science-catalogs 0.1.0b2__tar.gz

science_catalogs-0.1.0b2/.copier-answers.yml

@@ -0,0 +1,24 @@
+# Changes here will be overwritten by Copier
+_commit: v2.2.0-15-ga7522ba
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: ''
+author_name: LIneA IT
+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: science_catalogs
+project_description: Reusable toolkit for science-ready catalog preparation with Dask,
+    LSDB, and HATS.
+project_license: MIT
+project_name: science_catalogs
+project_organization: linea-it
+python_versions:
+- '3.12'
+test_lowest_version: none

science_catalogs-0.1.0b2/.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

science_catalogs-0.1.0b2/.gitattributes

@@ -0,0 +1,24 @@
+# For explanation of this file and uses see
+# https://git-scm.com/docs/gitattributes
+# https://developer.lsst.io/git/git-lfs.html#using-git-lfs-enabled-repositories
+# https://lincc-ppt.readthedocs.io/en/latest/practices/git-lfs.html
+#
+# Used by https://github.com/lsst/afwdata.git
+# *.boost filter=lfs diff=lfs merge=lfs -text
+# *.dat filter=lfs diff=lfs merge=lfs -text
+# *.fits filter=lfs diff=lfs merge=lfs -text
+# *.gz filter=lfs diff=lfs merge=lfs -text
+#
+# apache parquet files
+# *.parq	filter=lfs diff=lfs merge=lfs -text
+#
+# sqlite files
+# *.sqlite3	filter=lfs diff=lfs merge=lfs -text
+#
+# gzip files
+# *.gz	filter=lfs diff=lfs merge=lfs -text
+#
+# png image files
+# *.png	filter=lfs diff=lfs merge=lfs -text
+
+.git_archival.txt export-subst

science_catalogs-0.1.0b2/.github/ISSUE_TEMPLATE/0-general_issue.md

@@ -0,0 +1,8 @@
+---
+name: General issue
+about: Quickly create a general issue
+title: ''
+labels: ''
+assignees: ''
+
+---

science_catalogs-0.1.0b2/.github/ISSUE_TEMPLATE/1-bug_report.md

@@ -0,0 +1,30 @@
+---
+name: Bug report
+about: Tell us about a problem to fix
+title: 'Short description'
+labels: 'bug'
+assignees: ''
+
+---
+**Bug report**
+
+
+**Environment Information**
+
+
+<details>
+<summary>Traceback</summary>
+
+```
+FILL IN YOUR STACK TRACE HERE
+```
+
+</details>
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the situation in which the bug arose, including what code was executed, and any applicable data others will need to reproduce the problem.
+- [ ] I have included information about my environment, including the version of this package (e.g. `science_catalogs.__version__`)
+- [ ] I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a description of what I expected instead.
+- [ ] If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

science_catalogs-0.1.0b2/.github/ISSUE_TEMPLATE/2-feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Short description'
+labels: 'enhancement'
+assignees: ''
+
+---
+
+**Feature request**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the purpose of the suggested change, specifying what I need the enhancement to accomplish, i.e. what problem it solves.
+- [ ] I have included any relevant links, screenshots, environment information, and data relevant to implementing the requested feature, as well as pseudocode for how I want to access the new functionality.
+- [ ] If I have ideas for how the new feature could be implemented, I have provided explanations and/or pseudocode and/or task lists for the steps.

science_catalogs-0.1.0b2/.github/ISSUE_TEMPLATE/README.md

@@ -0,0 +1,9 @@
+# Configurations
+
+Templates for various different issue types are defined in this directory
+and a pull request template is defined as ``../pull_request_template.md``. Adding,
+removing, and modifying these templates to suit the needs of your project is encouraged.
+
+For more information about these templates, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/issue_pr_templating.html
+
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

science_catalogs-0.1.0b2/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

science_catalogs-0.1.0b2/.github/pull_request_template.md

@@ -0,0 +1,13 @@
+## Change Description
+<!--- 
+Closes #???
+-->
+
+## Solution Description
+
+
+## Code Quality
+- [ ] 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

