Merge branch 'main' into py312

.github/workflows/build.yml

@@ -211,7 +211,7 @@ jobs:
     env:
       PYTHON_COVREPORTS_VERSION: "3.11"
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -317,10 +317,9 @@ jobs:
         pip install pytest-cov
         # Turn astropy deprecation warnings into errors as well if astropy
         if $REQUIRES_ASTROPY; then export PYTEST_ADDOPTS="-W error::astropy.utils.exceptions.AstropyDeprecationWarning"; else export PYTEST_ADDOPTS=""; fi
-        export XDRLIB_DEPRECATION="-W ignore:\"'xdrlib' is deprecated and slated for removal in Python 3.13\":DeprecationWarning"
         export TQDM_DEPRECATION="-W ignore:\"datetime.datetime.utcfromtimestamp() is deprecated and scheduled for removal in a future version.\":DeprecationWarning -W ignore:\"datetime.datetime.utcnow() is deprecated and scheduled for removal in a future version. Use timezone-aware objects to represent datetimes in UTC\":DeprecationWarning"
         # eval necessary for -k 'not ...' in TEST_FILES
-        eval "pytest -W error::DeprecationWarning -W error::FutureWarning $PYTEST_ADDOPTS $XDRLIB_DEPRECATION $TQDM_DEPRECATION -v $TEST_FILES --cov galpy --cov-config .coveragerc --disable-pytest-warnings --durations=0 --cov-report=term --cov-report=xml"
+        eval "pytest -W error::DeprecationWarning -W error::FutureWarning $PYTEST_ADDOPTS $TQDM_DEPRECATION -v $TEST_FILES --cov galpy --cov-config .coveragerc --disable-pytest-warnings --durations=0 --cov-report=term --cov-report=xml"
     - name: Generate code coverage
       if: ${{ matrix.python-version == env.PYTHON_COVREPORTS_VERSION && matrix.os == 'ubuntu-latest' }}
       run: |

.github/workflows/build_pyodide_wheels.yml

@@ -35,7 +35,7 @@ jobs:
     name: Build pyodide/wasm wheels
     runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - uses: actions/setup-python@v4
         with:
           python-version: 3.10.2

.github/workflows/build_windows.yml

@@ -161,7 +161,7 @@ jobs:
             REQUIRES_NUMBA: false
             REQUIRES_JAX: false
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v4
       with:
@@ -240,6 +240,5 @@ jobs:
         pip install pytest-cov
         # Turn astropy deprecation warnings into errors as well if astropy
         if $REQUIRES_ASTROPY; then export PYTEST_ADDOPTS="-W error::astropy.utils.exceptions.AstropyDeprecationWarning"; else export PYTEST_ADDOPTS=""; fi
-        export XDRLIB_DEPRECATION="-W ignore:\"'xdrlib' is deprecated and slated for removal in Python 3.13\":DeprecationWarning"
         # eval necessary for -k 'not ...' in TEST_FILES
-        eval "pytest -W error::DeprecationWarning -W error::FutureWarning $PYTEST_ADDOPTS $XDRLIB_DEPRECATION -v $TEST_FILES --cov galpy --cov-config .coveragerc --disable-pytest-warnings --durations=0"
+        eval "pytest -W error::DeprecationWarning -W error::FutureWarning $PYTEST_ADDOPTS -v $TEST_FILES --cov galpy --cov-config .coveragerc --disable-pytest-warnings --durations=0"

