Merge pull request #346 from HERA-Team/fix-for-release

maint: use pypi version of hera-calibration

.github/workflows/publish.yaml

@@ -12,6 +12,8 @@ jobs:
   build-n-publish:
     name: Build and publish to PyPI
     runs-on: ubuntu-latest
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
     steps:
       - uses: actions/checkout@main
         with:
@@ -32,6 +34,3 @@ jobs:
       - name: Publish to PyPI
         if: startsWith(github.event.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@v1.12.3
-        with:
-          user: __token__
-          password: ${{ secrets.pypi_password }}

.pre-commit-config.yaml

@@ -23,11 +23,6 @@ repos:
   hooks:
     - id: rst-backticks
 
-- repo: https://github.com/asottile/setup-cfg-fmt
-  rev: v2.7.0
-  hooks:
-  - id: setup-cfg-fmt
-
 - repo: https://github.com/astral-sh/ruff-pre-commit
   # Ruff version.
   rev: v0.8.6

docs/tutorials/end_to_end_example.ipynb

@@ -40,21 +40,21 @@
     }
    ],
    "source": [
-    "import numpy as np\n",
-    "import matplotlib.pyplot as plt\n",
     "from pathlib import Path\n",
-    "from astropy import units, constants\n",
     "\n",
-    "import hera_sim\n",
-    "from hera_sim import Simulator, DATA_PATH\n",
-    "from hera_sim.visibilities import MatVis, ModelData, VisibilitySimulation\n",
-    "import pyuvsim\n",
+    "import matplotlib.pyplot as plt\n",
+    "import matvis\n",
+    "import numpy as np\n",
+    "import pyradiosky\n",
     "import pyuvdata\n",
+    "import pyuvsim\n",
     "import uvtools\n",
+    "from astropy import constants, units\n",
+    "from astropy.coordinates import Latitude, Longitude\n",
     "\n",
-    "import pyradiosky\n",
-    "import matvis\n",
-    "from astropy.coordinates import Latitude, Longitude"
+    "import hera_sim\n",
+    "from hera_sim import DATA_PATH, Simulator\n",
+    "from hera_sim.visibilities import MatVis, ModelData, VisibilitySimulation"
    ]
   },
   {

docs/tutorials/hera_sim_defaults.ipynb

@@ -20,13 +20,12 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "\n",
+    "import numpy as np\n",
     "import uvtools\n",
+    "\n",
     "import hera_sim\n",
-    "from hera_sim import Simulator\n",
-    "from hera_sim import DATA_PATH\n",
+    "from hera_sim import DATA_PATH, Simulator\n",
     "from hera_sim.config import CONFIG_PATH\n",
     "\n",
     "%matplotlib inline"

docs/tutorials/hera_sim_simulator.ipynb

@@ -37,10 +37,10 @@
     "import matplotlib.pyplot as plt\n",
     "import numpy as np\n",
     "from astropy import units\n",
+    "from uvtools.plot import labeled_waterfall\n",
     "\n",
     "import hera_sim\n",
-    "from hera_sim import Simulator, DATA_PATH, utils\n",
-    "from uvtools.plot import labeled_waterfall"
+    "from hera_sim import DATA_PATH, Simulator, utils"
    ]
   },
   {

docs/tutorials/hera_sim_tour.ipynb

@@ -21,11 +21,13 @@
    "outputs": [],
    "source": [
     "%matplotlib inline\n",
-    "import uvtools\n",
     "import numpy as np\n",
     "import pylab as plt\n",
+    "import uvtools\n",
     "from astropy.units import sday\n",
+    "\n",
     "from hera_sim import DATA_PATH\n",
+    "\n",
     "plt.rcParams[\"figure.figsize\"] = [14, 8]"
    ]
   },
@@ -35,7 +37,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "from hera_sim import foregrounds, noise, sigchain, rfi, defaults"
+    "from hera_sim import defaults, foregrounds, noise, rfi, sigchain"
    ]
   },
   {

docs/tutorials/mutual_coupling_example.ipynb

@@ -37,13 +37,14 @@
     }
    ],
    "source": [
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "import hera_sim\n",
+    "import numpy as np\n",
     "import uvtools\n",
     "from astropy import constants, units\n",
     "from pyuvdata import UniformBeam\n",
     "\n",
+    "import hera_sim\n",
+    "\n",
     "%matplotlib inline"
    ]
   },

docs/tutorials/polybeam_simulation.ipynb

@@ -28,14 +28,15 @@
     }
    ],
    "source": [
-    "from hera_sim.visibilities import VisibilitySimulation, ModelData, MatVis\n",
-    "from hera_sim.beams import PerturbedPolyBeam\n",
-    "from hera_sim import io\n",
-    "import numpy as np\n",
     "import matplotlib.pyplot as plt\n",
-    "from astropy.coordinates.angles import Latitude, Longitude\n",
+    "import numpy as np\n",
     "from astropy import units as un\n",
-    "from pyradiosky import SkyModel"
+    "from astropy.coordinates.angles import Latitude, Longitude\n",
+    "from pyradiosky import SkyModel\n",
+    "\n",
+    "from hera_sim import io\n",
+    "from hera_sim.beams import PerturbedPolyBeam\n",
+    "from hera_sim.visibilities import MatVis, ModelData, VisibilitySimulation"
    ]
   },
   {

