new template

.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

@@ -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

.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 descriprion 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/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/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@v3
+      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@v3
+      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@v4
+      with:
+        comment-id: ${{ steps.find-comment.outputs.comment-id }}
+        issue-number: ${{ steps.pr-info.outputs.pr }}
+        body-path: output
+        edit-mode: replace

.github/workflows/smoke-test.yml

@@ -10,12 +10,9 @@ on:
   # Runs this workflow automatically
   schedule:
     - cron: 45 6 * * *
-<<<<<<< before updating
-=======
 
   # Allows you to run this workflow manually from the Actions tab
   workflow_dispatch:
->>>>>>> after updating
 
 jobs:
   build:
@@ -42,4 +39,4 @@ jobs:
         pip list
     - name: Run unit tests with pytest
       run: |
-        python -m pytest
+        python -m pytest

.pre-commit-config.yaml

@@ -41,56 +41,6 @@ repos:
   - repo: https://github.com/python-jsonschema/check-jsonschema
     rev: 0.28.0
     hooks:
-<<<<<<< before updating
-      - id: isort
-        name: Run isort
-        description: Sort and organize imports in .py and .pyi files.
-        types_or: [python, pyi]
-
-
-
-    # Analyze the src code style and report code that doesn't adhere.
-  #- repo: local
-    #hooks:
-      #- id: pylint
-        #name: pylint (python files in src/)
-        #entry: pylint
-        #language: system
-        #types: [python]
-        #files: ^src/
-        #args:
-          #[
-            #"-rn", # Only display messages
-            #"-sn", # Don't display the score
-            #"--rcfile=src/.pylintrc",
-          #]
-#
-    # Analyze the tests code style and report code that doesn't adhere.
-  #- repo: local
-    #hooks:
-      #- id: pylint
-        #name: pylint (python files in tests/ and benchmarks/)
-        #entry: pylint
-        #language: system
-        #types: [python]
-        #files: ^(tests|benchmarks)/
-        #args:
-          #[
-            #"-rn", # Only display messages
-            #"-sn", # Don't display the score
-            #"--rcfile=tests/.pylintrc",
-          #]
-
-
-
-
-    # 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
-=======
       - id: check-github-workflows
         args: ["--verbose"]
   - repo: https://github.com/astral-sh/ruff-pre-commit
@@ -104,7 +54,6 @@ repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
     # Ruff version.
     rev: v0.2.1
->>>>>>> after updating
     hooks:
       - id: ruff-format
         name: Format code using ruff

.setup_dev.sh

@@ -0,0 +1,42 @@
+#!/usr/bin/env bash
+
+# This script should be run by new developers to install this package in
+# editable mode and configure their local environment
+
+echo "Checking virtual environment"
+if [ -z "${VIRTUAL_ENV}" ] && [ -z "${CONDA_PREFIX}" ]; then
+    echo 'No virtual environment detected: none of $VIRTUAL_ENV or $CONDA_PREFIX is set.'
+    echo
+    echo "=== This script is going to install the project in the system python environment ==="
+    echo "Proceed? [y/N]"
+    read -r RESPONCE
+    if [ "${RESPONCE}" != "y" ]; then
+        echo "See https://lincc-ppt.readthedocs.io/ for details."
+        echo "Exiting."
+        exit 1
+    fi
+
+fi
+
+echo "Checking pip version"
+MINIMUM_PIP_VERSION=22
+pipversion=( $(python -m pip --version | awk '{print $2}' | sed 's/\./ /g') )
+if let "${pipversion[0]}<${MINIMUM_PIP_VERSION}"; then
+    echo "Insufficient version of pip found. Requires at least version ${MINIMUM_PIP_VERSION}."
+    echo "See https://lincc-ppt.readthedocs.io/ for details."
+    exit 1
+fi
+
+echo "Installing package and runtime dependencies in local environment"
+python -m pip install -e . > /dev/null
+
+echo "Installing developer dependencies in local environment"
+python -m pip install -e .'[dev]' > /dev/null
+if [ -f docs/requirements.txt ]; then python -m pip install -r docs/requirements.txt; fi
+
+echo "Installing pre-commit"
+pre-commit install > /dev/null
+
+#######################################################
+# Include any additional configurations below this line
+#######################################################

