Changes for Python 3.13 support

.github/workflows/unit-tests-workflow.yml

@@ -6,7 +6,7 @@ jobs:
   test:
     strategy:
       matrix:
-        python-version: ['3.8', '3.9', '3.10', '3.11']
+        python-version: ['3.10', '3.11', '3.12', '3.13']
 
     runs-on: ubuntu-latest
 
@@ -23,13 +23,13 @@ jobs:
         with:
           python-version: ${{ matrix.python-version }}
 
-      - name: Install dependencies
-        run: python -m pip install --upgrade pip poetry
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          version: "latest"
 
       - name: Set up project
-        run: |
-          cd $GITHUB_WORKSPACE
-          poetry install
+        run: uv sync --dev
 
       - name: Run unit tests
-        run: poetry run pytest
+        run: uv run pytest

CONTRIBUTING.md

@@ -68,9 +68,7 @@ Follow these rules and you should succeed without a problem.
 ### Run the tests
 Before you submit a pull request, please run the entire test suite via:
 
-`$ export NUMBA_DISABLE_JIT=1`
-`$ python setup.py test`
-`$ unset  NUMBA_DISABLE_JIT`
+`$ uv run pytest`
 
 The first thing the core committers will do is run this command. Any pull request that fails this test suite will be rejected.
 
@@ -114,7 +112,7 @@ First we pull the code into a local branch:
 
 Then we run the tests:
 
-`$ python -m unittest tests/test_*.py`
+`$ uv run pytest`
 
 We finish with a merge and push to GitHub:
 

Dockerfile

@@ -0,0 +1,47 @@
+FROM python:3.11-slim AS builder
+
+LABEL authors="[email protected]"
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /bin/uv
+
+# Set working directory
+WORKDIR /app
+
+# Copy dependency files
+COPY pyproject.toml uv.lock ./
+
+# Install dependencies
+RUN uv sync --frozen --no-dev
+
+# Production stage
+FROM python:3.11-slim
+
+# Install runtime dependencies
+RUN apt-get update && apt-get --no-install-recommends install -y \
+    build-essential \
+    libhdf5-dev \
+    libnetcdf-dev \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy uv and virtual environment from builder
+COPY --from=builder /app/.venv /app/.venv
+COPY --from=builder /bin/uv /bin/uv
+
+# Set working directory
+WORKDIR /app
+
+# Copy source code
+COPY src/ ./src/
+COPY pyproject.toml ./
+
+# Create non-root user
+RUN useradd --create-home --shell /bin/bash climate
+USER climate
+
+# Set environment variables
+ENV PATH="/app/.venv/bin:$PATH"
+ENV PYTHONPATH="/app/src:$PYTHONPATH"
+
+# Set entrypoint
+ENTRYPOINT ["python", "-m", "climate_indices"]

docs/conf.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 #
 # Configuration file for the Sphinx documentation builder.
 #

docs/index.rst

@@ -64,14 +64,17 @@ Quick Start
    ::
 
     # create and activate a Python virtual environment with conda
-    conda create -n myvenv poetry pytest
+    conda create -n myvenv python=3.10
     conda activate myvenv
 
+    # install uv
+    pip install uv
+
     # install the package
-    python -m poetry install
+    uv sync --dev
 
     # optionally run the unit tests suite
-    python -m poetry run pytest
+    uv run pytest
 
 
 Installation
@@ -81,35 +84,33 @@ From PyPI
 
 Install directly from PyPI::
 
-    python -m pip install climate-indices
+    uv add climate-indices
 
 From source
 ^^^^^^^^^^^^^^
 
-In order to build and install the package from source we need to first install `poetry <https://python-poetry.org/>`__::
+In order to build and install the package from source we need to first install `uv <https://docs.astral.sh/uv/>`__::
 
-    python -m pip install poetry
+    pip install uv
 
 Then install the package from source::
 
-   python -m poetry install
+   uv sync --dev
 
 Next (optional) run the unit test suite to validate the installation::
 
-    python -m pytest tests
+    uv run pytest
 
 the above should display output similar to this::
 
    ======================= 38 passed, 18 warnings in 12.19s =======================
 
 Finally, show the package installed into the environment::
 
-   conda list climate-indices
+   uv list | grep climate-indices
 
-   # packages in environment at /Users/jadams/miniconda3/envs/climate381:
-   #
-   # Name                    Version                   Build  Channel
-   climate-indices           1.0.16                   pypi_0    pypi
+   # climate-indices v2.1.0 (editable)
+   #     + climate-indices==2.1.0 (from file:///path/to/climate_indices)
 