docs/tutorials/visibility_simulator.ipynb

@@ -76,7 +76,6 @@
     "from hera_sim import DATA_PATH\n",
     "from hera_sim.visibilities import MatVis, ModelData, VisibilitySimulation\n",
     "\n",
-    "\n",
     "# Path to the example pyuvsim configuration files.\n",
     "# These can be found in `hera_sim.DATA_PATH` to follow along.\n",
     "config_file = (\n",
@@ -310,8 +309,8 @@
     }
    ],
    "source": [
-    "from pyuvsim.simsetup import initialize_uvdata_from_params, _complete_uvdata\n",
     "from pyradiosky import SkyModel\n",
+    "from pyuvsim.simsetup import _complete_uvdata, initialize_uvdata_from_params\n",
     "\n",
     "# Here, the configuration file uses the `PolyBeam` defined in hera_sim directly in the\n",
     "# pyuvsim configuration file, as the format accepts custom beams.\n",
@@ -391,9 +390,9 @@
     }
    ],
    "source": [
-    "from pyradiosky import SkyModel\n",
-    "from astropy.coordinates import Longitude, Latitude\n",
     "from astropy import units as u\n",
+    "from astropy.coordinates import Latitude, Longitude\n",
+    "from pyradiosky import SkyModel\n",
     "\n",
     "# Point Soruce Model ##\n",
     "component_type = \"point\"\n",

pyproject.toml

@@ -1,25 +1,103 @@
 [build-system]
-requires = ["setuptools>=45", "wheel", "setuptools_scm>=6.2"]
+requires = ["setuptools>=64", "setuptools_scm>=8"]
 build-backend = "setuptools.build_meta"
 
 [tool.setuptools_scm]
 
-[tool.black]
-line-length = 88
-exclude = '''
-/(
-    \.eggs
-  | \.git
-  | \.hg
-  | \.mypy_cache
-  | \.tox
-  | \.venv
-  | _build
-  | buck-out
-  | build
-  | dist
-)/
-'''
+[project]
+name = "hera_sim"
+description = "A collection of simulation routines describing the HERA instrument."
+readme = "README.rst"
+authors = [
+  {name="HERA Team"},
+  {name="Steven Murray", email="murray.steveng@gmail.com"}
+]
+license = {text="MIT"}
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Intended Audience :: Science/Research",
+  "License :: OSI Approved",
+  "License :: OSI Approved :: MIT License",
+  "Natural Language :: English",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Topic :: Scientific/Engineering :: Astronomy",
+  "Topic :: Scientific/Engineering :: Physics",
+]
+dynamic=["version"]
+requires-python = ">=3.10"
+
+dependencies = [
+  "astropy",
+  "astropy-healpix",
+  "cached-property",
+  "deprecation",
+  "hera-cli-utils>=0.1.0",
+  "numpy>=2",
+  "pyuvdata>=3.1.2",
+  "pyuvsim>=1.4",
+  "pyyaml>=5.1",
+  "rich",
+  "scipy",
+  "typing-extensions;python_version<'3.11'",
+]
+
+[project.optional-dependencies]
+all = [
+  "hera-sim[vis,bda,cal,gpu]",
+]
+bda = [
+  "bda"
+]
+cal = [
+  "hera-calibration>3.6.1"
+]
+dev = [
+  "hera-sim[docs,tests]",
+]
+docs = [
+  "fftvis",
+  "furo",
+  "ipython",
+  "matvis>=1.3.0",
+  "nbsphinx",
+  "numpydoc>=0.8",
+  "pyradiosky>=0.1.2",
+  "sphinx>=1.8,<7.2",
+  "sphinx-autorun",
+]
+tests = [
+  "coverage>=4.5.1",
+  "hera-sim[bda,cal,vis]",
+  "matplotlib>=3.4.2",
+  "pre-commit",
+  "pytest>=3.5.1",
+  "pytest-cov>=2.5.1",
+  "uvtools",
+]
+vis = [
+  "fftvis>=0.1.0",
+  "line-profiler",
+  "matvis>=1.2.1",
+  "mpi4py",
+  "pyradiosky>=0.1.2",
+]
+
+[project.urls]
+Documentation = "https://hera_sim.readthedocs.org"
+Repository = "https://github.com/HERA-Team/hera_sim"
+
+[tool.setuptools]
+script-files = ["scripts/hera-sim-simulate.py", "scripts/hera-sim-vis.py"]
+
+[tool.pytest.ini_options]
+addopts = "--cov hera_sim --cov-config=.coveragerc --cov-report xml:./coverage.xml --durations=25 --verbose"
+norecursedirs = [
+  "dist",
+  "build",
+  ".tox",
+]
+testpaths = "hera_sim/tests"
 
 [tool.ruff]
 line-length = 88
@@ -35,6 +113,7 @@ select = [
   "E",    # pycodestyle
   "W",    # pycodestyle warning
   "NPY",  # numpy-specific rules
+  "I",    # isort
 ]
 
 ignore = [

scripts/hera-sim-simulate.py

@@ -16,9 +16,10 @@
 
 import argparse
 import copy
-import numpy as np
 import os
 import sys
+
+import numpy as np
 import yaml
 from astropy import units
 from astropy.coordinates import Angle