modernize orbitize install & fix ci tests

.github/workflows/joss-compile.yml

@@ -14,7 +14,7 @@ jobs:
           # This should be the path to the paper within your repo.
           paper-path: paper/paper.md
       - name: Upload
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v4
         with:
           name: paper
           # This is the output path where Pandoc will write the compiled

.github/workflows/python-package.yml

@@ -33,7 +33,7 @@ jobs:
     - name: Lint with flake8
       run: |
         # stop the build if there are Python syntax errors or undefined names
-        flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
+        flake8 . --count --select=E9,F63,F7,F82 --extend-ignore=F824 --show-source --statistics
         # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
         flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
     - name: Test with pytest

docs/index.rst

@@ -55,6 +55,10 @@ User Guide:
 Changelog:
 ++++++++++
 
+**3.2.0 (2025-7-18)**
+
+- modernize install: setup.py -> pyproject.toml (@sblunt)
+
 **3.1.0 (2024-9-09)**
 
 - JOSS paper published! (@sblunt et al)

orbitize/__init__.py

@@ -1,6 +1,6 @@
 import os
 
-__version__ = "3.1.0"
+__version__ = "3.2.0"
 
 # set Python env variable to keep track of example data dir
 orbitize_dir = os.path.dirname(__file__)

orbitize/system.py

@@ -554,9 +554,15 @@ def compute_all_orbits(self, params_arr, epochs=None, comp_rebound=False):
             deoff = dec_kepler + dec_perturb
 
         if self.fitting_basis == "XYZ":
+
             # Find and filter out unbound orbits
-            bad_orbits = np.where(np.logical_or(ecc >= 1.0, ecc < 0.0))[0]
-            if bad_orbits.size != 0:
+            bad_orbits = []
+            if isinstance(ecc, float):
+                if ecc >= 1.0 or ecc < 0.0:
+                    bad_orbits = [0]
+            else:
+                bad_orbits = np.where(np.logical_or(ecc >= 1.0, ecc < 0.0))[0]
+            if len(bad_orbits) > 0:
                 raoff[:, :, bad_orbits] = np.inf
                 deoff[:, :, bad_orbits] = np.inf
                 vz[:, :, bad_orbits] = np.inf

pyproject.toml

@@ -0,0 +1,34 @@
+[build-system]
+requires = [
+    "setuptools", 
+    "numpy",
+    "cython", 
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "orbitize"
+dynamic = ["version"]
+dependencies = [
+    "numpy",
+    "astropy>=4",
+    "scipy",
+    "emcee>=3",
+    "ptemcee_for_orbitize",
+    "matplotlib",
+    "corner",
+    "h5py",
+    "deprecation",
+    "pytest",
+    "pandas",
+    "pyerfa",
+    "astroquery",
+    "rebound",
+    "dynesty"
+]
+
+[tool.setuptools.dynamic]
+version = {attr = "orbitize.__version__"}
+
+[tool.setuptools.packages]
+find = {}

requirements.txt

@@ -12,7 +12,5 @@ pytest
 pandas
 pyerfa
 astroquery
-sphinx>=6
-docutils<0.17
 rebound
 dynesty

setup.py

@@ -1,70 +1,22 @@
-from setuptools import setup, find_packages, Extension
-import numpy, sys
-import re
-
-USE_C_KEPLER_MODULE = 1
-if "--disable-cython" in sys.argv:
-    sys.argv.remove("--disable-cython")
-    USE_C_KEPLER_MODULE = 0
-else:
-    try:
-        from Cython.Build import cythonize
-    except:
-        print("Error: Importing cython build environment failed")
-        USE_C_KEPLER_MODULE = 0
-
-
-# auto-updating version code stolen from RadVel
-def get_property(prop, project):
-    result = re.search(
-        r'{}\s*=\s*[\'"]([^\'"]*)[\'"]'.format(prop),
-        open(project + "/__init__.py").read(),
-    )
-    return result.group(1)
-
-
-def get_requires():
-    reqs = []
-    for line in open("requirements.txt", "r").readlines():
-        reqs.append(line)
-    return reqs
+from setuptools import setup, Extension
+import numpy
+from Cython.Build import cythonize
 
