Changelog

All notable changes to this project will be documented in this file.

The format is based on Keep a Changelog. This project adheres to Semantic Versioning.

[1.0.9] - 2024-07-24

Fixed

Fixed increase of version of fermo_core to 0.4.3

[1.0.8] - 2024-07-23

Changed

Bumped version of fermo_core to 0.4.3

[1.0.7] - 2024-07-10

Added

Example: added example result files for download

Fixed

Job URLs: when job was started after loading old parameters, result URL was malformed
Nginx config: fixed default upload file size
Dashboard: clarified download field names

[1.0.6] - 2024-06-19

Fixed

Fixed broken redirect for 'job_not_found'

[1.0.5] - 2024-06-19

Changed

Updated html templates

[1.0.4] - 2024-06-18

Fixed

Fixed required flag for Chrome and Edge Plotly rendering

[1.0.3] - 2024-06-18

Fixed

Additional fixing of malformed link in notification email

[1.0.2] - 2024-06-18

Fixed

Fixed malformed link in notification email

[1.0.1] - 2024-06-18

Fixed

Added 'restart' flags to docker-compose services for increased maintainability

[1.0.0] - 2024-06-16

Changed

Full rework of frontend and backend of fermo_gui
Use of fermo_core as processing backend
[Breaking Change] No compatibility with previous versions of FERMO

[0.9.1] - 2024-01-22

Changed

Full rework on fermo frontend and backend
Replaced legacy code with Flask application

[0.8.11] - 2023-04-16

Added

Re-introduced support for macOS
Startup script for macOS

Changed

Updated to MS2Query v 0.7.3.2 (by Niek de Jonge)

[0.8.10] - 2023-02-14

Fixed

Bugfix of modify_feature_info_df() in dashboard_functions.py

[0.8.9] - 2023-02-10

Added

Tracking of changes with CHANGELOG.md

Changed

Changed relative module import paths to absolute ones, making installation of tool via pip install -e . mandatory

Fixed

Bugfix by modifying requirements.txt: specifying package matchmsextras==0.3.0

[0.8.8] - 2023-01-24

Added

Expanded adduct detection functionality - FERMO now also recognizes [M+NH4]+, [M+K]+, [M+H2O+H]+, [M-H2O+H]+ (0.8.8.3)

Changed

Rework of fold-change filter on dashboard page: a range, and groups to be excluded or included can be specified (0.8.8.1)
Changed handling of webbrowser opening (0.8.8.2)

[0.8.7] - 2023-01-15

Added:

Installation via pip install . using pyproject.toml
Centralization of dependency metadata in requirements.txt
Bibliographic information using CITATION.cff
Initialization of testing via pytest package
Coverage of calculate_feature_overlap.py with unit tests
Build testing with GitHub actions workflow .github/workflows/CI_build.yml

Changed:

Changed directory structure: moved source code to src/fermo/...
Rewrite of calculate_feature_overlap.py to allow for testing and increase maintainability

[0.8.6] - 2022-12-25

Fixed:

Bugfix in quantitative biological data parsing related to issue Cannot upload quantitative biological data (*.csv) file

[0.8.5] - 2022-12-23

Added:

Initial public version of FERMO