.github/workflows/wheels.yml

@@ -35,9 +35,9 @@ jobs:
         - [macos-latest, macosx, x86_64]
         - [macos-latest, macosx, arm64]
         - [windows-2019, win, amd64]
-        python: ["cp38", "cp39", "cp310", "cp311"]
+        python: ["cp38", "cp39", "cp310", "cp311", "cp312"]
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - name: Install GSL (Windows / Mac OS x86_64)
         uses: mamba-org/setup-micromamba@v1
         if: matrix.buildplat[1] == 'win' || ( matrix.buildplat[1] == 'macosx' && matrix.buildplat[2] == 'x86_64' )
@@ -88,7 +88,7 @@ jobs:
           rsync -azv gsl/lib/ /usr/local/lib/
           echo "REPAIR_LIBRARY_PATH=/usr/local/lib/" >> $GITHUB_ENV # https://github.com/pypa/cibuildwheel/issues/816#issuecomment-916197079
       - name: Build wheels
-        uses: pypa/cibuildwheel@v2.15
+        uses: pypa/cibuildwheel@v2.16
         env:
           CIBW_BUILD: ${{ matrix.python }}-${{ matrix.buildplat[1] }}_${{ matrix.buildplat[2] }}
           CIBW_BUILD_VERBOSITY: 1
@@ -108,7 +108,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       # check-out this repository
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       # Setup python
       - name: Set up Python
         uses: actions/setup-python@v4
@@ -132,7 +132,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name == 'release' && github.event.action == 'created'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: |
           mkdir tmp_wheelhouse
           mkdir wheelhouse
@@ -152,7 +152,7 @@ jobs:
     runs-on: ubuntu-latest
     if: github.event_name != 'release' && github.event_name != 'pull_request' && github.ref == 'refs/heads/main'
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
       - run: |
           mkdir tmp_wheelhouse
           mkdir wheelhouse

.pre-commit-config.yaml

@@ -12,7 +12,7 @@ repos:
   - id: check-executables-have-shebangs
   - id: check-yaml
 - repo: https://github.com/asottile/pyupgrade
-  rev: v3.10.1
+  rev: v3.14.0
   hooks:
   - id: pyupgrade
     args: [--py38-plus]
@@ -30,12 +30,12 @@ repos:
   - id: isort
     name: isort (python)
 - repo: https://github.com/codespell-project/codespell
-  rev: "v2.2.5"
+  rev: "v2.2.6"
   hooks:
     - id: codespell
       args: ["-L", "thisE,thise,mye,tE,te,hist,ro,sav,ccompiler,aas",
       "-x","doc/source/_static/try-galpy.js"]
 - repo: https://github.com/psf/black
-  rev: 23.7.0
+  rev: 23.9.1
   hooks:
     - id: black

doc/source/basic_df.rst

@@ -430,7 +430,7 @@ The warm response is slightly smaller in amplitude
 although the numerical uncertainty in ``mvrwarm`` is large, because
 the grid is not sufficiently fine.
 
-We can then re-use this grid in calculations of other moments of
+We can then reuse this grid in calculations of other moments of
 the DF, e.g.,
 
 >>> print(edfcold.meanvT(0.9,phi=22.5,deg=True,t=0.,grid=gridcold))
@@ -468,7 +468,7 @@ A_{\mathrm{axi}}+0.05/(2\sqrt{2})` where :math:`A_{\mathrm{axi}} =
 >>> print(oortacold-(0.5/0.9+0.05/2./sqrt(2.)))
 # 0.0022613349141670236
 
-These grids can then be re-used for the other Oort functions, for
+These grids can then be reused for the other Oort functions, for
 example,
 
 >>> print(edfcold.oortB(0.9,phi=22.5,deg=True,t=0.,grid=gridcold,derivphiGrid=gridphicold,derivRGrid=gridrcold))

doc/source/installation.rst

@@ -147,7 +147,7 @@ If you are reading this, either the simple installation instructions at the top
         To compile ``galpy`` from source, you will first need to install the GSL. The
         easiest way to do this is using `Homebrew <http://brew.sh/>`__ as::
 
-            brew install gsl --universal
+            brew install gsl
 
         Alternatively, you can use ``conda`` to install the GSL and use ``conda`` to
         manage your Python environment. Install the GSL in your preferred environment
@@ -444,7 +444,7 @@ The easiest way to install this is using its Anaconda build::
 If you do not want to go that route, on a Mac, the next easiest way to install
 the GSL is using `Homebrew <http://brew.sh/>`_ as::
 
