Add base files

.github/workflows/build.yml

@@ -0,0 +1,36 @@
+# Package builds
+name: Build
+
+on:
+  release:
+    types:
+      - published
+
+jobs:
+  pypi:
+    name: PyPI Wheel
+    runs-on: "ubuntu-22.04"
+    steps:
+
+    - name: Checkout repo
+      uses: actions/[email protected]
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        pip install --editable .[dev]
+
+    - name: Build wheel
+      run: |
+        python -m build --wheel
+        twine check dist/*
+    
+    - name: Upload
+      env:
+        PYPI_TOKEN: ${{ secrets.PYPI_TOKEN }}
+      run: |
+        twine upload -u __token__ -p "$PYPI_TOKEN" dist/* --non-interactive --skip-existing --disable-progress-bar

.github/workflows/ci.yml

@@ -0,0 +1,70 @@
+# Continuous integration
+name: CI
+
+on:
+  push:
+    paths:
+      - "sleap_roots/**"
+      - "tests/**"
+      - ".github/workflows/ci.yml"
+      - "environment.yml"
+      - "setup.cfg"
+
+jobs:
+  # Tests with pytest
+  tests:
+
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-22.04", "windows-2022"]
+        python: [3.8]
+
+    name: Tests (${{ matrix.os }}, Python ${{ matrix.python }})
+    runs-on: ${{ matrix.os }}
+
+    steps:
+
+      - name: Checkout repo
+        uses: actions/[email protected]
+
+      - name: Cache conda
+        uses: actions/cache@v1
+        env:
+          # Increase this value to reset cache if environment.yml has not changed
+          CACHE_NUMBER: 0
+        with:
+          path: ~/conda_pkgs_dir
+          key: ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ hashFiles('environment.yml', 'setup.cfg') }}
+
+      - name: Setup Miniconda
+        # https://github.com/conda-incubator/setup-miniconda
+        uses: conda-incubator/[email protected]
+        with:
+          python-version: ${{ matrix.python }}
+          use-only-tar-bz2: true # IMPORTANT: This needs to be set for caching to work properly!
+          environment-file: environment.yml
+          activate-environment: sleap-roots
+
+      - name: Print environment info
+        shell: bash -l {0}
+        run: |
+          which python
+          conda info
+          conda list
+      - name: Test with pytest
+        if: ${{ !(startsWith(matrix.os, 'ubuntu') && matrix.python == 3.8) }}
+        shell: bash -l {0}
+        run: |
+          pytest
+      - name: Test with pytest (with coverage)
+        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.8 }}
+        shell: bash -l {0}
+        run: |
+          pytest --cov=sleap_roots --cov-report=xml tests/
+      - name: Upload coverage
+        uses: codecov/codecov-action@v3
+        if: ${{ startsWith(matrix.os, 'ubuntu') && matrix.python == 3.8 }}
+        with:
+          fail_ci_if_error: true
+          verbose: false

.github/workflows/lint.yml

@@ -0,0 +1,41 @@
+# This action runs:
+# 
+# 1. Linting with black
+#
+# 2. Docstring style checking with pydocstyle 
+# Note: This uses Google-style docstring convention
+# Ref: https://google.github.io/styleguide/pyguide.html
+
+name: Lint
+
+on:
+  push:
+    paths:
+      - "sleap_roots/**"
+      - "tests/**"
+      - ".github/workflows/lint.yml"
+
+jobs:
+  lint:
+    name: Lint
+    runs-on: "ubuntu-22.04"
+    steps:
+
+    - name: Checkout repo
+      uses: actions/[email protected]
+
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.8
+
+    - name: Install dependencies
+      run: |
+        pip install --editable .[dev]
+    - name: Run Black
+      run: |
+        black --check sleap_roots tests
+    
+    - name: Run pydocstyle
+      run: |
+        pydocstyle --convention=google sleap_roots/

.gitignore

@@ -127,3 +127,5 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+.DS_Store

README.md

@@ -1,2 +1,41 @@
 # sleap-roots
-Analysis tools for SLEAP-based root phenotyping.
+
+[![CI](https://github.com/talmolab/sleap-roots/actions/workflows/ci.yml/badge.svg)](https://github.com/talmolab/sleap-roots/actions/workflows/ci.yml)
+[![Lint](https://github.com/talmolab/sleap-roots/actions/workflows/lint.yml/badge.svg)](https://github.com/talmolab/sleap-roots/actions/workflows/lint.yml)
+[![codecov](https://codecov.io/gh/talmolab/sleap-roots/branch/main/graph/badge.svg)](https://codecov.io/gh/talmolab/sleap-roots)
+[![Release](https://img.shields.io/github/v/release/talmolab/sleap-roots?label=Latest)](https://github.com/talmolab/sleap-roots/releases/)
+[![PyPI](https://img.shields.io/pypi/v/sleap-roots?label=PyPI)](https://pypi.org/project/sleap-roots)
+
+Analysis tools for [SLEAP](https://sleap.ai)-based plant root phenotyping.
+
+## Installation
+```
+pip install sleap-roots
+```
+
+If you are using conda:
+```
+conda create -n sleap-roots python=3.8
+conda activate sleap-roots
+pip install sleap-roots
+```
+
+### Development
+For development, use the following syntax to install in editable mode:
+```
+conda env create -f environment.yml
+```
+This will create a conda environment called `sleap-roots`.
+
+To run tests, first activate the environment:
+```
+conda activate sleap-roots
+```
+Then run `pytest` with:
+```
+pytest tests
+```
+To start fresh, just delete the environment:
+```
+conda env remove -n sleap-roots
+```

codecov.yml

@@ -0,0 +1,12 @@
+coverage:
+  status:
+    project: # Measures overall project coverage.
+      default:
+        target: auto
+        threshold: 0.05%
+        informational: true # Project coverage for stats only.
+    patch: #  Only measures lines adjusted in the pull request.
+      default:
+        target: auto
+        threshold: 0.05%
+        informational: true # Patch coverage for stats only.