docs/index.rst

@@ -7,38 +7,7 @@
 
 .. rubric:: :header_no_toc:`kcorrect documentation`
 
-<<<<<<< before updating
 Overview
-=========================
-=======
-.. code-block:: console
-
-   >> conda create env -n <env_name> python=3.10
-   >> conda activate <env_name>
-
-
-Once you have created a new environment, you can install this project for local
-development using the following commands:
-
-.. code-block:: console
-
-   >> pip install -e .'[dev]'
-   >> pre-commit install
-   >> conda install pandoc
-
-
-Notes:
-
-1) The single quotes around ``'[dev]'`` may not be required for your operating system.
-2) ``pre-commit install`` will initialize pre-commit for this local repository, so
-   that a set of tests will be run prior to completing a local commit. For more
-   information, see the Python Project Template documentation on
-   `pre-commit <https://lincc-ppt.readthedocs.io/en/latest/practices/precommit.html>`_.
-3) Installing ``pandoc`` allows you to verify that automatic rendering of Jupyter notebooks
-   into documentation for ReadTheDocs works as expected. For more information, see
-   the Python Project Template documentation on
-   `Sphinx and Python Notebooks <https://lincc-ppt.readthedocs.io/en/latest/practices/sphinx.html#python-notebooks>`_.
->>>>>>> after updating
 
 This page has documentation for the kcorrect product to calculate
 astronomical K-corrections for galaxies.

docs/requirements.txt

@@ -1,21 +1,8 @@
-<<<<<<< before updating
-#sphinx==6.1.3
-#sphinx-rtd-theme==1.2.0
-#sphinx-autoapi==2.0.1
-#astroid==2.15.7
-sphinx
-sphinx-rtd-theme
-sphinx-autoapi
-nbsphinx
-=======
-
-ipykernel
->>>>>>> after updating
 ipython
 jupytext
 nbconvert
 nbsphinx
 sphinx
 sphinx-autoapi
 sphinx-copybutton
-sphinx-rtd-theme
+sphinx-rtd-theme

pyproject.toml

@@ -16,14 +16,6 @@ classifiers = [
 dynamic = ["version"]
 requires-python = ">=3.9"
 dependencies = [
-<<<<<<< before updating
-    "ipykernel", # Support for Jupyter notebooks
-    "matplotlib>=3.5.2",
-    "numpy>=1.18.1",
-    "scipy>=1.8.1",
-    "astropy>=3.0.0"
-=======
->>>>>>> after updating
 ]
 
 [project.urls]
@@ -37,24 +29,22 @@ dev = [
     "pre-commit", # Used to run checks before finalizing a git commit
     "pytest",
     "pytest-cov", # Used to report total code coverage
-<<<<<<< before updating
-    "pre-commit", # Used to run checks before finalizing a git commit
-    "sphinx", # Used to automatically generate documentation
-    "sphinx-rtd-theme", # Used to render documentation
-    "sphinx-autoapi", # Used to automatically generate api documentation
-    "pylint", # Used for static linting of files
-    # if you add dependencies here while experimenting in a notebook and you
-    # want that notebook to render in your documentation, please add the
-    # dependencies to ./docs/requirements.txt as well.
-    # "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
-    "nbsphinx", # Used to integrate Python notebooks into Sphinx documentation
-    # "ipython", # Also used in building notebooks into Sphinx
-    "matplotlib", # Used in sample notebook intro_notebook.ipynb
-    "numpy", # Used in sample notebook intro_notebook.ipynb
-    "asv==0.5.1", # Used to compute performance benchmarks
-=======
+# before updating
+  #  "pre-commit", # Used to run checks before finalizing a git commit
+  #  "sphinx", # Used to automatically generate documentation
+  #  "sphinx-rtd-theme", # Used to render documentation
+  #  "sphinx-autoapi", # Used to automatically generate api documentation
+  #  "pylint", # Used for static linting of files
+  #  # if you add dependencies here while experimenting in a notebook and you
+  #  # want that notebook to render in your documentation, please add the
+  #  # dependencies to ./docs/requirements.txt as well.
+  #  # "nbconvert", # Needed for pre-commit check to clear output from Python notebooks
+  #  "nbsphinx", # Used to integrate Python notebooks into Sphinx documentation
+  #  # "ipython", # Also used in building notebooks into Sphinx
+  #  "matplotlib", # Used in sample notebook intro_notebook.ipynb
+  #  "numpy", # Used in sample notebook intro_notebook.ipynb
+  #  "asv==0.5.1", # Used to compute performance benchmarks
     "ruff", # Used for static linting of files
->>>>>>> after updating
 ]
 
 [build-system]