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Changelog

Changelog

All notable changes to this project will be documented in this file. Dates are displayed in UTC.

Generated by auto-changelog.

3.14.0

21 March 2025

  • feat: ability to view docking results in 3D #166

3.13.0

20 March 2025

  • feat: overhauled docs #164
  • Bugfixes mar 18 2 #163
  • core: added comments about PyPI actions #162
  • fix: another small bugfix #161

3.12.1

18 March 2025

  • fix: small bugfixes #160

3.12

18 March 2025

  • Small fixes and improvements #159
  • Fixes 17 mar #158
  • fix: mistakes in docs #157
  • feat: simpler install #156

3.11.1

17 March 2025

  • feat: switched all docs to be python-first #155

3.11.0

17 March 2025

  • New Complex class, better support for ABFE/RBFE/Docking #154

3.10.0

11 March 2025

  • RBFE + docking support #153

3.9.0

10 March 2025

  • feat: improvements to SDF tools #152

3.8.1

5 March 2025

  • Abfe improvements #151

3.8.0

5 March 2025

  • Support for new FEP class that can do both ABFE and RBFE #150

3.7.0

3 March 2025

  • ABFE tools improvements #149
  • feat: better abfe workflow #148

3.6.0

3 February 2025

  • chore: bump platform SDK to 2.0.0 #147

3.5.0

31 January 2025

  • FEP: tooling to run ABFE #146
  • feat: update draco docs #145
  • feat: interrupting wait_for_jobs leads to a clean exit #144

3.4.0

23 January 2025

  • feat: high level toolkit for running ligand and docking #143
  • fix: reverting change in auth_domain #142

3.3.0

15 January 2025

  • feat: dashboard for jobs #139
  • feat: added images of databases #141
  • feat: better docs #140

3.2.0

8 January 2025

  • Draco #133
  • Better errors #138
  • feat: added pdb->pdbqt conferter #137

3.1.0

2 January 2025

  • feat: updated changelog #136
  • feat: more tool wrappers, more docs, assorted bugfixes #135
  • feat: simpler tool execution code #134
  • Fix conda docs #132
  • feat: tooling to run autodock vina on deep origin #131
  • Support for filtering rows in a database #130

3.0.5

9 December 2024

  • fix: works with new auth_domain #129

3.0.4

4 December 2024

  • fix: limit-python-version to 3.10+ #128
  • fix: dropped 3.9 #127

3.0.3

3 December 2024

  • fix: fixed a bug where expressions weren't being handled correctly in… #126

3.0.2

2 December 2024

  • fix: fix for dangerous indexing #125

3.0.1

2 December 2024

  • fix: bumped to v29 of SDK for httpx workaround #124
  • fix: removed ensure_client decorator #122
  • fix: removed download_file #121
  • fix: only patch the action #120
  • fix: better handling of text responses #118

3.0.0

22 November 2024

  • fix: start pr #117
  • Add rows #115
  • Support for platform API #116
  • Refactor of test stack #114
  • Live tests 2 #113
  • fix: parallelized tests #112
  • Live tests #111

2.5.3

14 November 2024

  • fix: fixed more type mismatch issues #110

2.5.2

14 November 2024

  • fix: hotfix for malformed types #109
  • fix: annotation improvements #107

2.5.1

29 October 2024

  • fix: bugfixes and debug hooks #106

2.5.0

29 October 2024

  • feat: moving to hover callback #105
  • refactor: moved JS callback into its own file #104
  • fix: insertion of series data into dataframe #102
  • fix: attempt to fix custom domain reset #103
  • fix: fixed site url #101
  • feat: ability to make plots from Deep Origin dataframes #100

2.4.1

25 October 2024

  • fix: fixed a bug in adding string columns #99

2.4.0

24 October 2024

  • feat: added changelog for new version #98
  • feat: slicing a dataframe using loc preserves attributes #97
  • fix: better typing for dataframes #96
  • feat: ability to delete terminated workstations #94
  • fix: suppress message about new version on lambda #93
  • feat: ability to decode tokens #92
  • fix: added docstrings for all modules #91
  • fix: fixed a bug where expired tokens were not being refreshed #90
  • feat: added ability to compute hash on file upload #89

2.3.0

7 October 2024

  • feat: added ability to download files in parallel #88

2.2.1

3 October 2024

  • fix: we don't send the hash #87

2.2.0

3 October 2024

  • refactor: dropped support for graphql secrets and variables #86
  • refactor: split up utils into different modules #85
  • feat: support for passing sha256 checksum to upload_file #84
  • fix: more bugfixes & improvements #83
  • fix: added list_files method back, matching docs #81

