Copier update and better readme links. (#60)

* Better readme links. * Copier update
astronomy-commons · Nov 6, 2023 · b44d539 · b44d539
1 parent d9e03f7
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Showing 9 changed files with 43 additions and 42 deletions.
diff --git a/.copier-answers.yml b/.copier-answers.yml
@@ -1,5 +1,5 @@
 # Changes here will be overwritten by Copier
-_commit: v1.4.3
+_commit: v1.4.4
 _src_path: gh:lincc-frameworks/python-project-template
 author_email: [email protected]
 author_name: LINCC Frameworks
@@ -13,5 +13,6 @@ package_name: lsdb
 preferred_linter: pylint
 project_license: BSD
 project_name: lsdb
+project_organization: astronomy-commons
 use_gitlfs: none
 use_isort: true
diff --git a/.github/workflows/asv-main.yml b/.github/workflows/asv-main.yml
@@ -66,7 +66,7 @@ jobs:
         run: |
           sudo apt-get update
           python -m pip install --upgrade pip
-          pip install asv==0.5.1 virtualenv tabulate
+          pip install asv==0.6.1 virtualenv tabulate
 
       - name: Configure git
         run: |
@@ -86,7 +86,7 @@ jobs:
           fi
 
       - name: Run ASV for the main branch
-        run: asv run ALL --skip-existing
+        run: asv run ALL --skip-existing --verbose
 
       - name: Submit new results to the "benchmarks" branch
         uses: JamesIves/github-pages-deploy-action@v4

diff --git a/.github/workflows/asv-nightly.yml b/.github/workflows/asv-nightly.yml
@@ -7,7 +7,8 @@ name: Run benchmarks nightly job
 on:
   schedule:
     - cron: 45 6 * * *
-
+  workflow_dispatch:
+
 env:
   PYTHON_VERSION: "3.10"
   WORKING_DIR: ${{ github.workspace }}/benchmarks
@@ -43,7 +44,7 @@ jobs:
         run: |
           sudo apt-get update
           python -m pip install --upgrade pip
-          pip install asv==0.5.1 virtualenv
+          pip install asv==0.6.1 virtualenv
 
       - name: Create ASV machine config file
         run: asv machine --machine gh-runner --yes
@@ -67,8 +68,8 @@ jobs:
 
           if [ -f $HASH_FILE ]; then          
             PREV_HASH=$(cat $HASH_FILE)
-            asv continuous $PREV_HASH $CURRENT_HASH || true
-            asv compare $PREV_HASH $CURRENT_HASH --sort ratio
+            asv continuous $PREV_HASH $CURRENT_HASH --verbose || true
+            asv compare $PREV_HASH $CURRENT_HASH --sort ratio --verbose
           fi
 
           echo $CURRENT_HASH > $HASH_FILE

diff --git a/.github/workflows/asv-pr.yml b/.github/workflows/asv-pr.yml
@@ -61,7 +61,7 @@ jobs:
         run: |
           sudo apt-get update
           python -m pip install --upgrade pip
-          pip install asv==0.5.1 virtualenv tabulate lf-asv-formatter
+          pip install asv==0.6.1 virtualenv tabulate lf-asv-formatter
 
       - name: Get current job logs URL
         uses: Tiryoh/gha-jobid-action@v0
@@ -77,31 +77,25 @@ jobs:
         run: |
           git remote add upstream https://github.com/${{ github.repository }}.git
           git fetch upstream
-          asv continuous upstream/main HEAD || true
-          asv compare upstream/main HEAD --sort ratio | tee output
-          python -m lf_asv_formatter
+          asv continuous upstream/main HEAD --verbose || true
+          asv compare upstream/main HEAD --sort ratio --verbose | tee output
+          python -m lf_asv_formatter --asv_version "$(echo asv --version)"
           printf "\n\nClick [here]($STEP_URL) to view all benchmarks." >> output
         env:
           STEP_URL: "${{ steps.jobs.outputs.html_url }}#step:8:1"
 
