Install (#93)

* Update env

* Update docs

* Fix tests

* Formatting

* style: pre-commit fixes

* Clean up CI

* Pre commit

* style: pre-commit fixes

* No sync

---------

Co-authored-by: Alec Thomson <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: 3 people

.github/dependabot.yml

@@ -1,13 +1,11 @@
-# To get started with Dependabot version updates, you'll need to specify which
-# package ecosystems to update and where the package manifests are located.
-# Please see the documentation for all configuration options:
-# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
-
 version: 2
 updates:
-  - package-ecosystem: "pip" # See documentation for possible values
-    directory: "/" # Location of package manifests
+  # Maintain dependencies for GitHub Actions
+  - package-ecosystem: "github-actions"
+    directory: "/"
     schedule:
       interval: "weekly"
-    reviewers:
-      - "AlecThomson"
+    groups:
+      actions:
+        patterns:
+          - "*"

.github/release.yml

@@ -0,0 +1,5 @@
+changelog:
+  exclude:
+    authors:
+      - dependabot
+      - pre-commit-ci

.github/workflows/ci.yml

@@ -0,0 +1,78 @@
+name: CI
+
+on:
+  workflow_dispatch:
+  pull_request:
+  push:
+    branches:
+      - main
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+env:
+  # Many color libraries just need this to be set to any value, but at least
+  # one distinguishes color depth, where "3" -> "256-bit color".
+  FORCE_COLOR: 3
+  # Jupyter is migrating its paths to use standard platformdirs
+  # given by the platformdirs library.  To remove this warning and
+  # see the appropriate new directories, set the environment variable
+  # `JUPYTER_PLATFORM_DIRS=1` and then run `jupyter --paths`.
+  # The use of platformdirs will be the default in `jupyter_core` v6
+  JUPYTER_PLATFORM_DIRS: 1
+
+jobs:
+  pre-commit:
+    name: Format
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --hook-stage manual --all-files
+
+  checks:
+    name: Check Python ${{ matrix.python-version }} on ${{ matrix.runs-on }}
+    runs-on: ${{ matrix.runs-on }}
+    needs: [pre-commit]
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.10", "3.11", "3.12", "3.13"]
+        runs-on: [ubuntu-latest]
+
+    steps:
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          allow-prereleases: true
+
+      - name: Install package
+        run: python -m pip install uv && uv pip install .[dev] --system
+
+      - name: Test package
+        run: >-
+          python -m pytest -ra --cov --cov-report=xml --cov-report=term
+          --durations=20 --junitxml=junit.xml -o junit_family=legacy --ignore=submit
+
+      - name: Upload coverage reports to Codecov
+        uses: codecov/codecov-action@v5
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}
+          slug: AlecThomson/arrakis
+
+      - name: Upload test results to Codecov
+        if: ${{ !cancelled() }}
+        uses: codecov/test-results-action@v1
+        with:
+          token: ${{ secrets.CODECOV_TOKEN }}

.github/workflows/mirror.yml

@@ -4,13 +4,13 @@ ci:
 
 repos:
   - repo: https://github.com/adamchainz/blacken-docs
-    rev: "1.19.1"
+    rev: "1.20.0"
     hooks:
       - id: blacken-docs
         additional_dependencies: [black==24.*]
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: "v5.0.0"
+    rev: "v6.0.0"
     hooks:
       - id: check-added-large-files
       - id: check-case-conflict
@@ -33,7 +33,7 @@ repos:
       - id: rst-inline-touching-normal
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: "v0.12.3"
+    rev: "v0.13.0"
     hooks:
       - id: ruff
         args: ["--fix", "--show-fixes"]
@@ -54,7 +54,7 @@ repos:
         additional_dependencies: ["validate-pyproject-schema-store[all]"]
 
   - repo: https://github.com/python-jsonschema/check-jsonschema
-    rev: "0.33.2"
+    rev: "0.33.3"
     hooks:
       - id: check-dependabot
       - id: check-github-workflows

.github/workflows/python-app.yml

@@ -6,9 +6,9 @@
 import argparse
 import logging
 import os
+from collections.abc import Callable
 from pathlib import Path
 from pprint import pformat
-from typing import Callable
 from typing import NamedTuple as Struct
 from urllib.error import URLError
 

.pre-commit-config.yaml

@@ -12,6 +12,7 @@
 from pathlib import Path
 from pprint import pformat
 from typing import NamedTuple as Struct
+from typing import overload
 
 import astropy.units as u
 import numpy as np
@@ -216,9 +217,21 @@ def genparset(
     return parset_file
 
 
+@overload
+def linmos(
+    parset: None, fieldname: str, image: str, holofile: Path | None = None
+) -> None: ...
+
+
+@overload
+def linmos(
+    parset: str, fieldname: str, image: str, holofile: Path | None = None
+) -> pymongo.UpdateOne: ...
+
+
 @task(name="Run linmos")
 def linmos(
-    parset: str | None, fieldname: str, image: str, holofile: Path
+    parset: str | None, fieldname: str, image: str, holofile: Path | None = None
 ) -> pymongo.UpdateOne | None:
     """Run linmos
 
@@ -248,12 +261,15 @@ def linmos(
     log_file = parset.replace(".in", ".log")
     linmos_command = shlex.split(f"linmos -c {parset}")
 
-    holo_folder = holofile.parent
+    bind_dir_str = f"{rootdir}:{rootdir}"
+    if holofile is not None:
+        holo_folder = holofile.parent
+        bind_dir_str += f",{holo_folder}:{holo_folder}"
 
     output = sclient.execute(
         image=image,
         command=linmos_command,
-        bind=f"{rootdir}:{rootdir},{holo_folder}:{holo_folder}",
+        bind=bind_dir_str,
         return_result=True,
         quiet=False,
         stream=True,

arrakis/frion.py

@@ -8,9 +8,10 @@
 import os
 import time
 import warnings
+from collections.abc import Callable
 from pathlib import Path
 from pprint import pformat
-from typing import Callable, NamedTuple
+from typing import NamedTuple
 
 import astropy.units as u
 import dask.dataframe as dd