 
 

notebooks/concurrent_shared_memory_example.ipynb

@@ -8,11 +8,8 @@
    "source": [
     "import concurrent.futures\n",
     "from multiprocessing import cpu_count, shared_memory\n",
-    "import sys\n",
-    "from typing import Dict\n",
     "\n",
-    "import numpy as np\n",
-    "import xarray as xr"
+    "import numpy as np"
    ]
   },
   {
@@ -59,7 +56,7 @@
    "outputs": [],
    "source": [
     "def shm_add_average(\n",
-    "    arguments: Dict,\n",
+    "    arguments: dict,\n",
     "):\n",
     "    existing_shm_input = shared_memory.SharedMemory(name=arguments[\"shm_name_input\"])\n",
     "    shm_ary_input = np.ndarray(\n",

notebooks/generate_fitting_parameters_nclimgrid.ipynb

@@ -7,16 +7,14 @@
    "outputs": [],
    "source": [
     "import sys\n",
-    "from typing import Dict\n",
     "\n",
-    "import matplotlib\n",
     "import numpy as np\n",
     "import xarray as xr\n",
     "\n",
     "climate_indices_home_path = \"/home/james/git/climate_indices\"\n",
     "if climate_indices_home_path not in sys.path:\n",
     "    sys.path.insert(climate_indices_home_path)\n",
-    "from climate_indices import compute, indices, utils\n",
+    "from climate_indices import compute, indices\n",
     "\n",
     "%matplotlib inline"
    ]
@@ -115,7 +113,7 @@
    "source": [
     "def compute_gammas(\n",
     "    da_precip: xr.DataArray,\n",
-    "    gamma_coords: Dict,\n",
+    "    gamma_coords: dict,\n",
     "    scale: int,\n",
     "    calibration_year_initial,\n",
     "    calibration_year_final,\n",
@@ -139,9 +137,7 @@
     "            values = da_precip[lat_index, lon_index]\n",
     "\n",
     "            # skip over this grid cell if all NaN values\n",
-    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(\n",
-    "                np.isnan(values)\n",
-    "            ):\n",
+    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(np.isnan(values)):\n",
     "                continue\n",
     "\n",
     "            # convolve to scale\n",
@@ -220,9 +216,7 @@
     "            values = da_precip[lat_index, lon_index]\n",
     "\n",
     "            # skip over this grid cell if all NaN values\n",
-    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(\n",
-    "                np.isnan(values)\n",
-    "            ):\n",
+    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(np.isnan(values)):\n",
     "                continue\n",
     "\n",
     "            gamma_parameters = {\n",
@@ -289,9 +283,7 @@
     "    \"geospatial_lat_units\",\n",
     "    \"geospatial_lon_units\",\n",
     "]\n",
-    "global_attrs = {\n",
-    "    key: value for (key, value) in ds_prcp.attrs.items() if key in attrs_to_copy\n",
-    "}"
+    "global_attrs = {key: value for (key, value) in ds_prcp.attrs.items() if key in attrs_to_copy}"
    ]
   },
   {
@@ -437,9 +429,7 @@
     "            values = da_precip[lat_index, lon_index]\n",
     "\n",
     "            # skip over this grid cell if all NaN values\n",
-    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(\n",
-    "                np.isnan(values)\n",
-    "            ):\n",
+    "            if (np.ma.is_masked(values) and values.mask.all()) or np.all(np.isnan(values)):\n",
     "                continue\n",
     "\n",
     "            # compute the SPI\n",

notebooks/spi_simple.ipynb

@@ -170,7 +170,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from climate_indices.compute import scale_values, Periodicity"
+    "from climate_indices.compute import Periodicity, scale_values"
    ]
   },
   {
@@ -328,9 +328,7 @@
     "# do it \"by hand\" by looping over each lat/lon point\n",
     "for lat_index in range(len(da_one_more_lo_looper[\"lat\"])):\n",
     "    for lon_index in range(len(da_one_more_lo_looper[\"lon\"])):\n",
-    "        da_one_more_lo_looper[lat_index, lon_index] = add_one(\n",
-    "            da_one_more_lo_looper[lat_index, lon_index]\n",
-    "        )"
+    "        da_one_more_lo_looper[lat_index, lon_index] = add_one(da_one_more_lo_looper[lat_index, lon_index])"
    ]
   },
   {
@@ -363,9 +361,7 @@
     "# do it \"by hand\" by looping over each lat/lon point\n",
     "for lat_index in range(len(da_one_more_hi_looper[\"lat\"])):\n",
     "    for lon_index in range(len(da_one_more_hi_looper[\"lon\"])):\n",
-    "        da_one_more_hi_looper[lat_index, lon_index] = add_one(\n",
-    "            da_one_more_hi_looper[lat_index, lon_index]\n",
-    "        )"
+    "        da_one_more_hi_looper[lat_index, lon_index] = add_one(da_one_more_hi_looper[lat_index, lon_index])"
    ]
   },
   {
@@ -426,10 +422,7 @@
     "    if len(shape) == 2:\n",
     "        values = values.flatten()\n",
     "    elif len(shape) != 1:\n",
-    "        message = (\n",
-    "            \"Invalid shape of input array: {shape}\".format(shape=shape)\n",
-    "            + \" -- only 1-D and 2-D arrays are supported\"\n",
-    "        )\n",
+    "        message = f\"Invalid shape of input array: {shape}\" + \" -- only 1-D and 2-D arrays are supported\"\n",
     "        _logger.error(message)\n",
     "        raise ValueError(message)\n",
     "\n",
@@ -484,9 +477,7 @@
     "        )\n",
     "\n",
     "    else:\n",
-    "        message = \"Unsupported distribution argument: \" + \"{dist}\".format(\n",
-    "            dist=distribution\n",
-    "        )\n",
+    "        message = \"Unsupported distribution argument: \" + f\"{distribution}\"\n",
     "        _logger.error(message)\n",
     "        raise ValueError(message)\n",
     "\n",