Migrate to pyproject.toml, update min Python to 3.9, consolidate dev workflows

.github/CONTRIBUTING.md

@@ -0,0 +1 @@
+Follow the instructions in our [contributing page](./contributing.md).

.github/dependabot.yml

@@ -0,0 +1,6 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/tests.yml

@@ -1,39 +1,46 @@
 name: Test pyglider
 on: [push, pull_request]
+
+defaults:
+  run:
+    shell: bash -el {0}
+
 jobs:
   test-gliders:
     name: pyglider (${{ matrix.python-version }}, ${{ matrix.os }})
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
         os: ["ubuntu-latest"]
-        python-version: ["3.9", "3.10", "3.11", "3.12"]
+        python-version: ["3.9", "3.10", "3.11", "3.12", "3.13"]
     steps:
       - uses: actions/checkout@v4
       - name: mamba setup enviroment
         uses: mamba-org/[email protected]
         with:
           environment-name: test-env
-          environment-file: tests/environment.yml
+          environment-file: environment.yml
           create-args: >-
             python=${{ matrix.python-version }}
-      - name: Conda info
-        shell: micromamba-shell {0}
-        run: conda info; conda list
       - name: install pyglider source
-        shell: micromamba-shell {0}
-        run: which pip; pip install -e .
+        run: |
+          pip install -e .
       - name: Process seaexplorer
-        shell: micromamba-shell {0}
-        run: which python; cd tests/example-data/example-seaexplorer; make clean-all; python process_deploymentRealTime.py
+        run: |
+          cd tests/example-data/example-seaexplorer
+          make clean-all
+          python process_deploymentRealTime.py
       - name: Process slocum
-        shell: micromamba-shell {0}
-        run: which python; cd tests/example-data/example-slocum; make clean-all; python process_deploymentRealTime.py
+        run: |
+          cd tests/example-data/example-slocum
+          make clean-all
+          python process_deploymentRealTime.py
       - name: Process seaexplorer-legato-flntu-arod-ad2cp
-        shell: micromamba-shell {0}
-        run: which python; cd tests/example-data/example-seaexplorer-legato-flntu-arod-ad2cp; make clean-all; python process_deploymentRealTime.py
+        run: |
+          cd tests/example-data/example-seaexplorer-legato-flntu-arod-ad2cp
+          make clean-all
+          python process_deploymentRealTime.py
       - name: Run tests
-        shell: micromamba-shell {0}
-        run: which python; pytest --cov --cov-report xml
+        run: pytest --cov --cov-report xml
       - name: Upload coverage to Codecov
         uses: codecov/codecov-action@v4

.readthedocs.yaml

@@ -1,41 +1,11 @@
-# Read the Docs configuration file for Sphinx projects
-# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-
-# Required
 version: 2
-
-# Set the OS, Python version and other tools you might need
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.12"
-    # You can also specify other tool versions:
-    # nodejs: "20"
-    # rust: "1.70"
-    # golang: "1.20"
+    python: mambaforge-22.9
 
-# Build documentation in the "docs/" directory with Sphinx
 sphinx:
   configuration: docs/conf.py
-  # You can configure Sphinx to use a different builder, for instance use the dirhtml builder for simpler URLs
-  # builder: "dirhtml"
-  # Fail on all warnings to avoid broken references
-  # fail_on_warning: true
-
-python:
-  install:
-    - requirements: docs-requirements.txt
-    # Install our python package before building the docs
-    - method: pip
-      path: .
-# Optionally build your docs in additional formats such as PDF and ePub
-# formats:
-#   - pdf
-#   - epub
 
-# Optional but recommended, declare the Python requirements required
-# to build your documentation
-# See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
-# python:
-#   install:
-#     - requirements: docs/requirements.txt
+conda:
+  environment: environment.yml

docs/Install.md

@@ -14,14 +14,4 @@ conda install -c conda-forge pyglider
 
 ## Editable installation
 
-If you want to be able to edit the files in `pyglider/pyglider` then install
-the dependencies as above. Fork of PyGlider on github, and then clone it locally:
-
-```
-git clone https://github.com/yourname/pyglider.git
-```
-
-Navigate to the new `pyglider` directory and then do `pip install -e .`.
-That will re-install pyglider with links to the local directory, so you
-can edit the library files. If you do so, consider making a pull-request
-with your changes!
+Follow the instructions in our [contributing page](./contributing.md).

docs/conf.py

@@ -25,7 +25,8 @@
 # The full version, including alpha/beta/rc tags
 release = __version__
 
