Add pyproject.toml (#99)

* transition to poetry

* reformat

* drop 3.7, add 3.11

* using new github actions

* caching pyproject

* install poetry

* adding matplotlib dependency

* sklearn version update

* using poetry install

* poetry pytest

* key value update

* install gdal osx

* using pyproject as version source

* dependency spec update

.github/workflows/deploy-docs.yml

@@ -12,10 +12,10 @@ jobs:
     runs-on: ubuntu-latest
     if: ${{ github.event.workflow_run.conclusion == 'success' }}
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
         with:
-          python-version: 3.7
+          python-version: 3.11
       - run: pip install mkdocs mkdocs-material mkdocstrings[python] mkdocs-jupyter livereload
       - run: pip install .
       - run: mkdocs gh-deploy --force

.github/workflows/os-tests.yml

@@ -15,18 +15,17 @@ jobs:
         os: [macos-latest, windows-latest]
     runs-on: ${{ matrix.os }}
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+
+    - name: Install poetry
+      run: pipx install poetry
 
     - name: Set up Python ${{ env.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ env.python-version }}
-        cache: 'pip'
-
-    - name: Install dependencies
-      run: |
-        python -m pip install --upgrade pip
-        pip install pytest pytest-cov pytest-xdist
+        cache: 'poetry'
+        cache-dependency-path: "pyproject.toml"
 
     - name: Install windows geo dependencies
       if: matrix.os == 'windows-latest'
@@ -42,10 +41,15 @@ jobs:
         pipwin install rtree
         pip install geopandas
 
+    - name: 'Install osx geo dependencies'
+      if: matrix.os == 'macos-latest'
+      run: |
+        brew install gdal
+
     - name: Install package
       run: |
-        pip install .
+        poetry install
 
     - name: Run pytest
       run: |
-        pytest -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered --cov-report xml:coverage.xml
+        poetry run pytest -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered --cov-report xml:coverage.xml

.github/workflows/run-pytest.yml

@@ -11,19 +11,20 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.8", "3.9", "3.10", "3.11"]
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
+    - name: Install poetry
+      run: pipx install poetry
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
+        cache: 'poetry'
+        cache-dependency-path: "pyproject.toml"
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
-        pip install pytest pytest-cov pytest-xdist
-        pip install .
+        poetry install
     - name: Run pytest
       run: |
-        pytest -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered --cov-report xml:coverage.xml
+        poetry run pytest -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered --cov-report xml:coverage.xml

.pre-commit-config.yaml

@@ -1,27 +1,27 @@
 default_language_version:
-  python: python3.8
+  python: python3.11
 
 repos:
   - repo: https://github.com/ambv/black
-    rev: 23.1.0
+    rev: 24.8.0
     hooks:
       - id: black
-        args: ["elapid", "--line-length=120", "--target-version=py37"]
+        args: ["elapid", "--line-length=120"]
 
   - repo: https://github.com/pycqa/flake8
-    rev: 6.0.0
+    rev: 7.1.0
     hooks:
       - id: flake8
         args: ["--select=C,E,F,W,B,B950", "--max-line-length=120", "--ignore=E203,E501,W503,F401,F403"]
 
   - repo: https://github.com/timothycrosley/isort
-    rev: 5.12.0
+    rev: 5.13.2
     hooks:
       - id: isort
         args: ["-l 120", "--profile", "black", "."]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.6.0
     hooks:
       - id: check-yaml
         exclude: recipe/meta.yaml

MANIFEST.in

@@ -1,6 +1,6 @@
 include LICENSE
 include README.md
-include requirements.txt
+include pyproject.toml
 
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]

Makefile

@@ -10,7 +10,6 @@ help:
 	@echo "--- [ $(NAME) developer tools ] --- "
 	@echo ""
 	@echo "make init        - initialize conda dev environment"
-	@echo "make utils       - install convenient packages"
 	@echo "make test        - run package tests"
 	@echo "make test-data   - generates new data for tests/data/"
 	@echo "make conda-clean - removes conda tempfiles"
@@ -20,14 +19,9 @@ help:
 # utils
 
 init:
-	conda env list | grep -q ${NAME} || conda create --name=${NAME} python=3.8 mamba -y -c conda-forge
-	${CONDA} mamba install gdal -c conda-forge -c nodefaults
-	${CONDA} pip install pre-commit pytest pytest-xdist pytest-cov
-	${CONDA} pre-commit install
-	${CONDA} pip install -e .
-
-utils:
-	${CONDA} pip install ipython jupyter matplotlib mkdocs-material mkdocstrings[python] mkdocs-jupyter
+	conda env list | grep -q ${NAME} || conda create --name=${NAME} python=3.11 mamba -y -c conda-forge -c nodefaults
+	${CONDA} mamba install gdal poetry -c conda-forge -c nodefaults -y
+	${CONDA} poetry install
 
 test:
 	${CONDA} pytest -n auto --cov --no-cov-on-fail --cov-report=term-missing:skip-covered

elapid/__init__.py

@@ -1,6 +1,5 @@
 """User entrypoint to elapid"""
 
