Merge pull request #45 from astronomy-commons/delucchi/bench_ppt

delucchi-cmu · web-flow · commit da796a5c0d7c · 2026-03-02T18:07:37.000-05:00
Update PTT to 2.2.0. Add single benchmark test.
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,10 +1,26 @@
 # Changes here will be overwritten by Copier
-_commit: v2.1.1
+_commit: v2.2.0
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: lincc-frameworks-team@lists.lsst.org
 author_name: LINCC Frameworks
-custom_install: false
+create_example_module: false
+custom_install: custom
+enforce_style:
+- ruff_lint
+- ruff_format
+failure_notification: []
+include_benchmarks: true
+include_docs: true
+include_notebooks: true
+mypy_type_checking: none
 package_name: hats_tap
+project_description: TAP(Table Access Protocol) server prototype for HATS data, queried
+    using LSDB.
 project_license: BSD
 project_name: hats-tap
 project_organization: astronomy-commons
+python_versions:
+- '3.11'
+- '3.12'
+- '3.13'
+test_lowest_version: none
diff --git a/.github/ISSUE_TEMPLATE/1-bug_report.md b/.github/ISSUE_TEMPLATE/1-bug_report.md
@@ -12,6 +12,13 @@ assignees: ''
 **Environment Information**
 
 
+<details>
+<summary>Traceback</summary>
+
+FILL IN YOUR STACK TRACE HERE
+
+</details>
+
 **Before submitting**
 Please check the following:
 
diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md
@@ -1,63 +1,13 @@
-<!-- 
-Thank you for your contribution to the repo :)
-
-Pull Request (PR) Instructions:
-Provide a general summary of your changes in the Title above. Fill out each section of the template, and replace the space with an `x` in all the boxes that apply. If you're unsure about any of these, don't hesitate to ask. We're here to help! Once you are satisfied with the pull request, click the "Create pull request" button to submit it for review.
-
-Before submitting this PR, please ensure that your input and responses are entered in the designated space provided below each section to keep all project-related information organized and easily accessible.
- 
-How to link to a PR:
-https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue 
--->
-
 ## Change Description
 <!--- 
-Describe your changes in detail. In your description, you should answer questions like "Why is this change required? What problem does it solve?".
-
-If it fixes an open issue, please link to the issue here. If this PR closes an issue, put the word 'closes' before the issue link to auto-close the issue when the PR is merged.
+Closes #???
 -->
-- [ ] My PR includes a link to the issue that I am addressing
-
-
 
 ## Solution Description
-<!-- Please explain the technical solution that I have provided and how it addresses the issue or feature being implemented -->
-
 
 
 ## Code Quality
-- [ ] I have read the Contribution Guide
+- [ ] I have read the Contribution Guide and agree to the Code of Conduct
 - [ ] My code follows the code style of this project
 - [ ] My code builds (or compiles) cleanly without any errors or warnings
 - [ ] My code contains relevant comments and necessary documentation
-
-## Project-Specific Pull Request Checklists
-<!--- Please only use the checklist that apply to your change type(s) -->
-
-### Bug Fix Checklist
-- [ ] My fix includes a new test that breaks as a result of the bug (if possible)
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
-
-### New Feature Checklist
-- [ ] I have added or updated the docstrings associated with my feature using the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
-- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
-- [ ] I have added unit/End-to-End (E2E) test cases to cover my new feature
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
-
-### Documentation Change Checklist
-- [ ] Any updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
-
-### Build/CI Change Checklist
-- [ ] If required or optional dependencies have changed (including version numbers), I have updated the README to reflect this
-- [ ] If this is a new CI setup, I have added the associated badge to the README
-
-<!-- ### Version Change Checklist [For Future Use] -->
-
-### Other Change Checklist
-- [ ] Any new or updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
-- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
-- [ ] I have added unit/End-to-End (E2E) test cases to cover any changes
-- [ ] My change includes a breaking change
-  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
diff --git a/.github/workflows/asv-main.yml b/.github/workflows/asv-main.yml
@@ -8,7 +8,7 @@ on:
     branches: [ main ]
 
 env:
-  PYTHON_VERSION: "3.11"
+  PYTHON_VERSION: "3.12"
   ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
 
diff --git a/.github/workflows/asv-nightly.yml b/.github/workflows/asv-nightly.yml
@@ -9,7 +9,7 @@ on:
   workflow_dispatch:
   