 
 def get_extensions():
     extensions = []
-    if USE_C_KEPLER_MODULE:
-        extensions = cythonize(
-            [
-                Extension(
-                    "orbitize._kepler",
-                    ["orbitize/_kepler.pyx"],
-                    include_dirs=[numpy.get_include()],
-                )
-            ]
-        )
+    extensions = cythonize(
+        [
+            Extension(
+                "orbitize._kepler",
+                ["orbitize/_kepler.pyx"],
+                include_dirs=[numpy.get_include()],
+            )
+        ]
+    )
     return extensions
 
 
 setup(
-    name="orbitize",
-    version=get_property("__version__", "orbitize"),
-    description="orbitize! Turns imaging data into orbits",
-    url="https://github.com/sblunt/orbitize",
-    author="",
-    author_email="",
-    license="BSD",
-    packages=find_packages(),
-    package_data={"": ["kernels/*.cu"]},
     ext_modules=get_extensions(),
-    include_dirs=[numpy.get_include()],
-    include_package_data=True,
-    zip_safe=False,
-    classifiers=[
-        "Intended Audience :: Science/Research",
-        "Topic :: Scientific/Engineering :: Astronomy",
-        "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 3.6",
-    ],
-    keywords="Orbits Astronomy Astrometry",
-    install_requires=get_requires(),
 )

tests/test_nested_sampler.py

@@ -6,6 +6,7 @@
 import numpy as np
 import pytest
 from orbitize.system import generate_synthetic_data
+import sys
 
 
 def test_nested_sampler():
@@ -24,29 +25,34 @@ def test_nested_sampler():
     ecc = 0.5
 
     # initialize orbitize `System` object
-    sys = system.System(1, data_table, mtot, plx)
-    lab = sys.param_idx
+    mySys = system.System(1, data_table, mtot, plx)
+    lab = mySys.param_idx
 
     ecc = 0.5  # eccentricity
 
     # set all parameters except eccentricity to fixed values (same as used to generate data)
-    sys.sys_priors[lab["inc1"]] = np.pi / 4
-    sys.sys_priors[lab["sma1"]] = sma
-    sys.sys_priors[lab["aop1"]] = np.pi / 4
-    sys.sys_priors[lab["pan1"]] = np.pi / 4
-    sys.sys_priors[lab["tau1"]] = 0.8
-    sys.sys_priors[lab["plx"]] = plx
-    sys.sys_priors[lab["mtot"]] = mtot
+    mySys.sys_priors[lab["inc1"]] = np.pi / 4
+    mySys.sys_priors[lab["sma1"]] = sma
+    mySys.sys_priors[lab["aop1"]] = np.pi / 4
+    mySys.sys_priors[lab["pan1"]] = np.pi / 4
+    mySys.sys_priors[lab["tau1"]] = 0.8
+    mySys.sys_priors[lab["plx"]] = plx
+    mySys.sys_priors[lab["mtot"]] = mtot
+
+    start_method="fork"
+    if sys.platform == "darwin":
+        start_method="spawn"
 
     # run both static & dynamic nested samplers
-    mysampler = sampler.NestedSampler(sys)
-    _ = mysampler.run_sampler(bound="multi", pfrac=0.95, static=False, num_threads=8)
+    mysampler = sampler.NestedSampler(mySys)
+    _ = mysampler.run_sampler(bound="multi", pfrac=0.95, static=False, start_method=start_method, num_threads=8)
     print("Finished first run!")
 
     dynamic_eccentricities = mysampler.results.post[:, lab["ecc1"]]
     assert np.median(dynamic_eccentricities) == pytest.approx(ecc, abs=0.1)
 
-    _ = mysampler.run_sampler(bound="multi", static=True, num_threads=8)
+
+    _ = mysampler.run_sampler(bound="multi", static=True, start_method=start_method, num_threads=8)
     print("Finished second run!")
 
     static_eccentricities = mysampler.results.post[:, lab["ecc1"]]