-	brew install gsl --universal
+	brew install gsl
 
 You should be able to check your version using (on Mac/Linux)::
 

galpy/actionAngle/actionAngleAdiabaticGrid.py

@@ -56,7 +56,7 @@ def __init__(
 
            nEz=, nEr=, nLz, nR= grid size
 
-           numcores= number of cpus to use to parallellize
+           numcores= number of cpus to use to parallelize
 
            c= if True, use C to calculate actions
 

galpy/actionAngle/actionAngleStaeckelGrid.py

@@ -55,7 +55,7 @@ def __init__(
 
            interpecc= (False) if True, also interpolate the approximate eccentricity, zmax, rperi, and rapo
 
-           numcores= number of cpus to use to parallellize
+           numcores= number of cpus to use to parallelize
 
            ro= distance from vantage point to GC (kpc; can be Quantity)
 

galpy/df/quasiisothermaldf.py

@@ -2075,7 +2075,7 @@ def meanlz(self, R, z, nsigma=None, mc=True, nmc=10000, **kwargs):
 
         PURPOSE:
 
-           calculate the mean angular momemtum by marginalizing over velocity
+           calculate the mean angular momentum by marginalizing over velocity
 
         INPUT:
 

galpy/df/sphericaldf.py

@@ -77,7 +77,7 @@ def __init__(self, pot=None, denspot=None, rmax=None, scale=None, ro=None, vo=No
             )
         phys = conversion.get_physical(pot, include_set=True)
         # if pot has physical units, transfer them (if already on, we know
-        # they are compaible)
+        # they are compatible)
         if phys["roSet"] and phys["voSet"]:
             self.turn_physical_on(ro=phys["ro"], vo=phys["vo"])
         if pot is None:  # pragma: no cover
@@ -731,7 +731,7 @@ def _call_internal(self, *args):
 
         INPUT:
 
-            E,L,Lz - The energy, angular momemtum magnitude, and its z component (only E is used)
+            E,L,Lz - The energy, angular momentum magnitude, and its z component (only E is used)
 
         OUTPUT:
 

galpy/orbit/Orbits.py

@@ -2705,7 +2705,7 @@ def _setupaA(self, pot=None, type="staeckel", **kwargs):
         return None
 
     def _setup_EccZmaxRperiRap(self, pot=None, **kwargs):
-        """Internal function to compute e,zmax,rperi,rap and cache it for re-use"""
+        """Internal function to compute e,zmax,rperi,rap and cache it for reuse"""
         self._setupaA(pot=pot, **kwargs)
         if hasattr(self, "_aA_ecc"):
             return None
@@ -2738,7 +2738,7 @@ def _setup_EccZmaxRperiRap(self, pot=None, **kwargs):
         return None
 
     def _setup_actionsFreqsAngles(self, pot=None, **kwargs):
-        """Internal function to compute the actions, frequencies, and angles and cache them for re-use"""
+        """Internal function to compute the actions, frequencies, and angles and cache them for reuse"""
         self._setupaA(pot=pot, **kwargs)
         if hasattr(self, "_aA_jr"):
             return None
@@ -2777,7 +2777,7 @@ def _setup_actionsFreqsAngles(self, pot=None, **kwargs):
         return None
 
     def _setup_actions(self, pot=None, **kwargs):
-        """Internal function to compute the actions and cache them for re-use (used for methods that don't support frequencies and angles)"""
+        """Internal function to compute the actions and cache them for reuse (used for methods that don't support frequencies and angles)"""
         self._setupaA(pot=pot, **kwargs)
         # Caching effectively checked in _setup_actionsFreqsAngles, because always called first
         # if hasattr(self, "_aA_jr"):

galpy/orbit/integrateFullOrbit.py

@@ -1142,7 +1142,7 @@ def _rectForce(x, pot, t=0.0, vx=None):
        x - current position
        t - current time
        pot - (list of) Potential instance(s)
-       vx = (None) if set, use this [vx,vy,vz] when evalulating dissipative forces
+       vx = (None) if set, use this [vx,vy,vz] when evaluating dissipative forces
     OUTPUT:
        force
     HISTORY:

