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 <https://github.com/open-strateos/txpy_jupyter_notebooks>_
• 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

Breaking Changes

• Existing direct imports from transcriptic.jupyter.objects will no longer work. Please import directly from the relevant object instead. E.g. transcriptic.jupyter.run. Common imports like from transcriptic import * and from transcriptic.jupyter import Run to access Jupyter objects remains unaffected.

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

build: v8.1.2 (#180)

Fixed
- Issue with bash syntax for Travis config

build: v8.1.0 (#169)

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 (#163)

Highlights

• Numerous dependency updates, notably Python 3.5 support is dropped, while Python 3.8 support is added
• Large Infrastructure Improvements, including using black for auto-formatting, pre-commit for lint and cleaner Travis builds
• Bugfixes and Improvements to Analysis package - Plotting functions and Dataset representations
• CLI http-signing support, standardized to kebab-case and auto-completion support for Fish

Full Changelog

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

v3.2.0

Summary

There has been a number of updates since the last major release (v3.0.0) covering additions to the API, changes to analysis objects as well as other misc. fixes.

On the CLI front, tab completion can now be enabled by sourcing transcriptic_complete.sh. Detailed instructions can be found in README.md. Also, the -h flag now prints help.

On the analysis front, the Instruction and Aliquot objects have been reworked. All the objects listed in the documentation are now stable and have complete functionality.

Changelog (since v3.0.0)

Added

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

Changed

• 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

Fixed

• Better handling of Datasets with no well_map property in kinetics.spectrophotometry
• Change check for ImagePlate to be more generic

Removed

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

v3.0.0

Summary

There are some major additions in v3.0.0 with the general direction towards being more developer friendly. Most notably, the underlying test framework has been updated to use py.test and documentation has been completely overhauled.
A Dockerfile has also been added for those interested in running TxPy with a pre-configured environment.

Last but certainly not least, the default connection object previously named ctx has now been renamed to api to reflect its usage and purpose. This changes a commonly used object in TxPy and is NOT backwards compatible, so please bear that in mind when upgrading.

Changelog

Added

• 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/
• New documentation for the new testing framework and on how to write tests

Changed

• 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

v2.3.0

Summary

A new Kinetics module has been added for analysis of kinetics experiments. In particular, multiple Spectrophotometry (e.g. Absorbance) datasets can now been batched together and plotted as a single curve.

As part of the ongoing Objects refactorization, more relevant properties and documentation has been added for the Dataset object. Note that Transcriptic objects are the recommended way of interacting with Transcriptic data in a Jupyter notebook environment.

Changelog

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