Merge pull request planetarypy#23 from michaelaye/main

implement GH workflow for running tests

.github/workflows/test.yaml

@@ -0,0 +1,66 @@
+# FILE: .github/workflows/test.yaml
+name: Run software tests
+
+on:
+  push:
+  pull_request:
+    branches:
+      - main
+
+jobs:
+  test:
+    name: Run tests
+    runs-on: ubuntu-latest
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    - name: Setup Conda
+      uses: conda-incubator/setup-miniconda@v3
+      with:
+        miniforge-variant: Miniforge3
+        miniforge-version: latest
+        activate-environment: test_env
+        use-mamba: true
+        python-version: "3.9"
+        channels: conda-forge
+        channel-priority: strict
+        auto-activate-base: false
+        conda-remove-defaults: true
+
+    - name: Cache conda env
+      uses: actions/cache@v3
+      with:
+        path: |
+          ~/.conda/pkgs
+          ~/.conda/envs
+        key: conda-${{ runner.os }}-py${{ matrix.python-version }}-${{ github.sha }}
+        restore-keys: |
+          conda-${{ runner.os }}-py${{ matrix.python-version }}-
+          conda-${{ runner.os }}-
+
+    - 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
+        
+        # Run the installation script
+        python install_dev_deps.py
+
+    - name: Install package
+      shell: bash -l {0}
+      run: |
+        pip install -e .
+
+    - name: Run tests
+      shell: bash -l {0}
+      run: |
+        pytest --cov=src/planetarypy --cov-report=xml --cov-report=term
+
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        files: ./coverage.xml
+        fail_ci_if_error: true

.gitignore

@@ -127,3 +127,8 @@ dmypy.json
 
 # Pyre type checker
 .pyre/
+
+# pixi environments
+.pixi
+*.egg-info
+*.code-workspace

Makefile

@@ -54,7 +54,6 @@ lintblack: ## check style with black
 	black --check src/planetarypy tests
 
 test: ## run tests quickly with the default Python
-	jupyter nbconvert --to python tests/test_*.ipynb
 	pytest --cov
 
 test-all: ## run tests on every Python version with tox

README.rst

@@ -9,6 +9,8 @@ planetarypy
         :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

install_dev_deps.py

@@ -0,0 +1,53 @@
+#!/usr/bin/env python
+from pathlib import Path
+import tomlkit
+import sh
+import sys
+
+# Define packages that should be installed via pip instead of conda
+PIP_PACKAGES = {'build', 'pip-tools'}
+
+def install_deps():
+    # Read pyproject.toml
+    pyproject_path = Path("pyproject.toml")
+    with open(pyproject_path) as f:
+        pyproject = tomlkit.load(f)
+
+    # Get both main and dev dependencies
+    main_deps = pyproject["project"]["dependencies"]
+    dev_deps = pyproject["project"]["optional-dependencies"]["dev"]
+    all_deps = main_deps + dev_deps
+
+    # Split dependencies into conda and pip packages
+    conda_deps = [dep for dep in all_deps if dep not in PIP_PACKAGES]
+    pip_deps = [dep for dep in all_deps if dep in PIP_PACKAGES]
+
+    # Install conda packages
+    if conda_deps:
+        try:
+            print("Installing with mamba:", ' '.join(conda_deps))
+            sh.mamba("install", "-y", "-c", "conda-forge", *conda_deps, 
+                    _err=sys.stderr, _out=sys.stdout)
+            print("Conda installation completed successfully!")
+        except sh.ErrorReturnCode as e:
+            print("Error installing conda packages!")
+            print("Exit code:", e.exit_code)
+            print("Stdout:", e.stdout.decode() if e.stdout else 'No stdout')
+            print("Stderr:", e.stderr.decode() if e.stderr else 'No stderr')
+            sys.exit(1)
+
+    # Install pip packages
+    if pip_deps:
+        try:
+            print("\nInstalling with pip:", ' '.join(pip_deps))
+            sh.pip("install", *pip_deps, _err=sys.stderr, _out=sys.stdout)
+            print("Pip installation completed successfully!")
+        except sh.ErrorReturnCode as e:
+            print("Error installing pip packages!")
+            print("Exit code:", e.exit_code)
+            print("Stdout:", e.stdout.decode() if e.stdout else 'No stdout')
+            print("Stderr:", e.stderr.decode() if e.stderr else 'No stderr')
+            sys.exit(1)
+
+if __name__ == "__main__":
+    install_deps() 

planetarypy.code-workspace

@@ -0,0 +1,11 @@
+{
+	"folders": [
+		{
+			"path": "."
+		},
+		{
+			"path": "../0_nbplanetary"
+		}
+	],
+	"settings": {}
+}

