Merge branch 'main' into maxgamill-sheffield/unet-crop-fix

.github/dependabot.yml

@@ -0,0 +1,11 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/pull_request_template.md

@@ -13,8 +13,11 @@ description of why a particular item is not relevant.
 Before submitting a Pull Request please check the following.
 
 - [ ] Existing tests pass.
-- [ ] Documentation has been updated and builds. Remember to update `configuration.md`, `usage.md`, and relevant
-      processing sections under `advanced.md`.
+- [ ] Documentation has been updated and builds. Remember to update as required...
+  - [ ] `docs/configuration.md`
+  - [ ] `docs/usage.md`
+  - [ ] `docs/data_dictionary.md`
+  - [ ] `docs/advanced.md` and new pages it should link to.
 - [ ] Pre-commit checks pass.
 - [ ] New functions/methods have typehints and docstrings.
 - [ ] New functions/methods have tests which check the intended behaviour is correct.

.github/workflows/add-issue-to-project.yaml

@@ -10,7 +10,7 @@ jobs:
     name: Add issue to project
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/add-to-project@v0.5.0
+      - uses: actions/add-to-project@v1.0.2
         with:
           # You can target a repository in a different organization
           # to the issue

.github/workflows/tests.yaml

@@ -50,7 +50,7 @@ jobs:
         run: |
           coverage xml
       - name: Upload coverage to Codecov
-        uses: codecov/codecov-action@v4
+        uses: codecov/codecov-action@v5
 
       - name: Setup tmate session
         if: ${{ failure() }}

.gitignore

@@ -1,13 +1,170 @@
-# Byte-compiled / optimized / DLL files
-__pycache__/
-*.py[cod]
-*.egg-info/*
-
-# Build directory
-build/*
-
-# User-Specific config file
-output/config.yaml
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+### Python Patch ###
+# Poetry local configuration file - https://python-poetry.org/docs/configuration/#local-configuration
+poetry.toml
+
+# ruff
+.ruff_cache/
+
+# LSP config files
+pyrightconfig.json
+
+# End of https://www.toptal.com/developers/gitignore/api/python
 
 # Source / output data
 .dropbox
@@ -26,7 +183,7 @@ output/config.yaml
 *.svg
 
 # Notebook checkpoints
-notebooks/.ipynb_checkpoints/
+notebooks/.ipynb_checkpoints
 
 # Example Data
 !minicircle.spm
@@ -35,6 +192,7 @@ notebooks/.ipynb_checkpoints/
 .vscode/
 .idea/
 *~
+\#*
 pytest-debug.ini
 
 # Documentation

.pre-commit-config.yaml

@@ -19,7 +19,7 @@ repos:
         types: [python, yaml, markdown]
 
   - repo: https://github.com/DavidAnson/markdownlint-cli2
-    rev: v0.14.0
+    rev: v0.15.0
     hooks:
       - id: markdownlint-cli2
         args: []
@@ -32,7 +32,7 @@ repos:
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
-    rev: v0.7.2
+    rev: v0.8.1
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix, --show-fixes]
@@ -58,13 +58,13 @@ repos:
     hooks:
       - id: codespell
 
-  - repo: https://github.com/pre-commit/mirrors-prettier
-    rev: v4.0.0-alpha.8
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.4.1
     hooks:
       - id: prettier
 
   - repo: https://github.com/kynan/nbstripout
-    rev: 0.8.0
+    rev: 0.8.1
     hooks:
       - id: nbstripout
 
@@ -73,6 +73,17 @@ repos:
     hooks:
       - id: numpydoc-validation
 
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: v1.10.0
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
+      - id: python-no-eval
+      - id: python-check-blanket-noqa
+      - id: python-check-blanket-type-ignore
+      - id: python-check-mock-methods
+
   - repo: local
     hooks:
       - id: pylint

.readthedocs.yaml

@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
+    python: "3.11"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:

CITATION.cff

@@ -38,6 +38,24 @@ authors:
     given-names: Mingxue
     family-names: Du
     orcid: "https://orcid.org/0009-0008-9452-5719"
+  - given-names: Joseph
+    family-names: Beton
+    affiliation: CSSB Hamburg, Hamburg, DE
+    orcid: 0000-0001-7499-3867
+  - given-names: Luzie
+    family-names: Helfmann
+    email: [email protected]
+    affiliation: Zuse Institute Berlin
+    orcid: 0000-0002-8188-8288
+  - given-names: Robert
+    family-names: Gray
+    affiliation: Institute of Structural and Molecular Biology, Birkbeck, University of London
+    orcid: 0000-0001-5035-4999
+  - given-names: Agnel Praveen
+    family-names: Joseph
+    email: [email protected]
+    affiliation: Collaborative Computational Project for Electron cryo-Microscopy, Science and Technology Facilities Council
+
 identifiers:
   - type: doi
     value: 10.15131/shef.data.22633528.v1

README.md

@@ -99,4 +99,8 @@ Please use the [Citation File Format](https://citation-file-format.github.io/) w
 
 ### Publications
 
-- [TopoStats – A program for automated tracing of biomolecules from AFM images](https://www.sciencedirect.com/science/article/pii/S1046202321000207)
+- [TopoStats - Atomic Force Microscopy image processing and
+  analysis](https://orda.shef.ac.uk/articles/software/TopoStats_-_Atomic_Force_Microscopy_image_processing_and_analysis/22633528)
+  [doi:10.15131/shef.data.22633528.v2](https://doi.org/10.15131/shef.data.22633528.v2)
+- **Pre-Print** [Under or Over? Tracing Complex DNA Structures with High Resolution Atomic Force Microscopy |
+  bioRxiv](https://www.biorxiv.org/content/10.1101/2024.06.28.601212v2) [doi:10.1101/2024.06.28.601212](https://doi.org/10.1101/2024.06.28.601212)