first implementation of bandsilo and band scan annotation

.flake8

@@ -7,3 +7,5 @@ exclude =
     venv, 
     .conda
 max-complexity = 10
+# Black's PEP 8-compliant slice formatting conflicts with pycodestyle E203.
+extend-ignore = E203

.github/workflows/test_and_lint.yml → .github/workflows/lint.yml

@@ -1,4 +1,4 @@
-name: Lint and run tests
+name: Lint
 
 on:
   pull_request:
@@ -18,9 +18,7 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
-      run: | 
+      run: |
         python -m pip install -e . --group dev --no-cache-dir
     - name: Run linter checks
-      run: flake8 . && interrogate --verbose .
-    - name: Run tests and coverage
-      run: coverage run -m unittest discover && coverage report
+      run: flake8 . && interrogate --verbose .

.github/workflows/tag_and_publish.yml

@@ -3,8 +3,7 @@ on:
   push:
     branches:
       - main
-# Remove line 65 to enable automated semantic version bumps.
-# Change line 71 from "if: false" to "if: true" to enable PyPI publishing. 
+# Set the publish job's "if" condition to true to enable PyPI publishing.
 # Requires that svc-aindscicomp be added as an admin to repo.
 jobs:
   update_badges:
@@ -41,19 +40,6 @@ jobs:
             new_interrogate_badge="interrogate-$interrogate_val%25-yellow"
         fi
         sed -i "s/$interrogate_badge/$new_interrogate_badge/g" README.md
-    - name: Get Coverage values and Update README.md
-      run: |
-        coverage run -m unittest discover
-        coverage_val=$(coverage report | grep "^TOTAL" | grep -o '[0-9]\+%' | grep -o '[0-9]\+')
-        coverage_badge=$(grep '^\!\[Coverage\]' README.md | sed -n 's/.*\(coverage-[^)]*\).*/\1/p')
-        if (( $(echo "$coverage_val >= 90.00" | bc -l) )); then 
-            new_coverage_badge="coverage-$coverage_val%25-brightgreen"
-        elif (( $(echo "$coverage_val < 80.00" | bc -l) )); then
-            new_coverage_badge="coverage-$coverage_val%25-red"
-        else
-            new_coverage_badge="coverage-$coverage_val%25-yellow"
-        fi
-        sed -i "s/$coverage_badge/$new_coverage_badge/g" README.md
     - name: Commit changes
       uses: EndBug/add-and-commit@v10
       with:

.gitignore

@@ -37,19 +37,8 @@ MANIFEST
 pip-log.txt
 pip-delete-this-directory.txt
 
-# Unit test / coverage reports
-htmlcov/
-.tox/
-.nox/
-.coverage
-.coverage.*
+# Tool caches
 .cache
-nosetests.xml
-coverage.xml
-*.cover
-*.py,cover
-.hypothesis/
-.pytest_cache/
 
 # Translations
 *.mo
@@ -135,5 +124,8 @@ dmypy.json
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 .idea/
 
+# VS Code
+.vscode/
+
 # MacOs
 **/.DS_Store

CONTRIBUTING.md

@@ -1,15 +1,19 @@
 # Contributing
 
-### Linters and testing
+### Development setup
 
-There are several libraries used to run linters, check documentation, and run tests.
-
-- Please test your changes using the **coverage** library, which will run the tests and log a coverage report:
+From the repository root, install the package and development tools with pip 25.1 or later:
 
 ```bash
-coverage run -m unittest discover && coverage report
+pip install -e . --group dev
 ```
 
+Alternatively, use `uv sync`. Interactive ROI work also requires tkinter in the Python installation.
+
+### Code quality
+
+Use the following tools to check documentation and maintain code style.
+
 - Use **interrogate** to check that modules, methods, etc. have been documented thoroughly:
 
 ```bash
@@ -47,7 +51,6 @@ where scope (optional) describes the packages affected by the code changes and t
 - **fix**: A bugfix
 - **perf**: A code change that improves performance
 - **refactor**: A code change that neither fixes a bug nor adds a feature
-- **test**: Adding missing tests or correcting existing tests
 
 ### Semantic Release
 
@@ -60,15 +63,17 @@ The table below, from [semantic release](https://github.com/semantic-release/sem
 | `perf(pencil): remove graphiteWidth option`<br><br>`BREAKING CHANGE: The graphiteWidth option has been removed.`<br>`The default graphite width of 10mm is always used for performance reasons.` | ~~Major~~ Breaking Release <br /> (Note that the `BREAKING CHANGE: ` token must be in the footer of the commit and need to be all caps as shown) |
 
 ### Documentation
-To generate the rst files source files for documentation, run
-```bash
-sphinx-apidoc -o docs/source/ src
-```
-Then to create the documentation HTML files, run
+
+The maintained Sphinx pages include a curated public API reference; do not regenerate them with `sphinx-apidoc`.
+Build the documentation and treat warnings as errors:
+
 ```bash
-sphinx-build -b html docs/source/ docs/build/html
+sphinx-build -b html -n -W --keep-going docs/source/ docs/build/html
 ```
-More info on sphinx installation can be found [here](https://www.sphinx-doc.org/en/master/usage/installation.html).
+
+External API links use Python, NumPy, and h5py inventories downloaded by Sphinx; a clean build requires network access to those documentation sites.
+
+Keep the README focused on running BandSILo. Put option and staging details in [API and data conventions](docs/source/migration.rst), scientific details in [trace estimation](docs/source/traces.rst), schemas in [file formats](docs/source/file_formats.rst), and ownership decisions in [architecture](docs/source/architecture.rst).
 
 ### Read the Docs Deployment
 Note: Private repositories require **Read the Docs for Business** account. The following instructions are for a public repo.