OPSIM-1079: Update pyproject.toml and workflows

.github/workflows/python-docs-only.yml → .github/workflows/build_docs.yaml

@@ -1,59 +1,67 @@
-name: Build and Push Documentation
+name: Build and Upload Docs
 
-on:
-  release:
-    types:
-      - created
+"on":
+  push:
+    tags:
+      - "*"
+    branches:
+      - "main"
+  pull_request: {}
   workflow_dispatch:
 
 jobs:
-  Docs:
-    name: Build and push documentation
-    runs-on: "ubuntu-latest"
+  build_sphinx_docs:
+    name: Build and upload documentation
+    runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: "3.10"
-          channels: conda-forge,defaults
+          python-version: "3.11"
+          channels: conda-forge
           channel-priority: strict
           show-channel-urls: true
-      - name: configure and install conda and requirements
+
+      - name: configure and install requirements and documenteer
         shell: bash -l {0}
         run: |
           conda config --set always_yes yes
           conda install --quiet --file=requirements.txt
-          conda install lsst-documenteer-pipelines
+          conda install --quiet pip
+          pip install "documenteer[guide]"
+
       - name: install rubin_sim
         shell: bash -l {0}
         run: |
           echo `pwd`
           ls ${{ github.workspace }}
           python -m pip install .
+
       - name: download rubin_sim_data components needed to set up metrics for metricList
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}
           rs_download_data --tdqm_disable -d 'maf,throughputs'
-      - name: conda list
+
+      - name: check conda and documenteer
         shell: bash -l {0}
-        run: conda list
-      - name: build documentation
+        run: |
+          conda list
+
+      - name: build docs
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}
           cd doc
           python metric_list.py
-          make html
-      - name: Install LTD Conveyor
-        shell: bash -l {0}
-        run: |
-          python -m pip install ltd-conveyor        
+          package-docs build
+
       - name: upload documentation
-        shell: bash -l {0}
-        env:
-          LTD_PASSWORD: ${{ secrets.LTD_PASSWORD }}
-          LTD_USERNAME: ${{ secrets.LTD_USERNAME }}
-        run: |
-          ltd upload --gh --dir doc/_build/html --product rubin-sim
+        uses: lsst-sqre/ltd-upload@v1
+        with:
+          project: "rubin-sim"
+          dir: "docs/_build/html"
+          username: ${{ secrets.ltd_username }}
+          password: ${{ secrets.ltd_password }}
+

.github/workflows/build_pypi.yml

@@ -0,0 +1,89 @@
+name: Build and Publish PyPI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+
+jobs:
+  tests:
+    name: Check Tests (${{ matrix.python-version }}, ${{ matrix.os }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: ["ubuntu-latest"]
+        python-version: ["3.11"]
+    steps:
+      - uses: actions/checkout@v4
+      - uses: conda-incubator/setup-miniconda@v2
+        with:
+          python-version: ${{ matrix.python-version }}
+          auto-update-conda: true
+          channels: conda-forge,defaults
+          miniforge-variant: Mambaforge
+          use-mamba: true
+          channel-priority: strict
+          show-channel-urls: true
+
+      - name: configure conda and install requirements
+        shell: bash -l {0}
+        run: |
+          mamba config --set always_yes yes
+          mamba install --quiet --file=requirements.txt
+          mamba install --quiet --file=test-requirements.txt
+
+      - name: install rubin_sim
+        shell: bash -l {0}
+        run: |
+          echo `pwd`
+          python -m pip install .
+
+      - name: conda list
+        shell: bash -l {0}
+        run: conda list
+
+      - name: run unit tests
+        shell: bash -l {0}
+        run: |
+          pytest -r a -v --cov=rubin_sim --cov=tests --cov-report=xml --cov-report=term --cov-branch
+
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v2
+        with:
+          file: coverage.xml
+
+  pypi:
+    name: Build and upload to PyPI
+    runs-on: ubuntu-latest
+    needs: [tests]
+    if: startsWith(github.ref, 'refs/tags/')
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          # Need to clone everything to embed the version.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.11
+          cache: "pip"
+
+      - name: Install dependencies for build
+        run: |
+          python -m pip install --upgrade pip
+          pip install --upgrade setuptools build
+
+      - name: Build and create distribution
+        run: |
+          python -m build --skip-dependency-check
+
+      - name: Upload to lsst-sp PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          user: __token__
+          password: ${{ secrets.SP_PYPI_UPLOADS }}

