planetarypy · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025 · Mar 7, 2025
diff --git a/.coveragerc b/.coveragerc
diff --git a/.github/workflows/test.yaml b/.github/workflows/test.yaml
@@ -9,8 +9,13 @@ on:
 
 jobs:
   test:
-    name: Run tests
+    name: Python ${{ matrix.python-version }} tests
     runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10"]
+      fail-fast: false
+
     steps:
     - name: Checkout repository
       uses: actions/checkout@v4
@@ -20,9 +25,9 @@ jobs:
       with:
         miniforge-variant: Miniforge3
         miniforge-version: latest
-        activate-environment: test_env
+        activate-environment: test_env_py${{ matrix.python-version }}
         use-mamba: true
-        python-version: "3.9"
+        python-version: ${{ matrix.python-version }}
         channels: conda-forge
         channel-priority: strict
         auto-activate-base: false
@@ -42,16 +47,16 @@ jobs:
     - name: Install dependencies
       shell: bash -l {0}
       run: |
-        # Install tomlkit and sh first to run the installation script
-        mamba install -y -c conda-forge tomlkit sh
+        # Install core dependencies via mamba first
+        mamba install -y -c conda-forge tomlkit sh gdal
         
         # Run the installation script
         python install_dev_deps.py
 
     - name: Install package
       shell: bash -l {0}
       run: |
-        pip install -e .
+        pip install -e ".[spice]"
 
     - name: Run tests
       shell: bash -l {0}
@@ -63,4 +68,5 @@ jobs:
       with:
         token: ${{ secrets.CODECOV_TOKEN }}
         files: ./coverage.xml
-        fail_ci_if_error: true
+        fail_ci_if_error: true
+        name: codecov-py${{ matrix.python-version }}
diff --git a/.gitignore b/.gitignore
@@ -132,3 +132,6 @@ dmypy.json
 .pixi
 *.egg-info
 *.code-workspace
+run_migration.py
+src/planetarypy/pds/migrate_config.py
+src/planetarypy/scripts/migrate_pds_config.py
diff --git a/MODERNIZATION.md b/MODERNIZATION.md
@@ -0,0 +1,43 @@
+# Package Modernization
+
+This project has been modernized to use `pyproject.toml` as the primary configuration file, following PEP 517 and PEP 518 standards.
+
+## Changes Made
+
+1. Updated `pyproject.toml` to include:
+   - All project metadata
+   - Dependencies from requirements.txt
+   - Development dependencies from requirements-dev.txt
+   - Package build configuration
+   - Tool configurations from setup.cfg (pytest, flake8, etc.)
+   - Bumped version settings
+
+2. Updated version in `src/planetarypy/__init__.py` to match `pyproject.toml`
+
+## Files That Can Be Removed
+
+The following files are now redundant and can be safely removed:
+
+- `setup.py` - All configuration now in pyproject.toml
+- `setup.cfg` - All tool configurations moved to pyproject.toml under appropriate [tool.*] sections
+- `requirements.txt` - Dependencies now in pyproject.toml
+- `requirements-dev.txt` - Development dependencies now in pyproject.toml
+- `requirements_dev.txt` - Redundant with requirements-dev.txt
+
+## Installation
+
+With this modernization, you can install the package using:
+
+```bash
+# For development installation with all dev dependencies
+pip install -e ".[dev]"
+
+# For regular installation
+pip install .
+```
+
+## Future Improvements
+
+1. Consider using standardized tools for version management like `hatch` instead of `bumpversion`
+2. Update documentation to reflect the new project structure
+3. Update CI/CD pipelines to use the new configuration 
diff --git a/README.rst → README.md b/README.rst → README.md
@@ -1,21 +1,12 @@
-planetarypy
-===========
+# planetarypy
 
+[![PyPI](https://img.shields.io/pypi/v/planetarypy.svg)](https://pypi.python.org/pypi/planetarypy)
+[![Documentation Status](https://readthedocs.org/projects/planetarypy/badge/?version=latest)](https://planetarypy.readthedocs.io/en/latest/?badge=latest)
+[![codecov](https://codecov.io/gh/planetarypy/planetarypy/branch/main/graph/badge.svg)](https://codecov.io/gh/planetarypy/planetarypy)
 
-.. image:: https://img.shields.io/pypi/v/planetarypy.svg
-        :target: https://pypi.python.org/pypi/planetarypy
-
-.. image:: https://readthedocs.org/projects/planetarypy/badge/?version=latest
-        :target: https://planetarypy.readthedocs.io/en/latest/?badge=latest
-        :alt: Documentation Status
-
-.. image:: https://codecov.io/gh/planetarypy/planetarypy/branch/main/graph/badge.svg
-        :target: https://codecov.io/gh/planetarypy/planetarypy
-
 Core package for planetary science tools.
 
