Merge branch 'oblate_coord_rot' into debug

.readthedocs.yaml

@@ -20,6 +20,7 @@ build:
   jobs:
     pre_build:
       - ford fortran_docs.md 
+      - pip install pyshtools
       - DOC_BUILD=1 pip install .
 python:
   install:

environment.yml

@@ -5,22 +5,22 @@ channels:
   - defaults
 
 dependencies:
-  - python>=3.9
-  - numpy>=1.24.3
-  - scipy>=1.10.1
-  - xarray>=2022.11.0
-  - distributed>=2022.1
-  - dask>=2022.1
-  - bottleneck>=1.3.5
-  - h5netcdf>=1.0.2
-  - netcdf4>=1.6.2
-  - matplotlib>=3.7.1
-  - astropy>=5.1
+  - python==3.9
+  - numpy>=1.26.4
+  - scipy>=1.12.0
+  - xarray>=2024.2.0
+  - distributed>=2024.2.1
+  - dask>=2024.2.1
+  - bottleneck>=1.3.8
+  - h5netcdf>=1.3.0
+  - netcdf4>=1.6.5
+  - matplotlib>=3.8.3
+  - astropy>=6.0.0
   - astroquery>=0.4.6
-  - tqdm>=4.65.0
+  - tqdm>=4.66.2
   - x264>=1!157.20191217
   - ffmpeg>=4.3.2
-  - cython>=3.0.0
+  - cython>=3.0.8
   - pkg-config
   - meson-python>=0.14
   - setuptools_scm>=8

pyproject.toml

@@ -13,7 +13,7 @@ maintainers = [
     {name = 'David A. Minton', email='daminton@purdue.edu'},
 ]
 readme = "README.md"
-requires-python=">=3.8"
+requires-python=">=3.9"
 license={file = "LICENSE"}
 classifiers=[
 'Development Status :: 3 - Alpha',
@@ -24,20 +24,20 @@ classifiers=[
 ]
 keywords=['astronomy','astrophysics', 'planetary', 'n-body',  'integrator', 'symplectic', 'wisdom-holman', 'symba']
 dependencies = [
-    'numpy>=1.24.3',
-    'scipy>=1.10.1',
-    'xarray>=2023.1',
-    'dask>=2023.5',
-    'distributed>=2023.5',
-    'bottleneck>=1.3.5',
-    'h5netcdf>=1.1',
-    'h5py>=3.9',
-    'netcdf4>=1.6.2',
-    'matplotlib>=3.7.1',
-    'astropy>=5.2',
+    'numpy>=1.26.4',
+    'scipy>=1.12.0',
+    'xarray>=2024.2.0',
+    'dask>=2024.2.1',
+    'distributed>=2024.2.1',
+    'bottleneck>=1.3.8',
+    'h5netcdf>=1.3.0',
+    'h5py>=3.10.0',
+    'netcdf4>=1.6.5',
+    'matplotlib>=3.8.3',
+    'astropy>=6.0.0',
     'astroquery>=0.4.6',
-    'tqdm>=4.65',
-    'cython>=3.0.0',
+    'tqdm>=4.66.2',
+    'cython>=3.0.8',
 ]
 
 [project.optional-dependencies]
@@ -48,8 +48,8 @@ Repository = 'https://github.itap.purdue.edu/MintonGroup/swiftest'
 
 [build-system]
 requires = [
-    "scikit-build-core>=0.8",
-    "cython>=3.0",
+    "scikit-build-core>=0.8.2",
+    "cython>=3.0.8",
 ]
 build-backend = "scikit_build_core.build"
 
@@ -133,7 +133,7 @@ PATH="${HDF5_ROOT}/bin:${PATH}"
 CMAKE_INSTALL_LIBDIR="lib"
 