.github/workflows/ruff.yaml

@@ -0,0 +1,24 @@
+name: Ruff and iSort
+on:
+  # Trigger the workflow on push (to main) or pull request
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  workflow_dispatch:
+
+jobs:
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: isort/isort-action@v1
+        with:
+          requirements-files: "requirements.txt test-requirements.txt"
+  ruff:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - uses: chartboost/ruff-action@v1

.github/workflows/python-all-tests.yml → .github/workflows/run_all_tests.yaml

@@ -1,4 +1,4 @@
-name: Run All Tests
+name: Run All of the Tests
 
 on:
   push:
@@ -16,39 +16,50 @@ jobs:
       fail-fast: True
       matrix:
         os: ["ubuntu-latest-8-cores"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
-
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           channels: conda-forge,defaults
+          miniforge-variant: Mambaforge
+          use-mamba: true
           channel-priority: strict
           show-channel-urls: true
+
       - name: configure conda and install requirements
         shell: bash -l {0}
         run: |
-          conda config --set always_yes yes
-          conda install --quiet --file=requirements.txt
-          conda install --quiet --file=test-requirements.txt
+          mamba config --set always_yes yes
+          mamba install --quiet --file=requirements.txt
+          mamba install --quiet --file=test-requirements.txt
+
       - name: install rubin_sim
         shell: bash -l {0}
         run: |
           echo `pwd`
           ls ${{ github.workspace }}
           python -m pip install .
+
       - name: download rubin_sim_data components needed for unit tests
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}/data_dir
           rs_download_data --force --tdqm_disable
+
       - name: conda list
         shell: bash -l {0}
         run: conda list
+
       - name: run tests
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}/data_dir
-          pytest
+          pytest -r a -v --cov=rubin_sim --cov=tests --cov-report=xml --cov-report=term --cov-branch
+
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v2
+        with:
+          file: coverage.xml

.github/workflows/python-tests-doc.yml → .github/workflows/run_tests_docs.yaml

@@ -18,54 +18,60 @@ jobs:
       fail-fast: false
       matrix:
         os: ["ubuntu-latest", "macos-latest"]
-        python-version: ["3.10"]
+        python-version: ["3.11"]
     steps:
-      - uses: actions/checkout@v3
-
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
           python-version: ${{ matrix.python-version }}
           channels: conda-forge,defaults
+          miniforge-variant: Mambaforge
+          use-mamba: true
           channel-priority: strict
           show-channel-urls: true
+
       - name: configure conda and install requirements
         shell: bash -l {0}
         run: |
-          conda config --set always_yes yes
-          conda install --quiet --file=requirements.txt
-          conda install --quiet --file=test-requirements.txt
+          mamba config --set always_yes yes
+          mamba install --quiet --file=requirements.txt
+          mamba install --quiet --file=test-requirements.txt
+
       - name: install rubin_sim
         shell: bash -l {0}
         run: |
           echo `pwd`
           ls ${{ github.workspace }}
           python -m pip install .
+
       - name: download rubin_sim_data components needed for unit tests
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}/data_dir
           rs_download_data --tdqm_disable -d 'site_models,throughputs,skybrightness,skybrightness_pre'
           rs_download_data --tdqm_disable -d tests --force
+
       - name: conda list
         shell: bash -l {0}
         run: conda list
+
       - name: run tests
         shell: bash -l {0}
         run: |
           export RUBIN_SIM_DATA_DIR=${{ github.workspace }}/data_dir
-          pytest
+          pytest -r a -v
 
   Docs:
     name: Build and push documentation
     needs: Tests
     runs-on: "macos-latest"
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: conda-incubator/setup-miniconda@v2
         with:
           auto-update-conda: true
-          python-version: "3.10"
+          python-version: "3.11"
           channels: conda-forge,defaults
           channel-priority: strict
           show-channel-urls: true

.pre-commit-config.yaml

@@ -1,5 +1,27 @@
 repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+      - id: check-toml
   - repo: https://github.com/psf/black
     rev: 23.7.0
     hooks:
       - id: black
+        # It is recommended to specify the latest version of Python
+        # supported by your project here, or alternatively use
+        # pre-commit's default_language_version, see
+        # https://pre-commit.com/#top_level-default_language_version
+        language_version: python3.11
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    # Ruff version.
+    rev: v0.0.278
+    hooks:
+      - id: ruff