science_catalogs-0.1.0b2/.github/workflows/README.md

@@ -0,0 +1,9 @@
+# Workflows
+
+The .yml files in this directory are used to define the various continuous
+integration scripts that will be run on your behalf e.g. nightly as a smoke check,
+or when you create a new PR.
+
+For more information about CI and workflows, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci.html
+
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

science_catalogs-0.1.0b2/.github/workflows/asv-main.yml

@@ -0,0 +1,68 @@
+# This workflow will run benchmarks with airspeed velocity (asv), 
+# store the new results in the "benchmarks" branch and publish them
+# to a dashboard on GH Pages.
+name: Run ASV benchmarks for main
+
+on:
+  push:
+    branches: [ main ]
+
+env:
+  PYTHON_VERSION: "3.12"
+  ASV_VERSION: "0.6.5"
+  WORKING_DIR: ${{github.workspace}}/benchmarks
+
+concurrency:
+  group: ${{github.workflow}}-${{github.ref}}
+  cancel-in-progress: true
+
+jobs:
+  asv-main:
+    runs-on: ubuntu-latest
+    permissions:
+      contents: write
+    defaults:
+      run:
+        working-directory: ${{env.WORKING_DIR}}
+    steps:
+    - name: Set up Python ${{env.PYTHON_VERSION}}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{env.PYTHON_VERSION}}
+    - name: Checkout main branch of the repository
+      uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+    - name: Install dependencies
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}}
+    - name: Configure git
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+    - name: Create ASV machine config file
+      run: asv machine --machine gh-runner --yes
+    - name: Fetch previous results from the "benchmarks" branch
+      run: |
+        if git ls-remote --exit-code origin benchmarks > /dev/null 2>&1; then
+          git merge origin/benchmarks \
+            --allow-unrelated-histories \
+            --no-commit
+          mv ../_results .
+        fi
+    - name: Run ASV for the main branch
+      run: asv run ALL --skip-existing --verbose || true
+    - name: Submit new results to the "benchmarks" branch
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: benchmarks
+        folder: ${{env.WORKING_DIR}}/_results
+        target-folder: _results
+    - name: Generate dashboard HTML
+      run: |
+        asv show
+        asv publish
+    - name: Deploy to Github pages
+      uses: JamesIves/github-pages-deploy-action@v4
+      with:
+        branch: gh-pages
+        folder: ${{env.WORKING_DIR}}/_html

science_catalogs-0.1.0b2/.github/workflows/asv-nightly.yml

@@ -0,0 +1,72 @@
+# This workflow will run daily at 06:45.
+# It will run benchmarks with airspeed velocity (asv)
+# and compare performance with the previous nightly build.
+name: Run benchmarks nightly job
+
+on:
+  schedule:
+    - cron: 45 6 * * *
+  workflow_dispatch:
+  
+env:
+  PYTHON_VERSION: "3.12"
+  ASV_VERSION: "0.6.5"
+  WORKING_DIR: ${{github.workspace}}/benchmarks
+  NIGHTLY_HASH_FILE: nightly-hash
+
+jobs:
+  asv-nightly:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ${{env.WORKING_DIR}}
+    steps:
+    - name: Set up Python ${{env.PYTHON_VERSION}}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{env.PYTHON_VERSION}}
+    - name: Checkout main branch of the repository
+      uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+    - name: Install dependencies
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}}
+    - name: Configure git
+      run: |
+        git config user.name "github-actions[bot]"
+        git config user.email "41898282+github-actions[bot]@users.noreply.github.com"
+    - name: Create ASV machine config file
+      run: asv machine --machine gh-runner --yes
+    - name: Fetch previous results from the "benchmarks" branch
+      run: |
+        if git ls-remote --exit-code origin benchmarks > /dev/null 2>&1; then
+          git merge origin/benchmarks \
+            --allow-unrelated-histories \
+            --no-commit
+          mv ../_results .
+        fi
+    - name: Get nightly dates under comparison
+      id: nightly-dates
+      run: |
+        echo "yesterday=$(date -d yesterday +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+        echo "today=$(date +'%Y-%m-%d')" >> $GITHUB_OUTPUT
+    - name: Use last nightly commit hash from cache
+      uses: actions/cache@v5
+      with:
+        path: ${{env.WORKING_DIR}}
+        key: nightly-results-${{steps.nightly-dates.outputs.yesterday}}
+    - name: Run comparison of main against last nightly build
+      run: |
+        HASH_FILE=${{env.NIGHTLY_HASH_FILE}}
+        CURRENT_HASH=${{github.sha}}
+        if [ -f $HASH_FILE ]; then
+          PREV_HASH=$(cat $HASH_FILE)
+          asv continuous $PREV_HASH $CURRENT_HASH --verbose || true
+          asv compare $PREV_HASH $CURRENT_HASH --sort ratio --verbose
+        fi
+        echo $CURRENT_HASH > $HASH_FILE
+    - name: Update last nightly hash in cache
+      uses: actions/cache@v5
+      with:
+        path: ${{env.WORKING_DIR}}
+        key: nightly-results-${{steps.nightly-dates.outputs.today}}

