aertslab · SeppeDeWinter · Sep 30, 2025 · Oct 7, 2025 · Oct 7, 2025 · Oct 14, 2025
diff --git a/.cruft.json b/.cruft.json
@@ -1,7 +1,7 @@
 {
   "template": "https://github.com/scverse/cookiecutter-scverse",
-  "commit": "6ad2d42351bf968ef4962b2f5e664a6e29c090bc",
-  "checkout": null,
+  "commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec",
+  "checkout": "v0.6.0",
   "context": {
     "cookiecutter": {
       "project_name": "tfmindi",
@@ -36,8 +36,8 @@
         "trim_blocks": true
       },
       "_template": "https://github.com/scverse/cookiecutter-scverse",
-      "_commit": "6ad2d42351bf968ef4962b2f5e664a6e29c090bc"
+      "_commit": "d383d94fadff9e4e6fdb59d77c68cb900d7cedec"
     }
   },
   "directory": null
-}
+}
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -78,11 +78,15 @@ jobs:
           MPLBACKEND: agg
           PLATFORM: ${{ matrix.os }}
           DISPLAY: :42
-        run: uvx hatch run ${{ matrix.env.name }}:run-cov
+        run: uvx hatch run ${{ matrix.env.name }}:run-cov -v --color=yes -n auto
       - name: generate coverage report
-        run: uvx hatch run ${{ matrix.env.name }}:coverage xml
+        run: |
+          # See https://coverage.readthedocs.io/en/latest/config.html#run-patch
+          test -f .coverage || uvx hatch run ${{ matrix.env.name }}:cov-combine
+          uvx hatch run ${{ matrix.env.name }}:cov-report   # report visibly
+          uvx hatch run ${{ matrix.env.name }}:coverage xml # create report for upload
       - name: Upload coverage
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
 
   # Check that all tests defined above pass. This makes it easy to set a single "required" test in branch
   # protection instead of having to update it frequently. See https://github.com/re-actors/alls-green#why.

diff --git a/.gitignore b/.gitignore
@@ -14,6 +14,7 @@ __pycache__/
 # Tests and coverage
 /data/
 /node_modules/
+/.coverage*
 
 # docs
 /docs/generated/

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -6,25 +6,20 @@ default_stages:
   - pre-push
 minimum_pre_commit_version: 2.16.0
 repos:
-  - repo: https://github.com/biomejs/pre-commit
-    rev: v1.9.4
-    hooks:
-      - id: biome-format
-        exclude: ^\.cruft\.json$ # inconsistent indentation with cruft - file never to be modified manually.
   - repo: https://github.com/tox-dev/pyproject-fmt
     rev: v2.6.0
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.11.13
+    rev: v0.13.2
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]
         args: [--fix, --exit-non-zero-on-fix]
       - id: ruff-format
         types_or: [python, pyi, jupyter]
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
       - id: detect-private-key
       - id: check-ast
@@ -36,12 +31,3 @@ repos:
       # Check that there are no merge conflicts (could be generated by template sync)
       - id: check-merge-conflict
         args: [--assume-in-merge]
-  - repo: local
-    hooks:
-      - id: forbid-to-commit
-        name: Don't commit rej files
-        entry: |
-          Cannot commit .rej files. These indicate merge conflicts that arise during automated template updates.
-          Fix the merge conflicts manually and remove the .rej files.
-        language: fail
-        files: '.*\.rej$'
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -8,6 +8,26 @@ and this project adheres to [Semantic Versioning][].
 [keep a changelog]: https://keepachangelog.com/en/1.0.0/
 [semantic versioning]: https://semver.org/spec/v2.0.0.html
 
+## 1.2.0
+
+This version accompanies the human neural development paper preprint.
+
+### Features
+
+- updated to scverse template v0.6.0
+- added parameter to select pca svd solver for running PCA instead of hardcoded "covariance_eigh"
+- added functionality to save and load patterns to and from disk (`tfmindi.save_patterns` and `tfmindi.load_patterns`)
+- now allows for patterns to be generated by any annotation in .obs, not only by `leiden`
+- can now concatenate multiple TF-MINDI anndatas together using `tfmindi.concat`
+- changed behaviour of seqlet most frequent-occurence for annotating clusters to binomial tests
+- added MAFFT-based backend as option for pattern creation (much faster than TomTom or k-mer)
+
+### Bugfixes
+
+- fix extra 0-position being included in `Pattern.ic_trim`
+- fix failure case in in `Pattern.ic_trim` when all nucleotides are above IC threshold
+- plotting legends are filtered on colors in `adata.obs[color_by]`
+
 ## 1.1.0
 