-Warning
--------
+## Warning
 
 This package is in early alpha.
 
@@ -27,19 +18,77 @@ That package will be open for public contribution and collaboration.
 The approximate feature set (also see below) that this package will cover can be checked out at
 https://michaelaye.github.io/nbplanetary where the documentation for the current package lives.
 
-
 * Free software: BSD-3 license
-* Documentation (not yet deployed): https://planetarypy.readthedocs.io.
-* Part of the `PlanetaryPy`_ Organisation.
+* Documentation (not yet deployed): https://planetarypy.readthedocs.io
+* Part of the [PlanetaryPy](https://planetarypy.org/) Organisation.
+
+## Installation
+
+From PyPI (once published):
+
+```bash
+pip install planetarypy
+```
+
+From GitHub:
+
+```bash
+pip install git+https://github.com/planetarypy/planetarypy.git
+```
+
+For development installation:
+
+```bash
+# Clone the repository
+git clone https://github.com/planetarypy/planetarypy.git
+cd planetarypy
+
+# Install in development mode with dev dependencies
+pip install -e ".[dev]"
+```
+
+## Features
 
+### PDS Index Tools
 
-Installation
-------------
+The package includes robust tools for working with PDS (Planetary Data System) indices:
 
-`pip install git@github.com:planetarypy/planetarypy`
+- **Index Configuration**: Manage URLs and access timestamps in separate configuration files
+- **Dynamic URL Discovery**: Automatically find and use the latest index files for mission data
+- **Index Browsing**: Easily explore available missions, instruments, and indices
 
-General scope
--------------
+```python
+from planetarypy.pds import print_pds_tree, list_missions, list_instruments, list_indexes
+
+# Display all available PDS indices in a tree structure
+print_pds_tree()
+
+# Get a list of all missions
+missions = list_missions()
+
+# Get all instruments for a specific mission
+instruments = list_instruments('mro')
+
+# Get all indices for a specific mission and instrument
+indices = list_indexes('cassini', 'iss')
+```
+
+- **Index Management**: Download, update, and convert indices to high-performance parquet format
+
+```python
+from planetarypy.pds import Index
+
+# Create an index object
+idx = Index('cassini.iss.ring_summary')
+
+# Check if updates are available
+idx.check_for_updates()
+
+# Download the index
+idx.download()
+```
+
+## General scope
 
 First and foremost this package shall provide support in working with planetary science data.
 
@@ -52,8 +101,7 @@ With working we mean:
 
 of data.
 
-Locating
-^^^^^^^^
+### Locating
 
 This library manages, via its PDS tools, multiple PDS3 index files per instrument that can be
 used for identifying data of interest.
@@ -62,16 +110,14 @@ These index files are automatically downloaded and converted to the very perform
 Parquet is able to store advanced datatypes like nan-capable integer and full datetime objects,
 as opposed to HDF5.
 
-Retrieving
-^^^^^^^^^^
+### Retrieving
 
 The interface to getting data is via a path-retrieving function based on a PDS product-id.
 If that product-id is available locally, the path will be returned.
 If it is not, it will previously be downloaded, stored in a systematic fashion organized by
 mission and instrument, and then the local path will be returned.
 
-Reading
-^^^^^^^
+### Reading
 
 For now, the library only returns the path to the object and the user needs to sort out the
 reading process.
@@ -88,20 +134,15 @@ There will exist larger other packages that focus on working with a given instru
 in which case that package could become an affiliated package with the `planetarypy` GitHub
 organization, if so desired.
 
-Further processing
-^^^^^^^^^^^^^^^^^^
+### Further processing
 
 In the future, additional frequently used procedures will be added to this library, e.g.
 
 - frequently used GDAL/rasterio procedures
 - frequently used SPICE operations, e.g. surface illumination on a given body
 
-Contributing
-------------
+## Contributing
 
 Feedback, issues, and contributions are always gratefully welcomed. See the
 contributing guide for details on how to help and setup a development
-environment, see :ref:Contributing .
-
-
-.. _PlanetaryPy: https://planetarypy.org/
+environment.