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

ABFE: recursively validate all nested dt values are within [0.001, 0.004]
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