galpy/orbit/integratePlanarOrbit.py

@@ -1590,7 +1590,7 @@ def _planarRectForce(x, pot, t=0.0, vx=None):
        x - current position
        t - current time
        pot - (list of) Potential instance(s)
-       vx = (None) if set, use this [vx,vy] when evalulating dissipative forces
+       vx = (None) if set, use this [vx,vy] when evaluating dissipative forces
     OUTPUT:
        force
     HISTORY:

galpy/orbit/orbit_c_ext/integrateFullOrbit.c

@@ -932,7 +932,7 @@ void evalRectDeriv(double t, double *q, double *a,
 
 void evalSOSDeriv(double psi, double *q, double *a,
 		              int nargs, struct potentialArg * potentialArgs){
-  // q= (x,y,vx,vy,A,t,psi); to save operations, we re-use a first for the
+  // q= (x,y,vx,vy,A,t,psi); to save operations, we reuse a first for the
   // rectForce then for the actual RHS
   // Note also that we keep track of psi in q+6, not in psi! This is
   // such that we can avoid having to convert psi to psi+psi0

galpy/orbit/orbit_c_ext/integratePlanarOrbit.c

@@ -876,7 +876,7 @@ void evalPlanarRectDeriv(double t, double *q, double *a,
 
 void evalPlanarSOSDerivx(double psi, double *q, double *a,
 		                 int nargs, struct potentialArg * potentialArgs){
-  // q= (y,vy,A,t,psi); to save operations, we re-use a first for the
+  // q= (y,vy,A,t,psi); to save operations, we reuse a first for the
   // rectForce then for the actual RHS
   // Note also that we keep track of psi in q+4, not in psi! This is
   // such that we can avoid having to convert psi to psi+psi0
@@ -910,7 +910,7 @@ void evalPlanarSOSDerivx(double psi, double *q, double *a,
 
 void evalPlanarSOSDerivy(double psi, double *q, double *a,
 		                 int nargs, struct potentialArg * potentialArgs){
-  // q= (x,vx,A,t,psi); to save operations, we re-use a first for the
+  // q= (x,vx,A,t,psi); to save operations, we reuse a first for the
   // rectForce then for the actual RHS
   // Note also that we keep track of psi in q+4, not in psi! This is
   // such that we can avoid having to convert psi to psi+psi0

galpy/potential/SnapshotRZPotential.py

@@ -489,7 +489,7 @@ def _setup_potential(self, R, z, use_pkdgrav=False, dr=0.0001):
                 )
 
             # do the same for the mixed radial-vertical component
-            if self._interpepifreq and self._interpverticalfreq:  # re-use this
+            if self._interpepifreq and self._interpverticalfreq:  # reuse this
                 Rzgrad = numpy.zeros(len(points_new))
                 for i, racc in enumerate(
                     rgrad_acc.reshape((len(rgrad_acc) // 2, 2, 3))

galpy/potential/potential_c_ext/NonInertialFrameForce.c

@@ -114,7 +114,7 @@ void NonInertialFrameForcexyzforces_xyz(double R,double z,double phi,double t,
         v0x= (*(*(potentialArgs->tfuncs+6)))(t);
         v0y= (*(*(potentialArgs->tfuncs+7)))(t);
         v0z= (*(*(potentialArgs->tfuncs+8)))(t);
-        // Re-use variable
+        // Reuse variable
         Omegatimesvecx= Omegax * x0x + Omegay * x0y + Omegaz * x0z;
         *Fx+=  2. * ( Omegaz * v0y - Omegay * v0z ) + Omega2 * x0x - Omegax * Omegatimesvecx;
         *Fy+= -2. * ( Omegaz * v0x - Omegax * v0z ) + Omega2 * x0y - Omegay * Omegatimesvecx;

galpy/util/bovy_rk.c

@@ -313,7 +313,7 @@ void bovy_rk6_onestep(void (*func)(double t, double *q, double *a,
   //calculate k6
   func(tn+dt/2.,ynk,a,nargs,potentialArgs);
   for (ii=0; ii < dim; ii++) *(yn1+ii) -= 32.* dt * *(a+ii) / 120.;
-  for (ii=0; ii < dim; ii++) *(k5+ii)= dt * *(a+ii); //re-use k5 for k6
+  for (ii=0; ii < dim; ii++) *(k5+ii)= dt * *(a+ii); //reuse k5 for k6
   for (ii=0; ii < dim; ii++) *(ynk+ii)= *(yn+ii) + ( 9. * *(k1+ii)
 						     - 36. * *(k2+ii)
 						     +63.* *(k3+ii)

