Refactor for post-unblinding data taking

.github/dependabot.yml

@@ -0,0 +1,7 @@
+version: 2
+updates:
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"

.github/workflows/main.yml

@@ -0,0 +1,59 @@
+name: lgdo
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+      - "releases/**"
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  FORCE_COLOR: 3
+
+jobs:
+  build-and-test:
+    name: Test lgdo with Python
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.11", "3.12"]
+        os: [ubuntu-latest, macos-13]
+
+    steps:
+      - uses: actions/checkout@v4
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+      - name: Get dependencies and install legend-dataflow
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install --upgrade .[test]
+      - name: Run unit tests
+        run: |
+          python -m pytest
+
+  test-coverage:
+    name: Calculate and upload test coverage
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 2
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Generate Report
+        run: |
+          python -m pip install --upgrade pip wheel setuptools
+          python -m pip install --upgrade .[test]
+          python -m pytest --cov=legenddataflow --cov-report=xml
+      - name: Upload Coverage to codecov.io
+        uses: codecov/codecov-action@v5

.gitignore

@@ -1,3 +1,6 @@
+.snakemake
+workflow/src/legenddataflow/_version.py
+
 # New additions go at the top!
 *.c
 .DS_Store
@@ -10,6 +13,13 @@
 *~
 *.csv
 
+# uv
+uv.lock
+
+#prodenv_stuff
+inputs
+software
+generated
 
 # -------------------- github-generated stuff -------------------
 # Byte-compiled / optimized / DLL files
@@ -77,7 +87,7 @@ instance/
 .scrapy
 
 # Sphinx documentation
-/docs/build/
+/docs/_build/
 /docs/source/generated
 
 # PyBuilder
@@ -113,3 +123,5 @@ venv.bak/
 
 # mypy
 .mypy_cache/
+
+docs/source/api

.pre-commit-config.yaml

@@ -4,89 +4,103 @@ ci:
   autofix_commit_msg: "style: pre-commit fixes"
 
 repos:
-- repo: https://github.com/pre-commit/pre-commit-hooks
-  rev: "v5.0.0"
-  hooks:
-  - id: check-added-large-files
-  - id: check-case-conflict
-  - id: check-merge-conflict
-  - id: check-symlinks
-  - id: check-yaml
-  - id: check-json
-  - id: check-toml
-  - id: check-docstring-first
-  - id: debug-statements
-  - id: end-of-file-fixer
-  - id: forbid-new-submodules
-  - id: mixed-line-ending
-  - id: name-tests-test
-    args: ["--pytest-test-first"]
-  - id: requirements-txt-fixer
-  - id: trailing-whitespace
+  - repo: https://github.com/adamchainz/blacken-docs
+    rev: "1.19.1"
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==24.*]
 
-- repo: https://github.com/psf/black
-  rev: "24.10.0"
-  hooks:
-  - id: black-jupyter
-    args: ["--line-length", "99"]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: "v5.0.0"
+    hooks:
+      - id: check-added-large-files
+      - id: check-case-conflict
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-yaml
+      - id: check-json
+      - id: check-toml
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: end-of-file-fixer
+      - id: forbid-new-submodules
+      - id: mixed-line-ending
+      - id: name-tests-test
+        args: ["--pytest-test-first"]
+      - id: requirements-txt-fixer
+      - id: trailing-whitespace
 
-- repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: "v0.8.6"
-  hooks:
-    - id: ruff
-      args: ["--fix", "--show-fixes"]
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.8.6"
+    hooks:
+      - id: ruff
+        args: ["--fix", "--show-fixes"]
+      - id: ruff-format
 
-- repo: https://github.com/asottile/setup-cfg-fmt
-  rev: "v2.7.0"
-  hooks:
-  - id: setup-cfg-fmt
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: "v0.23"
+    hooks:
+      - id: validate-pyproject
+        additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
-- repo: https://github.com/pre-commit/mirrors-mypy
-  rev: "v1.14.1"
-  hooks:
-    - id: mypy
-      files: src
-      stages: [manual]
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: "0.30.0"
+    hooks:
+      - id: check-dependabot
+      - id: check-github-workflows
+      - id: check-readthedocs
 
-- repo: https://github.com/kynan/nbstripout
-  rev: "0.8.1"
-  hooks:
-    - id: nbstripout
-      args: ["--drop-empty-cells",
-             "--extra-keys", "metadata.kernelspec metadata.language_info"]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: "v1.14.1"
+    hooks:
+      - id: mypy
+        files: src
+        stages: [manual]
 
