🚀 Features

• 9510946 added peptide mass prediction and B/Y ion drawing
• f278508 added adduct calculation and reformatted isotopic distribution plotting
• 2f70499 added plotting in different colors + legend entries
• ed4d6d5 added dynamic adding and removal of ion list features, too
• ba3091c added preliminary theoretical spectrum calculation and drawing

🐛 Bug Fixes

• 40ec9f5 set proper ctypes types for TerminateProcess on 64-bit Windows
• eec85a7 use TerminateProcess on Windows to avoid access violation during pytest shutdown
• 026727c fixed a bug where the tests would fail because of segfault after calling the garbage collector
• 5866c5f fixed a bug where Edit integration wouldn't work for peptides
• 698a1d4 fixed a bug where the theoretical spectra would disappear after changing adducts

🛠 Refactoring

• 6f85904 revamped the MS2 functionality
• dcd1825 swapped adducts dropdown and help icon
• 8b125b9 removed the big arrow on adducts dropdown

Other Changes

• 2fbdf5b Merge pull request #24 from MateuszFido/proteomics
• 7e7485f Update lcmspector/ui/tabs/upload_tab.py
• 5adf104 Update lcmspector/ui/tabs/upload_tab.py
• 93b4478 Update lcmspector/utils/theoretical_spectrum.py
• 5063c48 Update tests/unit/test_ms2_lookup.py
• af0685a Update tests/unit/test_ms2_lookup.py
• 4c689fe Merge pull request #23 from MateuszFido/theoretical-spectrum
• 6c15a80 Update lcmspector/ui/tabs/upload_tab.py
• 71af2bd Update lcmspector/ui/widgets.py
• b6dcaa0 Update lcmspector/ui/tabs/upload_tab.py
• 2828d10 Update lcmspector/ui/tabs/upload_tab.py
• aa86f03 Update lcmspector/ui/widgets.py

🚀 Features

• 33d2557 added a visual label for where the m/z values are placed in IntegrationWidget
• 5cd838a Added integration window for each compound available by right-clicking on its IonTable entry
• ee1aa2d added a custom file reader based on lxml
• fe3fb45 added a tooltip explaining the use of ion lists
• 1fa90f8 added PubChem lookup for m/z value from name

🐛 Bug Fixes

• 61626ba update README logo URL to point to main branch

🛠 Refactoring

• 00b8d29 uncoupled plotting from calibrateButton and removed Calibration checkboxes
• 9048553 formatting and ResultsTab UI changes

🧹 Chores & Maintenance

• f59909a update README.md
• ff4c9a3 updated Dockerfile to match v0.13.2

🚀 Features

• 76ea053 added tooltips for LC and MS file upload
• 97037cb added a tooltip next to ion selection in QuantitationTab
• a40f6f3 added fully functional ion switching for one-by-one manual integration

🐛 Bug Fixes

• e7cff45 remove unused import in lcmspector/ui/plotting.py
• 6b06b91 fixed a bug where columns were overwritten in UnifiedResultsTable when no ion_info was present
• 6c9ebae fixed a bug where filling comboBox_currentFile in ResultsTab would trigger plotting in UploadTab
• 511882b changed label_calibrate to match setup

🛠 Refactoring

• 0b04ce9 removed unused plotting methods from classes
• 2934646 changed the QuantitationTab layout to clarify file/compound selection
• f3985fd changed plot placeholders
• 439e41d changed placeholder text on UploadTab
• aa79266 changed how peak labeling behaves in canvas_avgMS to make it more consistent

Other Changes

• ace10af Merge pull request #22 from MateuszFido/bugfixes

🚀 Features

• db9f650 added signal emission for worker termination from executor
• 63b422b added working checkbox-plotting to canvas_avgMS
• 7fa5dc9 added working file selection for canvas LC
• 100e2d8 add comprehensive UI testing suite for UploadTab
• 87d227a added complete wipe + confirmation on mode change
• a39120b implemented line retrieval from plot
• 57e6bbc got half-working updating of integration in UnifiedResultsTable
• 66a0b27 added non-functional buttons for resetting the window, need to fix widget alignment
• ffd0cc6 added functional moving lines
• 0ff705f added InfLines to the integration plot
• 9b53ac5 added vertical line to compound integration display
• a3ad5c9 added plotting of the selected compounds XIC's in quantitation tab
• d4c9a00 incorporated peak_integration algoritmhs into construct_xics

🐛 Bug Fixes

• 5458399 CI test failures on Ubuntu and Windows
• 171b7b1 properly mock MS data.time accessor in tests
• d081105 fixed a bug where the crosshair lines would only appear after processing
• d54e46f fixed a bug where canvasXICs would stop responding to clicks
• aa40a2e casting to str for ion when returned from bounds
• eca123d removed updating m/z labels from integration plot to improve drawing speed

🛠 Refactoring

• d403c44 separated more view.py into tabs
• d6c9038 started improving tab separation

Other Changes

• f8883c4 Merge pull request #21 from MateuszFido/manual-integration
• b6459b5 Merge branch 'main' into manual-integration

🐛 Bug Fixes

• cd15b8d changed executable name in CD
• 5951117 corrected the exe check to still use main.dist before renaming
• a237405 added additional Qt6 deps
• 62dbeea add libxcb-cursor-dev for Qt6 binary check on Ubuntu
• f02d8c5 refactored plotting in annotated_XICs to get rid of the window pop-up bug
• 9aab2ca downgraded Python to 3.13 (no Nuitka support for 3.14)

🛠 Refactoring

• 9ff5544 updated CD to properly resolve modules
• a6b957a moved backend modules to calculation/

🧹 Chores & Maintenance

• 8b53693 bump nuitka to 2.8.10
• 307b310 update Python version from 3.13 to 3.14 and sync dependencies

⚙️ CI/CD

• b689ab8 updated executable check before releases

🧹 Chores & Maintenance

• 1fc0072 bumped python version to 3.14 and updated dependencies

🐛 Bug Fixes

• ed6e81b trying to stop the executable from hanging after shutdown

🐛 Bug Fixes

• 5e16cff added getter and setter funcs for calibration_parameters
• be78994 moved ui/plotting imports inside class plotting functions

🛠 Refactoring

• 9f5b433 moved plotting to ui/ again
• 7f06071 merged logging with UI changes
• 443b7dc improved logging and refactored view interface

Other Changes

• d7858b6 merged local and remote

• Bugfix: trying to pinpoint an issue with Nuitka mulitprocessing breaking
• Refactor: or: remove legacy CI/CD configs

• Refactor: or: moved CI to uv
• Chore: increased history search in release job
• Chore: add pydantic to uv.lock