Add CI/CD workflows

.github/workflows/ci.yml

@@ -0,0 +1,52 @@
+name: CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+
+permissions:
+  contents: read
+
+concurrency:
+  group: ci-${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  checks:
+    name: Python ${{ matrix.python-version }}
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version:
+          - "3.12"
+          - "3.13"
+          - "3.14"
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+
+      - name: Install uv and python
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          python-version: ${{ matrix.python-version }}
+          enable-cache: true
+          cache-dependency-glob: uv.lock
+
+      - name: Install the project
+        run: uv sync --locked --dev --extra analysis
+
+      - name: Check formatting
+        run: uv run ruff format --check
+
+      - name: Lint
+        run: uv run ruff check
+
+      - name: Type check
+        run: uv run pyrefly check
+
+      - name: Test
+        run: uv run pytest -v

.github/workflows/publish.yml

@@ -0,0 +1,74 @@
+name: Publish to PyPI
+
+on:
+  push:
+    tags:
+      - "v*"
+
+concurrency:
+  group: pypi-publish
+  cancel-in-progress: false
+
+jobs:
+  build:
+    name: Build distributions
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          persist-credentials: false
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@20cfd1bf945f4377ade1205e4dbc17946fc9a30d # v10.0.1
+        with:
+          enable-cache: false
+
+      - name: Verify tag matches package version
+        shell: bash
+        run: |
+          tag_version="${GITHUB_REF_NAME#v}"
+          project_version="$(uv version --short)"
+          if [[ "$tag_version" != "$project_version" ]]; then
+            echo "Tag version $tag_version does not match package version $project_version" >&2
+            exit 1
+          fi
+
+      - name: Build distributions
+        run: uv build
+
+      - name: Smoke test wheel
+        run: uv run --isolated --no-project --with dist/*.whl python -c "import routing_pyramids"
+
+      - name: Smoke test source distribution
+        run: uv run --isolated --no-project --with dist/*.tar.gz python -c "import routing_pyramids"
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
+        with:
+          name: distributions
+          path: dist/
+          if-no-files-found: error
+
+  publish:
+    name: Publish distributions
+    needs: build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/project/routing-pyramids/
+    permissions:
+      id-token: write
+
+    steps:
+      - name: Download distributions
+        uses: actions/download-artifact@3e5f45b2cfb9172054b4087a40e8e0b5a5461e7c # v8.0.1
+        with:
+          name: distributions
+          path: dist/
+
+      - name: Publish distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@dc37677b2e1c63e2034f94d8a5b11f265b73ba33 # v1.14.2