 Bugfixes, an updated seqlet calling algorithm, and new k-mer pattern tooling.

diff --git a/LICENSE b/LICENSE
@@ -1,21 +1,59 @@
-MIT License
 
-Copyright (c) 2025, Stein Aerts Lab
+Academic Non-commercial Software License Agreement
 
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+The Licensed Software is developed by and on behalf of the Laboratory of Computational Biology of VIB-KU Leuven and is owned by VIB vzw, located at Rijvisschestraat 120, B-9052 Zwijnaarde, Belgium (hereinafter referred to as "VIB"). By downloading or installing the Licensed Software, the user agrees with the terms and conditions below.
+
+Definitions
+
+“Licensed Software” shall mean TF-MINDI as available on GitHub.
+
+"Effective Date" shall mean the date on which you download or install TF-MINDI (as available on GitHub) on your system and which provide you access to the TF-MINDI tool.
+
+“Commercial Purposes” shall include (1) the use of Licensed Software to provide a service, information or data that is directly or indirectly conveyed to any third party against compensation, (2) any type of transfer of the Licensed Software for compensation, and (3) any other use of Licensed Software that supports commercial entities.
+
+License
+
+1.	Licensed Software is the work of the Aerts lab. The copyright in Licensed Software is owned by VIB.
+
+2.	Subject to the terms and conditions of this Agreement, VIB hereby grants and the user accepts a non-exclusive, non-transferable license to use the Licensed Software for strictly internal academic research use only, on your own behalf or on behalf of your institution, and not for Commercial Purposes.
+
+3.	The user confirms to be an academic user. For academic users, there is no license fee.
+
+4. The user shall acknowledge VIB as the provider of Licensed Software and shall include the following reference “De Winter, S., & et al. (2025). aertslab/TF-MInDi. Zenodo. https://doi.org/10.5281/zenodo.17202107” in any manuscript describing data obtained using Licensed Software.
+
+5.	This license does not entitle the user to receive from VIB hard-copy documentation, technical support, telephone assistance, or enhancements or updates to the Licensed Software, and nothing contained herein shall be interpreted as to require VIB, its faculty, employees or students to provide maintenance, installation services, debugging, consultation or end-user support of any kind.
+
+6.	The title and copyright to Licensed Software and any associated programs and documentation shall remain with VIB. The user agrees to preserve the same.
+
+7.	The user agrees not to make any copies of Licensed Software except for use in the user’s laboratory, without VIB’s prior written consent.  The user agrees to place the appropriate copyright notice on any such copies.
+
+8.	The user shall not distribute Licensed Software to other laboratories within user’s institution. The user shall not transfer Licensed Software to another location or person outside of user’s institution without VIB’s prior and written permission.
+
+9.	The user shall not market or otherwise benefit commercially from any product utilizing any portion of Licensed Software, nor any derivative works of Licensed Software, without first entering into a separate commercial license with VIB.
+
+10.	Except as otherwise expressly permitted in this Agreement, the user must not (i) modify or create any derivative works of the Licensed Software or documentation, including customization, translation or localization; (ii) decompile, disassemble, reverse engineer, or otherwise attempt to derive the source code for the Licensed Software; (iii) remove or alter any trademark, logo, copyright or other proprietary notices, legends, symbols or labels in the Licensed Software.
+
+11.	The user acknowledges that the Licensed Software is proprietary to VIB. The software code shall be treated as trade secrets and confidential information of VIB, and the user agrees to use all reasonable efforts to hold the same in confidence. The user’s obligation for confidentiality shall not extend to any information which (i) is or becomes generally available to the public, (ii) is already known to or subsequently disclosed by third parties to the user and at its free disposal, or (iii) is independently developed by the user or its affiliates without the use of the confidential information disclosed by VIB, or (iv) is required by law or legal process to be disclosed.
+
+12.	The user acknowledges that Licensed Software is a research tool and provided free of charge, it is only provided “as is”. VIB makes no representations or warranties of any type whatsoever, express or implied, regarding the Licensed Software. VIB expressly disclaims all representations and warranties regarding the Licensed Software, including but not limited to any representations or warranties of merchantability or fitness for any particular application or that the use of the Licensed Software will not infringe any patents, copyrights or trademarks or other rights of third parties, or any warranty that the rights and licenses granted hereunder comprise all the rights and licenses necessary or desirable to use the Licensed Software for internal non-commercial research purposes as permitted by this Agreement. The entire risk as to the quality and performance of the Licensed Software is borne by the user.
+
+13.	VIB shall not be responsible for losses of any kind resulting from the use of Licensed Software, and can in no way provide compensation for any losses sustained, including but not limited to, any obligation, liability, right, claim or remedy for tort, or for any actual or alleged infringement of patents, copyrights, trade secrets, or similar rights of third parties, nor any business expense, machine downtime or damages caused by any deficiency, defect or error in Licensed Software or mal-function thereof, nor any incidental or consequential damages, however caused.
+
+14.	The user will indemnify, defend and hold harmless VIB, its directors, officers, employees and agents from and against all liability, losses, damages and expenses (including attorney’s fees and costs) arising out of any claims, demands, actions or other proceedings made or instituted by any third party against any of them and arising out of or relating to any breach of this Agreement by the user, or any use of the Licensed Software by the user, except insofar as such claims or liability result from VIB’s gross negligence or willful misconduct.
+
+15.	This Agreement and the license rights granted herein shall become effective as of the date the user downloaded the Licensed Software and shall continue in full force until the user deletes the Licensed Software and any and all related files from the user’s computing system, unless terminated in accordance with this Section. Upon one party's breach of any agreement, covenant, or representation made in this Agreement, the agreement will automatically end thirty (30) days after such breach. Either party shall have the right, at any time, to terminate this Agreement without cause by written notice to the other party specifying the date of termination. Upon termination, the user shall destroy all full and partial copies of the Licensed Software. The user shall forward written notice to VIB that all programs containing Licensed Software have been deleted from all computer libraries and storage or memory devices and are no longer stored therein.
+
+16.	This Agreement shall be construed in accordance with the laws of Belgium. The courts of Belgium shall have exclusive jurisdiction.
+
+17.	The parties agree that this Agreement is the complete and exclusive agreement among the parties and supersedes all proposals and prior agreements whether written or oral, and all other communications among the parties relating to the subject matter of this Agreement. This Agreement cannot be modified except in writing and signed by both parties. Failure by either party at any time to enforce any of the provisions of this Agreement shall not constitute a waiver by such party of such provision nor in any way affect the validity of this Agreement.
+
+18.	The invalidity of singular provisions does not affect the validity of the entire understanding. The parties are obligated, however, to replace the invalid provisions by a regulation, which comes closest to the economic intent of the invalid provision. The same shall apply mutatis mutandis in case of a gap.
 
