CHANGELOG.md

Changelog

Unreleased

Changed

• Reworked the GitLab CI/CD pipeline: unit tests now run on every merge request and the default branch (decoupled from the docs deploy) and block on failure; the tests run across Python 3.10/3.11/3.12 on stock slim images via a matrix; hardened the CI shell scripts (set -eu) and replaced the broken custom SAST job with the GitLab-managed template.
• resources/ci_cd/debug_run_docker.sh now mirrors the entire pipeline locally in Docker — the unit-test matrix on every Python version and the docs build, in GitLab stage order — reading the version list and images from .gitlab-ci.yml so it stays in sync with CI. It is portable: the repo root and docs build dir are auto-detected and Docker availability is pre-checked, so it runs on any machine (not just the maintainer's). The host-side scripts (debug_run_docker.sh, run_docker.sh) are macOS-compatible — GNU-only readlink -f and head -n -1 were replaced with cd … && pwd -P and sed '$d'.
• Simplified the pages docs job: the package install moved into pages.sh and the separate before_script.sh + its .before_script_template anchor were removed. make is now baked into the docs image (PERSISTENT_DEPS) instead of being re-installed via apk add on every run.

Removed

• resources/ci_cd/before_script.sh and the .before_script_template anchor in .gitlab-ci.yml; the docs job now runs pages.sh directly (which installs the package then builds the docs).

• Dead bioinformatics-template leftovers from the docs Docker image (resources/docker/plot-misc/master/Dockerfile): the libdeflate/ libdeflate-dev (cyvcf), openssh (only used by the removed ssh-agent), and commented llvm11/numba build dependencies. The image now requires a rebuild and push to take effect in CI.

Fixed

• plot_misc.machine_learning imported Self from typing, which only exists on Python 3.11+, breaking imports on the declared-supported Python 3.10. It now falls back to typing_extensions.Self on 3.10, and typing_extensions is declared as a runtime dependency in requirements.txt (marker python_version < "3.11") and in the conda recipe / env files (unconditional, as conda noarch packages have no install-time python selector).

2.2.2 - 2026-06-23

Added

• plot_misc.heatmap.masked_heatmap, a two-layer heatmap that draws a single-colour background and overlays the heatmap only on the cells flagged by a binary indicator table the same shape as data.
• examples.qc_matrix, a dummy quality-control data set (signed standardised deviations plus a binary pass/fail indicator) showcasing masked_heatmap.
• Masked-heatmap cells added to the resources/examples/heatmap.ipynb and resources/examples/tldr/heatmap.ipynb notebooks.
• Example notebooks for the plot_misc.utils.utils helpers: a concise TLDR notebook resources/examples/tldr/utils.ipynb and a detailed worked-out notebook resources/examples/utils.ipynb.
• Corresponding .nblink files under docs/source/examples/plots/ and docs/source/examples/plots/tldr/, linked into the nbgallery and the "Worked out examples" toctree in docs/source/index.rst.
• calc_matrices symbol argument to set the significance marker glyph to any text/unicode string (e.g. '●', '◆'); previously fixed to '★'.
• calc_matrices annotate='symbol' option, replacing 'star' as the significance-marker selector.
• calc_matrices p-value annotation options 'pvalues_signed', 'pvalues_unsigned', and 'pvalues_raw', controlling whether the annotation shows signed -log10, unsigned -log10, or the raw p-value. The numeric value matrix remains signed -log10 regardless.
• MatrixHeatmapResults now exposes two further numeric p-value tables, curated_matrix_value_unsigned_log (unsigned -log10) and curated_matrix_value_raw (raw p-values), alongside the signed -log10 curated_matrix_value.

Changed

• calc_matrices annotate now defaults to 'symbol' (was 'star'); the default output is unchanged. The annotate argument is now a typed Literal of the supported options.
• _format_matrices no longer takes a log argument; p-values are always -log10 transformed and the numeric curated_matrix_value is consistently signed -log10.
• calc_matrices alpha is now a raw p-value in (0, 1] (default 0.05), consistent with volcano; it is converted internally to a -log10 threshold. Values outside (0, 1] raise InputValidationError.
• calc_matrices ptrun is now a raw p-value in (0, 1] (default 1e-16), consistent with alpha; the old exponent convention was removed. Values outside (0, 1] raise InputValidationError.

