Release History

Orion Version

Orion Platform Version

Release Date

End of Support

2023.3.1

6.1.2

2024/02

2025/02

2023.2.1

6.0.0

2023/09

2024/09

2023.1.2

5.1.1

2023/07

2024/07

2023.1.1

5.0.0

2023/04

2024/04

2022.3.1

4.5.0

2022/11

2023/11

2022.2.1

4.4.0

2022/06

2023/06

2022.1.1

4.3.0

2022/02

2023/02

2021.2.1

4.2.2

2021/11

2022/11

2021.1.1

4.0.0

2021/06

2022/06

This table does not cover versioning of all subcomponents in Orion.

Caution

Compatibility Notes

Although releases are supported for one year, Orion maintains high levels of compatibility between versions. However, the following notes should be kept in mind.

  • Old Cubes may not be able to be connected to newer Cubes if the Floe specification version is mismatched.

  • There may be external reasons involving pip or 3rd party dependencies that prevent an old Floe package from being uploaded.

  • Newer versions of Orion Platform may not run against older Orion stacks, and they will raise an error if they require a new API or version of an API.

Orion 2021.1.1 introduced a check on the minimum version of Orion Platform for new Floe package uploads.

Version 2023.3.1 Highlights for Cube and Floe Developers

Orion Integration, Version 2023.3.1

The following dependencies should be observed by Cube and Floe developers.

Dependency

Previous

Current

requests

2.30

2.31

requests-toolbelt

0.10.0

1.0.0

packaging

22.0

24.0

flatbuffers

2.0

23.1.21

v6.1.2

Orion Client

  • Updated example docker files were added with Amazon Linux 2023 and Ubuntu 22 commands.

  • WorkFloeJob.start() now accepts the notify=True flag to send a job completion email.

  • ocli datasets download now supports the –fieldlist argument to optionally export only select dataset columns. This comma-delimited list can contain either column names or column IDs.

  • OrionSession.delete_resource and ocli TYPE delete now support an immediate flag for files, datasets, collections, and projects.

  • Orion server minimum version has been upgraded to 19, thus requiring use of an Orion 2023.3.1 stack.

  • ocli jobs summary-export has been added to generate a job summary CSV file for an organization according to the request parameters. See Retrieving Summary of Jobs Within an Organization.

Bug Fixes

  • When you share a job via orionclient with session.share_resource (WorkFloeJob_instance, project_id), other members of the project can see the job in the UI. There are cases, however, where a user has access to a job but not the underlying Floe (e.g., a custom Floe that was not shared). The user could see the job but reached an uninformative blank screen when they clicked on it. The action now produces an error message.

Orion Platform

  • Columns can now be optionally ignored when exporting datasets to files. This functionality is available only in Orion.

  • A bug has been fixed in which floes using the RecordsToFileConverter Cube produced bloated files when only in Orion.

  • A bug has been fixed in which Floes using the RecordsToFileConverter Cube produced bloated files when exporting to CSV.

Floe

  • A new Cube parameter, max_backlog_wait, has been added. This parameter specifies the maximum number of seconds a Cube will be backlogged on a scaling group before being reevaluated for placement on another scaling group.

Version 2023.2.1 Highlights

  • Version 2023.2.1 includes a host of performance and stability improvements.

  • Package ingestion within Orion has been improved.

    • The environment log is now available during processing.

    • Log messages are clearer, with timestamps and phase timing.

    • Conda error messages are now more fully preserved.

  • Support for Python 3.11 has been added.

  • Support for docker-based Orion packages based on Amazon Linux 2023 (AL2023) and Ubuntu 22 (ubuntu22) has been added.

Orion Integration, Version 2023.2.1

  • The dependency attrs>=23.0.0,<24.0.0 is pinned to avoid an upstream RuntimeWarning.

  • Python ≥ 3.9 is required.

v6.0.0

Floe

  • A new cube parameter pids_per_cpu_limit has been added. This parameter allows users to configure the amount of available pids (processes/threads) in a cube.

Orion Client

  • Serial cubes will now retry http codes 409, 429, 460, 500, 502, 503, and 504 indefinitely

  • File download uses helper to check for incomplete download, retries three times

  • Project tags are tags on resources in Team Data on the Project Data page. They are visible to all project members and are colored pink in the user interface. Any member of a project can now add project tags to any resource in Team Data. Resources are now searchable via their project tags in the Orion user interface and with Orion Client. Tags are managed with ocli jobs commands.

Orion Platform

  • Molecule titles are now preserved when exporting records to CSV format.

