Merge pull request #19 from astronomy-commons/delucchi/copier

Re-run copier

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v0.0.3
+_commit: v0.0.5
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: Melissa DeLucchi

.github/workflows/python-package.yml

@@ -30,3 +30,6 @@ jobs:
         pip install .
         pip install .[dev]
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest --cov=. --cov-report=xml

.pre-commit-config.yaml

@@ -0,0 +1,60 @@
+repos:
+
+    # Clear output from jupyter notebooks so that only the input cells are committed.
+  - repo: local
+    hooks:
+      - id: jupyter-nb-clear-output
+        name: jupyter-nb-clear-output
+        description: Clear output from Jupyter notebooks.
+        files: \.ipynb$
+        stages: [commit]
+        language: system
+        entry: jupyter nbconvert --ClearOutputPreprocessor.enabled=True --inplace
+
+    # Run unit tests, verify that they pass
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: pytest-check
+        description: Run unit tests with pytest.
+        entry: pytest --cov=. --cov-report=html
+        language: system
+        pass_filenames: false
+        always_run: true
+
+    # prevents committing directly branches named 'main' and 'master'.
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: no-commit-to-branch
+        name: Don't commit to main or master branch
+        description: Prevent the user from committing directly to the primary branch.
+
+    # verify that pyproject.toml is well formed
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+        name: Validate syntax of pyproject.toml
+        description: Verify that pyproject.toml adheres to the established schema.
+
+    # Automatically sort the imports used in .py files
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+        description: Sort and organize imports in .py files.
+
+  - repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args:
+          [
+            "-rn", # Only display messages
+            "-sn", # Don't display the score
+          ]

nb/README.md

@@ -0,0 +1 @@
+Put your Jupyter notebooks here :)

nb/example.ipynb

@@ -0,0 +1,32 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "a = 2 + 2"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "copier_test",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "name": "python",
+   "version": "3.10.8 | packaged by conda-forge | (main, Nov 22 2022, 08:25:29) [Clang 14.0.6 ]"
+  },
+  "orig_nbformat": 4,
+  "vscode": {
+   "interpreter": {
+    "hash": "49ec39369c99805342b11327ac0d7c4ce794e7071ab73521f56ecad9648013da"
+   }
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

pyproject.toml

@@ -20,8 +20,11 @@ dependencies = [
 # On a mac, install optional dependencies with `pip install '.[dev]'` (include the single quotes)
 [project.optional-dependencies]
 dev = [
-    "pytest", 
-    "pytest-cov",
+    "pytest",
+    "pytest-cov", # Used to report total code coverage
+    "pre-commit", # Used to run checks before finalizing a git commit
+    "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
+    "pylint", # Used for static linting of files
 ]
 
 [metadata]
@@ -32,3 +35,8 @@ url = "https://github.com/astronomy-commons/hipscat"
 [build-system]
 requires = ["setuptools","wheel"]
 build-backend = "setuptools.build_meta"
+
+[tool.pylint.'MESSAGES CONTROL']
+disable = """
+    missing-module-docstring,
+"""

src/hipscat/catalog/__init__.py

@@ -2,3 +2,5 @@
 
 from .catalog import Catalog
 from .catalog_parameters import CatalogParameters
+from .pixel_node import PixelNode
+from .pixel_node_type import PixelNodeType

src/hipscat/catalog/catalog_parameters.py

@@ -1,6 +1,7 @@
 """Conatiner class for properties of a catalog that is being created"""
 
 import os
+from typing import List
 
 
 class CatalogParameters:
@@ -9,7 +10,7 @@ class CatalogParameters:
     def __init__(
         self,
         catalog_name=None,
-        input_paths: list[str] = None,
+        input_paths: List[str] = None,
         input_format="csv",
         output_path=None,
         highest_healpix_order=10,

tests/hipscat/catalog/test_pixel_node.py

@@ -127,4 +127,4 @@ def test_get_leaf_descendants_with_root_node(root_pixel_node, leaf_pixel_node):
 def test_get_leaf_descendants_with_multiple_leafs(root_pixel_node, leaf_pixel_node, leaf_pixel_node_data):
     leaf_pixel_node_data["hp_pixel"] += 1
     second_leaf = PixelNode(**leaf_pixel_node_data)
-    assert root_pixel_node.get_all_leaf_descendants() == [leaf_pixel_node, second_leaf]
+    assert root_pixel_node.get_all_leaf_descendants() == [leaf_pixel_node, second_leaf] or root_pixel_node.get_all_leaf_descendants() == [second_leaf, leaf_pixel_node]