CHANGELOG.rst

Changelog

v9.6.3

Fixed

• Allow empty body in put post patch requests with rsa requests

v9.6.2

Fixed

• Always rebuild authorization headers even on redirects

Updated

• Pin CI environment to Ubuntu 20.04 to support running Py 36 tests

v9.6.1

Updated

• Transcriptic CLI to use "strateos" not "transcriptic" as default API root

Updated

• Preferring Bearer token over user token when configuring Connection session.
• Using json-api runs endpoint to fetch project runs instead of previous project-runs endpoint. Change was made to avoid possible timeouts, and improve efficiency. Fields returned from the original project-runs api call were limited to the fields used by the cli. This may be a BREAKING CHANGE if using config.runs method.

v9.6.0

Fixed

• requests dependency to requests>2.21.0,<3
• upload-release command to release archive requires the user_id of the session.
• Linting, equivalence, and docstring issues.

Updated

• Updated pillow version <=8,<9
• Pandas version to >=1, <2 to support Python 3.9

Added

• Python 3.9 support

v9.5.0

Updated

• Jinja2 version >=3.0 to be compatible with the data-processor-service.

Fixed

• upgraded base docker image to 3.7 to fix nbgitpuller error

v9.4.2

Added

• Stdout the detail error_info of the generation_errors in the launch request.

v9.4.1

Added

• optional predecessor_id argument in commands.launch. and config.submit_launch_request If passed, will populate on web.

v9.4.0

Added

• New -e/--exclude and -i/--include flags to exec. It filters out the autoprotocol instructions in the backend.

v9.3.1

Fixed

• Adapt the backend url resolution with the new configuration of the frontend client.

v9.3.0

Added

• A new -tc-suggestion/--time-constraints-are-suggestion flag to exec.
• A new --no-redirect flag to exec. It allows the endpoint of the scle test workcell instance to be used, instead of the client dashboard.

Fixed

• The workcell id in exec was forced to be wcN. There is now no restrictions.

Updated

• Added support for sessions and absolute time constraint in exec CLI command. Added "--sessionId", "--schedule-at", and "--schedule-delay" flags.
• The api url expected by the exec method has been changed to be the url of the new dashboard (unless --no-redirect is used). It has the shape: base_url/facility/workcell. It does not require http to be added anymore.

v9.2.0

Added

• A new generated_containers attribute to the Instruction object

v9.1.0

Added

• A new exec command to send autoprotocol to a test workcell
• isort for automatic import sorting
• Example initial tests for commands file using responses pattern, starting with submit and projects.
• Deprecation warning for existing -i option for projects command.
• Binder build cache step
• All API requests will now pass the organization context as a request header

Fixed

• Issue with CodeCov for GitHub action CI
• -i option for projects command did not output anything to console when called from cli.
• Pinned numpy to <=1.19.5 due to an incompatibility issue with numpy 1.20.0 on python 3.7

Updated

• Added new option "--names" to projects CLI command. This is meant as a better named and more intuitive replacement for the existing -i option.
• Returned more explicit error statuses for projects and submit commands.
• Remove notebooks directory as we break it out into a separate repository
• Plumbed test posargs through to allow local execution of specific test files.
• Autoprotocol dependency to >=7.6.1,<8 for Instruction informatics attribute

v9.0.0

Added

• example notebook for Analysis package exploration
• sample Absorbance and Kinetics datasets
• transcriptic.sampledata module for enabling mocked Jupyter object exploration without establishing an explicit connection
• example notebook for Jupyter object exploration
• Downloads badge to keep track of usage