Deprecated

• calc_matrices annotate='star' is deprecated in favour of 'symbol'.
• calc_matrices annotate='pvalues' is deprecated in favour of 'pvalues_signed'.
• calc_matrices without_log is deprecated and no longer changes behaviour (p-values are always -log10 transformed); use curated_matrix_value_raw for raw p-values.

Fixed

• annotate_heatmap no longer raises MaskError on masked arrays; masked cells (e.g. from masked_heatmap) are skipped so only visible cells are annotated.
• masked_heatmap now rejects a shape mismatch between data and indicator on the full 2D shape (previously only the row count was checked, so a column mismatch raised an opaque IndexError), and applies background_zorder to the background grid lattice.
• segment_labelled now rotates the midpoint label to align with the drawn segment. The second endpoint was transformed with the wrong x-coordinate (y[0] instead of x[1]), producing an incorrect text angle whenever x[1] != y[0].
• masked_heatmap per-cell outlines are no longer clipped by the axes boundary on edge cells (outline patches now default to clip_on=False).

2.2.1 - 2026-05-30

Added

• TLDR notebooks split into per-plot files under resources/examples/tldr/ (barcharts, bubblechart, forestplot, heatmap, incidencematrix, machine_learning, pychart, survival, treeplot, volcanoplot), each with minimal self-contained examples. The original tldr.ipynb has been removed.
• Corresponding .nblink files added under docs/source/examples/plots/tldr/ and linked in docs/source/index.rst.
• New load_forest_preprocessed dataset loader in plot_misc/example_data/examples.py, returning a plot-ready DataFrame with colour and shape columns attached.
• Barchart group_positions parameter to control bar positions within groups.
• Examples for saving metadata with PDFs and applying compression with TIFFs added to the publication-ready notebook.

Changed

• resources/build/inc_version.sh improved: simplified git branch detection and now also updates CHANGELOG.md automatically on version bump.
• CI/CD: unified pip dependencies across pipeline stages and removed stale code and comments.

Fixed

• Heatmap: threshold now applied to raw values instead of normalised values.
• Barchart: grouped bar charts were using the same position for every bar within a group.
• Function and class naming inconsistencies corrected; boolean handling brought in line with coding standards.

Removed

• Redundant conftest.py removed from the test suite.

v2.2.0 - 18-02-2026

Fixed

• Fixed a pytest.raises error for plot_table.
• Added missing test_survival test.
• Renamed commit-spell.sh to pre-commit to comply with git hook name conventions.

Added

• Git hook enforcing commit message standards.
• Added the .githooks directory and script.
• codespellrc and ignore word list.
• Makefile: generalised GitLab install and path to the git hooks setup script; git hook install now handled via make install.
• Started a publication-ready tips notebook, expanding tutorials on tick labels and locations.

Changed

• Incidencematrix parameter arguments updated.
• Volcano module refactored: updated colour arguments, added vline_kwargs_dict, and updated the example notebook.
• Heatmap refactored: removed redundant tests and cleaned the example file.
• Example notebooks updated, correcting spelling mistakes and removing redundant help calls.
• Numerous spelling and grammar fixes across documentation.

Deprecated

Nothing

Removed

• Clustermap removed from the heatmap module, as it no longer fits the package aim.
• Seaborn dependency removed.

v2.1.0 - 30-10-2025

Fixed

• forestplot notebook.

Added

• Added midpoints parameter to annotate_axis_midpoints function which overwrites the gap argument.
• Added survival module and notebook supporting survival plots with bottom survival table.
• Additional colour schemes to the utils.colour module.
• text_wrap function in utils.formatting to automatically break a string into multiple lines with optional line break character.
• introduced x and y coordinate parameters in incidencematrix allowing the user to match coordinates when creating multiple plots in for example a gridspec.

Changed

• Documentation improvements.

Deprecated

Nothing

Removed

Nothing

v2.0.4 - 14-08-2025

Fixed

• Added missing versioning in the pyproject.toml for the required and optional packages.

Added

Nothing

Changed

• Improved the example notebooks and documentation.
• Brought the docker requirements image in line with the current software versions.
• stack_bar now uses bar internally instead of matplotlib.Axes.bar.
• split the requirements.txt into requirements.txt and requirements-dev.txt, updating the CI/CD scripts to pip install both.

