Update imports in notebooks

.copier-answers.yml

@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.5.2
+_commit: v1.5.3
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks

.github/workflows/pre-commit-ci.yml

@@ -1,17 +1,17 @@
-# This workflow runs pre-commit hooks on pull requests to enforce coding style.
-# To ensure correct configuration, please refer to:
-#   https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
-
+# This workflow runs pre-commit hooks on pushes and pull requests to main
+# to enforce coding style. To ensure correct configuration, please refer to:
+#  https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
 name: Run pre-commit hooks
 
 on:
+  push:
+    branches: [ main ]
   pull_request:
+    branches: [ main ]
 
 jobs:
   pre-commit-ci:
     runs-on: ubuntu-latest
-    env: 
-      SKIP: "check-lincc-frameworks-template-version,pytest-check,no-commit-to-branch,validate-pyproject,check-added-large-files,sphinx-build"
     steps:
     - uses: actions/checkout@v4
       with:
@@ -28,6 +28,8 @@ jobs:
         if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
     - uses: pre-commit/[email protected]
       with:
-        extra_args: --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
+        extra_args: --all-files --verbose
+      env:
+        SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
     - uses: pre-commit-ci/[email protected]
-      if: always()
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

.pre-commit-config.yaml

@@ -1,4 +1,3 @@
-fail_fast: true
 repos:
     # Compare the local template version to the latest remote template version
     # This hook should always pass. It will print a message if the local version 
@@ -38,6 +37,12 @@ repos:
       - id: validate-pyproject
         name: Validate pyproject.toml
         description: Verify that pyproject.toml adheres to the established schema.
+    # Verify that GitHub workflows are well formed
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.28.0
+    hooks:
+      - id: check-github-workflows
+        args: ["--verbose"]
     # Automatically sort the imports used in .py files
   - repo: https://github.com/pycqa/isort
     rev: 5.12.0
@@ -88,20 +93,6 @@ repos:
         # pre-commit's default_language_version, see
         # https://pre-commit.com/#top_level-default_language_version
         language_version: python3.10
-    # Run unit tests, verify that they pass. Note that coverage is run against
-    # the ./src directory here because that is what will be committed. In the 
-    # github workflow script, the coverage is run against the installed package
-    # and uploaded to Codecov by calling pytest like so:
-    # `python -m pytest --cov=<package_name> --cov-report=xml`
-  - repo: local
-    hooks:
-      - id: pytest-check
-        name: Run unit tests
-        description: Run unit tests with pytest.
-        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
-        language: system
-        pass_filenames: false
-        always_run: true
     # Make sure Sphinx can build the documentation while explicitly omitting 
     # notebooks from the docs, so users don't have to wait through the execution 
     # of each notebook or each commit. By default, these will be checked in the 
@@ -128,3 +119,17 @@ repos:
             "-D", # Flag to override settings in conf.py
             "exclude_patterns=notebooks/*", # Exclude our notebooks from pre-commit
           ]
+    # Run unit tests, verify that they pass. Note that coverage is run against
+    # the ./src directory here because that is what will be committed. In the
+    # github workflow script, the coverage is run against the installed package
+    # and uploaded to Codecov by calling pytest like so:
+    # `python -m pytest --cov=<package_name> --cov-report=xml`
+  - repo: local
+    hooks:
+      - id: pytest-check
+        name: Run unit tests
+        description: Run unit tests with pytest.
+        entry: bash -c "if python -m pytest --co -qq; then python -m pytest --cov=./src --cov-report=html; fi"
+        language: system
+        pass_filenames: false
+        always_run: true

docs/conf.py

@@ -30,6 +30,16 @@
 extensions.append("nbsphinx")
 extensions.append("myst_parser")
 
+# -- sphinx-copybutton configuration ----------------------------------------
+extensions.append("sphinx_copybutton")
+## sets up the expected prompt text from console blocks, and excludes it from
+## the text that goes into the clipboard.
+copybutton_exclude = ".linenos, .gp"
+copybutton_prompt_text = ">> "
+
+## lets us suppress the copy button on select code blocks.
+copybutton_selector = "div:not(.no-copybutton) > div.highlight > pre"
+
 templates_path = []
 exclude_patterns = ["_build", "**.ipynb_checkpoints"]
 

docs/notebooks/catalog_size_inspection.ipynb

@@ -33,23 +33,23 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import hipscat\n",
     "import os\n",
     "\n",
-    "from hipscat.loaders import read_from_hipscat\n",
-    "from hipscat.io import paths\n",
-    "\n",
     "### Change this path!!!\n",
     "catalog_dir = \"../../tests/data/small_sky_order1\"\n",
     "\n",
     "### ----------------\n",
     "### You probably won't have to change anything from here.\n",
     "\n",
-    "catalog = read_from_hipscat(catalog_dir)\n",
+    "catalog = hipscat.read_from_hipscat(catalog_dir)\n",
     "\n",
     "info_frame = catalog.partition_info.as_dataframe()\n",
     "\n",
     "for index, partition in info_frame.iterrows():\n",
-    "    file_name = result = paths.pixel_catalog_file(catalog_dir, partition[\"Norder\"], partition[\"Npix\"])\n",
+    "    file_name = result = hipscat.io.paths.pixel_catalog_file(\n",
+    "        catalog_dir, partition[\"Norder\"], partition[\"Npix\"]\n",
+    "    )\n",
     "    info_frame.loc[index, \"size_on_disk\"] = os.path.getsize(file_name)\n",
     "\n",
     "info_frame = info_frame.astype(int)\n",

docs/notebooks/cone_search.ipynb

@@ -16,12 +16,10 @@
    "metadata": {},
    "outputs": [],
    "source": [
+    "import hipscat\n",
     "import healpy as hp\n",
     "import numpy as np\n",
     "\n",
-    "from hipscat.loaders import read_from_hipscat\n",
-    "from hipscat import inspection\n",
-    "\n",
     "## Fill in these variables with what's relevant in your use case:\n",
     "\n",
     "### Change this path!!!\n",
@@ -40,7 +38,7 @@
    "source": [
     "## Load catalog\n",
     "\n",
-    "catalog = read_from_hipscat(catalog_path)"
+    "catalog = hipscat.read_from_hipscat(catalog_path)"
    ]
   },
   {
@@ -51,7 +49,7 @@
    "source": [
     "## Plot catalog pixels\n",
     "\n",
-    "inspection.plot_pixels(catalog)"
+    "hipscat.inspection.plot_pixels(catalog)"
    ]
   },
   {
@@ -82,7 +80,7 @@
     "\n",
     "filtered_catalog = catalog.filter_by_cone(ra, dec, radius)\n",
     "\n",
-    "inspection.plot_pixels(filtered_catalog)"
+    "hipscat.inspection.plot_pixels(filtered_catalog)"
    ]
   }
  ],

docs/requirements.txt

@@ -1,6 +1,7 @@
 sphinx
 sphinx-rtd-theme
 sphinx-autoapi
+sphinx-copybutton
 nbsphinx
 ipykernel
 ipython

src/hipscat/__init__.py

@@ -1,4 +1,4 @@
 """High-level namespace, hipscat"""
 
-from . import catalog, io, pixel_math
+from . import catalog, inspection, io, pixel_math
 from .loaders import read_from_hipscat