Updated

• Migrated from travis to github actions as a CI backend
• Remove unused scipy dependency
• Break out Jupyter objects into individual files. This affects direct imports from transcriptic.jupyter.objects

v8.1.2

Fixed

• Issue with bash syntax for Travis config

v8.1.1

Added

• Codecov configuration for coverage
• Binder badge and updated Dockerfile

Fixed

• Repeated deploy issue with Travis config
• Encoding error when using dataset upload API with request signing enabled
• Bad request error when making calls to non-Strateos endpoints (e.g. S3) with authorization headers set

v8.1.0

Added

• Support bearer token authentication

Updated

• Pin black version to 20.8b1 for local dev env consistency
• Remove util.robotize/humanize and change callers to use autoprotocol directly

v8.0.0

Added

• .readthedocs.yml configuration for docs building, corresponding badge
• pre-commit framework and linting
• auto-deploy functionality
• Fish completions
• Autoprotocol dependency for analysis package

Updated

• Transitioned all .md files to .rst files
• Doc dependencies, Sphinx to 2.4, releases to 1.6.3, sphinx-rtd-theme to 0.4.3
• Test dependencies, pytest to 5.4, pylint to 2.5.2, tox to 3.15
• Travis build reorganized to distinct jobs
• Support for Python 3.8
• Made adding autocomplete functionality more explicit
• Base CLI test framework
• Standardize on kebab-case for cli commands
• Plotly dependency to 1.13
• Matplotlib dependency to 3.0.3
• Spectrophotometry plots now render offline
• Dataset object html representation increased

Fixed

• Kinetics.Spectrophotometry.plot() function now works again
• Spectrophotometry.Absorbance/Fluorescence/Luminescence plot() works again

Removed

• References to Phabricator
• Support for Python 3.5

v7.1.0

Added

• Add optional Run title to Launch command

Fixed

• Removal of can_submit_autoprotocol feature group in the default .transcriptic

v7.0.0

Added

• zsh auto-completion support

Updated

• Support only Python >=3.5, drop Python 2 support
• Pin dependencies
• Email references to point towards strateos

v6.0.0

Added

• Added Connection.from_default_config() method and tests
• Added Connection.modify_aliquot_properties() for aliquot property managment

Updated

• Lint and docs, test cleanup
• Starter work on testing Connection methods.
• Updated dependencies to only support python 2.7 and python >=3.5

v5.6.0

Updated

• run tox tests against python 3.5 instead of 3.4

Added

• lint and build docs with tox
• DataObject class which should help ease the transition from Datasets to DataObjects with regards to fetching data.

Fixed

• doc and lint errors

v5.5.1

Fixed

• Docstring building

v5.5.0

Added

• attachments attribute on Dataset

Fixed

• Analyzed Dataset content-disposition

v5.4.1

Updated

• Separated out the CLI logic into programatically callable functions.

v5.4.0

Added

• Ability to filter by package id when using transcriptic launch

v5.3.10

Updated

• Made transcriptic analyze command visible to all

v5.3.9

Updated

• Analyze handles missing pricing information.

v5.3.8

Updated

• Jinja2 dependency made less strict

v5.3.7

Fixed

• Fixed dataset and release uploading.

v5.3.6

Fixed

• Fixed encoding bug with Python 3

v5.3.5

Fixed

• Fixed backwards compatibility bug with using makedirs with Python 2

v5.3.4

Updated

• Added transcriptic generate_protocol <NAME> that generates a scaffold of a python protocol.

v5.3.3

Updated

• transcriptic summarize now has an optional --html argument. When specified it will return a url to view the autoprotocol.

v5.3.2

Updated

• transcriptic select_org now has an optional organization argument. When specified, i.e. transcriptic select_org my_org, it’ll skip the prompt and set the organization value to my_org directly.

