24 accelerate io on photometric data by using hdf5 files

.copier-answers.yml

@@ -0,0 +1,10 @@
+# Changes here will be overwritten by Copier
+_commit: v2.0.3
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: sylvie.dagoret-campagne@ijclab.in2p3.fr
+author_name: Boris Leistedt
+custom_install: false
+package_name: delight
+project_license: MIT
+project_name: delight
+project_organization: LSSTDESC

.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: $Format:%D$

.gitattributes

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+# 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

.github/ISSUE_TEMPLATE/0-general_issue.md

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

.github/ISSUE_TEMPLATE/1-bug_report.md

@@ -0,0 +1,17 @@
+---
+name: Bug report
+about: Tell us about a problem to fix
+title: 'Short description'
+labels: 'bug'
+assignees: ''
+
+---
+**Bug report**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
+- [ ] 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.

.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.

.github/LINCC_README.md

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+# The .github directory
+
+This directory contains various configurations and .yml files that are used to
+define GitHub actions and behaviors.
+
+## Workflows
+
+The .yml files in ``./workflows`` 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
+
+## Configurations
+
+Templates for various different issue types are defined in ``./ISSUE_TEMPLATE``
+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

.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"

.github/pull_request_template.md

@@ -0,0 +1,63 @@
+<!-- 
+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.
+-->
+- [ ] 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
+- [ ] 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)

.github/workflows/asv-main.yml

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+# 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: "3.10"
+  ASV_VERSION: "0.6.4"
+  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@v5
+      with:
+        python-version: ${{env.PYTHON_VERSION}}
+    - name: Checkout main branch of the repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Install dependencies
+      run: pip install "asv[virtualenv]==${{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

.github/workflows/asv-nightly.yml

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+# 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: "3.10"
+  ASV_VERSION: "0.6.4"
+  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@v5
+      with:
+        python-version: ${{env.PYTHON_VERSION}}
+    - name: Checkout main branch of the repository
+      uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+    - name: Install dependencies
+      run: pip install "asv[virtualenv]==${{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@v4
+      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@v4
+      with:
+        path: ${{env.WORKING_DIR}}
+        key: nightly-results-${{steps.nightly-dates.outputs.today}}