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Changelog

All notable changes to VLab4Mic are documented here in user-facing terms.

The project started as supra_molecular_simulator, was renamed to supramolsim, and later became vlab4mic. Older entries preserve that package history so releases can be traced back to the corresponding version bumps.

[0.1.0] - 2026-06-01

Preprint submission release.

Added

  • Added and refreshed the publication-oriented example suite used to generate article and supplementary figure panels, including primary/secondary labelling, probe examples, localisation simulations, NPC quantification, depth-of-field examples, structural-integrity examples, multiple structures, and structure-parsing workflows.
  • Added smoke tests for notebooks and core workflows so Colab/Jupyter entry points are checked automatically.
  • Added clearer issue templates for the project scope.

Changed

  • Marked the package as preprint-ready by bumping the package version from 0.0.21 to 0.1.0.
  • Moved the user-facing MkDocs website out of the main Python package repository so the website can be hosted and built independently.
  • Updated Colab notebooks and notebook CI so the public notebooks are tested closer to how users run them.
  • Improved package metadata, supported Python version claims, modality tables, and API examples.

Fixed

  • Fixed the download-structures command so it works from an installed package context.
  • Fixed CI and packaging issues, including the missing IPython runtime dependency.
  • Fixed runtime correctness bugs in workflows and sweep generation.
  • Fixed Colab notebook problems around Google Drive setup, broken links, and notebook framing.
  • Fixed structural-integrity upper-bound behaviour in the publication examples.

[0.0.21] - 2026-04-29

Publication examples and localisation-analysis release.

Added

  • Added scripts for the main figure panels, supplementary examples, and article-ready validation workflows.
  • Added localisation-table simulation for SMLM-like outputs, including localisation parameter handling in modality configuration.
  • Added structure/probe visualisation improvements used by the article examples.
  • Added output date stamping for experiment outputs.

Changed

  • Updated SMLM modality configuration and example scripts to support localisation outputs.
  • Removed outdated notebooks in favour of the current codeless notebook workflow.
  • Standardised and renamed several article figure scripts for clearer use.

Fixed

  • Fixed edge cases when localisation sampling produces no emitters.
  • Fixed modality parameter updates and missing modality keys.
  • Fixed primary-probe degree-of-labelling handling.

[0.0.20] - 2026-04-09

Randomness and reproducibility patch.

Fixed

  • Fixed random-seed reset behaviour when generating image simulations, improving reproducibility across repeated runs.

[0.0.19] - 2026-04-08

Structural-integrity parameter handling release.

Changed

  • Centralised structural-integrity setup in the experiment object.
  • Updated high-level experiment functions and parameter sweeps to use the same structural-integrity setter.

[0.0.18] - 2026-04-08

Structural-integrity bugfix release.

Fixed

  • Released a patch for structural-integrity handling immediately after 0.0.17.

[0.0.17] - 2026-04-08

Capsid examples and labelled-structure preview release.

Changed

  • Updated capsid scripts and configuration values.
  • Improved labelled-structure preview plot limits.

[0.0.16] - 2026-04-02

Revised structural-integrity model.

Changed

  • Revised how structural integrity is modelled so the sampled structure better matches the requested integrity percentage.
  • Updated labelled-particle visualisation to show only available epitopes after structural-integrity modelling.
  • Reduced test runtime by avoiding redundant experiment fixture work.

Fixed

  • Fixed stopping conditions during structural-integrity iteration.
  • Fixed fracture-point sampling so each iteration samples independently.

[0.0.15] - 2026-03-30

Custom models, positioning, and reproducibility release.

Added

  • Added support for using custom model files and image-derived positions as virtual-sample inputs.
  • Added structure-axis Euler rotation controls and initial-orientation handling.
  • Added global normal-direction options for structure epitopes.
  • Added optional random seeds to experiments, sweeps, and high-level functions.
  • Added controls for explicit rotations, orientations, offsets, and per-particle placement from high-level functions.

Fixed

  • Fixed handling of missing assembly-operation fields in CIF files.
  • Fixed structure path reset behaviour when switching away from local files.
  • Fixed probe visualisation with degree of labelling.