  • Conversion of datasets to CSV has been streamlined by removing the need to read all records prior to conversion.

  • A nonprimary molecule field is used if available when a primary molecule field is not present when converting a record to an OEMol.

  • DatasetReader cubes may now be used inside or outside of a CubeGroup without the need to set fast_read.

DRConvert

  • Placeholders are now written within OEFields instead of images when converting records to molecular file formats.

  • Columns containing primary molecules are now added as the first column when exporting datasets to CSV files, with their titles exported as the second column.

Version 2023.1.2 Highlights

  • Version 2023.1.2 is a maintenance release containing performance and stability improvements developed at OpenEye.

  • Python ≥ 3.9 is required.

Orion Integration, Version 2023.1.2

  • The dependency requests==2.29 is pinned to avoid conflicts.

  • A memory leak was causing large numbers of simultaneous jobs to fail. The leak, now fixed, could cause failure with ≥ 100 jobs running simultaneously. A symptom was a message with:

    [...., State=Suspect] removed: Error[NoError]]

v5.1.1

Orion Client

  • We have modified rate limiting. We have added a mechanism to help the Orion client tell if it is running in Orion as a serial cube or as a parallel cube. If the current client is a parallel cube running in Orion, retries are limited to 2; if the current client is a serial cube, retries continue indefinitely.

Orion Integration, Version 2023.1.1

v5.0.0

  • Bumps __api_version__ to 16.0

Orion Client

  • Improved support for V2 ShardCollections

Floe

  • This is the last release before the local runtime v1 will be deprecated. To use the new local runtime, specify FLOERUNTIME=v2.

  • Cyclic CubeGroups are now supported locally and in orion.

  • A bug in Floe connections has been fixed.

  • A bug in Floe detect has been fixed.

  • URLToFileCube has been added.

  • A bug with cycle configuration has been fixed in cases where component has no external source and none of the cubes in the component are sources.

  • The default string representation for Cubes has been changed to prioritize using a cube’s name instead of title.

  • A validation check has been added to prevent floes from containing any disconnected cubes.

  • A FloeSpecConverter utility is documented, to convert between two different floe specification versions.

Orion Platform

  • Expose nullable argument to FieldParameters.

Orion Integration, Version 2022.3.1

  • NVIDIA driver during package inspection on GPU has been provided.

  • Floe and cube tags with nested lists will be flattened during package inspection.

  • Bug where writing empty molecule would fail a floe has been fixed.

  • Better error message when package failed inspection due to lack of memory has been implemented.

  • Requirement parsing during package ingestion was not always handling local paths properly. This has been fixed

  • Openeye-orionplatform[artemis] works with more recent versions of pytest.

  • Uploaded Docker images were always saved in a user’s data. There is now an option to delete the files after they are used.

  • Package uploading and processing has been improved.

v4.5.4

Orion Client

  • A bug affecting ShardCollection creation has been fixed.

v4.5.3

Orion Client

  • A bug was fixed that was preventing ocli packages create-environment-yaml from working with standard manifest files.

v4.5.2

Orion Client

  • A bug in support for collections in Orion releases older than 2022.2.1 has been fixed.

v4.5.1

Floe

  • A bug in floe description length validation has been fixed

v4.5.0

  • The minimum release of Orion now supported is 2021.2.1

Artemis

  • The maximum allowed version of pytest is now <=7.3.0

Orion Platform

  • A bug in BaseDatasetFieldAddOrReplaceCube where datasets were not finalized has been fixed.

Orion Client

  • ocli upload-package-image and ocli import-from-orion-file now include an option to delete the image file after processing.

  • ocli packages init now includes an example of how to use prebuild and postbuld hooks.

  • ocli cost export generates spending/storage cost reports.

  • orionclient.types.accounting.export_cost_report triggers cost report generation.

Floe

  • A bug causing a circular import when running floe unit tests has been fixed.

  • A new cube parameter, shared_memory_mb, has been added. This parameter allows manipulation of docker’s --shm_size parameter when containers are launched, thus modifying the amount of RAM available to /dev/shm/ within the container.

  • A bug preventing nested list tags from being corrected has been fixed.

  • Validation of floe description has been added. Descriptions must be <= 2712 characters.

v4.4.1 September 2022

Orion Client

  • An issue where orionclient.types.Shard.download() could receive less data than expected has been fixed. An IOError will be raised and orionclient.types.Shard.download_to_file() will catch and retry.

  • An issue where mutable default function parameters were defined has been fixed. Mutable default parameters are parameters with a default value of [] or {} that get initialized once at runtime and not per function call.