2.1.4

19 September 2024

  • fix: dataframe printing errors shouldn't cause an error #79

2.1.3

18 September 2024

  • fix: check file_ids length prior to listing files #78

2.1.2

5 September 2024

  • fix: version number printed correctly #77
  • fix: better testing for config #76
  • feat: much faster file name resolution using ListFiles #75

2.1.1

29 August 2024

  • fix: number of small bugfixes with dataframes #74

2.1.0

22 August 2024

  • feat: better way of interacting with databases #72
  • fix: fixed some small bugs #71

2.0.5

13 August 2024

  • feat: updated to new version of deleting database columns #70

2.0.4

9 August 2024

  • feat(docs): minor edits to docs #69
  • feat: ability to create/delete objects #68
  • feat: clarified and standardized error messages #67

2.0.3

7 August 2024

  • Minor improvements and bug fixes #66
  • Updates to documentation #65
  • feat: changed 'document' terminology to 'notebook' #64
  • fix: minor improvements #63
  • feat: clarified the help strings of the data hub in the CLI #62
  • fix: removed a file that shouldn't be included #60
  • ci: changed codeowners from documentation writers to platform documentation writers #61

2.0.2

31 July 2024

  • fix: many small fixes to python client #59
  • fix: fixed a bug in get_dataframe where HID prefix had a - #58

2.0.1

30 July 2024

  • docs: clarified configuration documentation #57

2.0.0

29 July 2024

  • feat: refined UX and docs #56
  • Updated and modernized docs and CLI #55
  • refactor: switched to low-level generated code #54

1.6.0

9 July 2024

  • feat: disabled printing context for compute cluster and hardware which the platform no longer provides #53
  • fix: dataframe better matches DB #50
  • feat: nicer headers for docs #48
  • chore: added documentation writers and designers to code owners #49
  • feat(docs): updated theme to new brand identity #47

1.5.0

21 June 2024

  • Support for uploading data #46
  • feat: expanded docs to talk about uploading files #45

1.4.2

13 June 2024

  • fix: URLs for nucleus now have a trailing slash #44

1.4.1

12 June 2024

  • feat: shortcut when running in AWS lambda; read config values from env #43

1.4.0

11 June 2024

  • feat: supports reading tokens from env #42

1.3.2

11 June 2024

  • fix: fixed client not having the right props #41

1.3.1

11 June 2024

  • fix: fixed a bug where attributes were't being set correctly #40

1.3.0

11 June 2024

  • feat(client): client can now be configured without config files #39
  • fix: renamed formiclabs to deeporiginbio #38
  • Dataframe improvements #37
  • fix: set default configuration to production settings #35

1.2.0

29 May 2024

  • refactor(testing): moved mock client out of source #34
  • fix(managed-data): improvemented to managed-data #33

0.1.1

17 May 2024

  • fix(CLI): fixed a bug where deep-origin was still being used #32
  • fix(docs): added info about variables #31
  • feat(docs): added pypi badge #29

0.1.0

10 May 2024

  • refactor(CLI): overhauled how tokens are handled and cached #28
  • feat(managed-data): support for more functionality #26
  • fix(testing): re-enabled test on windows #27
  • fix(testing): added windows tests #25

0.0.7

2 May 2024

  • refactor(CLI): removed a controller and added a config command #24
  • fix(managed-data): many small improvements #23

0.0.6

1 May 2024

  • fix(managed-data): fixed a bug with multiple root items #22

0.0.5

1 May 2024

  • feat(infra): avoided error messages in repeated installations #20
  • fix(managed-data): fixed a bug in dynamic git version #21
  • feat(docs): expanded docs to show auth #19

0.0.4

26 April 2024

  • feat(docs): expanded docs #18
  • feat(docs): refined documentation #17
  • Started work on documentation system + support for merging DBs from CLI #16
  • fix(testing): better coverage #15
  • fix(infra): better install that links the executable #14
  • feat(pypi): publishing to pypi #13

0.0.3

18 April 2024

  • feat(pypi): ready to publish 937e78e

0.0.2

18 April 2024

  • fix(pypi): restoring author info 55204f0

0.0.1

18 April 2024

  • fix(docs): cleaned up readme #12
  • fix(testing): all tests pass locally now #11
  • fix(testing): made some more tests work #10
  • feat(managed-data): Support for multiple databases and operations on them #9
  • feat(managed-data): support for getting cell data #8
  • refactor(cli): changed how endpoints are stored in config file #7
  • Better Testing #1
  • initial commit e95b4ad
  • feat(pypi): publishing to pypi b20a72e
  • feat(pypi): wheel should build now e49fc79