Merge overleaf-2024-06-17-1638 into main

PSTN-056.tex

@@ -1,5 +1,5 @@
 \documentclass[PST,authoryear,toc]{lsstdoc}
-\input{meta}
+%\input{meta}
 
 % Package imports go here.
 
@@ -42,7 +42,7 @@
 % Fields: VERSION, DATE, DESCRIPTION, OWNER NAME.
 % See LPM-51 for version number policy.
 \setDocChangeRecord{%
-  \addtohist{1}{YYYY-MM-DD}{Unreleased.}{federica bianco (she/her/hers)}
+  \addtohist{1}{YYYY-MM-DD}{Unreleased.}{Federica Bianco and the Survey Cadence Optimization Committee}
 }
 
 

lsst-texmf-main/.github/CONTRIBUTING.md

@@ -0,0 +1,5 @@
+Thank you for contributing to lsst-texmf!
+
+Please review our [developer documentation](https://lsst-texmf.lsst.io/developer.html) that covers updating the class and style files, bibliographies, examples, and documentation.
+
+https://lsst-texmf.lsst.io/developer.html

lsst-texmf-main/.github/workflows/ci.yaml

@@ -0,0 +1,116 @@
+name: CI
+
+on: [push, pull_request]
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install dependancies and linters
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install uv
+          python -m uv pip install --system pybtex
+          python -m uv pip install --system -r requirements.txt
+
+      - name: Run pybtex
+        run: make test-pybtex
+
+      - name: Run author check
+        run: make test-authors
+
+      - name: Run pytest
+        env:
+          PYTHONPATH: bin
+        run: pytest
+
+      - name: Run as test generateBibfile.py
+        run: |
+          bin/generateBibfile.py generated.bib
+          wc -l generated.bib
+
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install uv
+          python -m uv pip install --system -r docs/requirements.txt
+          python -m uv pip install --system ltd-conveyor
+
+      - name: Pull existing images
+        run: |
+          docker pull lsstsqre/lsst-texmf:base || true
+          docker pull lsstsqre/lsst-texmf:dependencies || true
+          docker pull lsstsqre/lsst-texmf:latest || true
+
+      - name: Build the base Docker image
+        run: |
+          DOCKER_BUILDKIT=1 docker build \
+            --build-arg BUILDKIT_INLINE_CACHE=1 \
+            --target base \
+            --cache-from=lsstsqre/lsst-texmf:base \
+            --tag lsstsqre/lsst-texmf:base .
+
+      - name: Build the dependencies Docker image
+        run: |
+          DOCKER_BUILDKIT=1 docker build \
+            --build-arg BUILDKIT_INLINE_CACHE=1 \
+            --target dependencies \
+            --cache-from=lsstsqre/lsst-texmf:dependencies \
+            --tag lsstsqre/lsst-texmf:dependencies .
+
+      - name: Build the runtime Docker image
+        run: |
+          DOCKER_BUILDKIT=1 docker build \
+            --build-arg BUILDKIT_INLINE_CACHE=1 \
+            --target runtime \
+            --cache-from=lsstsqre/lsst-texmf:latest \
+            --tag lsstsqre/lsst-texmf:latest .
+
+      - name: Compile test and example documents
+        run: |
+          docker run --rm -v `pwd`:/workspace -w /lsst-texmf lsstsqre/lsst-texmf:latest sh -c 'make all && cp *.pdf /workspace'
+
+      - name: Test generateAcronyms.py
+        run: |
+          docker run -w /lsst-texmf lsstsqre/lsst-texmf:latest sh -c "make test-acronyms"
+
+      - name: Compile documentation
+        run: |
+          make docs
+
+      - name: Upload documentation
+        if: ${{ github.event_name == 'push' }}
+        env:
+          LTD_PASSWORD: ${{ secrets.LTD_PASSWORD }}
+          LTD_USERNAME: ${{ secrets.LTD_USERNAME }}
+        run: |
+          ltd upload --product lsst-texmf --gh --dir docs/_build/html
+
+      - name: Log into Docker Hub
+        run: echo ${{ secrets.DOCKER_TOKEN }} | docker login --username ${{ secrets.DOCKER_USERNAME }} --password-stdin
+
+      - name: Push Docker images
+        if: ${{ github.ref == 'refs/heads/main' && github.event_name == 'push' }}
+        run: |
+          docker push lsstsqre/lsst-texmf:base
+          docker push lsstsqre/lsst-texmf:dependencies
+          docker push lsstsqre/lsst-texmf:latest

lsst-texmf-main/.github/workflows/dockercache.yaml

@@ -0,0 +1,41 @@
+# This workflow runs weekly. Its purpose is to rebuild the base Docker images
+# to get the latest security updates and versions of Python dependencies
+# (otherwise the regular CI workflow will continue to use the existing base
+# images).
+
+name: Refresh Docker cache
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 4 * * MON"
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Build the dependencies Docker image without caching
+        run: |
+          DOCKER_BUILDKIT=1 docker build \
+            --build-arg BUILDKIT_INLINE_CACHE=1 \
+            --target dependencies \
+            --no-cache \
+            --tag lsstsqre/lsst-texmf:dependencies .
+
+      - name: Build the base Docker image (for pushing as a separate tag)
+        run: |
+          DOCKER_BUILDKIT=1 docker build \
+            --build-arg BUILDKIT_INLINE_CACHE=1 \
+            --target base \
+            --tag lsstsqre/lsst-texmf:base .
+
+      - name: Log into Docker Hub
+        run: echo ${{ secrets.DOCKER_TOKEN }} | docker login --username ${{ secrets.DOCKER_USERNAME }} --password-stdin
+
+      - name: Push Docker images
+        run: |
+          docker push lsstsqre/lsst-texmf:base
+          docker push lsstsqre/lsst-texmf:dependencies

