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Merge branch 'main' into 22-consistent-test-struct
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‎.github/workflows/ci.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: ["3.10", "3.12", "3.13"]
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python-version: ["3.11", "3.12", "3.13"]
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steps:
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- uses: actions/checkout@v4
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# Run tests in the venv
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- name: Run tests
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env:
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TMEQ_RUN_CURVELETS: "0"
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QT_QPA_PLATFORM: "offscreen"
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run: |
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source venv/bin/activate

‎.github/workflows/manual-test.yml‎

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name: Manual Testing Stub
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# This action allows manual testing of other actions from branches, without
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# requiring them to be on main themselves.
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on:
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# Enable manual execution from GitHub UI
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workflow_dispatch:
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jobs:
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test-run:
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# Create this file on your branch as the action to test
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uses: ./.github/workflows/test-action.yml
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secrets: inherit

‎.gitignore‎

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*.pydevproject
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.project
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.metadata
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bin/
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tmp/
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*.tmp
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*.bak
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publish
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# Others
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[Bb]in
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[Oo]bj
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sql
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TestResults
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*.py[co]
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# uv
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uv.lock
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# Packages
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*.egg
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*.egg-info
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dist
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build
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eggs
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parts
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bin
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var
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sdist
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develop-eggs

‎Makefile‎

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# Makefile for tme-quant
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# Convenience commands for common tasks
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.PHONY: help setup test check clean
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help:
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@echo "tme-quant Makefile Commands"
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@echo ""
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@echo "Setup & Installation:"
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@echo " make setup - Automated installation with curvelops (uses bin/install.sh)"
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@echo ""
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@echo "Development:"
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@echo " make test - Run test suite"
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@echo " make check - Run linting"
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@echo " make clean - Clean build artifacts"
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@echo ""
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setup:
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@echo "Running automated installation..."
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bash bin/install.sh
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test:
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uv run pytest -v
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check:
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uv run ruff check .
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clean:
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rm -rf build/ dist/ *.egg-info
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find . -type d -name __pycache__ -exec rm -r {} +
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find . -type f -name "*.pyc" -delete
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rm -rf .pytest_cache .coverage htmlcov