-
+master_doc = 'index'
+source_suffix = ['.rst', '.md']
 # -- General configuration ---------------------------------------------------
 
 # Add any Sphinx extension module names here, as strings. They can be
@@ -36,7 +37,7 @@
     'myst_parser',
     'sphinx.ext.autodoc',
     'sphinx.ext.inheritance_diagram',
-    'autoapi.sphinx',
+    'autoapi.extension',
 ]
 
 extensions.append('sphinx.ext.intersphinx')
@@ -46,7 +47,7 @@
     'python': ('https://docs.python.org/3/', None),
 }
 
-autoapi_modules = {'pyglider': None}
+autoapi_dirs = ['../pyglider']
 
 # Add any paths that contain templates here, relative to this directory.
 templates_path = ['_templates']

docs/contributing.md

@@ -0,0 +1,57 @@
+# Contributing
+
+## Create a fork
+
+```{note}
+TODO: Create contributing page noting:
+- the forking process (trimmed down)
+```
+
+## Development environment
+
+Assuming that you have Anaconda/Miniconda installed, you can create a new environment for development:
+
+```bash
+conda create -n pyglider-dev python=3.9
+conda activate pyglider-dev
+```
+
+Then install the dependencies:
+
+```bash
+conda env update -f environment.yml -n pyglider-dev
+```
+
+And install the package in editable mode:
+
+```bash
+pip install -e . --no-build-isolation --no-deps
+```
+
+Done!
+
+---
+
+From here, you can make the changes you want, and add tests. When you are ready, you can create a pull request into the codebase.
+
+## Running tests
+
+Once the development environment is set up, you can run the tests with:
+
+```bash
+pytest
+```
+
+## Building documentation
+
+```{note}
+TODO
+```
+
+## [Optional] Running pre-commit
+
+We use pre-commit [TODO link] to run tooling on the code to make sure that it adheres to standards that we have adopted in the codebase. This is done automatically in the cloud on all pull requests, however this can also be done locally.
+
+Pre-commit is already a dependency in the `environment.yml` file, so you only have to do `pre-commit install` in the repository (this will install the hooks in the repository so that they run when you commit changes).
+
+That's it! If you want to, you can manually run the hooks by doing `pre-commit run --all-files` (or `pre-commit run` if you only want to run on staged files).

docs/index.md

@@ -29,6 +29,7 @@ Install
 getting-started-seaexplorer
 getting-started-slocum
 pyglider/pyglider
+contributing
 
 ```
 

environment.yml

@@ -1,8 +1,9 @@
-name: pyglider
+name: pyglider-dev
 channels:
   - conda-forge
 dependencies:
-  - python>=3.10
+  # Core
+  - python>=3.9
   - numpy
   - pip
   - xarray
@@ -13,5 +14,24 @@ dependencies:
   - scipy
   - bitstring
   - pooch
+
+  # Testing
+  - pytest
+  - pytest-cov
+  - matplotlib
+  - compliance-checker
+  - cc-plugin-glider
+
+  # Docs
+  - pydata-sphinx-theme
+  - sphinx
+  - sphinx-autoapi
+  - numpydoc
+  - myst-parser
+
+  # QAQC
+  - pre_commit
+
   - pip:
+      # Core
       - dbdreader

pyproject.toml

@@ -1,3 +1,49 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "pyglider"
+dynamic = ["version"]
+description = "Glider data to netCDF translation in python"
+readme = "README.md"
+license = { file = "LICENSE" }
+requires-python = ">=3.9"
+classifiers = [
+  "License :: OSI Approved :: Apache Software License",
+  "Programming Language :: Python :: 3.9",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Operating System :: OS Independent",
+  "Topic :: Scientific/Engineering",
+  "Intended Audience :: Science/Research",
+]
+authors = [
+  { name = "Jody Klymak", email = "[email protected]" },
+]
+dependencies = [
+  "bitstring",
+  "dask",
+  "gsw",
+  "netcdf4",
+  "polars",
+  "pooch",
+  "scipy",
+  "xarray",
+]
+
+[project.urls]
+Homepage = "https://pyglider.readthedocs.io"
+
+[tool.hatch.version]
+path = "pyglider/_version.py"
+
+[tool.hatch.build.targets.sdist]
+include = [
+  "/pyglider",
+]
 [tool.pytest.ini_options]
 addopts = ["--strict-config", "--strict-markers"]
 testpaths = ["tests"]