Initial code and docs commit

.github/pull_request_template.md

@@ -0,0 +1,4 @@
+## Checklist
+
+- [ ] ran Jenkins
+- [ ] added a release note for user-visible changes to `doc/changes`

.github/workflows/build.yaml

@@ -0,0 +1,55 @@
+name: build_and_test
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "*"
+  pull_request:
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # Need to clone everything for the git tags.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "setup.cfg"
+
+      - name: Install yaml
+        run: sudo apt-get install libyaml-dev
+
+      - name: Install prereqs for setuptools
+        run: pip install wheel
+
+      # We have two cores so we can speed up the testing with xdist
+      - name: Install xdist, openfiles and flake8 for pytest
+        run: >
+          pip install pytest-xdist pytest-openfiles pytest-flake8
+          pytest-cov "flake8<5"
+
+      - name: Build and install
+        run: pip install -v -e .
+
+      - name: Install documenteer
+        run: pip install 'documenteer[pipelines]<0.7'
+
+      - name: Run tests
+        run: >
+          pytest -r a -v -n 3 --open-files --cov=tests
+          --cov=lsst.rubintv.analysis.service
+          --cov-report=xml --cov-report=term
+          --doctest-modules --doctest-glob="*.rst"
+
+      - name: Upload coverage to codecov
+        uses: codecov/codecov-action@v2
+        with:
+          file: ./coverage.xml

.github/workflows/build_docs.yaml

@@ -0,0 +1,41 @@
+name: docs
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  build_sphinx_docs:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+        with:
+          # Need to clone everything for the git tags.
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: "3.10"
+          cache: "pip"
+          cache-dependency-path: "setup.cfg"
+
+      - name: Update pip/wheel infrastructure
+        run: |
+          python -m pip install --upgrade pip
+          pip install wheel
+
+      - name: Build and install
+        run: pip install -v -e .
+
+      - name: Show compiled files
+        run: ls python/lsst/rubintv/analysis/service
+
+      - name: Install documenteer
+        run: pip install 'documenteer[pipelines]<0.7'
+
+      - name: Build documentation
+        working-directory: ./doc
+        run: package-docs build

.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

.github/workflows/lint.yaml

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

.github/workflows/yamllint.yaml

@@ -0,0 +1,11 @@
+name: Lint YAML Files
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+jobs:
+  call-workflow:
+    uses: lsst/rubin_workflows/.github/workflows/yamllint.yaml@main

.pre-commit-config.yaml

@@ -0,0 +1,32 @@
+repos:
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-yaml
+        args:
+          - "--unsafe"
+      - id: end-of-file-fixer
+      - id: trailing-whitespace
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    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: python3.10
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        name: isort (python)
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8

doc/.gitignore

@@ -0,0 +1,10 @@
+# Doxygen products
+html
+xml
+*.tag
+*.inc
+doxygen.conf
+
+# Sphinx products
+_build
+py-api

doc/SConscript

@@ -0,0 +1,3 @@
+# -*- python -*-
+from lsst.sconsUtils import scripts
+scripts.BasicSConscript.doc()

doc/conf.py

@@ -0,0 +1,12 @@
+"""Sphinx configuration file for an LSST stack package.
+This configuration only affects single-package Sphinx documentation builds.
+For more information, see:
+https://developer.lsst.io/stack/building-single-package-docs.html
+"""
+
+from documenteer.conf.pipelinespkg import *
+
+project = "rubintv_analysis_service"
+html_theme_options["logotext"] = project
+html_title = project
+html_short_title = project

doc/index.rst

@@ -0,0 +1,12 @@
+##############################################
+rubintv_analysis_service documentation preview
+##############################################
+
+.. This page is for local development only. It isn't published to pipelines.lsst.io.
+
+.. Link the index pages of package and module documentation directions (listed in manifest.yaml).
+
+.. toctree::
+   :maxdepth: 1
+
+   lsst.rubintv.analysis.service/index

doc/lsst.rubintv.analysis.service/index.rst

@@ -0,0 +1,40 @@
+.. py:currentmodule:: lsst.rubintv.analysis.service
+
+.. _lsst.rubintv.analysis.service:
+
+#############################
+lsst.rubintv.analysis.service
+#############################
+
+.. Paragraph that describes what this Python module does and links to related modules and frameworks.
+
+.. _lsst.rubintv.analysis.service-using:
+
+Using lsst.rubintv.analysis.service
+=======================
+
+toctree linking to topics related to using the module's APIs.
+
+.. toctree::
+   :maxdepth: 2
+
+.. _lsst.rubintv.analysis.service-contributing:
+
+Contributing
+============
+
+``lsst.rubintv.analysis.service`` is developed at https://github.com/lsst-ts/rubintv_analysis_service.
+
+.. If there are topics related to developing this module (rather than using it), link to this from a toctree placed here.
+
+.. .. toctree::
+..    :maxdepth: 2
+
+.. _lsst.rubintv.analysis.service-pyapi:
+
+Python API reference
+====================
+
+.. automodapi:: lsst.rubintv.analysis.service
+   :no-main-docstr:
+   :no-inheritance-diagram:

doc/manifest.yaml

@@ -0,0 +1,12 @@
+# Documentation manifest.
+
+# List of names of Python modules in this package.
+# For each module there is a corresponding module doc subdirectory.
+modules:
+  - "lsst.rubintv.analysis.service"
+
+# Name of the static content directories (subdirectories of `_static`).
+# Static content directories are usually named after the package.
+# Most packages do not need a static content directory (leave commented out).
+# statics:
+#   - "_static/example_standalone"

mypy.ini

@@ -0,0 +1,22 @@
+[mypy]
+warn_unused_configs = True
+warn_redundant_casts = True
+plugins = pydantic.mypy
+
+[mypy-astropy.*]
+ignore_missing_imports = True
+
+[mypy-matplotlib.*]
+ignore_missing_imports = True
+
+[mypy-numpy.*]
+ignore_missing_imports = True
+
+[mypy-scipy.*]
+ignore_missing_imports = True
+
+[mypy-sqlalchemy.*]
+ignore_missing_imports = True
+
+[mypy-yaml.*]
+ignore_missing_imports = True

pyproject.toml

@@ -30,7 +30,9 @@ dependencies = [
     "scipy",
     "matplotlib",
     "pydantic",
-    "pyyaml"
+    "pyyaml",
+    "sqlalchemy",
+    "astropy",
 ]
 #dynamic = ["version"]
 
@@ -65,9 +67,6 @@ line_length = 110
 [tool.lsst_versions]
 write_to = "python/lsst/rubintv/analysis/service/version.py"
 
-[tool.pytest.ini_options]
-addopts = "--flake8"
-flake8-ignore = ["W503", "E203"]
 # The matplotlib test may not release font files.
 open_files_ignore = ["*.ttf"]
 

python/lsst/__init__.py

@@ -1,3 +1,3 @@
 import pkgutil
 
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__ = pkgutil.extend_path(__path__, __name__)

python/lsst/rubintv/__init__.py

@@ -1,3 +1,3 @@
 import pkgutil
 
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__ = pkgutil.extend_path(__path__, __name__)

python/lsst/rubintv/analysis/__init__.py

@@ -1,3 +1,3 @@
 import pkgutil
 
-__path__ = pkgutil.extend_path(__path__, __name__)
+__path__ = pkgutil.extend_path(__path__, __name__)

python/lsst/rubintv/analysis/service/__init__.py

@@ -0,0 +1 @@
+from . import command, database, query