 env:
-  PYTHON_VERSION: "3.11"
+  PYTHON_VERSION: "3.12"
   ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
   NIGHTLY_HASH_FILE: nightly-hash
diff --git a/.github/workflows/asv-pr.yml b/.github/workflows/asv-pr.yml
@@ -15,7 +15,7 @@ concurrency:
   cancel-in-progress: true
 
 env:
-  PYTHON_VERSION: "3.11"
+  PYTHON_VERSION: "3.12"
   ASV_VERSION: "0.6.5"
   WORKING_DIR: ${{github.workspace}}/benchmarks
   ARTIFACTS_DIR: ${{github.workspace}}/artifacts
diff --git a/.github/workflows/build-documentation.yml b/.github/workflows/build-documentation.yml
@@ -21,16 +21,18 @@ jobs:
 
     steps:
     - uses: actions/checkout@v6
-    - name: Set up Python 3.11
+    - name: Set up Python 3.12
       uses: actions/setup-python@v6
       with:
-        python-version: '3.11'
+        python-version: '3.12'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
     - name: Install dependencies
       run: |
         sudo apt-get update
-        python -m pip install --upgrade pip
-        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
-        pip install .
+        uv pip install --system -e .
+        if [ -f docs/requirements.txt ]; then uv pip install --system -r docs/requirements.txt; fi
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
     - name: Install notebook requirements
       run: |
         sudo apt-get install pandoc
diff --git a/.github/workflows/pre-commit-ci.yml b/.github/workflows/pre-commit-ci.yml
@@ -20,7 +20,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install uv
       uses: astral-sh/setup-uv@v7
     - name: Install dependencies
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -27,7 +27,7 @@ jobs:
     - name: Set up Python
       uses: actions/setup-python@v6
       with:
-        python-version: '3.11'
+        python-version: '3.12'
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -4,7 +4,7 @@ repos:
     # This hook should always pass. It will print a message if the local version 
     # is out of date.
   - repo: https://github.com/lincc-frameworks/pre-commit-hooks
-    rev: v0.1.2
+    rev: v0.2.2
     hooks:
       - id: check-lincc-frameworks-template-version
         name: Check template version
@@ -60,32 +60,15 @@ repos:
       - id: ruff-format
         name: Format code using ruff
         types_or: [ python, pyi, jupyter ]
-    # 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 
-    # GitHub workflows.
-  - repo: local
+  - repo: https://github.com/lincc-frameworks/pre-commit-hooks
+    rev: v0.2.2
     hooks:
-      - id: sphinx-build
-        name: Build documentation with Sphinx
-        entry: sphinx-build
-        language: system
-        always_run: true
-        exclude_types: [file, symlink]
+      - id: pre-executed-nb-never-execute
+        name: Check pre-executed notebooks
+        files: ^docs/pre_executed/.*\.ipynb$
+        verbose: true
         args:
-          [
-            "-M", # Run sphinx in make mode, so we can use -D flag later
-                  # Note: -M requires next 3 args to be builder, source, output
-            "html", # Specify builder
-            "./docs", # Source directory of documents
-            "./_readthedocs", # Output directory for rendered documents
-            "-T", # Show full trace back on exception
-            "-E", # Don't use saved env; always read all files
-            "-d", # Flag for cached environment and doctrees
-            "./docs/_build/doctrees", # Directory
-            "-D", # Flag to override settings in conf.py
-            "exclude_patterns=notebooks/*,_build", # Exclude notebooks and build dir from pre-commit
-          ]
+          ["docs/pre_executed/"]
     # 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
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -9,7 +9,7 @@ version: 2
 build:
   os: ubuntu-22.04
   tools:
-    python: "3.11"
+    python: "3.12"
 
 # Build documentation in the docs/ directory with Sphinx
 sphinx:
@@ -19,5 +19,6 @@ sphinx:
 python:
    install:
    - requirements: docs/requirements.txt
+   - requirements: requirements.txt
    - method: pip
      path: .
diff --git a/benchmarks/asv.conf.json b/benchmarks/asv.conf.json
@@ -37,7 +37,7 @@
     // The Pythons you'd like to test against. If not provided, defaults
     // to the current version of Python used to run `asv`.
     "pythons": [
-        "3.11"
+        "3.12"
     ],
     // The matrix of dependencies to test. Each key is the name of a
     // package (in PyPI) and the values are version numbers.  An empty
diff --git a/benchmarks/benchmarks.py b/benchmarks/benchmarks.py
@@ -3,14 +3,30 @@
 For more information on writing benchmarks:
 https://asv.readthedocs.io/en/stable/writing_benchmarks.html."""
 