[0.0.14] - 2026-01-15

Sweep step-size and structure-format release.

Added

  • Added package badges and coverage upload support.
  • Added structure-format handling for local PDB/CIF files.

Changed

  • Changed parameter-sweep ranges to use step size rather than number of values.
  • Updated scripts and tests to match the new sweep range interpretation.

Fixed

  • Fixed modality parameter updates in parameter sweeps.
  • Fixed parsing fallbacks when PDB/CIF files do not contain expected protein-name metadata.

[0.0.13] - 2026-01-12

PyPI installation and sweep usability release.

Changed

  • Updated notebooks and installation instructions to install from PyPI.
  • Switched progress imports away from notebook-specific tqdm.
  • Simplified and reduced redundant parameter-sweep tests.

Fixed

  • Fixed parameter-sweep figure saving and feedback messages.
  • Fixed warning-prone plotting paths, subplot indexing, and file naming.

[0.0.12] - 2026-01-07

Parameter-sweep channel patch.

Added

  • Added a high-level parameter-sweep test.

Fixed

  • Fixed channel-index handling in parameter sweeps.

[0.0.11] - 2026-01-06

Expanded high-level simulation controls.

Added

  • Added expansion-factor support to high-level functions and experiment methods.
  • Added an AiryScan modality configuration.

Changed

  • Updated multicolour and Figure 3 scripts to use the new controls.

Fixed

  • Fixed modality handling in image_vsample.

[0.0.10] - 2025-12-12

Multichannel fluorophore release.

Added

  • Added support for two fluorophores/channels in image simulation.
  • Added article example scripts for primary/secondary probes and NPC quantification.

Fixed

  • Fixed changing fluorophores in probe configurations.

[0.0.9] - 2025-12-10

Jupyter separation release.

Changed

  • Removed Jupyter widgets from the core vlab4mic package so widget code can live in the companion vlab4micjupyter package.
  • Updated notebooks to import widgets from vlab4micjupyter.
  • Removed JupyterLab/widget dependencies from the core package dependency list.
  • Updated installation instructions for the split package workflow.

Added

  • Added an option to save simulated images locally from high-level functions.

Fixed

  • Fixed notebook imports after moving widget code out of the core package.

[0.0.8] - 2025-11-17

Examples and beginner-facing documentation release.

Added

  • Added example outputs and references for real-vs-simulation scripts.
  • Added a tutorial GIF and clearer README presentation.

Changed

  • Improved script README tables and descriptions.
  • Improved widget feedback text and local-structure loading descriptions.
  • Removed duplicated structure loading in the main experiment flow.

[0.0.7] - 2025-11-11

Notebook naming and cleanup release.

Changed

  • Renamed the main notebook to VLab4Mic_main.ipynb and fixed links to it.
  • Cleaned up completed TODO comments and structure-related imports.

[0.0.6] - 2025-11-11

Repository documentation release.

Added

  • Added Code of Conduct and initial changelog files.
  • Added Google Drive mounting guidance for Colab notebooks.

Changed

  • Reworked the manual and README around codeless notebooks, Colab troubleshooting, and Python-package usage.
  • Updated repository links and notebook instructions after the VLab4Mic rename.

[0.0.5] - 2025-10-22

Colab and CIF parsing patch.

Added

  • Added Colab-facing titles to the main notebook.

Fixed

  • Fixed CIF database reading when operation lists are missing.

[0.0.4] - 2025-10-17

Sweep widget usability release.

Added

  • Added HTML display of selected parameters in sweep widgets.
  • Added methods to update sweep sliders programmatically.

Fixed

  • Fixed sweep widget slider values and manual typos.

[0.0.3] - 2025-10-16

Reference-image workflow release.

Added

  • Added optional reference masks for sweep analysis.
  • Added support for TIFF/TIF reference images.
  • Added widgets for uploading reference images and masks.
  • Added notebook guidance for local structure selection and advanced reference parameters.