v5.3.1

Updated

• transcriptic login now properly respects the --api-root option and persists the result into the dotfile

v5.3.0

Updated

• transcriptic launch --save_input now outputs the same type of JSON ### Added
• test flag to transcriptic launch, enabling the submission of test runs via the launch command

v5.2.0

Added

• warp_events, a new property of the Instruction object is added. This provides information on discrete monitoring events ### Updated
• Instruction object now has an Id field ### Fixed
• Fixed issue with broken direct imports of Jupyter objects (e.g. from transcriptic import Run)

v5.1.0

Updated

• Shifted non-core cli dependencies (i.e. those used in analysis) to the extras_require field
• Shifted relative imports in base __init__ file to make this possible
• Shifted objects to a separate Jupyter module, but preserved existing relative imports path for backwards compatibility
• Documentation updated to reflect the changes

v5.0.4

Fixed

• Error with transcriptic launch --local when a file is provided

v5.0.3

Fixed

• FileNotFound incompatibility error for Python2 (when ~/.transcriptic file isn’t specified)

v5.0.2

Fixed

• Made cookie updates actually update headers

v5.0.1

Fixed

• in Connection.upload_dataset(), only convert io.StringIO instance to bytes, not StringIO.StringIO instance
• Issue with upload-release

v5.0.0

Added

• Added concept of HiddenOption and email and token as input parameters ### Updated
• Use Sessions object for maintaining persistent api connection
• Reworked env_args and headers setting and getting to be clearer and more consistent
• CLI now automatically fits flags in the order of: –flag, environment variable, .transcriptic
• More formal support for cookie-based authentication ### Fixed
• Improvements to the way non-unique projects are handled
• Improved error handling for Py2 ### Removed
• use_environ flag is now deprecated in Connection. Please specify environment parameters directly
• organization is now deprecated from Connection. Please use organization_id instead

v4.3.0

Updated

• Reworked the structure of run.data to be more verbose

v4.2.1

Added

• transcriptic upload_dataset to CLI

v4.2.0

Added

• upload_dataset to api object and surrounding infrastructure ### Updated
• Dataset object is now initialized via a more stable route ### Fixed
• Reworked run.data route based on changes to web response

v4.1.2

Fixed

• Quick bugfix to run.data route due to breaking web change

v4.1.1

Fixed

• Minor bug with default behavior with select_org prompt in select_org and login

v4.1.0

Added

• transcriptic payments to view payment methods and their corresponding ids
• --payment flag to launch and submit to allow specification of payment methods ### Updated
• transcriptic launch now presents and the price and asks for a confirmation before proceeding. --accept_quote flag is added which will override the confirmation

v4.0.1

Fixed

• Remote behavior of transcriptic protocols
• Missing container key in Dataset initialization now returns a warning instead of an error

v4.0.0

Added

• Conditional display of views based on enabled feature_flags ### Updated
• Default behavior of protocols and launch to remote instead

v3.12.0

Added

• New –json flag for runs, projects and protocols for fetching JSON ### Fixed
• Fixed bug in PlateRead that caused data overwrites if multiple instances of the same group_label were present

v3.11.0

Updated

• Handling of 403 routes
• Documentation to reflect permissions changes
• Minor rework of launch_request

v3.10.3

Fixed

• Bug with launch_request

v3.10.2

Fixed

• AP2EN_test failures still requiring protocol
• object.py requirement for autoprotocol.container_types

v3.10.1

Fixed

• Minor bugfix for _parse_protocol

v3.10.0

Updated

• Removed setup.py requirement for autoprotocol-python

v3.9.2

Fixed

• Bugfix to resolve error caused by attempting to print unicode characters on the CLI.

v3.9.1

Fixed

• Bugfix to remove data_keys from Absorbance function, which is no longer returned from webapp

v3.9.0

Added

• Add raw_data property to the Dataset object
• Add ability to cross reference aliquots with their data using the Dataset object

v3.8.0

Added

• Ability to add --dye_test flag to transcriptic preview to convert a run into a water/dye test

v3.7.1

Fixed

• Fixed minor bug in launching local protocols with transcriptic launch

v3.7.0

Added

• Ability to browse your inventory using the transcriptic inventory command E.g. transcriptic inventory water
• Ability to launch protocols remotely using the --remote flag. E.g. transcriptic launch Pipetting --remote
• Ability to view available remote protocols for launching using transcriptic protocols --remote
• Ability for transcriptic summarize to retrieve resource strings with the --lookup flag