science_catalogs-0.1.0b2/.github/workflows/asv-pr.yml

@@ -0,0 +1,70 @@
+# This workflow will run benchmarks with airspeed velocity (asv) for pull requests.
+# It will compare the performance of the main branch with the performance of the merge
+# with the new changes. It then publishes a comment with this assessment by triggering
+# the publish-benchmarks-pr workflow.
+# Based on https://securitylab.github.com/research/github-actions-preventing-pwn-requests/.
+name: Run benchmarks for PR
+
+on:
+  pull_request:
+    branches: [ main ]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{github.workflow}}-${{github.ref}}
+  cancel-in-progress: true
+
+env:
+  PYTHON_VERSION: "3.12"
+  ASV_VERSION: "0.6.5"
+  WORKING_DIR: ${{github.workspace}}/benchmarks
+  ARTIFACTS_DIR: ${{github.workspace}}/artifacts
+
+jobs:
+  asv-pr:
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        working-directory: ${{env.WORKING_DIR}}
+    steps:
+    - name: Set up Python ${{env.PYTHON_VERSION}}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{env.PYTHON_VERSION}}
+    - name: Checkout PR branch of the repository
+      uses: actions/checkout@v6
+      with:
+        fetch-depth: 0
+    - name: Display Workflow Run Information
+      run: |
+        echo "Workflow Run ID: ${{github.run_id}}"
+    - name: Install dependencies
+      run: pip install asv[virtualenv]==${{env.ASV_VERSION}} lf-asv-formatter
+    - name: Make artifacts directory
+      run: mkdir -p ${{env.ARTIFACTS_DIR}}
+    - name: Save pull request number
+      run: echo ${{github.event.pull_request.number}} > ${{env.ARTIFACTS_DIR}}/pr
+    - name: Get current job logs URL
+      uses: Tiryoh/gha-jobid-action@v1
+      id: jobs
+      with:
+        github_token: ${{secrets.GITHUB_TOKEN}}
+        job_name: ${{github.job}}
+    - name: Create ASV machine config file
+      run: asv machine --machine gh-runner --yes
+    - name: Save comparison of PR against main branch
+      run: |
+        git remote add upstream https://github.com/${{github.repository}}.git
+        git fetch upstream
+        asv continuous upstream/main HEAD --verbose || true
+        asv compare upstream/main HEAD --sort ratio --verbose | tee output
+        python -m lf_asv_formatter --asv_version "$(asv --version | awk '{print $2}')"
+        printf "\n\nClick [here]($STEP_URL) to view all benchmarks." >> output
+        mv output ${{env.ARTIFACTS_DIR}}
+      env:
+        STEP_URL: ${{steps.jobs.outputs.html_url}}#step:10:1
+    - name: Upload artifacts (PR number and benchmarks output)
+      uses: actions/upload-artifact@v6
+      with:
+        name: benchmark-artifacts
+        path: ${{env.ARTIFACTS_DIR}}