‎README.md‎

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Base requirements:
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- macOS, Linux, or Windows (see notes below)
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- Conda (recommended) or Python 3.10–3.13
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- For napari: a Qt binding (PyQt or PySide)
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- Python 3.11+
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- [uv](https://docs.astral.sh/uv/) (recommended) or pip
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- napari uses PyQt6 (included in dependencies)
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### Quick start (without curvelets)
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Install the package and the napari GUI. This path avoids the native curvelet build.
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```bash
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conda create -y -n napari-env -c conda-forge python=3.11 pip
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conda activate napari-env
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# project install (editable)
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pip install -e .
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# napari + Qt
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conda install -y -c conda-forge napari pyqt qtpy
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uv sync
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uv run napari
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```
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### Optional: curvelet backend (curvelops)
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To enable curvelet-powered features and tests you must build and install FFTW 2.1.5 and CurveLab, then install `curvelops`.
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macOS/Linux outline:
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To enable curvelet-powered features and tests you must build FFTW 2.1.5 and CurveLab, then install with curvelops. Use the automated script:
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**Prerequisites:** Clone this repo, install [uv](https://docs.astral.sh/uv/), and download CurveLab to `../utils` (see [doc/INSTALL.md](doc/INSTALL.md)).
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macOS/Linux:
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```bash
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# 1) Build FFTW 2.1.5 (C only)
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curl -L -O http://www.fftw.org/fftw-2.1.5.tar.gz
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tar xzf fftw-2.1.5.tar.gz
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cd fftw-2.1.5
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# If configure fails on macOS due to outdated config.{sub,guess}, update them from your system
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./configure --prefix="$HOME/opt/fftw-2.1.5" --disable-fortran
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make -j$(sysctl -n hw.logicalcpu 2>/dev/null || nproc)
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make install
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export FFTW="$HOME/opt/fftw-2.1.5"
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# 2) Build CurveLab 2.1.x
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export FDCT="/path/to/CurveLab-2.1.x"
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cd "$FDCT/fdct_wrapping_cpp/src" && make
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cd "$FDCT/fdct/src" && make
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cd "$FDCT/fdct3d/src" && make
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# 3) Install build tooling and curvelops
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conda activate napari-env
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python -m pip install -U pip
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pip install pybind11 scikit-build-core cmake ninja
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export FFTW="$HOME/opt/fftw-2.1.5"
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export FDCT="/path/to/CurveLab-2.1.x"
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pip install -v "curvelops @ git+https://github.com/PyLops/curvelops@0.23"
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bash bin/install.sh
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# or: make setup
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```
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Windows options:
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- Recommended: use WSL2 (Ubuntu). Follow the macOS/Linux steps inside WSL.
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- Native Windows: use MSYS2 (for `gcc`, `make`) or Visual Studio toolchain; build FFTW 2.1.5 and CurveLab from source, set `FFTW` and `FDCT` env vars to their install roots, then install `curvelops` as above. Supervisors can validate these steps on a Windows host.
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- Native Windows: use MSYS2 (for `gcc`, `make`) or Visual Studio toolchain; build FFTW 2.1.5 and CurveLab from source, set `FFTW` and `FDCT` env vars to their install roots, then use `uv` commands as above.
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### Development
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See [doc/DEVELOPMENT.md](doc/DEVELOPMENT.md) for plugin setup and troubleshooting. Running tests:
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### Development: running the tests
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- Headless (no GUI): set Qt to offscreen
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- macOS/Linux: `export QT_QPA_PLATFORM=offscreen`
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- Core tests (no curvelets):
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```bash
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pytest -q
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make test
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```
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- Full tests with curvelets (after installing `curvelops`):
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```bash
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export TMEQ_RUN_CURVELETS=1
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pytest -q
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```
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- Full tests with curvelets (after installing `curvelops`): `make test` — curvelet tests run automatically when curvelops is available; otherwise skipped.
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Notes:
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- The napari test is an import-only smoke test (no `Viewer` is created); it runs headless.
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### Continuous integration
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- CI installs the package without `curvelops` to avoid building FFTW/CurveLab on runners.
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- CI environment:
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- Curvelet tests skipped (curvelops not installed on CI)
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- `QT_QPA_PLATFORM=offscreen` (headless napari import)
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### Working with secrets in GitHub Actions
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This project uses GitHub Actions secrets for tasks that require authentication or access to private resources. Secrets can be configured in the [Settings tab of the repostiory](https://github.com/uw-loci/tme-quant/settings/secrets/actions). For more information about secrets, see:
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- [Secrets as a concept](https://docs.github.com/en/actions/concepts/security/secrets)
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- [Secrets in actions](https://docs.github.com/en/actions/security-for-github-actions/security-guides/using-secrets-in-github-actions).
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#### Manual testing workflow
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The `manual-test` workflow allows developers to manually trigger workflows from the GitHub UI without committing changes to `main`. This is useful for testing workflows that require secrets on topic branches.
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**How to use it:**
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1. Create or edit `.github/workflows/test-action.yml` to define your workflow's structure and declare which secrets it needs via the `secrets:` input in `workflow_call`:
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```yaml
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on:
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workflow_call:
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secrets:
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MY_SECRET_NAME:
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ANOTHER_SECRET:
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jobs:
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my-job:
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runs-on: ubuntu-latest
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steps:
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- name: Use a secret
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run: echo "Secret is ${{ secrets.MY_SECRET_NAME }}"
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```
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2. The `manual-test` workflow (`.github/workflows/manual-test.yml`) will call `test-action.yml` and pass repository secrets to it via `secrets: inherit`.
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3. To trigger the workflow:
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- Push your branch with the updated `test-action.yml` to GitHub.
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- Go to the **Actions** tab in the repository and select the **[Manual Testing Stub](https://github.com/uwloci/tme-quant/actions/workflows/manual-test.yml)** workflow.
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- Click **Run workflow** and select your branch.
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- The workflow will execute with access to all secrets configured for the repository.
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**NOTE**
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- Never hardcode secrets or access tokens in workflow files; always use the `secrets:` context.
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### Troubleshooting
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- Qt error ("No Qt bindings could be found"): install `pyqt` (or `pyside2`) from conda-forge.
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- Qt error ("No Qt bindings could be found"): ensure `uv sync` completed; pyproject includes PyQt6.
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- Segfault on Viewer creation: avoid creating a `napari.Viewer()` in tests; we only import napari and run offscreen.
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- curvelops build errors: ensure `FFTW` and `FDCT` point to your install roots and the 2D/3D libraries were built.

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