CONTRIBUTING.md

@@ -10,3 +10,19 @@ uv run pyrefly check
 # test
 uv run pytest
 ```
+
+## Releasing
+
+Publishing uses PyPI trusted publishing with GitHub Actions.
+For each release, update and commit the version and lockfile:
+
+```sh
+uv version 0.2.0
+git add pyproject.toml uv.lock
+git commit -m "release 0.2.0"
+```
+
+Wait for CI to pass on the version commit,
+then create and push the matching version tag.
+The tag must be the package version prefixed with `v`.
+Pushing it starts the publishing [workflow](.github/workflows/publish.yml).

examples/visualize_bbbc013_latents.py

@@ -3,13 +3,11 @@
 from dataclasses import dataclass
 from pathlib import Path
 
-import betterplots
 import matplotlib.pyplot as plt
 import numpy as np
 import pandas as pd
 import seaborn as sns
 import torch
-from betterplots.boxstripplot import boxstripplot
 from cmap import Colormap as CmapColormap
 from matplotlib.axes import Axes
 from matplotlib.cm import ScalarMappable
@@ -24,6 +22,8 @@
 from torch.utils.data import DataLoader
 from umap import UMAP
 
+from routing_pyramids._vendor.betterplots import set_style
+from routing_pyramids._vendor.betterplots.boxstripplot import boxstripplot
 from routing_pyramids.data.temporal_datamodule import BBBC013VideoDataModule
 from routing_pyramids.pyramid_flow_system import (
     PyramidFlowDecoder2d,
@@ -77,7 +77,7 @@
 
 device = torch.device("cpu" if FORCE_CPU or not torch.cuda.is_available() else "cuda")
 print(f"Using device: {device}")
-betterplots.set_style(
+set_style(
     usetex=False,
     serif=True,
     font_size=8,

examples/visualize_flow_aics_object_posterior.py

@@ -5,11 +5,11 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import torch
-from betterplots import set_style
 from matplotlib.colors import hsv_to_rgb
 from torch import Tensor
 from torch.nn import functional as F
 
+from routing_pyramids._vendor.betterplots import set_style
 from routing_pyramids.data.temporal_video_dataset import OMEZarrVideoDataset
 from routing_pyramids.data.transforms import get_normalization, get_transforms
 from routing_pyramids.pyramid_flow_system import (

pyproject.toml

@@ -24,7 +24,6 @@ analysis = [
     "seaborn>=0.13.2",
     "scikit-learn>=1.9.0",
     "umap-learn>=0.5.12",
-    "betterplots @ git+https://github.com/maweigert/betterplots@3a2c3bd7646290c5748e463553f33368ea8253bd",
 ]
 
 [build-system]

src/routing_pyramids/_vendor/__init__.py

@@ -0,0 +1 @@
+"""Private vendored dependencies."""

src/routing_pyramids/_vendor/betterplots/__init__.py

@@ -0,0 +1,76 @@
+# Vendored from https://github.com/maweigert/betterplots
+# 3a2c3bd7646290c5748e463553f33368ea8253bd.
+# Copyright Martin Weigert (BSD-3-Clause).
+
+from typing import Literal
+
+from cycler import cycler
+
+PALETTES = {
+    "mw": ["#4B6584", "#7A6FAF", "#B99B52", "#5F8F7A", "#A45A6A", "#5B8FA8"],
+    "tab10": [
+        "#1f77b4",
+        "#ff7f0e",
+        "#2ca02c",
+        "#d62728",
+        "#9467bd",
+        "#8c564b",
+        "#e377c2",
+        "#7f7f7f",
+        "#bcbd22",
+        "#17becf",
+    ],
+}
+
+
+def set_style(
+    usetex=False,
+    serif=True,
+    font_size=12,
+    legend_font_size=10,
+    label_size=10,
+    tick_size=10,
+    colors: Literal["mw", "tab10"] | None = "tab10",
+):
+    import matplotlib as mpl
+
+    mpl.rc("text", usetex=usetex)
+    # mpl.rc('font',family='serif')
+    # mpl.rc('font',serif=['Palatino'])
+    mpl.rcParams["font.family"] = "serif" if serif else "sans-serif"
+    mpl.rcParams["font.serif"] = ["Palatino"]
+    mpl.rcParams["font.sans-serif"] = [
+        "Inter 18pt",
+        "Myriad Pro",
+        "Neue Haas Grotesk Display Pro",
+    ]
+    mpl.rc("font", size=font_size)
+    mpl.rc("legend", fontsize=legend_font_size)
+    mpl.rc("axes", labelsize=label_size)
+    mpl.rc("xtick", labelsize=tick_size)
+    mpl.rc("ytick", labelsize=tick_size)
+    mpl.rcParams["axes.titleweight"] = "semibold"
+
+    if colors is None:
+        colors = "tab10"
+    if colors not in PALETTES:
+        raise ValueError(
+            f"colors must be one of {list(PALETTES)} or None, got {colors!r}"
+        )
+    mpl.rcParams["axes.prop_cycle"] = cycler(color=PALETTES[colors])
+
+    if usetex:
+        mpl.rcParams["text.latex.preamble"] = r"\usepackage{mathtools,amssymb,bm}"
+        print(
+            "in case latex is not working, make sue that the following packages are installed:"
+        )
+        print(
+            "sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super"
+        )
+
+    # xtick.major.size : 5
+    # xtick.minor.size : 3
+    # ytick.major.size : 5
+    # ytick.minor.size : 3
+    # axes.linewidth : 0.8
+    # legend.handlelength : 2.0