-- repo: https://github.com/mgedmin/check-manifest
-  rev: "0.50"
-  hooks:
-  - id: check-manifest
-    stages: [manual]
+  - repo: https://github.com/kynan/nbstripout
+    rev: "0.8.1"
+    hooks:
+      - id: nbstripout
+        args:
+          [
+            "--drop-empty-cells",
+            "--extra-keys",
+            "metadata.kernelspec metadata.language_info",
+          ]
 
-- repo: https://github.com/codespell-project/codespell
-  rev: "v2.3.0"
-  hooks:
-  - id: codespell
-    args: ["-L", "nd,unparseable,compiletime,livetime,fom,puls"]
+  - repo: https://github.com/mgedmin/check-manifest
+    rev: "0.50"
+    hooks:
+      - id: check-manifest
+        stages: [manual]
 
-- repo: https://github.com/shellcheck-py/shellcheck-py
-  rev: "v0.10.0.1"
-  hooks:
-  - id: shellcheck
+  - repo: https://github.com/codespell-project/codespell
+    rev: "v2.3.0"
+    hooks:
+      - id: codespell
+        args: ["-L", "nd,unparseable,compiletime,livetime,fom,puls"]
 
-- repo: https://github.com/pre-commit/pygrep-hooks
-  rev: "v1.10.0"
-  hooks:
-  - id: rst-backticks
-  - id: rst-directive-colons
-  - id: rst-inline-touching-normal
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: "v0.10.0.1"
+    hooks:
+      - id: shellcheck
 
-- repo: https://github.com/pre-commit/mirrors-prettier
-  rev: "v4.0.0-alpha.8"
-  hooks:
-    - id: prettier
-      types_or: [json]
+  - repo: https://github.com/pre-commit/pygrep-hooks
+    rev: "v1.10.0"
+    hooks:
+      - id: rst-backticks
+      - id: rst-directive-colons
+      - id: rst-inline-touching-normal
 
-- repo: https://github.com/snakemake/snakefmt
-  rev: v0.10.2
-  hooks:
-    - id: snakefmt
-      files: Snakefile*|\.smk
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v4.0.0-alpha.8"
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown, json, toml]
+
+  - repo: https://github.com/snakemake/snakefmt
+    rev: v0.10.2
+    hooks:
+      - id: snakefmt
+        files: Snakefile*|\.smk
+        exclude: channel_merge.smk

.readthedocs.yaml

@@ -0,0 +1,23 @@
+version: 2
+
+build:
+  os: "ubuntu-22.04"
+  tools:
+    python: "3.12"
+  commands:
+    # FIXME: dependencies should not be explicitly listed here!
+    - asdf plugin add uv
+    - asdf install uv latest
+    - asdf global uv latest
+    - uv venv
+    - uv pip install .[docs]
+    - rm -rf docs/source/api
+    - .venv/bin/python -m sphinx.ext.apidoc
+      --private
+      --module-first
+      --force
+      --output-dir docs/source/api
+      workflow/src
+      workflow/rules
+    - .venv/bin/python -m sphinx -T -b html -d docs/_build/doctrees -D
+      language=en docs/source $READTHEDOCS_OUTPUT/html

.ruff.toml

@@ -12,7 +12,7 @@ lint.select = [
   "PIE",         # flake8-pie
   "PL",          # pylint
   "PT",          # flake8-pytest-style
-  # "PTH",         # flake8-use-pathlib
+  "PTH",         # flake8-use-pathlib
   "RET",         # flake8-return
   "RUF",         # Ruff-specific
   "SIM",         # flake8-simplify
@@ -29,7 +29,6 @@ lint.extend-ignore = [
   "G004",   # Logging statement uses f-string
   "PLR",    # Design related pylint codes
   "E501",   # Line too long
-  "PT004",  # Use underscore for non-returning fixture (use usefixture instead)
   "RET505", # Unnecessary `else` after `return` statement
   "E402", # Module level imports at top of file need disable for numba default imports
   "NPY201", # Numpy 2 warnings ignore for the moment

LICENSE.md

@@ -1,9 +1,11 @@
-The legend-dataflow-hades package is licensed under the MIT "Expat" License:
+The legend-dataflow package is licensed under the MIT "Expat" License:
 
 > Copyright (c) 2021:
 >
->    Matteo Agostini <[email protected]>
->    Oliver Schulz <[email protected]>
+> Matteo Agostini <[email protected]>
+> Oliver Schulz <[email protected]>
+> George Marshall <[email protected]>
+> Luigi Pertoldi <[email protected]>
 >
 > Permission is hereby granted, free of charge, to any person obtaining a copy
 > of this software and associated documentation files (the "Software"), to deal
@@ -22,4 +24,3 @@ The legend-dataflow-hades package is licensed under the MIT "Expat" License:
 > LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 > OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 > SOFTWARE.
->