lsst-texmf-main/.github/workflows/formatting.yaml

@@ -0,0 +1,11 @@
+name: Check Python formatting
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/formatting.yaml@main

lsst-texmf-main/.github/workflows/generatebib.yaml

@@ -0,0 +1,68 @@
+name: generatebib
+
+on:
+  workflow_dispatch:
+  schedule:
+    #  UTC min hour day month dayOfWeek
+    - cron: '03 6 * * *'
+
+jobs:
+  bib:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install uv
+          python -m uv pip install --system pyyaml algoliasearch latexcodec pybtex
+
+      - name: Generate bibfile
+        run: |
+          wc -l texmf/bibtex/bib/lsst.bib
+          make lsst.bib
+          wc -l texmf/bibtex/bib/lsst.bib
+
+      - name: Check diff
+        run: | #  set an environment variable
+           if git diff --exit-code; then
+              echo "CHANGED=false" >> ${GITHUB_ENV}
+              echo "No changes - no PR"
+           else
+              echo "CHANGED=true" >> ${GITHUB_ENV}
+              echo "Git changes - should make PR"
+           fi
+
+      - name: Commit new bib
+        if: env.CHANGED == 'true'
+        run: |
+          git config user.name github-actions
+          git config user.email github-actions@github.com
+          git commit -m " generated lsst.bib " texmf/bibtex/bib/lsst.bib
+
+      - name: Create Pull Request
+        id: cpr
+        if: env.CHANGED == 'true'
+        uses: peter-evans/create-pull-request@v6
+        with:
+          token: ${{ secrets.WOM_UPDATEBIB_PAT }}
+          branch: update-bibfile
+          branch-suffix: short-commit-hash
+          title: Automatic bibfile  update
+          commit-message: bibfile update
+          body: Update bibfile from lsst.io and etc/static_entries.bib
+
+      - name: Enable Pull Request Automerge
+        if: steps.cpr.outputs.pull-request-operation == 'created'
+        uses: peter-evans/enable-pull-request-automerge@v3
+        with:
+          token: ${{ secrets.WOM_UPDATEBIB_PAT }}
+          pull-request-number: ${{ steps.cpr.outputs.pull-request-number }}
+          merge-method: merge

lsst-texmf-main/.github/workflows/lint.yaml

@@ -0,0 +1,16 @@
+name: lint
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/lint.yaml@main
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: chartboost/ruff-action@v1

lsst-texmf-main/.github/workflows/rebase_checker.yaml

@@ -0,0 +1,7 @@
+name: Check that 'main' is not merged into the development branch
+
+on: pull_request
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/rebase_checker.yaml@main

lsst-texmf-main/.github/workflows/yamllint.yaml

@@ -0,0 +1,25 @@
+name: Lint YAML Files
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  lint:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.11
+          cache: "pip"
+
+      - name: Install
+        run: pip install yamllint
+
+      - name: Run linter
+        run: yamllint .

lsst-texmf-main/Dockerfile

@@ -0,0 +1,56 @@
+# Dockerized lsst-texmf
+#
+# This is a multi-stage docker build composed of three images:
+# 1. "base" is an official Python image with additional system dependencies
+#    (such as texlive) installed via the "docker/install-base-packages.sh"
+#    script. Add additional apt-get dependencies through that script.
+# 2. "dependencies" installs the Python dependencies defined in
+#     requirements.txt.
+# 3. "runtime" is the final image for end users. It is based on the "base"
+#    image and includes both the Python depndencies and a copy of lsst-texmf.
+
+FROM python:3.7-slim-buster AS base
+
+# Copy a file to prevent docs from being installed
+COPY docker/01_nodoc /etc/dpkg/dpkg.cfg.d
+
+# Update system packages
+COPY docker/install-base-packages.sh .
+RUN ./install-base-packages.sh
+
+FROM base AS dependencies
+
+# Create a Python virtual environment
+ENV VIRTUAL_ENV=/opt/venv
+RUN python -m venv $VIRTUAL_ENV
+# Make sure we use the virtualenv
+ENV PATH="$VIRTUAL_ENV/bin:$PATH"
+# Put the latest pip and setuptools in the virtualenv
+RUN pip install --upgrade --quiet --no-cache-dir pip setuptools wheel
+# Install the Python runtime dependencies
+COPY requirements.txt .
+RUN pip install --quiet --no-cache-dir -r requirements.txt
+
+FROM base AS runtime
+
+# Create a directory for the lsst-texmf installation
+RUN mkdir lsst-texmf
+
+# Disable git safe directory checks, particularly for the /workspace
+# working directory that documents are mounted into.
+RUN git config --global --add safe.directory '*'
+
+# Point $TEXMFHOME to the container's lsst-texmf. This environment variable
+# exists for container runs by a user.
+ENV TEXMFHOME "/lsst-texmf/texmf"
+
+# Make sure we use the virtualenv; also add lsst-texmf's scripts to the path.
+ENV PATH="/lsst-texmf/bin:/opt/venv/bin:$PATH"
+
+# Install Python dependencies
+COPY --from=dependencies /opt/venv /opt/venv
+
+# Copy lsst-texmf repo in /lsst-texmf/
+COPY . /lsst-texmf
+
+CMD ["/bin/echo", "See https://lsst-texmf.lsst.io/docker.html for usage."]