Fixed

• resources route has been updated to match web return
• Ap2En for dispense and provision
• resources route now accepts resource IDs

v3.6.0

Added

• Object helpers to allow more natural property access. E.g. myRun.instructions.Instructions = myRun.Instructions

Updated

• Misc formatting changes for HTML representation

Fixed

• Underyling handle_response code to be more robust

v3.5.1

Added

• Row index of the Container.aliquots DataFrame object now corresponds to the well index

Fixed

• Stored volume in the Container.aliquots DataFrame as a Unit object instead of unicode

v3.5.0

Added

• timeout property for Run objects
• data_ids property for Run objects

Updated

• data property for Run objects gives more informative errors when failing due to timeout
• .monitoring method is now shifted to the Instruction object from the Run object
• Optional parameters can now be handled by get_route ### Fixed
• Existing route for monitoring data

v3.4.3

Fixed

• Made local commands robust to lack of internet access

v3.4.2

Fixed

• Broaden exception clause for general Python compatibility

v3.4.1

Added

• Usage analytics support to CLI ### Updated
• Minor documentation fixes

v3.4.0

Added

• transcriptic select_org in CLI now allows you to switch organizations without re-authenticating
• User-agent information to headers
• Run.containers to return a list of containers used within the run

v3.3.1

Fixed

• Updated transcriptic runs route to reflect reality

v3.3.0

Added

• Ability for api.get_zip to handle larger zip-files by downloading to a local file
• cover and storage attributes to Container object
• Ability to construct and visualize a given protocol’s job tree using a flag on the CLI ### Updated
• Updated english’s summarize to handle all currently-implemented instructions

v3.2.5

Fixed

• Fixed initialization of Container object

v3.2.4

Added

• Helper function flatmap into util ### Fixed
• Fixed resources route in CLI. transcriptic resources 'query' now works

v3.2.3

Updated

• Simplified Container._parse_container_type to use matching AP-Py container-type object whenever possible

v3.2.2

Added

• additional documentation for Connection object ### Updated
• update relevant documentation.rst files

v3.2.1

Updated

• Updated “url” reference in run attributes to use “id” instead, in-line with a web update ### Fixed
• Update docs/requirements.txt to be PEP440 compatible

v3.2.0

Updated

• Reworked Instruction object
• Reworked Run.instructions to return a Dataframe of Instruction objects
• Aliquot object has been reworked into Container object as an aliquots property

Removed

• Resource object has been removed from the library as its currently unused

Fixed

• Change check for ImagePlate to be more generic
• Setup now requires plotly 1.9.6 (for plotly offline/ipython compatibility reasons)

v3.1.0

Added

• Tab completion for CLI (enabled by sourcing transcriptic_complete.sh)
• New API route for getting zipfiles: api.get_zip
• Made -h option synonymous with –help

v3.0.2

Updated

• Setup now requires plotly 1.9.6 or greater

v3.0.1

Fixed

• Better handling of Datasets with no well_map property in kinetics.spectrophotometry

v3.0.0

Added

• New documentation for the new testing framework and how to write tests
• Added Dockerfile for running Transcriptic containers. Compatible with CI tools (e.g. Jenkins) as well
• New documentation added and hosted on http://transcriptic.readthedocs.io/en/latest/

Updated

• Migrated the test framework from vanilla unittest2 to py.test
• Rewrote documentation structure and added misc. documentation related changes
• api module has been removed and merged into config module. The Connection object now handles all api calls.
• All references to ctx has been renamed to api

Fixed

• Fixed bug in spectrophotometry handling attributes
• Fixed compatibility issue with running transcriptic preview on python3

v2.3.1

Updated

• Transcriptic CLI subcommands: compile, init, preview, summarize no longer require login

