Migrate to uv (#189)

Author: JWCook

.dockerignore

@@ -0,0 +1,4 @@
+*
+!uv.lock
+!pyproject.toml
+!user-settings/

.github/workflows/deploy.yml

@@ -7,7 +7,7 @@ on:
   push:
     paths:
       - 'Dockerfile'
-      - 'poetry.lock'
+      - 'uv.lock'
   workflow_dispatch:
     inputs:
       version:

.pre-commit-config.yaml

@@ -0,0 +1,9 @@
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: check-toml
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: mixed-line-ending
+      - id: trailing-whitespace

Dockerfile

@@ -6,39 +6,37 @@ ARG PACKAGE_VERSION='latest'
 
 ENV JUPYTER_SETTINGS="/home/${NB_USER}/.jupyter/lab/user-settings" \
     PATH="/home/${NB_USER}/.local/bin:${PATH}" \
-    POETRY_INSTALLER="https://install.python-poetry.org/install-poetry.py" \
-    POETRY_VIRTUALENVS_CREATE=false \
+    UV_INSTALLER="https://astral.sh/uv/install.sh" \
     VIRTUAL_ENV="${CONDA_DIR}"
 RUN mkdir -p ${JUPYTER_SETTINGS}
 COPY user-settings/ ${JUPYTER_SETTINGS}/
-COPY poetry.lock pyproject.toml ./
 
 # Install utilities for plot & animation rendering
 RUN \
-    apt update \
-    && apt install -y imagemagick ffmpeg \
+    apt-get update \
+    && apt-get install -y imagemagick ffmpeg \
     && apt-get clean \
     && rm -rf /var/lib/apt/lists/*
 
+# Use conda to install geospatial libraries (due to binary dependencies)
 RUN \
-    # Use conda to install geospatial libraries (due to binary dependencies)
     conda config --set channel_priority strict \
     && conda install -yq -c conda-forge \
-    'gdal==3.6.2' \
-    'geoviews==1.9.6' \
-    'geopandas==0.12.2' \
-    # Use poetry to install all other packages from lockfile
-    && fix-permissions "/home/${NB_USER}" \
-    && wget $POETRY_INSTALLER \
-    && python install-poetry.py -y \
-    && poetry add "pyinaturalist@${PACKAGE_VERSION}" \
-    && poetry install -v \
-    # Cleanup
-    && poetry cache clear -q --all . \
-    && python install-poetry.py --uninstall -y \
-    && rm poetry.lock pyproject.toml install-poetry.py \
+    'gdal==3.10' \
+    'geoviews==1.14' \
+    'geopandas==1.0' \
     && conda clean -yaf || echo 'Failed to clear Conda cache' \
-    && echo 'Fixing permissions' \
+    && fix-permissions "${CONDA_DIR}"
+
+# Install all other packages from lockfile via uv
+COPY uv.lock pyproject.toml ./
+RUN \
+    fix-permissions "/home/${NB_USER}" \
+    && curl -LsSf $UV_INSTALLER | sh \
+    && uv add "pyinaturalist@${PACKAGE_VERSION}" \
+    && uv sync \
+    && uv cache clean \
+    && rm uv.lock pyproject.toml \
     && fix-permissions "${CONDA_DIR}" \
     && fix-permissions "/home/${NB_USER}"
 

README.md

@@ -3,10 +3,11 @@
 [![Docker Image Version](https://img.shields.io/docker/v/jxcook/pyinaturalist-notebook)](https://hub.docker.com/r/jxcook/pyinaturalist-notebook)
 [![Run with Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/pyinat/pyinaturalist/main?filepath=examples)
 
-This is a simple extension of the Jupyter notebook server
+This is an extension of the Jupyter notebook server
 ([jupyter/scipy-notebook](https://jupyter-docker-stacks.readthedocs.io/en/latest/using/selecting.html#jupyter-scipy-notebook))
 for working with [iNaturalist](https://www.inaturalist.org) data, which adds
-[pyinaturalist](https://github.com/pyinat/pyinaturalist) plus some extra packages for data exploration & visualization.
+[pyinaturalist](https://github.com/pyinat/pyinaturalist) and all dependencies needed for running
+[pyinaturalist example notebooks](https://pyinaturalist.readthedocs.io/en/stable/examples.html).
 
 ## Usage
 ```bash

poetry.lock

@@ -1,42 +1,32 @@
-[tool.poetry]
+[project]
 name = "pyinaturalist-notebook"
-version = "0.20.0"
+version = "0.21.0"
 description = "A Jupyter notebook image for iNaturalist data exploration & visualization"
-authors = ["Jordan Cook"]
-license = "MIT"
-package-mode = false
-
-[tool.poetry.dependencies]
-python = "^3.10"
-altair = ">=4.1"
-altair-saver = ">=0.5"
-bar_chart_race = ">=0.1"
-beautifulsoup4 = ">=4.0"
-black = ">=22.3"
-ipyplot = ">=1.1"
-isort = ">=5.10"
-jupyterlab-code-formatter = ">=2.2"
-jupyterlab-geojson = ">=3.1"
-pillow = ">=9.1.1"
-plotly = ">=5.1"
-pyinaturalist-convert = {extras = ["all"], version = ">=0.6"}
-pyopenssl = ">=23.2"
-vega-datasets = ">=0.9"
-websocket-client = ">=1.3"
-xarray = ">=0.18"
-
-# Version solving sometimes get stuck on trying every combination of these
-# urllib3 = "^2.0.7"
-# boto3 = "^1.34.13"
-# botocore = "^1.34.13"
-
-# Specific version is optionally set via workflow variable -> Docker build arg
-pyinaturalist = {extras = ["all"], version = "*"}
+authors = [
+    {name = "Jordan Cook"}
+]
+license = {text = "MIT"}
+requires-python = ">=3.10"
+dependencies = [
+    "altair>=4.1",
+    "altair-saver>=0.5",
+    "bar_chart_race>=0.1",
+    "beautifulsoup4>=4.0",
+    "ipyplot>=1.1",
+    "isort>=5.10",
+    "jupyterlab-geojson>=3.1",
+    "pillow>=9.1.1",
+    "plotly>=5.1",
+    "pyinaturalist-convert>=0.7.5",
+    "pyarrow>=10.0",
+    "pyopenssl>=23.2",
+    "vega-datasets>=0.9",
+    "websocket-client>=1.3",
+    "xarray>=0.18",
+    "xmltodict>=0.12",
+    "pyinaturalist",
+]
 
 [build-system]
-requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
-
-[tool.black]
-skip-string-normalization = true
-line-length = 100
+requires = ["hatchling"]
+build-backend = "hatchling.build"

pyproject.toml

@@ -7,4 +7,4 @@
         "line_length": 100
     },
     "formatOnSave": true
-}
+}