-      - name: Publish comment to PR
-        uses: actions/github-script@v6
+      - name: Find benchmarks comment
+        uses: peter-evans/find-comment@v2
+        id: find-comment
         with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          script: |
-            const fs = require('fs');
-            const path = require('path');
-
-            const workingDir = process.env.WORKING_DIR;
-            try {
-              process.chdir(workingDir);
-              const comment = fs.readFileSync('output', 'utf-8');
-              const { data } = await github.rest.issues.createComment({
-                ...context.repo,
-                issue_number: context.issue.number,
-                body: comment,
-              });
-              console.log('Comment published:', data.html_url);
-            } catch (err) {
-              console.error(err);
-            }
+          issue-number: ${{ github.event.pull_request.number }}
+          comment-author: 'github-actions[bot]'
+          body-includes: view all benchmarks
+
+      - name: Create or update benchmarks comment
+        uses: peter-evans/create-or-update-comment@v3
+        with:
+          comment-id: ${{ steps.find-comment.outputs.comment-id }}
+          issue-number: ${{ github.event.pull_request.number }}
+          body-path: ${{ env.WORKING_DIR }}/output
+          edit-mode: replace
diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml
@@ -33,3 +33,4 @@ jobs:
       run: |
         pylint -rn -sn --recursive=y ./src --rcfile=./src/.pylintrc
         pylint -rn -sn --recursive=y ./tests --rcfile=./tests/.pylintrc
+        pylint -rn -sn --recursive=y ./benchmarks --rcfile=./tests/.pylintrc
diff --git a/.github/workflows/publish-to-pypi.yml b/.github/workflows/publish-to-pypi.yml
@@ -1,5 +1,5 @@
 # This workflow will upload a Python Package using Twine when a release is created
-# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python#publishing-to-package-registries
+# 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
@@ -19,7 +19,8 @@ jobs:
   deploy:
 
     runs-on: ubuntu-latest
-
+    permissions:
+      id-token: write
     steps:
     - uses: actions/checkout@v3
     - name: Set up Python
@@ -33,7 +34,4 @@ jobs:
     - name: Build package
       run: python -m build
     - name: Publish package
-      uses: pypa/gh-action-pypi-publish@27b31702a0e7fc50959f5ad993c78deac1bdfc29
-      with:
-        user: __token__
-        password: ${{ secrets.PYPI_API_TOKEN }}
+      uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/README.md b/README.md
@@ -5,9 +5,11 @@
 
 [![Template](https://img.shields.io/badge/Template-LINCC%20Frameworks%20Python%20Project%20Template-brightgreen)](https://lincc-ppt.readthedocs.io/en/latest/)
 
-[![GitHub release (latest SemVer)](https://img.shields.io/github/v/release/astronomy-commons/lsdb)](https://pypi.org/project/lsdb/)
-![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/astronomy-commons/lsdb/testing-and-coverage.yml)
-[![Read the Docs](https://img.shields.io/readthedocs/lsdb)](https://lsdb.readthedocs.io/en/latest/)
+[![PyPI](https://img.shields.io/pypi/v/lsdb?color=blue&logo=pypi&logoColor=white)](https://pypi.org/project/lsdb/)
+[![GitHub Workflow Status](https://img.shields.io/github/actions/workflow/status/astronomy-commons/lsdb/smoke-test.yml)](https://github.com/astronomy-commons/lsdb/actions/workflows/smoke-test.yml)
+[![codecov](https://codecov.io/gh/astronomy-commons/lsdb/branch/main/graph/badge.svg)](https://codecov.io/gh/astronomy-commons/lsdb)
+[![Read the Docs](https://img.shields.io/readthedocs/lsdb)](https://lsdb.readthedocs.io/)
+[![benchmarks](https://img.shields.io/github/actions/workflow/status/astronomy-commons/lsdb/asv-main.yml?label=benchmarks)](https://astronomy-commons.github.io/lsdb/)
 
 ## LSDB - Large Survey DataBase
 

diff --git a/docs/index.rst b/docs/index.rst
@@ -36,7 +36,7 @@ Notes:
    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) Install ``pandoc`` allows you to verify that automatic rendering of Jupyter notebooks
+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>`_.

diff --git a/pyproject.toml b/pyproject.toml
@@ -42,9 +42,13 @@ dev = [
     "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
+    "asv==0.6.1", # Used to compute performance benchmarks
 ]
 
+[metadata]
+long_description = { file = "README.md" }
+url = "https://github.com/astronomy-commons/lsdb"
+
 [build-system]
 requires = [
     "setuptools>=62", # Used to build and package the Python project