Fixed

• transcriptic runs command now works in CLI

v2.3.0

Added

• __version__ variable for checking version. Enable version checking in CLI using transcriptic --version
• New Analysis module: Kinetics; Kinetics base object and Kinetics.Spectrophotometry for analyzing kinetics-based data such as growth curves
• Expose additional properties of Dataset object: operation, container, data_type

v2.2.1

Updated

• Objects module has been heavily reworked and documentation added. This is especially true for Project, Run and Dataset objects

Fixed

• Fixed package related CLI issues

v2.2.0

Added

• api module for handling all calls including responses and exceptions
• Connection object now mirrors most of the CLI functionality
• basic test infrastructure and examples for testing API module

Updated

• all separate requests, context or connection object calls are now consolidated and re-routed to go through the api and routes module

Removed

• all direct api calls (get, put, push, pull) are removed from Connection. Users are encouraged to use the corresponding calls from the api module instead

v2.1.2

Fixed

• Change in datasets route

Updated

• Removed additional shadowed variable names

v2.1.1

Added

• imaging module with ImagePlate as the first class for representing plate images. Focus is placed on IPython rendering
• PIL dependency for image manipulation

v2.1.0

Updated

• Major refactor of code to be in-line with PEP8
• Removed unnecessary modules and renamed shadowed variables

v2.0.11

Updated

• Updated behavior of transcriptic login to be clearer and to return appropriate error messages

Fixed

• print statement for launch

v2.0.10

Added

• pypi tags for setup.py such as classifiers and license

Fixed

• Updated Container object to automatically populate safe_min_volume_ul

Removed

• Unused dependency: scikit-learn

v2.0.9

Added

• Updated manifest json parsing to deserialize into an OrderedDict, preserving key order, which enables quick launch inputs to be ordered

v2.0.8

Added

• launch command now supports –save_input option to save the protocol input as a local file

Fixed

• launch command now properly supported either a project name or project id for the project option
• typo AutoProtocol -> Autoprotocol

v2.0.7

Added

• launch command to configure and run protocols without needing to package and upload them first

v2.0.6

Fixed

• RMSE calculation in spectrophotometry.py now reports correct RMSE
• transcriptic submit now correctly parses new autopick group
• containter attributes are correctly requested from transcriptic via spectrophotometry.py

v2.0.5

Added

• List runs in a specific project using the transcriptic runs <project_name_or_id command

v2.0.4

Added

• Enabled analyze and submit to work for Protocol objects
• Additional functionality to Container object: Use your favorite autoprotocol ContainerType functions
• Additional properties of Container object exposed: Use wellMap to return a mapping of the well indices to aliquot names

Fixed

• Set plot to default to use mpl=true (not all users have plotly credentials)

v2.0.3

Added

• cost breakdown in analyze
• Python 3 compatibility
• use transcriptic preview --view to return a URL that displays the instruction cards produced by the run you want to preview (this URL expires after two hours)
• use the ‘transcriptic resources ’ CLI command to search the catalog for a resource’s vendor and id
• plotly and future are now required

Fixed

• dataset helpers and embedding

Removed

• ipython module

v2.0.2

Updated

• Refactored analysis.spectrophotometry into Fluorescence, Absorbance and Luminescence classes that inherit from PlateRead

Added

• More documentation and related configuration
• Python 3 support
• Added cost breakdown to analyze CLI

Fixed

• bug with initializing runs with Project object

v2.0.1

Added

• project url and description to setup.py
• Aliquot, Resource and Container object types
• documentation setup and configuration

Updated

• moved submit from cli to __init__

Fixed

• critical bug in submit
• bug in analyze
• bug in create_project

v2.0.0

Updated

• migrated content from transcriptic/runner to here, converted that code to a Python Client Library,
• CLI functionality has not changed other than renaming some commands:
  • release –> build-release
  • upload –> upload-release
  • new-project –> create-project
  • new-package –> create-package
  • run –> compile