Migrate dependencies to pyproject

.github/workflows/pr.yaml

@@ -29,8 +29,7 @@ jobs:
       run: |
         python -m pip install --upgrade pip
         python -m pip install --upgrade setuptools wheel
-        pip install -r requirements-dev.txt
-        pip install -e .
+        python -m pip install -e ".[dev]"
     - name: Test with pytest
       run: |
         pytest

.github/workflows/pypi.yaml

@@ -34,7 +34,7 @@ jobs:
         python-version: "3.12"
 
     - name: Install dependencies
-      run: python -m pip install --upgrade pip build setuptools>=64.0.0 setuptools_scm[toml]>=8.0 wheel
+      run: python -m pip install --upgrade pip build "setuptools>=64.0.0" "setuptools_scm[toml]>=8.0" wheel
 
     - name: Build distributions
       run: |

.readthedocs.yaml

@@ -40,6 +40,7 @@ sphinx:
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
   install:
-    - requirements: docs/requirements.txt
     - method: pip
       path: .
+      extra_requirements:
+        - docs

README.md

@@ -2,8 +2,8 @@
   <a href="https://doi.org/10.5281/zenodo.11454148">
     <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.11454148.svg" alt="DOI">
   </a>
-  <a href="https://raw.githubusercontent.com/OSOceanAcoustics/echopop/master/LICENSE">
-    <img alt="GitHub License" src="https://img.shields.io/github/license/OSOceanAcoustics/echopop">
+  <a href="https://raw.githubusercontent.com/echostack-org/echopop/master/LICENSE">
+    <img alt="GitHub License" src="https://img.shields.io/github/license/echostack-org/echopop">
   </a>
 </div>
 

docs/_config.yml

@@ -24,7 +24,7 @@ parse:
 
 # Information about where the book exists on the web
 repository:
-  url: https://github.com/OSOceanAcoustics/echopop  # Online location of your book
+  url: https://github.com/echostack-org/echopop  # Online location of your book
   path_to_book: docs  # Optional path to your book, relative to the repository root
   branch: main  # Which branch of the repository should be used when creating links (optional)
 

docs/conf.py

@@ -1,17 +1,3 @@
-import sys
-from pathlib import Path
+"""Sphinx configuration for Echopop documentation."""
 
-# Add the '_ext' directory to sys.path
-# sys.path.append(str(Path('_ext').resolve()))
-# sys.path.insert(0, str(Path(__file__).parent / "_ext"))
-
-sys.path.append(str(Path("_ext").resolve()))
-
-
-# Import the echoautobody extension
-# extensions = ['echoautobody', 'helloworld']
-extensions = ["echoautobody"]
-
-# Manually import extension (this registers the directives)
-# import echoautobody
-# import helloworld
+extensions = ["echopop._sphinx_ext.echoautobody"]

docs/general/install.md

@@ -10,7 +10,7 @@ Ensure you have Python 3.12 or 3.13 installed, as Python 3.14 has known dependen
 
 [![PyPI version](https://img.shields.io/pypi/v/echopop)](https://pypi.org/project/echopop/)
 
-Install Echopop directly from PyPi:
+Install Echopop directly from PyPI:
 
 ```shell
 pip install echopop
@@ -31,19 +31,17 @@ We recommend using the ``libmamba`` solver instead of the classic solver.
 ```
 
 ## Latest source
-[![GitHub release](https://img.shields.io/github/v/release/OSOceanAcoustics/echopop)](https://github.com/OSOceanAcoustics/echopop/releases)
+[![GitHub release](https://img.shields.io/github/v/release/echostack-org/echopop)](https://github.com/echostack-org/echopop/releases)
 
 If you need the latest development version or want to contribute, clone the repository and install from source:
 
 ```shell
 # Clone the repository
-git clone https:://github.com/OSOceanAcoustics/echopop.git
+git clone https://github.com/echostack-org/echopop.git
 cd echopop
 
-# Create a conda environment using the supplied requirements files
-conda create -c conda-forge -n echopop --yes python=3.12 --file requirements.txt
-
-# Switch to the newly built environment
+# Create and activate a conda environment
+conda create -c conda-forge -n echopop --yes python=3.12
 conda activate echopop
 
 # Optional: Install ipykernel for JupyterLab support
@@ -53,11 +51,12 @@ conda install -c conda-forge ipykernel
 pip install -e .
 ```
 
-For a full development environment that includes docs building and testing, use:
+For a full development environment that includes testing and documentation tools, use:
 
 ```shell
-conda create -c conda-forge -n echopop --yes python=3.12 --file requirements.txt --file requirements-dev.txt --file docs/requirements.txt
-pip install -e .
+conda create -c conda-forge -n echopop-dev --yes python=3.12
+conda activate echopop-dev
+pip install -e ".[dev,docs]"
 ```
 
 :::{admonition} Development mode

pyproject.toml

@@ -63,11 +63,31 @@ dependencies = [
     "holoviews",
     "hvplot",
     "ipywidgets"
+]
+
+[project.optional-dependencies]
+dev = [
+    "black",
+    "coverage",
+    "isort",
+    "pre-commit",
+    "pytest",
+    "ruff",
+]
 
+docs = [
+    "docutils>=0.18,<0.22",
+    "jupyter-book==1.0.4.post1",
+    "numpydoc",
+    "setuptools",
+    "sphinx-automodapi",
+    "sphinxcontrib-bibtex",
+    "sphinx-tippy",
+    "sphinx-togglebutton",
 ]
 
 [project.urls]
-Homepage = "https://github.com/OSOceanAcoustics/echopop"
+Homepage = "https://github.com/echostack-org/echopop"
 
 [tool.setuptools.packages.find]
 where = ["."]
@@ -85,12 +105,12 @@ write_to_template = 'version = "{version}"  # noqa'
 line-length = 100
 target-version = "py312"
 extend-exclude = [
-    "echopop/workflows/nwfsc_feat/workflows",
+   "echopop/workflow_examples",
     "*.ipynb"
 ]
 
 [tool.ruff.lint]
-# E/F = Flake8 basics, I = Isort, D = Docstrings (pydocstyle)
+# E/F = pycodestyle/pyflakes basics, I = import sorting, D = docstrings
 select = ["E", "F", "I", "D", "UP", "B"]
 ignore = [
     "D100", # Missing docstring in public module