  • Parallel To Serial Initializer Cube scenarios that cause deadlock are now validated.

Orion Platform

  • Documentation for Collections has been improved.

v4.4.0 June 2022

Floe

  • A new runtime for running floes locally, which can be used by setting the environment variable FLOERUNTIME=v2, has been added.

  • The ability to more intelligently choose when to start cubes, which can be used by setting the environment variable EAGER=false, has been added. Only available with new floe runtime. This option is experimental and only available locally, not in Orion.

  • Validation of cube and floe tags and classification has been fixed. If tags are nested lists, they will be flattened.

  • Support for pathlib.PurePath in floe classification has been added.

  • Support for floe brief attribute, for a <= 280 character overview description of the floe, has been added.

  • Floe spec version 1.3 has been introduced.

Orion Client

  • ocli workfloes list-classifications has been added to browse classifications.

  • ocli workfloes list now supports classification and classification_depth filters.

  • orionclient.utils.TemporaryPath has been deprecated. utils.TemporaryPath should be used instead.

  • ocli packages init default template has been updated to pass opts to floe lint floes

  • python setup.py test-all/cubes/orion has been fixed to return a correct exit code on failure

  • An issue with importing convert_path has been fixed.

  • Setup_tasks.py package command logic has been relocated into orionclient helper functions. Package command logic now able to be maintained via orionplatform updates.

  • ocli projects leave has been added

  • ocli projects unshare has been modified to accept the new-owner option

DRConvert

  • Support for fields with None values and the nullable parameter set to True has been improved.

Orion Platform

  • ~orionplatform.parameters.fields.FieldSelectorParameter is now able to handle multiple field names when many=True.

  • --system-param option has been added to ocli jobs start for specifying system parameters.

  • --path option has been added to ocli jobs start for specifying the location for job output.

  • --project option has been added to ocli jobs start for specifying the project for job output.

  • --cost-notification option has been added to ocli jobs start for specifying job cost notification threshold.

  • --cost-termination option has been added to ocli jobs start for specifying job cost termination threshold.

v4.3.2 May 2022

DRConvert

  • An issue with import drconvert has been fixed.

v4.3.1 February 2022

Orion Client

  • An issue in the template ‘setup.py’ preventing python setup.py package from updating the version in ‘manifest.json’ has been fixed.

  • Curl has been added to template Dockerfile.

  • Template Dockerfile has been updated so resulting image is close to the one in Orion.

v4.3.0 February 2022

drconvert

Orion Client

  • Snowball dependency from template for ocli packages init command has been removed.

  • ocli files upload now reports uploaded location and filename.

  • ocli datasets upload now reports uploaded location and filename.

  • ocli collections upload now reports uploaded location and directory name, as well as containing dataset for shards.

  • ocli packages check-image now fails if floe inspection report contains errors.

Floe

  • An issue with Floe’s parameter default value validation has been fixed.

  • An error in floe detect when using a relative path from the command line has been fixed.

v4.2.7 November 2021

  • Floe parameter validation now always validates default values.

v4.2.6 November 2021

  • Upload timeout errors have been reduced.

  • The effect of the --timeout option on ocli commands is now more consistent.

  • Metric period in cube parameters has been modified to contain list of valid choices.

  • ‘dev’ and ‘convert’ extras requirement installations have been added.

  • Types.Chem.DesignUnit has been added to types stored on a molecule as generic data.

  • Improvements to the boilerplate Dockerfile printed by ocli packages show-dockerfile have been made.

v4.2.5 October 2021

Orion Client

  • A new command ocli packages import-from-registry for creating a package from an image pulled from a docker registry has been added.

  • A new command ocli packages import-from-orion-file for creating a package from an existing file in Orion has been added.

v4.2.4 October 2021

Orion Platform

  • CreateCollectionCube changes:

Orion Client

  • Snowball version pin and bounded orion-platform version in scaffold package generation has been removed.

v4.2.3 October 2021

Orion Platform

  • A bug causing ‘ShardReaderCube’ to fail when the ‘collection’ parameter is not required has been fixed.

v4.2.2 October 2021

Datarecord

  • A toolkit serialization bug affecting datarecord in orionplatform 4.1.0 and 4.2.0 has been mitigated.

v4.2.1 October 2021

Floe

  • A bug causing parameter modifications to be incorrectly parsed has been fixed.

v4.2.0 October 2021

Orion Client

  • ocli packages commands to download base images, create & upload packages images to Orion have been added.

  • The total number of parts are printed for each part uploaded during a multi-part file upload.