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
 
 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.
diff --git a/README.md b/README.md
@@ -1,12 +1,23 @@
-# TF-MInDi: Transcription Factor Motifs and Instances Discovery
+<div align="center">
+    <img src="https://raw.githubusercontent.com/aertslab/TF-MINDI/main/docs/_static/TF-MINDI_LOGO_nobg_notext.png"
+    height=50%
+    >
+</div>
+
+# TF-MINDI: Transcription Factor Motif Instance Neighborhood Decomposition and Interpretation
 
 [![Tests][badge-tests]][tests]
 [![Documentation][badge-docs]][documentation]
 
 [badge-tests]: https://img.shields.io/github/actions/workflow/status/aertslab/TF-MInDi/test.yaml?branch=main
 [badge-docs]: https://img.shields.io/readthedocs/tf-mindi
 
-**TF-MInDi** is a Python package for analyzing transcription factor binding patterns from deep learning model attribution scores. It identifies and clusters sequence motifs from contribution scores, maps them to DNA-binding domains, and provides comprehensive visualization tools for regulatory genomics analysis.
+**TF-MINDI** is a Python package for analyzing transcription factor binding patterns from deep learning model attribution scores. It identifies and clusters sequence motifs from contribution scores, maps them to DNA-binding domains, and provides comprehensive visualization tools for regulatory genomics analysis.
+
+<div align="center">
+   <img src="https://raw.githubusercontent.com/aertslab/TF-MINDI/main/docs/_static/tf_mindi_overview.png"
+   height=700>
+</div>
 
