<0.7.0
  - Minor bugfixes have been made.
  - Additional features for the CubeTestRunner have been added.
  - Improvements have been made to the network protocol.
- OpenEye-drconvert>=0.6.16,<0.7.0
  - Minor bug fixes have been made.

Bugfixes¶

RecordToCollectionCube no longer crashes when given records without metadata.

v0.2.0 January 2019¶

Cuberecord has been removed as a dependency in favor of simplified API added to the orionplatform library.
- This API will replace Cuberecord going forward, though Cuberecord will continue to be usable within Orion.

v0.1.14 February 2019¶

Requirement changes:
- OpenEye-drconvert>=0.6.15,<0.7.0
  - More options for conversions have been added. In addition, only a single pass for molecular formats that don’t contain SD data is now required.
- OpenEye-datarecord>=0.12.9,<0.13.0
  - A new Link type and support with links have been added.
- OpenEye-orionclient>=0.6.12,<0.7.0
  - New APIs have been provided for creating links from Orion Resources and retrieving the link data.
- OpenEye-Floe>=0.6.22,<0.7.0
  - Local failures of parallel jobs has been fixed.
  - The default memory usage of cubes has been reduced from 2048 MB to 1800 MB.
  - The many argument to Parameters is now supported.
- OpenEye-schemagen>=0.3.4,<0.4.0
  - More options for generating schemas has been added.

v0.1.13 January 2019¶

Requirement changes:
- OpenEye-drconvert>=0.6.13,<0.7.0
  - Now calls:py:meth:flush() before returning records from MolFileConverter.
- OpenEye-datarecord>=0.12.7,<0.13.0
  - A new method flush() has been added to OERecord that writes all cached values to bytes.
- OpenEye-schemagen>=0.3.3,<0.4.0
  - Minor cleanup has been performed.

v0.1.12 December 2018¶

Requirement changes:
- OpenEye-drconvert>=0.6.12,<0.7.0
  - Whitespace in SD data is now handled.
- OpenEye-floe>=0.6.19,<0.7.0
  - A bug where ProxyCubes had their specs cleared has been fixed.
- OpenEye-orionclient>=0.6.10,<0.7.0
  - The Orion Client is now more robust to handling API changes.
  - Sharing no longer requires default permissions.
  - An issue with unsharing resources shared with organizations has been fixed.

v0.1.11 November 2018¶

Requirement changes:
- OpenEye-floe>=0.6.18,<0.7.0
  - parameter_overrides are now honored locally.
- OpenEye-datarecord>=0.12.6,<0.13.0
  - An issue which caused conformer titles to be missing has been fixed.

v0.1.10 November 2018¶

Requirement changes:
- OpenEye-schemagen>=0.3.2,<0.4.0
- SD data consisting of only whitespace now survives.
- OpenEye-datarecord>=0.12.5,<0.13.0
- More testing for metadata has been added.
- A new metadata flag, Meta.Flags.Predicted, has been added to datarecord.
- OpenEye-floe>=0.6.17,<0.7.0
- A default value of 1000 for max_parallel parameter on Parallel cubes has been added.
- The assumption that platform supports POSIX signal handling has been fixed.

v0.1.9 October 2018¶

Requirement changes:
- OpenEye-schemagen>=0.3.1,<0.4.0
  - Delimiters now ordered by descending priority.
- OpenEye-orionclient>=0.6.9,<0.7.0
  - 0.6.9
    - Adds headers to improve debugging capabilities.
  - 0.6.8
    - A new exception, OrionTimeout, has been added that indicates that a request couldn’t be made to the specified Orion within the expected time.
    - Several exceptions that were being raised in the CLI have been resolved.
- OpenEye-floe>=0.6.15,<0.7.0
  - 0.6.15
    - An issue that caused parallel workers to incorrectly propagate failures when run in Orion has been fixed.
  - 0.6.14
    - A bug with promoted parameter titles in hypercubes has been fixed.
  - 0.6.13
    - Workfloe specification validation has been improved.
- cuberecord>=0.16.3,<0.17.0
  - An issue with using fast_read parameter outside of Orion has been fixed.

v0.1.8 October 2018¶

Requirement changes:
- OpenEye-orionclient>=0.6.7,<0.7.0
  - The reliability of configuring profiles using ocli config profile has been improved.
  - Uploading and downloading of shards is now retried.
  - A new ocli jobs watch command has been added.
  - The memory footprint of Dataset.records() iterator has been reduced.
- OpenEye-datarecord>=0.12.4,<0.13.0
  - A minor bug where child records would get a extra field when deserialized has been fixed.
- OpenEye-cuberecord>=0.16.2,<0.17.0
  - A memory leak in DatasetReaderCube has been fixed.
  - Improves the robustness of Collection handling

v0.1.6 September 2018¶

Requirement changes:
- OpenEye-floe>=0.6.12,<0.7.0
  - 0.6.12
    - Includes parameter name in all validation errors.
    - A flag has been added to input buffers for whether an input request has been sent has been added.
- OpenEye-orionclient>=0.6.5,<0.7.0
  - 0.6.5
    - A new organization_feedback_email attribute has been added to UserProfile.
  - 0.6.4
    - An open method has been added to ShardCollection.
    - open and close sub-commands have been added to the collections command.
    - Additional keyword arguments to list commands on the CLI.
    - ocli files list now has the --name and --project filters.
    - ocli datasets list now has the --name and --project filters.
    - ocli workfloes list now has the --name and --package filters.
    - ocli collections list-shards now has the --name filter.
    - ocli jobs list now has the --name filter.
    - ocli secrets list now has the --name filter.
    - ocli services list now has the --name filter.
    - An issue that caused the lose of filters on pagination when paginating large numbers of resources has been fixed.

v0.1.5 September 2018¶

Requirement changes:
- OpenEye-cuberecord>=0.16.1,<0.17.0
- OpenEye-datarecord>=0.12.3,<0.13.0
- OpenEye-drconvert>=0.6.11,<0.7.0
- OpenEye-schemagen>=0.3.0,<0.4.0
- OpenEye-floe>=0.6.11,<0.7.0
- OpenEye-orionclient>=0.6.3,<0.7.0

v0.1.4 September 2018¶

Explicit requirements for drconvert and schemagen have been added.
Trust semantic versioning is being honored for patches