DRConvert

  • A failure caused by CSV files containing no data for some columns has been fixed.

  • IUPAC names are no longer parsed, resulting in fewer column splits and ETL speedup.

  • A failure parsing lists of numbers has been fixed.

  • A bug in the naming of split columns has been fixed.

  • A failure when converting a record to OEB has been fixed. Fields with data that cannot be properly attached as generic data to a molecule are now skipped by default.

  • The drconvert command now supports a --verbose option.

v4.1.0 September 2021

  • Requirement changes:

    • Require OpenEye-toolkits >=2020.2.4

    • Bump maximum version of attrs

    • Bump minimum and maximum versions of chardet

    • Bump maximum version of click

    • Bump maximum version of requests-toolbelt

    • Remove structlog

    • Remove floe package dependency (functionality now built in)

Orion Client

  • A new command ocli packages init to create a Floe package template has been added.

  • A bug where ocli datasets list --project 1234 could fail to retrieve all data for large numbers of datasets due to a pagination error which would eventually create an unusable URL has been fixed.

  • ocli commands for sharing File, Dataset, and ShardCollection have been disabled in favor of Shared Workspaces and will now raise an exception instead.

  • ocli config project no longer unnecessarily prints all projects a user has access to.

  • ocli workspaces commands to create and list workspaces as well as add or remove users from a workspace have been added.

  • ocli config directory/profile is now forced to be created with read/write permissions for the owner only. All other access is disabled.

  • orionclient.types has been refactored into multiple modules; consumers should not be impacted.

Artemis

  • Issues related to internal testing have been fixed.

drconvert

  • A regression in perceiving basic molecular properties for SMILES and CSV has been fixed.

Floe

  • A bug causing cyclic floes to deadlock has been fixed.

  • A bug related to the termination of cyclic floes has been fixed.

v4.0.0 May 2021

Important

  • OpenEye-artemis, OpenEye-datarecord, OpenEye-drconvert, OpenEye-floe, and OpenEye-orionclient are no longer separate packages.

  • Orion Platform >= 4.0.0 will not work with stacks older than 2021.1 due to usage of new APIs

  • These packages MUST all be removed from Floe package requirements and from virtual environments. The OpenEye-artemis requirement should be replaced with ‘OpenEye-orionplatform[artemis]==4.x.y’, matching the version of the main Orion Platform package. Failing to make these changes will cause imports to fail.

  • Bumps OpenEye-toolkits to 2020.2.4

  • Bumps __api_version__ to 12.0

Orion Client

  • A field path has been added to Dataset, File, and ShardCollection.

    • Folder paths have the following forms:

      • /project/<project-id>/[user/<username>|workspace/<workspace-id>|team]/<path>

      • /organization/<path>

    • Folder paths begin with a /project/<project-id>/ OR /organization/ prefix. The project id is an int.

  • session.create_resource() now uses path as a key in params when resource_type is one of these types.

  • OrionSession methods added:

    • assign_paths calls the backend API for assign-path on a list of dictionary assignments mapping an object to its intended path

    • ls_path calls the backend API for ls with the given path and query parameters and returns the results.

    • stat_path calls the backend API for stat-path with the given path to determine the resource_type.

    • get_paths calls the backend API for get-path for the specified objects and returns their corresponding path(s)

    • create_paths calls the backend API for create-path to create folders with the specified paths

    • remove_paths calls the backend API for remove-path to remove the items at the specified paths

    • move_folder calls the backend API for move-folders to move the item at the specified path to the specified destination path.

    • A new command ocli cp to copy to/from an Orion folder has been added.

    • A new command ocli ls to list contents has been added.

    • A new command ocli mv to move a folder on Orion has been added.

    • A new command ocli rm to remove an item on Orion has been added.

    • A new command ocli head to peek inside a file or dataset has been added.

    • A new command ocli mkdir to create a folder on Orion has been added.

  • OrionSession changes:

    • is_authenticated has been simplified and now returns true if the session is properly configured

    • Increased retry_timeout from 5 minutes to 15 minutes

  • :py class:~orionclient.utils.Backoff changes:

    • Increased default cap from 30 to 90 seconds

    • Increased DEFAULT_BACKOFF_DICT cap to 90 seconds, except for status 500 which remains at 30 seconds

  • Dataset has been upgraded to use get_converter() and SmilesFileConverter.

  • 429s are now retried.

  • ocli timeout has been increased from 5 to 10 seconds.

  • ocli backoff cap is now relative to the timeout and max retries.

Orion Platform

Artemis

  • A new option, --rebuild-packages, ensures all packages are freshly built, deleting old packages.