science_catalogs-0.1.0b2/.github/workflows/build-documentation.yml

@@ -0,0 +1,41 @@
+
+# This workflow will install Python dependencies, build the package and then build the documentation.
+
+name: Build documentation
+
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        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
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

science_catalogs-0.1.0b2/.github/workflows/pre-commit-ci.yml

@@ -0,0 +1,37 @@
+
+# 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
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        uv pip install --system .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
+    - uses: pre-commit/action@v3.0.1
+      with:
+        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/lite-action@v1.1.0
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

science_catalogs-0.1.0b2/.github/workflows/publish-benchmarks-pr.yml

@@ -0,0 +1,53 @@
+# This workflow publishes a benchmarks comment on a pull request. It is triggered after the
+# benchmarks are computed in the asv-pr workflow. This separation of concerns allows us limit
+# access to the target repository private tokens and secrets, increasing the level of security.
+# Based on https://securitylab.github.com/research/github-actions-preventing-pwn-requests/.
+name: Publish benchmarks comment to PR
+
+on:
+  workflow_run:
+    workflows: ["Run benchmarks for PR"]
+    types: [completed]
+
+jobs:
+  upload-pr-comment:
+    runs-on: ubuntu-latest
+    if: >
+      github.event.workflow_run.event == 'pull_request' &&
+      github.event.workflow_run.conclusion == 'success'
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+    - name: Display Workflow Run Information
+      run: |
+        echo "Workflow Run ID: ${{ github.event.workflow_run.id }}"
+        echo "Head SHA: ${{ github.event.workflow_run.head_sha }}"
+        echo "Head Branch: ${{ github.event.workflow_run.head_branch }}"
+        echo "Conclusion: ${{ github.event.workflow_run.conclusion }}"
+        echo "Event: ${{ github.event.workflow_run.event }}"
+    - name: Download artifact
+      uses: dawidd6/action-download-artifact@v14
+      with:
+        name: benchmark-artifacts
+        run_id: ${{ github.event.workflow_run.id }}
+    - name: Extract artifacts information
+      id: pr-info
+      run: |
+        printf "PR number: $(cat pr)\n"
+        printf "Output:\n$(cat output)"
+        printf "pr=$(cat pr)" >> $GITHUB_OUTPUT
+    - name: Find benchmarks comment
+      uses: peter-evans/find-comment@v4
+      id: find-comment
+      with:
+        issue-number: ${{ steps.pr-info.outputs.pr }}
+        comment-author: 'github-actions[bot]'
+        body-includes: view all benchmarks
+    - name: Create or update benchmarks comment
+      uses: peter-evans/create-or-update-comment@v5
+      with:
+        comment-id: ${{ steps.find-comment.outputs.comment-id }}
+        issue-number: ${{ steps.pr-info.outputs.pr }}
+        body-path: output
+        edit-mode: replace

science_catalogs-0.1.0b2/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,39 @@
+
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

science_catalogs-0.1.0b2/.github/workflows/smoke-test.yml

@@ -0,0 +1,43 @@
+# This workflow will run daily at 06:45.
+# It will install Python dependencies and run tests with a variety of Python versions.
+# See documentation for help debugging smoke test issues:
+#    https://lincc-ppt.readthedocs.io/en/latest/practices/ci_testing.html#version-culprit
+
+name: Unit test smoke test
+
+on:
+
+  # Runs this workflow automatically
+  schedule:
+    - cron: 45 6 * * *
+    
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12']
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        uv pip install --system -e .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
+    - name: List dependencies
+      run: |
+        pip list
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest

science_catalogs-0.1.0b2/.github/workflows/testing-and-coverage.yml

@@ -0,0 +1,40 @@
+
+# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit test and code coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12']
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install uv
+      uses: astral-sh/setup-uv@v7
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        uv pip install --system -e .[dev]
+        if [ -f requirements.txt ]; then uv pip install --system -r requirements.txt; fi
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest --cov=science_catalogs --cov-report=xml
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v5
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}