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Brendan/merge #22

Merged
merged 303 commits into from
Aug 19, 2024
Merged

Brendan/merge #22

merged 303 commits into from
Aug 19, 2024

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leb2
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@leb2 leb2 commented Aug 5, 2024

How the feature works? / How did you fix the issue?

(Screenshots, videos, or GIFs, if applicable)

Check list

  • unit-tests written
  • e2e-tests written
  • documentation updated
  • PR name follows the pattern #1234 – issue name
  • branch name doesn't contain '#'
  • PR is linked with the issue
  • base branch (master or release/xx) is correct
  • task status changed to "Code review"
  • reviewers are notified about the pull request

NataliaLoginova and others added 30 commits April 3, 2024 13:03
…-system-lost-most-substitution-count-values-export-to-molfile

epam#3957 - Atom Query feature export System lost MOST Substitution count values export to Molfile
Bumps [webpack-dev-middleware](https://github.com/webpack/webpack-dev-middleware) from 5.3.3 to 5.3.4.
- [Release notes](https://github.com/webpack/webpack-dev-middleware/releases)
- [Changelog](https://github.com/webpack/webpack-dev-middleware/blob/v5.3.4/CHANGELOG.md)
- [Commits](webpack/webpack-dev-middleware@v5.3.3...v5.3.4)

---
updated-dependencies:
- dependency-name: webpack-dev-middleware
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [vite](https://github.com/vitejs/vite/tree/HEAD/packages/vite) from 4.5.2 to 4.5.3.
- [Release notes](https://github.com/vitejs/vite/releases)
- [Changelog](https://github.com/vitejs/vite/blob/v4.5.3/packages/vite/CHANGELOG.md)
- [Commits](https://github.com/vitejs/vite/commits/v4.5.3/packages/vite)

---
updated-dependencies:
- dependency-name: vite
  dependency-type: direct:development
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Bumps [express](https://github.com/expressjs/express) from 4.18.2 to 4.19.2.
- [Release notes](https://github.com/expressjs/express/releases)
- [Changelog](https://github.com/expressjs/express/blob/master/History.md)
- [Commits](expressjs/express@4.18.2...4.19.2)

---
updated-dependencies:
- dependency-name: express
  dependency-type: indirect
...

Signed-off-by: dependabot[bot] <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
- also updated ketcher to 2.21.0-rc.1
- temporary marked tests as failed
timeout rose up to 60 mins
…pace-button-that-is-wrong

Backmerge: epam#4369 - Del button works as Backspace button that is wrong
…-redirects-1.15.6

Bump follow-redirects from 1.15.5 to 1.15.6
…oms-with-charge-value-out-or-range

epam#3943 - System allow to create atoms with Charge value out or range
…toms-and-bonds-in-ket-schema

 epam#3934 Support selection entity selection flag in KET format
…d from some monomers (epam#4489)

- added AttachmentPoint instance binding to it's html elements
- added pointer-events: none by default for all elements of attachment point and explicitly pointer-events: auto to it's hover area
- fixed screenshot
- fixed case with switching tool by hotkeys

---------

Co-authored-by: Roman Rodionov <[email protected]>
…4442)

* First draft

* second draft

* Adding tests, screencshots for issue 3805

* Adding tests, screencshots for issue 3805 - correction of lint file

* Changed to one browser per thread for toggle-explicit-hydrogens-with-respect-to-selected-atoms in order to save execution time

* Changed execution to one browser for zoom-tool and for import-saving-files
…4517)

* 3808 - connection rules for phosphate monomers

* Some tests disabled

* Extra correction

* one more

* Global Timeout introduced

* Number of retries - 0

* Restart browser solution

* eslint-disable prettier/prettier removing
…epam#4515)

- migrated monomers library from sdf to ket
- added rna presets to ket library and removed hardcoded rna presets
- moved library import and storage to core package
- fixed chems displaying in sequence view and favorites tab of library
- Rotation was missing z coordinate when switching into chemistry coordinate system.
…-sequence-edit-in-rna-builder

epam#4388 - Macro: Allow Nucleoside of sequence edit in RNA builder
…s-in-browser-local-cache

epam#4427 - Macro: Store custom presets in browser local cache
leb2 and others added 29 commits August 5, 2024 00:50
…pam#5188)

* epam#5172 - updated ket image format

* epam#5172 - fixed failing types

* epam#5172 - fixed regex

* epam#5172 - fixed package-lock file

* epam#5172 - updated file mime regexp
…one build process (epam#5212)

- added ketcher-standalone builds for indigo without render module
- added structService reinitialization
)

- unlocked monomers library for sequence mode
- implemented monomer/rna replacing by selecting in sequence mode and clicking by item in library

---------

Co-authored-by: Roman Rodionov <[email protected]>
…in sequence mode, increase debounce time (epam#5160)

- added changes according new requirements for IDT aliases
- added util function to add H to O leaving group
- fixed idt aliases in preview for unresolved monomers
- updated screenshots

---------

Co-authored-by: Roman Rodionov <[email protected]>
- also updated ketcher to 2.24.0-rc.1
- fixed test data
…on canvas (epam#5165)

* - added tests for Images test cases;
- added helper functions;
- added test files;
- added expected snapshots

* - tests refactored

* - added tests;
- added test file;
- added expected snapshots

* - updated tests

* - updated tests

* - added tests;
- added test files;
- added expected snapshots

* - added tests;
- added test file;
- added expected snapshots

* - added tests;
- added expected snapshots

* - added tests;
- added expected snapshots

* - added tests;
- added test files;
- added helper method;
- added expected snapshots

* - updated snapshots for fixed tests

* - added tests;
- added expected snapshots

* - added tests;
- added test files;
- added helper method;
- added expected snapshots

* refactored all tests for images

* - updated snapshots

* - added tests;
- added test files;
- added expected snapshots

* - added tests;
- added test file;
- added expected snapshots

* added tests

* added tests
…s cycled polymer (epam#5259)

- changed usage of previous/next node to previous/next node in same chain for replacing sequence items through the library
- fixed replacement of single selection of two chains
…plit nucleotides after load from file (KET/MOL doesn't matter) (epam#5251)

- added check for cyclic chain beginning
…on preset w/out base works wrong (epam#5278)

- moved rna node addition in sequence mode to separate function
- removed restriction of insertion/replacing rna without base
- fixed conditions sequence in rna addition method for sequence mode
…canvas even if it shouldn't (and error message is wrong) (epam#5279)

- fixed case with adding new sequence items using replace from library in case if there is no attachment points
- fixed R1/R2 missed attachment points cases
* 5215 - first draft

* 5215 - second draft

* 5215 - negative tests added

* 5215 - bug fixes

* 5215 - bug fix 2

* 5215 - fixes 3

* 5215 - One more try

* 5215 - more fixed

* 5215 - more fixes

* 5215 - last fix
- added fallback to text mimetype if custom mimetypes not supported

---------

Co-authored-by: Nikita Chistousov <[email protected]>
@leb2 leb2 merged commit b42df98 into master Aug 19, 2024
2 of 4 checks passed
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