  • A new option, --use-released-packages, disables package hashing and only uses packages that are already uploaded to Orion. Intended as a way to test packages once released to users.

Floe

  • Floe level promoted parameter groups to influence user interface display have been added. Created via floe.add_parameter_group(cube.existing_group) or floe.create_parameter_group("my_group_name", title="My Group", parameters=[cube.param, cube.param2, cube2.param])

  • Support for parameter group name attribute has been added.

  • Support for parameter group order and collapsed attributes to influence user interface display have been added.

  • cube.modify_parameter_group(cube.param_group, **fields) for modifying cube level parameter groups has been added.

  • floe.modify_parameter_group(floe.param_group, **fields) for modifying floe level parameter groups has been added.

  • A bug causing serial group output double counting when emitting to grouped neighbors has been fixed.

Bugfixes

  • A bug where an argument parser constructed in a floe package could conflict with floe detection has been fixed.

  • A deadlock caused by greater than 2GB aggregate of data emitted for a single item of work for a parallel cube has been fixed.

  • A bug where debug information requests to parallel cubes would hang has been fixed

DRConvert

  • A new Converter, SmilesFileConverter, has been added.

  • When converting CSV and SMILES format files to records, the original smiles are stored on output records.

  • A new function, get_converter(), has been added.

  • Link and JSONObject field data will no longer cause an error in record_to_mol.

Datarecord

  • py:class

    deprecated datarecord.utils.TemporaryPath has been removed

v3.1.3 January 2021

  • Requirement changes:

    • OpenEye-floe==0.12.2

      • FloeSpecConverter no longer raises error when converting to higher version.

      • Minor documentation fix for the default value of a Floe package’s base_os.

v3.1.2 December 2020

  • Requirement changes:

    • OpenEye-orionclient==3.1.2

      • AWS request ids are now logged from failed shard download/upload operations.

      • The timeout for shard downloads/uploads has been increased.

v3.1.1 December 2020

  • Requirement changes:

    • OpenEye-drconvert==1.1.3

      • Bump maximum supported version of attrs

    • OpenEye-orionclient==3.1.1

      • Bump maximum supported version of attrs

      • Bump maximum supported version of structlog

v3.1.0 November 2020

  • orionplatform.cubes.datasets.BaseDatasetFieldAddOrReplaceCube has been added.

  • If no file extension is provided to orionplatform.cubes.datasets.DatasetWriterCube’s output file parameter, the file format is now OEDB.

  • Requirement changes:

    • OpenEye-floe==0.12.0

      • Support for versioning of WorkFloes has been added.

      • Support for ordering of Parameters in the Orion UI has been added.

      • An issue that resulted in Serial Cube Group initializer ports not incrementing the counts has been resolved.

    • OpenEye-drconvert==1.1.2

      • Bump OpenEye Toolkits

    • OpenEye-orionclient==3.1.0

      • Bump OpenEye Toolkits

    • OpenEye-datarecord==3.0.1

      • Bump OpenEye Toolkits

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 orionplatform.cubes.FileToRecordConverter and orionplatform.cubes.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 == 1,048,576 bytes) 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 datarecord.Types.Chem.DesignUnit from “DesignUnit” to “Chem.DesignUnit”

      • datarecord.utils.TemporaryPath has been deprecated. orionclient.utils.TemporaryPath should be used instead.

      • A field type datarecord.Types.Chem.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.Dataset.records() now yields openeye.oechem.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:

    • orionplatform.cubes.collections.CollectionResizeCube

    • orionplatform.cubes.collections.CollectionToRecordsCube

    • orionplatform.cubes.collections.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 IDs 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 py:class:floe.api.parameters.BaseParameter

v2.2.0 November 2019

  • Requirement changes:

    • OpenEye-floe==0.8.9

      • An error is now raised 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 orionplatform.cubes.datasets.DatasetWriterCube Options parameter group has been removed.

v2.1.0 October 2019

  • orionplatform.cubes.datasets.BooleanSwitch and orionplatform.cubes.datasets.ParallelBooleanSwitch have been added.

  • FieldSelectorParameter which allows selecting fields by name has been added.

  • RecordBytesOutputPort 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.

      • floe.api.floes.WorkFloe.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 Secret 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, ORION_PROJECT, and 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 FieldParameter.

  • 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

      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

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

  • RecordsToCollectionCube 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

    • 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 are now ordered by descending priority.

    • OpenEye-orionclient>=0.6.9,<0.7.0

      • 0.6.9

        • Headers to improve debugging capabilities have been added.

      • 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.