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
Fixed¶
upgraded base docker image to 3.7 to fix nbgitpuller error
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.
v9.3.0¶
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.
v9.1.0¶
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
v8.1.1¶
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 testsAdded
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
v5.3.4¶
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 optionalorganization
argument. When specified, i.e.transcriptic select_org my_org
, it’ll skip the prompt and set the organization value tomy_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 ### Addedtest
flag totranscriptic launch
, enabling the submission of test runs via the launch command
v5.2.0¶
Added¶
warp_events
, a new property of theInstruction
object is added. This provides information on discrete monitoring events ### UpdatedInstruction object now has an
Id
field ### FixedFixed 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
fieldShifted relative imports in base
__init__
file to make this possibleShifted
objects
to a separate Jupyter module, but preserved existing relative imports path for backwards compatibilityDocumentation updated to reflect the changes
v5.0.3¶
Fixed¶
FileNotFound incompatibility error for Python2 (when ~/.transcriptic file isn’t specified)
v5.0.1¶
Fixed¶
in
Connection.upload_dataset()
, only convert io.StringIO instance to bytes, not StringIO.StringIO instanceIssue 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 connectionReworked 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 inConnection
. Please specify environment parameters directlyorganization
is now deprecated fromConnection
. Please useorganization_id
instead
v4.2.0¶
Added¶
upload_dataset
to api object and surrounding infrastructure ### UpdatedDataset object is now initialized via a more stable route ### Fixed
Reworked
run.data
route based on changes to web response
v4.1.0¶
Added¶
transcriptic payments
to view payment methods and their corresponding ids--payment
flag tolaunch
andsubmit
to allow specification of payment methods ### Updatedtranscriptic 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
andlaunch
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
v3.10.2¶
Fixed¶
AP2EN_test failures still requiring protocol
object.py requirement for
autoprotocol.container_types
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
objectAdd ability to cross reference aliquots with their data using the
Dataset
object
v3.8.0¶
Added¶
Ability to add
--dye_test
flag totranscriptic preview
to convert a run into a water/dye test
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 objectOptional parameters can now be handled by
get_route
### FixedExisting route for monitoring data
v3.4.0¶
Added¶
transcriptic select_org
in CLI now allows you to switch organizations without re-authenticatingUser-agent
information to headersRun.containers
to return a list of containers used within the run
v3.3.0¶
Added¶
Ability for
api.get_zip
to handle larger zip-files by downloading to a local filecover
andstorage
attributes to Container objectAbility 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
v3.2.4¶
Added¶
Helper function
flatmap
into util ### FixedFixed 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 ### Updatedupdate 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
objectReworked
Run.instructions
to return a Dataframe ofInstruction
objectsAliquot
object has been reworked into Container object as analiquots
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
v3.0.0¶
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 intoconfig
module. The Connection object now handles all api calls.All references to
ctx
has been renamed toapi
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 usingtranscriptic --version
New Analysis module: Kinetics;
Kinetics
base object andKinetics.Spectrophotometry
for analyzing kinetics-based data such as growth curvesExpose 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 exceptionsConnection
object now mirrors most of the CLI functionalitybasic 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
v2.1.1¶
Added¶
imaging
module withImagePlate
as the first class for representing plate images. Focus is placed on IPython renderingPIL 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
andlicense
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 theproject
optiontypo 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
andsubmit
to work for Protocol objectsAdditional 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
andfuture
are now required
Fixed¶
dataset helpers and embedding
Removed¶
ipython module
v2.0.2¶
Updated¶
Refactored analysis.spectrophotometry into
Fluorescence
,Absorbance
andLuminescence
classes that inherit fromPlateRead
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
andContainer
object typesdocumentation setup and configuration
Updated¶
moved
submit
fromcli
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