setup.py -> pyproject.toml

.github/workflows/pytest.yml

@@ -13,7 +13,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.9", "3.10", "3.11"]
         os: [ubuntu-latest, macos-latest]
     runs-on: ${{ matrix.os }}
 
@@ -24,7 +24,6 @@ jobs:
       uses: actions/setup-python@v2
       with:
         python-version: ${{ matrix.python-version }}
-        cache: 'pip'
 
     - name: Set up Conda
       uses: conda-incubator/setup-miniconda@v2
@@ -41,7 +40,7 @@ jobs:
       shell: /bin/zsh {0}
       run: |
         conda env create --file environment.yaml
-        conda run -n ${{ env.PACKAGE }} --no-capture-output pip install .
+        conda run -n ${{ env.PACKAGE }} --no-capture-output poetry install
       if: matrix.os == 'macos-latest'
 
     - name: Run pytest

.gitignore

@@ -3,9 +3,6 @@ __pycache__/
 *.py[cod]
 *$py.class
 
-# C extensions
-*.so
-
 # Distribution / packaging
 .Python
 build/

Makefile

@@ -2,8 +2,6 @@
 
 .DEFAULT: help
 help:
-	@echo "make init"
-	@echo "	initialize dev environment."
 	@echo "make create"
 	@echo "	create env and install dependencies."
 	@echo "make update"
@@ -17,7 +15,7 @@ help:
 
 ENV=xleaf
 PYTHON_VERSION=3.9
-ENV_CONDA=conda run -n ${ENV} --no-capture-output
+CONDA_ENV=conda run -n ${ENV} --no-capture-output
 
 UNAME_S := $(shell uname -s)
 ifeq ($(UNAME_S),Linux)
@@ -27,25 +25,35 @@ ifeq ($(UNAME_S),Darwin)
 	CONDA_LOCK=conda-osx-arm64.lock
 endif
 
-init:
-	conda-lock --mamba -f environment.yaml -k explicit
-
 create:
 	conda create -n ${ENV} --file ${CONDA_LOCK}
-	${ENV_CONDA} pip install -e .
-	${ENV_CONDA} pre-commit install
+	${CONDA_ENV} poetry install
+	${CONDA_ENV} pre-commit install
 
 update:
 	conda-lock --mamba -f environment.yaml -k explicit
-	${ENV_CONDA} conda update --file ${CONDA_LOCK}
+	${CONDA_ENV} conda update --file ${CONDA_LOCK}
 
 test:
-	${ENV_CONDA} pytest -n auto
+	${CONDA_ENV} pytest -n auto
+
+deploy:
+	rm -rf dist/
+	${CONDA_ENV} python3 setup.py sdist bdist_wheel
+	${CONDA_ENV} twine upload dist/*
 
 destroy:
 	conda env remove -n ${ENV}
 
-deploy:
+# dev utilities
+init:
+	conda-lock --mamba -f environment.yaml -k explicit
+
+fortran:
+	f2py -c -m prosail prosail/MODULE_PRO4SAIL.f90 prosail/dataSpec_PDB.f90 prosail/main_PROSAIL.f90 prosail/LIDF.f90 prosail/dladgen.f prosail/PRO4SAIL.f90 prosail/prospect_DB.f90 prosail/tav_abs.f90 prosail/volscatt.f90 \
+		&& mv *.so xleaf/
+
+pypi:
 	rm -rf dist/
-	${ENV_CONDA} python3 setup.py sdist bdist_wheel
-	${ENV_CONDA} twine upload dist/*
+	${CONDA_ENV} poetry build
+	twine upload dist/*

environment.yaml

@@ -3,16 +3,10 @@ channels:
   - conda-forge
   - nodefaults
 dependencies:
-  - python=3.9.*
+  - python=3.10
   - pip
-  - numpy
+  - poetry
   - gfortran
-  - pre-commit
-  - pytest
-  - pytest-xdist
-  - wheel
-  - ipython
-  - matplotlib
 platforms:
   - linux-64
   - osx-arm64

pyproject.toml

@@ -0,0 +1,30 @@
+[tool.poetry]
+name = "xleaf"
+version = "1.0.1"
+description = "Leaf and canopy radiative transfer modeling tools built on PROSPECT-D and SAIL"
+authors = ["Christopher Anderson <cbanders@alumni.stanford.edu>"]
+license = "MIT"
+readme = "README.md"
+include = ["xleaf/*.so"]
+keywords = ["prosail", "prospect", "radiative transfer modeling", "simulation modeling", "remote sensing"]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+numpy = ">=1.21.5"
+
+[tool.poetry.group.dev.dependencies]
+ipython = "^8.18.1"
+jupyter = "^1.0.0"
+pre-commit = "^3.6.0"
+pytest = "^7.4.3"
+pytest-cov = "^4.1.0"
+pytest-xdist = "^3.5.0"
+twine = "^4.0.2"
+mkdocs-material = "^9.5.2"
+mkdocs-jupyter = "^0.24.6"
+livereload = "^2.6.3"
+mkdocstrings = "^0.24.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"