-from elapid.__version__ import __doc__ as __version__
 from elapid.features import (
     CategoricalTransformer,
     HingeTransformer,
@@ -27,3 +26,4 @@
 from elapid.stats import normalize_sample_probabilities
 from elapid.train_test_split import BufferedLeaveOneOut, GeographicKFold, checkerboard_split
 from elapid.utils import download_sample_data, load_object, load_sample_data, save_object
+from elapid.version import __version__

elapid/config.py

@@ -1,4 +1,5 @@
 """SDM model configuration parameters."""
+
 from typing import Tuple, Union
 
 

elapid/features.py

@@ -349,13 +349,13 @@ def fit(self, x: ArrayLike) -> "CategoricalTransformer":
         self.estimators_ = []
         x = np.array(x)
         if x.ndim == 1:
-            estimator = OneHotEncoder(dtype=np.uint8, sparse=False)
+            estimator = OneHotEncoder(dtype=np.uint8, sparse_output=False)
             self.estimators_.append(estimator.fit(x.reshape(-1, 1)))
         else:
             nrows, ncols = x.shape
             for col in range(ncols):
                 xsub = x[:, col].reshape(-1, 1)
-                estimator = OneHotEncoder(dtype=np.uint8, sparse=False)
+                estimator = OneHotEncoder(dtype=np.uint8, sparse_output=False)
                 self.estimators_.append(estimator.fit(xsub))
 
         return self

elapid/models.py

@@ -1,4 +1,5 @@
 """Classes for training species distribution models."""
+
 from typing import List, Tuple, Union
 
 import matplotlib.pyplot as plt
@@ -20,7 +21,7 @@
     compute_weights,
 )
 from elapid.types import ArrayLike, validate_feature_types
-from elapid.utils import NCPUS, make_band_labels, square_factor
+from elapid.utils import NCPUS, make_band_labels
 
 # handle windows systems without functioning gfortran compilers
 FORCE_SKLEARN = False
@@ -181,7 +182,7 @@ def partial_dependence_scores(
             )
             mean[idx] = pd["individual"][0].mean(axis=0)
             stdv[idx] = pd["individual"][0].std(axis=0)
-            bins[idx] = pd["values"][0]
+            bins[idx] = pd["grid_values"][0]
 
         return bins, mean, stdv
 

elapid/types.py

@@ -1,4 +1,5 @@
 """Custom maxent and typing data types."""
+
 from typing import Any, Union
 
 import geopandas as gpd

elapid/utils.py

@@ -5,7 +5,7 @@
 import os
 import pickle
 import sys
-from typing import Any, Callable, Dict, Iterable, List, Tuple, Union
+from typing import Any, Callable, Dict, Iterable, List, Tuple
 from urllib import request
 
 import geopandas as gpd

elapid/version.py

@@ -0,0 +1,3 @@
+import importlib.metadata
+
+__version__ = importlib.metadata.version(__package__)

pyproject.toml

@@ -0,0 +1,42 @@
+[tool.poetry]
+name = "elapid"
+version = "1.0.2"
+description = "Species distribution modeling tools"
+authors = ["Christopher Anderson <cbanderson08@gmail.com>"]
+license = "MIT"
+readme = "README.md"
+keywords = ["biogeography", "ecology", "maxent", "SDM", "species distribution modeling"]
+include = [
+    { path = "elapid/data/*", format = "sdist" }
+]
+
+[tool.poetry.dependencies]
+python = ">=3.8"
+numpy = ">=1.18,<2.0"
+pandas = ">=1.0.3"
+pyproj = ">3.0"
+geopandas = ">=0.7"
+rasterio = ">=1.2.1"
+tqdm = ">=4.60"
+rtree = ">=0.9"
+scikit-learn = ">=1.2"
+matplotlib = ">=3.7"
+
+[tool.poetry.group.dev.dependencies]
+descartes = ">=1.1"
+pytest = ">=8.3"
+pytest-xdist = ">=3.6"
+pytest-cov = ">=5.0"
+pre-commit = ">=3.0"
+ipython = ">=8.0"
+jupyter = ">=1.0"
+mkdocs-material = ">=9.5"
+mkdocstrings = {extras = ["python"], version = ">=0.25"}
+mkdocs-jupyter = ">=0.24"
+
+[tool.poetry.extras]
+glmnet = ["glmnet"]
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"