tests/test_SpiralArmsPotential.py

@@ -3,8 +3,8 @@
 
 _NUMPY_VERSION = parse_version(numpy.__version__)
 _NUMPY_1_23 = (_NUMPY_VERSION > parse_version("1.22")) * (
-    _NUMPY_VERSION < parse_version("1.26")
-)  # For testing 1.23/1.24/1.25 precision issues
+    _NUMPY_VERSION < parse_version("1.27")
+)  # For testing 1.23/1.24/1.25/1.26 precision issues
 import unittest
 
 from numpy.testing import assert_allclose

tests/test_coords.py

@@ -3073,8 +3073,8 @@ def test_radec_to_custom_pal5():
     )
     xieta = coords.radec_to_custom(_RAPAL5, _DECPAL5, T=_TPAL5, degree=False)
 
-    def checkrng(x, xpct, dom, shft):
-        return numpy.fabs(((numpy.fabs(x - xpct) + shft) % dom) - shft)
+    def checkrng(x, xpct, dom, shift):
+        return numpy.fabs(((numpy.fabs(x - xpct) + shift) % dom) - shift)
 
     # 0 < xieta[0] < 2 * pi
     assert (
@@ -3231,8 +3231,8 @@ def test_custom_to_radec_pal5():  # FIXME COMPARE TO DOCUMENT
     )
     xieta = coords.custom_to_radec(_RAPAL5, _DECPAL5, T=_TPAL5.T, degree=False)
 
-    def checkrng(x, xpct, dom, shft):
-        return numpy.fabs(((numpy.fabs(x - xpct) + shft) % dom) - shft)
+    def checkrng(x, xpct, dom, shift):
+        return numpy.fabs(((numpy.fabs(x - xpct) + shift) % dom) - shift)
 
     # 0 < xieta[0] < 2 * pi
     assert (

tests/test_evolveddiskdf.py

@@ -1311,7 +1311,7 @@ def test_plot_grid():
         gridpoints=_GRIDPOINTS,
     )
     grid.plot()
-    # w/ list of tiems
+    # w/ list of times
     mvr, grid = edf.meanvR(
         0.9,
         t=[0.0, -2.5, -5.0, -7.5, -10.0],
@@ -1342,7 +1342,7 @@ def test_plot_hierarchgrid():
         gridpoints=_GRIDPOINTS,
     )
     grid.plot()
-    # w/ list of tiems
+    # w/ list of times
     mvr, grid = edf.meanvR(
         0.9,
         t=[0.0, -2.5, -5.0, -7.5, -10.0],

tests/test_potential.py

@@ -6026,7 +6026,7 @@ def pot(R, z, amp=1.0, a=0.75):
                 * special.jv(0, k * a)
                 * numpy.exp(-k * numpy.fabs(z)),
                 0.0,
-                numpy.infty,
+                numpy.inf,
             )[0]
         )
 
@@ -7284,13 +7284,13 @@ def test_TimeDependentAmplitudeWrapperPotential_inputerrors():
         match="A= input to TimeDependentAmplitudeWrapperPotential should be a function",
     ):
         tp = TimeDependentAmplitudeWrapperPotential(pot=lp)
-    # TypeError when suppplying a function with no argument
+    # TypeError when supplying a function with no argument
     with pytest.raises(
         TypeError,
         match="A= input to TimeDependentAmplitudeWrapperPotential should be a function that can be called with a single parameter",
     ):
         tp = TimeDependentAmplitudeWrapperPotential(pot=lp, A=lambda: 1.0)
-    # TypeError when suppplying a function with more than 1 argument
+    # TypeError when supplying a function with more than 1 argument
     with pytest.raises(
         TypeError,
         match="A= input to TimeDependentAmplitudeWrapperPotential should be a function that can be called with a single parameter",