 ## Getting Started
 
@@ -49,7 +60,7 @@ You might have to explicitly set your LD_LIBRARY_PATH for cuml as described [her
 
 ## Quick Start
 
-TF-MInDi follows a scanpy-inspired workflow:
+TF-MINDI follows a scanpy-inspired workflow:
 
 1. **Preprocessing (`tm.pp`)**: Extract seqlets, calculate motif similarities, and create an Anndata object
 2. **Tools (`tm.tl`)**: Cluster seqlets and create consensus patterns
@@ -114,7 +125,7 @@ If you found a bug, please use the [issue tracker](https://github.com/aertslab/T
 
 ## Citation
 
-> t.b.a
+> [De Winter S. *et al.* (2026). System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development. BioRxiv. https://doi.org/10.64898/2026.01.14.699402](https://doi.org/10.64898/2026.01.14.699402)
 
 [uv]: https://github.com/astral-sh/uv
 [issue tracker]: https://github.com/aertslab/TF-MInDi/issues

diff --git a/biome.jsonc b/biome.jsonc
@@ -1,9 +1,10 @@
 {
-    "$schema": "https://biomejs.dev/schemas/1.9.4/schema.json",
+    "$schema": "https://biomejs.dev/schemas/2.2.0/schema.json",
+    "vcs": { "enabled": true, "clientKind": "git", "useIgnoreFile": true },
     "formatter": { "useEditorconfig": true },
     "overrides": [
         {
-            "include": ["./.vscode/*.json", "**/*.jsonc"],
+            "includes": ["./.vscode/*.json", "**/*.jsonc"],
             "json": {
                 "formatter": { "trailingCommas": "all" },
                 "parser": {

diff --git a/docs/_static/TF-MINDI_LOGO.png b/docs/_static/TF-MINDI_LOGO.png
diff --git a/docs/_static/TF-MINDI_LOGO_nobg_notext.png b/docs/_static/TF-MINDI_LOGO_nobg_notext.png
diff --git a/docs/_static/tf_mindi_overview.png b/docs/_static/tf_mindi_overview.png
diff --git a/docs/api.md b/docs/api.md
@@ -14,4 +14,5 @@ api/io
 api/datasets
 api/types
 api/backends
+api/merge
 ```
diff --git a/docs/api/merge.md b/docs/api/merge.md
@@ -0,0 +1,12 @@
+# Merge
+
+Concatenation of TF-MInDi AnnData objects.
+
+```{eval-rst}
+.. currentmodule:: tfmindi
+
+.. autosummary::
+    :toctree: ../generated
+
+    concat
+```
diff --git a/docs/api/plotting.md b/docs/api/plotting.md
@@ -16,6 +16,9 @@ Visualization functions for seqlet analysis and motif exploration.
     pl.region_contributions
     pl.dbd_logos
     pl.dbd_cluster_logos
+    pl.pattern_logo
     pl.region_topic_tsne
+    pl.distance_bias_profile
+    pl.distance_bias_heatmap
     pl.render_plot
 ```
diff --git a/docs/api/tools.md b/docs/api/tools.md
@@ -13,5 +13,7 @@ Analysis tools for clustering seqlets and pattern discovery.
     tl.create_patterns
     tl.run_topic_modeling
     tl.evaluate_topic_models
+    tl.detect_distance_bias
+    tl.extend_biased_seqlets
 
 ```
diff --git a/docs/api/types.md b/docs/api/types.md
@@ -8,4 +8,6 @@ Core data types used throughout TF-MInDi.
 .. autoclass:: Pattern
 
 .. autoclass:: Seqlet
+
+.. autoclass:: BiasDetectionResult
 ```
diff --git a/docs/conf.py b/docs/conf.py
@@ -115,6 +115,7 @@
 html_theme = "sphinx_book_theme"
 html_static_path = ["_static"]
 html_css_files = ["css/custom.css"]
+html_logo = "_static/TF-MINDI_LOGO_nobg_notext.png"
 
 html_title = project_name