 [tool.cibuildwheel.linux]
-skip = "cp312-* pp* -manylinux_i686* *-musllinux*"
+skip = "pp* -manylinux_i686* *-musllinux*"
 before-all = [
     "yum install epel-release -y",
     "yum install doxygen libxml2-devel libcurl-devel fftw-static openblas-devel lapack-devel -y",

tests/test_swiftest.py

@@ -28,24 +28,32 @@
 from numpy.random import default_rng
 from astroquery.jplhorizons import Horizons
 import datetime
+import tempfile
 
 rng = default_rng(seed=123)
 
 major_bodies = ["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune"]
 param = {}
 
 class TestSwiftest(unittest.TestCase):
+    def setUp(self):
+        # Initialize a target and surface for testing
+        self.tmpdir=tempfile.TemporaryDirectory()
+        self.simdir = self.tmpdir.name
+
+    def tearDown(self):
+        # Clean up temporary directory
+        self.tmpdir.cleanup() 
 
     def test_gen_ic(self):
         """
         Tests that Swiftest is able to successfully generate a set of initial conditions in a file without any exceptions being raised
         """
         print("\ntest_gen_ic: Test whether we can generate simulation initial conditions test")
         # Files that are expected to be generated:
-        simdir = "simdata"
-        file_list = [simdir, os.path.join(simdir,"param.in"), os.path.join(simdir,"init_cond.nc")]
+        file_list = [self.simdir, os.path.join(self.simdir,"param.in"), os.path.join(self.simdir,"init_cond.nc")]
 
-        sim = swiftest.Simulation()
+        sim = swiftest.Simulation(simdir=self.simdir)
         sim.clean()
 
         # Add the modern planets and the Sun using the JPL Horizons Database.
@@ -62,7 +70,7 @@ def test_read_ic(self):
         Tests that Swiftest is able to read a set of pre-existing initial conditions files and that they contain the correct data
         """
         print("\ntest_read_ic: Test whether we can read back initial conditions files created by test_gen_ic")
-        sim = swiftest.Simulation()
+        sim = swiftest.Simulation(simdir=self.simdir)
         sim.clean()
 
         # Add the modern planets and the Sun using the JPL Horizons Database.
@@ -81,7 +89,7 @@ def test_integrators(self):
         Tests that Swiftest is able to integrate a collection of massive bodies and test particles with all available integrators
         """ 
         print("\ntest_integrators: Tests that Swiftest is able to integrate a collection of massive bodies and test particles with all available integrators")
-        sim = swiftest.Simulation()
+        sim = swiftest.Simulation(simdir=self.simdir)
 
         # Add the modern planets and the Sun using the JPL Horizons Database.
         sim.add_solar_system_body(major_bodies)
@@ -116,18 +124,18 @@ def test_conservation(self):
         print("\ntest_conservation: Tests that Swiftest conserves mass, energy, and momentum to within acceptable tolerances.")
 
         # Error limits
-        L_slope_limit = 1e-10
-        E_slope_limit = 1e-8
+        L_slope_limit = 1e-9
+        E_slope_limit = 1e-7
         GM_limit = 1e-14
 
-        sim = swiftest.Simulation()
+        sim = swiftest.Simulation(simdir=self.simdir)
         sim.clean()
 
         sim.add_solar_system_body(major_bodies)
 
         dt = 0.01
-        nout = 1000
-        tstop = 1e4
+        nout = 100
+        tstop = 1e3
         tstep_out = tstop / nout
 
         sim.run(tstart=0.0, tstop=tstop, dt=dt, tstep_out=tstep_out, dump_cadence=0, compute_conservation_values=True, integrator="symba")
@@ -182,7 +190,7 @@ def test_gr(self):
 
         # Initialize the simulation object as a variable. Define the directory in which the output will be placed.
         tstep_out = 10.0
-        sim = swiftest.Simulation(tstop=1000.0, dt=0.005, tstep_out=tstep_out, dump_cadence=0,general_relativity=True)
+        sim = swiftest.Simulation(simdir=self.simdir, tstop=1000.0, dt=0.005, tstep_out=tstep_out, dump_cadence=0,general_relativity=True)
         sim.add_solar_system_body(["Sun","Mercury","Venus","Earth","Mars","Jupiter","Saturn","Uranus","Neptune"])
 
         # Get the start and end date of the simulation so we can compare with the real solar system.