pyproject.toml

@@ -0,0 +1,53 @@
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[project]
+name = "planetarypy"
+version = "0.2.0"
+description = "Core package for planetary data tools."
+readme = "README.rst"
+requires-python = ">= 3.9, <4"
+license = {text = "BSD license"}
+license-file = "LICENSE"
+authors = [
+    {name = "Planetarypy Developers", email = "[email protected]"}
+]
+keywords = ["planetarypy", "planetary", "space", "science"]
+classifiers = [
+    "Development Status :: 2 - Pre-Alpha",
+    "Intended Audience :: Developers",
+    "License :: OSI Approved :: BSD License",
+    "Natural Language :: English",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+dependencies = [
+    "tomlkit",
+    "requests",
+    "tqdm",
+    "pandas",
+    "astropy",
+    "spiceypy",
+    "yarl",
+    "matplotlib",
+]
+repository = "https://github.com/planetarypy/planetarypy"
+
+[project.optional-dependencies]
+dev = [
+    "pytest",
+    "pytest-cov",
+    "build",
+    "twine",
+    "pip-tools",
+    "make"
+]
+
+[project.scripts]
+planetarypy = "planetarypy.cli:main"
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/planetarypy"]

src/planetarypy/config.py

@@ -9,7 +9,7 @@
 from pathlib import Path
 from typing import Union
 
-import toml
+import tomlkit
 
 
 def reset_non_urls(
@@ -57,7 +57,7 @@ def _read_config(self):
 
         `storage_root` will be stored as attribute.
         """
-        self.tomldoc = toml.loads(self.path.read_text())
+        self.tomldoc = tomlkit.loads(self.path.read_text())
         if not self.tomldoc["storage_root"]:
             path = Path.home() / "planetarypy_data"
             path.mkdir(exist_ok=True)
@@ -78,7 +78,7 @@ def __getitem__(self, key: str):
             key = "missions." + key
         try:
             return reduce(lambda c, k: c[k], key.split("."), self.d)
-        except toml.exceptions.NonExistentKey:
+        except KeyError:
             return ""
 
     def get_value(
@@ -90,7 +90,7 @@ def get_value(
             key = "missions." + key
         try:
             return reduce(lambda c, k: c[k], key.split("."), self.d)
-        except toml.exceptions.NonExistentKey:
+        except KeyError:
             return ""
 
     def set_value(
@@ -119,7 +119,7 @@ def __setitem__(self, nested_key: str, value: Union[float, str]):
 
     def save(self):
         """Write the TOML doc to file."""
-        self.path.write_text(toml.dumps(self.tomldoc))
+        self.path.write_text(tomlkit.dumps(self.tomldoc))
 
     @property
     def missions(self):

src/planetarypy/spice/kernels.py

@@ -41,7 +41,6 @@
 import requests
 import spiceypy as spice
 from astropy.time import Time
-from dask.distributed import Client
 from tqdm.auto import tqdm
 from tqdm.contrib.concurrent import process_map
 from yarl import URL
@@ -237,17 +236,11 @@ def get_local_path(self, url) -> Path:
         return basepath / u.parent.name / u.name
 
     def _non_blocking_download(self, overwrite: bool = False):
-        "Use dask for a parallel download."
-        with Client() as client:
-            futures = []
-            for url in tqdm(self.kernel_urls, desc="Kernels downloaded"):
-                local_path = self.get_local_path(url)
-                if local_path.exists() and not overwrite:
-                    print(local_path.parent.name, local_path.name, "locally available.")
-                    continue
-                local_path.parent.mkdir(exist_ok=True, parents=True)
-                futures.append(client.submit(url_retrieve, url, local_path))
-            return [f.result() for f in futures]
+        "Use multiprocessing for parallel download."
+        paths = [self.get_local_path(url) for url in self.kernel_urls]
+        args = zip(self.kernel_urls, paths, repeat(overwrite))
+        _ = process_map(download_one_url, args, max_workers=cpu_count() - 2, 
+                       desc="Kernels downloaded")
 
     def _concurrent_download(self, overwrite: bool = False):
         paths = [self.get_local_path(url) for url in self.kernel_urls]

src/planetarypy/utils.py

@@ -140,9 +140,19 @@ def file_variations(filename: Union[str, Path], extensions: list) -> list:
 
     Parameters
     ----------
-    filename : str
+    filename : str or Path
         The original filename to use as a base.
     extensions : list
         List of extensions to use for variations.
+
+    Raises
+    ------
+    TypeError
+        If extensions is not a list
+    ValueError
+        If any extension doesn't start with a dot
     """
+    if not isinstance(extensions, list):
+        raise TypeError("extensions must be a list")
+
     return [Path(filename).with_suffix(extension) for extension in extensions]