Fixed

  • Fixed reference-sample handling when using local structure files.
  • Fixed image generation and acquisition-parameter behaviour in the experiment widget.

[0.0.2] - 2025-10-09

First public example scripts release.

Added

  • Added installation/testing instructions for TestPyPI.
  • Added example scripts for imaging a virtual sample and running a parameter sweep.
  • Moved example scripts into their current folder layout.

Fixed

  • Fixed mask-index handling.

[0.0.1] - 2025-10-09

Alpha package-testing release.

Changed

  • Reset the package version from the earlier 0.1.0 baseline to 0.0.1 for alpha-stage TestPyPI deployment.

[vlab4mic 0.1.0 baseline] - 2025-08-14

Renaming release before the alpha version reset.

Changed

  • Renamed the package from supramolsim to vlab4mic.
  • Updated package metadata, coverage settings, and console entry points to use the VLab4Mic name.
  • Added particle-defect controls to notebooks and improved notebook markdown.

Fixed

  • Fixed a reported issue around the renamed package workflow.

[supramolsim 0.1.0] - 2025-05-16

Setuptools packaging baseline.

Changed

  • Deprecated the old setup.cfg workflow and moved package metadata into pyproject.toml.
  • Declared setuptools package discovery, package data, dependencies, optional dependency groups, and the structure-download command.

[2024.10.18] - 2024-10-18

Added

  • Added test fixtures for structure and coordinate-field workflows.

[2024.10.15] - 2024-10-15

Changed

  • Moved the project from Poetry to setuptools.
  • Added GitHub Actions, Makefile commands, pdoc documentation generation, and Python packaging commands.

Fixed

  • Fixed the test setup after the packaging migration.

[2024.10.09] - 2024-10-09

Fixed

  • Fixed label display in the Jupyter widget workflow.
  • Updated generated CIF ignore rules.

[2024.10.08] - 2024-10-08

Added

  • Added image-noise transforms, image convolution tools, text/TIFF writing utilities, and multi-modality imaging workflows.
  • Added widget controls for acquisition parameters and running simulations.
  • Added a demo notebook and local configuration retrieval.

Fixed

  • Fixed imaging imports and multi-modality image-generation tests.

[2024.10.07] - 2024-10-07

Fixed

  • Fixed data-visualisation imports.

[2024.10.04] - 2024-10-04

Added

  • Added PSF generation and initial image-generation modules.
  • Added workflows for creating an imaging system from field data.

[2024.10.03] - 2024-10-03

Added

  • Added widget-driven structural-model creation.
  • Added label construction from configuration files.
  • Added labelled-particle creation, particle defects, coordinate-field generation, and associated tests.
  • Added scikit-learn and test coverage support.

[2024.10.02] - 2024-10-02

Changed

  • Updated project files and custom widget imports during the refactor.

[2024.10.01] - 2024-10-01

Changed

  • Continued the large refactor into generate, utils, visualisation, workflow, and IO modules.
  • Updated formatting and linting configuration.

[2024.09.27] - 2024-09-27

Added

  • Added initial Jupyter widget module and ipykernel dependency.

Changed

  • Renamed the package from supra_molecular_simulator to supramolsim.

[2024.06.14] - 2024-06-14

Added

  • Added templates for structures, labels, fluorophores, detectors, modalities, and PSFs.
  • Added configuration metadata for the early simulator workflow.

Changed

  • Ignored generated coverage files.

[2024.06.13] - 2024-06-13

Changed

  • Moved the project back into a src/ package layout.
  • Updated pre-commit and test tooling.
  • Declared the package path in pyproject.toml.

[2024.06.12] - 2024-06-12

Changed

  • Renamed the structure-download console command to download-structures.
  • Performed early cleanup around packaging and scripts.

[2024.06.07] - 2024-06-07

Added

  • Added the first structure downloader command.
  • Added example CIF data and additional development dependencies.

[2024.06.06] - 2024-06-06

Initial package skeleton.

Added

  • Added the first supra_molecular_simulator package metadata.
  • Added initial dependencies, package declaration, and development/test tooling.