Deprecated

Nothing

Removed

Nothing

v2.0.3 - 08-08-2025

Fixed

Nothing

Added

Nothing

Changed

• Updated the sci_notation parameters to include both max and min windsoring.
• MatrixHeatmapResults now inherits from the general Results class.
• Improved the documentation - added a design_philosophy.rst to explain how the design philosophy of the module and explain how code contributions can best adhere to this.
• Introduced the Real type hint for the utils code.

Deprecated

Nothing

Removed

Nothing

v2.0.1 - 29-07-2025

Fixed

• Upgraded adjustText to 1.3 or higher to deal with an error where the lim keyword was incorrectly passed to FancyArrowPatch.

Added

Nothing.

Changed

• Slightly changed the pyproject.toml and meta.yaml file to handle the license correctly (changed to US spelling instead of licence).

Deprecated

Nothing.

Removed

Nothing.

v2.0.0 - 24-07-2025

Fixed

• Minor bug fixes.

Added

• Expanded code based to publish package on conda.
• annotate_axis_midpoints was added to utils.utils. The function adds a string placed exactly in the mid of two points. Useful to create headers in plots with lots of groups.
• Added Real type hint to replace int | float.
• Included further pytests for modules with low coverage (below 80%).
• Included a raising issues tutorial.

Changed

• The entire documentation has been refactored to be numpy compliant.
• All notebooks have been updated showcasing the new functionality.
• The following modules were refactored, where needed replacing function by classes: barchart, forest, incidencematrix, pychart.
• assign_distance can now deal with groups of different sizes.
• moved much of the function and classes outside the constants module into the errors.py module instead.
• The plot-table now standardise the x-axis to the [0, 1] range to improve alignments.

Deprecated

Nothing.

Removed

• assign_distance is replaced by set_y_coordinates.

v1.1.1 - 29-03-2025

Fixed

• Bug fixes to pychart.
• Bug fixes to utils.utils.calc_matrix.

Added

• Where relevant add repr
• Added some additional colours.
• Added a grouped bar chart.

Changed

• Migrated to pyproject.toml instead of setup.py
• Where relevant ensure all functions return ax.figure if an ax is supplied. This replaces returning a None value.
• Document clarifications.
• assign_distance can now deal with groups of different sizes.

Deprecated

Nothing

Removed

Nothing

v1.1.0 - 23-02-2024

Fixed

Nothing

Added

• A DecisionCurve class in the machine_learning.

Changed

• Updated examples.
• Changed the default behaviour of assign_distance to not sort rows.

Deprecated

Nothing

Removed

• Removes KD test function.
• Removes table module.

v1.0.0 - 15-02-2024

Fixed

Nothing

Added

• Piechart module pychart.
• A point estimate formatting function in utils.formatting.
• A empirical support class to plot trees.
• Pytest for the new functions.
• Adding sphinx documentation
• Gitlab CI/CD

Changed

• Updated the python requirements, currently build for python 3.12.

Deprecated

Nothing

Removed

Nothing

v0.3.0 - 29-06-2023

Fixed

• Fixed documentation
• Various fixes to forest.py

Added

• Expanded the number of input tests.
• Added a _dict_string_argument function to test the content of pd.DataFrame columns or pd.Series.
• Started a test_constants.py module.
• Verbose argument to some functions.

Changed

• volcano.py now calls ax instead of plt to set limits and labels.

Deprecated

Nothing

Removed

Nothing

v0.2.0 - 27-03-2023

Fixed

• Updated installation instructions and removed redundancies.
• Fixed documentation

Added

• seaborn clustermap wrapper.
• Added additional arguments for plot_forest.
• Added plot_table function to forest, including example and tests.

Changed

Nothing

Deprecated

Nothing

Removed

Nothing

v0.1.0 - 12-02-2023

Fixed

• Various minor changes in the arguments, improving logic and fixing some bugs
• kwargs in nested functions can now be overwritten by simply using the kwargs_dicts using _update_kwargs to ensure the kwargs_dicts take precedence .

Added

• Added unit tests for all plotting modules
• Added example data
• Added additional examples under resources
• Various naming objects in constants.py

Changed

• Updated examples reflecting minor changes in the code base
• Moved colour.py to utils.
• Dependencies: matplotlib 3.5.*

Deprecated

• Added a futurewarning warning that plot_misc.table.layout will be moved to the module data_clean (outside of plot_misc).

Removed

Nothing

v0.0.1.a0 - 05-01-2023

Fixed

Nothing

Added

• Started a changelog.

Changed

Nothing

Deprecated

Nothing

Removed

Nothing