-from hats_tap import example_benchmarks
+import pathlib
 
+from hats_tap.adql_to_lsdb import parse_adql_entities
 
-def time_computation():
+
+def time_sample1_parse():
     """Time computations are prefixed with 'time'."""
-    example_benchmarks.runtime_computation()
+    samples_dir = pathlib.Path(__file__).parent.parent / "src" / "hats_tap" / "samples"
 
+    adql = (samples_dir / "sample1.adql").read_text()
+    result = parse_adql_entities(adql)
 
-def mem_list():
-    """Memory computations are prefixed with 'mem' or 'peakmem'."""
-    return example_benchmarks.memory_computation()
+    assert result["tables"] == ["gaia_dr3.gaia"]
+    assert result["columns"] == [
+        "source_id",
+        "ra",
+        "dec",
+        "phot_g_mean_mag",
+        "phot_variable_flag",
+    ]
+    assert result["spatial_search"] == {
+        "type": "ConeSearch",
+        "ra": 270.0,
+        "dec": 23.0,
+        "radius": 0.25,
+    }
+    assert result["limits"] == 15
diff --git a/docs/index.rst b/docs/index.rst
@@ -6,6 +6,8 @@
 Welcome to hats_tap's documentation!
 ========================================================================================
 
+TAP(Table Access Protocol) server prototype for HATS data, queried using LSDB.
+
 Dev Guide - Getting Started
 ---------------------------
 
@@ -16,7 +18,7 @@ create and activate a new environment.
 
 .. code-block:: console
 
-   >> conda create env -n <env_name> python=3.11
+   >> conda create env -n <env_name> python=3.12
    >> conda activate <env_name>
 
 
diff --git a/docs/requirements.txt b/docs/requirements.txt
@@ -7,4 +7,4 @@ nbsphinx
 sphinx
 sphinx-autoapi
 sphinx-copybutton
-sphinx-rtd-theme
+sphinx-rtd-theme>=3.0
diff --git a/pyproject.toml b/pyproject.toml
@@ -7,6 +7,7 @@ readme = "README.md"
 authors = [
     { name = "LINCC Frameworks", email = "lincc-frameworks-team@lists.lsst.org" }
 ]
+description = "TAP(Table Access Protocol) server prototype for HATS data, queried using LSDB."
 classifiers = [
     "Development Status :: 4 - Beta",
     "Intended Audience :: Developers",
@@ -67,7 +68,6 @@ addopts = "--doctest-modules --doctest-glob=*.rst"
 
 [tool.ruff]
 line-length = 110
-target-version = "py39"
 [tool.ruff.lint]
 select = [
     # pycodestyle
diff --git a/requirements.txt b/requirements.txt
diff --git a/src/hats_tap/__init__.py b/src/hats_tap/__init__.py
@@ -10,9 +10,8 @@
 This server uses the adql_to_lsdb module to convert ADQL queries
 """
 
+from ._version import __version__
 from .import_tap_schema import TAPSchemaImporter
 from .tap_schema_db import TAPSchemaDatabase
 
-__all__ = ["TAPSchemaDatabase", "TAPSchemaImporter"]
-
-__version__ = "0.2.0"
+__all__ = ["TAPSchemaDatabase", "TAPSchemaImporter", "__version__"]
diff --git a/tests/hats_tap/test_adql_to_lsdb.py b/tests/hats_tap/test_adql_to_lsdb.py
@@ -336,9 +336,9 @@ def test_cone_search_structure(self):
         assert "ra" in spatial
         assert "dec" in spatial
         assert "radius" in spatial
-        assert isinstance(spatial["ra"], (int, float))
-        assert isinstance(spatial["dec"], (int, float))
-        assert isinstance(spatial["radius"], (int, float))
+        assert isinstance(spatial["ra"], int | float)
+        assert isinstance(spatial["dec"], int | float)
+        assert isinstance(spatial["radius"], int | float)
 
     def test_polygon_search_structure(self):
         """Test that PolygonSearch has correct structure."""