environment.yml

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+name: sleap-roots
+
+dependencies:
+  - python=3.8
+  - pip
+  - pip:
+    - "--editable=.[dev]"

pyproject.toml

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+[build-system]
+requires = ["setuptools"]
+build-backend = "setuptools.build_meta

setup.cfg

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+[metadata]
+name = sleap-roots
+version = attr: sleap_roots.__version__
+author = Talmo Pereira
+author_email = [email protected]
+maintainer = Talmo Pereira
+maintainer_email = [email protected]
+url = https://github.com/talmolab/sleap-roots
+description = Analysis tools for SLEAP-based plant root phenotyping.
+long_description = file: README.md, LICENSE
+long_description_content_type = text/markdown
+keywords = sleap, plants, roots
+license = BSD 3-Clause License
+classifiers =
+    Programming Language :: Python :: 3
+
+[options]
+packages = find:
+install_requires =
+    numpy
+    attrs
+    matplotlib
+
+[options.extras_require]
+dev =
+    pytest
+    pytest-cov
+    black
+    pydocstyle
+    toml
+    twine
+    build
+
+[options.exclude_package_data]
+tests = *
+docs = *
+
+[options.packages.find]
+exclude =
+    tests*
+    docs*
+
+[pydocstyle]
+convention = google
+match-dir = 'sleap_roots'

sleap_roots/__init__.py

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+"""High-level imports."""
+
+from sleap_roots.series import Series
+
+# Define package version.
+# This is read dynamically by setuptools in setup.cfg to determine the release version.
+__version__ = "0.0.1"

sleap_roots/bases.py

@@ -0,0 +1 @@
+"""Trait calculations that rely on bases (i.e., dicot-only)."""

sleap_roots/convhull.py

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+"""Convex hull fitting and derived trait calculation."""

sleap_roots/ellipse.py

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+"""Ellipse fitting and derived trait calculation."""

sleap_roots/series.py

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+"""Series-level data loader."""
+
+import attrs
+from typing import Optional, Tuple
+from pathlib import Path
+
+try:
+    import sleap
+except:
+    import sleap_io as sleap
+
+
+@attrs.define
+class Series:
+    h5_path: Optional[str] = None
+    primary_name: str = "primary_multi_day"
+    lateral_name: str = "lateral__nodes"
+    primary_labels: Optional[sleap.Labels] = None
+    lateral_labels: Optional[sleap.Labels] = None
+
+    @classmethod
+    def load(cls, h5_path: str, primary_name: str = "primary_multi_day", lateral_name: str = "lateral__nodes"):
+        primary_path = Path(h5_path).with_suffix(f".{primary_name}.predictions.slp").as_posix()
+        lateral_path = Path(h5_path).with_suffix(f".{lateral_name}.predictions.slp").as_posix()
+
+        return cls(
+            h5_path,
+            primary_name=primary_name,
+            lateral_name=lateral_name,
+            primary_labels=sleap.load_file(primary_path),
+            lateral_labels=sleap.load_file(lateral_path),
+        )
+
+    @property
+    def series_name(self) -> str:
+        return Path(self.h5_path).stem
+
+    @property
+    def video(self) -> sleap.Video:
+        return self.primary_labels.video
+
+    def __len__(self) -> int:
+        return len(self.video)
+
+    def __getitem__(self, idx: int) ->  Tuple[sleap.LabeledFrame, sleap.LabeledFrame]:
+        return self.get_frame(idx)
+
+    def __iter__(self):
+        for i in range(len(self)):
+            yield self[i]
+
+    def get_frame(self, frame_idx: int) -> Tuple[sleap.LabeledFrame, sleap.LabeledFrame]:
+        """Return labeled frames for primary and lateral predictions.
+        
+        Args:
+            frame_idx: Integer frame number.
+        
+        Returns:
+            Tuple of (primary_lf, lateral_lf) corresponding to the
+            sleap.LabeledFrames from each set of predictions on the same frame.
+        """
+        lf_primary = self.primary_labels.find(self.primary_labels.video, frame_idx, return_new=True)[0]
+        lf_lateral = self.lateral_labels.find(self.lateral_labels.video, frame_idx, return_new=True)[0]
+        return lf_primary, lf_lateral
+
+    def plot(self, frame_idx: int, scale: float = 1.0, **kwargs):
+        primary_lf, lateral_lf = self.get_frame(frame_idx)
+        sleap.nn.viz.plot_img(primary_lf.image, scale=scale)
+        sleap.nn.viz.plot_instances(primary_lf.instances, cmap=["r"], **kwargs)
+        sleap.nn.viz.plot_instances(lateral_lf.instances, cmap=["g"], **kwargs)
+
+
+def find_all_series(data_folders: list[str]) -> list[str]:
+    """Find all .h5 series from a list of folders.
+    
+    Args:
+        data_folders: List of paths to folders containing .h5 series.
+    
+    Returns:
+        A list of filenames to .h5 series.
+    """
+    if type(data_folders) != list:
+        data_folders = [data_folders]
+
+    h5_series = []
+    for data_folder in data_folders:
+        h5_series.extend([Path(p).as_posix() for p in Path(data_folder).glob("*.h5")])
+    return h5_series