Merge pull request #69 from mattpitkin/setup_update

Update setup methods and Python version requirements

Author: siyuan-chen

.flake8

@@ -20,7 +20,7 @@ jobs:
       fail-fast: false
       matrix:
         os: [ubuntu-latest, macos-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10']
+        python-version: ['3.8', '3.9', '3.10', '3.11', '3.12']
 
     steps:
     - name: Checkout repository
@@ -33,7 +33,7 @@ jobs:
       if: runner.os == 'macOS'
       run: |
         brew unlink gcc && brew link gcc
-        brew install automake
+        brew install automake libtool
         ./install_tempo2.sh
     - name: Install tempo2 on linux
       if: runner.os == 'Linux'
@@ -42,8 +42,7 @@ jobs:
     - name: Install dependencies and package
       run: |
         python -m pip install --upgrade pip
-        python -m pip install -r requirements_dev.txt
-        pip install -e .[astropy]
+        pip install -e .[astropy,dev]
     - name: Run lint
       run: make lint
     - name: Test with pytest
@@ -60,7 +59,7 @@ jobs:
     - name: Set up Python 
       uses: actions/setup-python@v2
       with:
-        python-version: '3.7'
+        python-version: '3.10'
     - name: Install tempo2 on mac
       if: runner.os == 'macOS'
       run: |
@@ -73,8 +72,8 @@ jobs:
         ./install_tempo2.sh
     - name: Build
       run: |
-        python -m pip install --upgrade pip setuptools wheel
-        pip install -r requirements.txt
+        python -m pip install --upgrade pip setuptools wheel build
+        python -m build --sdist --outdir dist
         make dist
     - name: Test the sdist
       run: |
@@ -114,4 +113,4 @@ jobs:
         TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
         TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
       run: |
-        twine upload dist/*
+        twine upload dist/*

.github/workflows/ci_tests.yml

@@ -0,0 +1,3 @@
+_version.py
+*.so
+*.cpp

libstempo/.gitignore

@@ -1,5 +1,3 @@
-__version__ = "2.4.7"
-
 import os
 from ._find_tempo2 import find_tempo2_runtime
 
@@ -14,3 +12,8 @@
 
 
 from libstempo.libstempo import *  # noqa F401,F402,F403
+
+try:
+    from ._version import version as __version__
+except ModuleNotFoundError:
+    __version__ = ""

libstempo/__init__.py

@@ -4,30 +4,12 @@ import os, sys, math, re, time
 from packaging import version
 
 import collections
+from collections import OrderedDict
 
-try:
-    from collections import OrderedDict
-except ImportError:
-    # this is for Python 2.6 compatibility, we may be able to drop it
-    from ordereddict import OrderedDict
-
-# Python 2/3 compatibility
+# what is the default encoding here?
+string = lambda s: s.decode()
+string_dtype = 'U'
 
-if sys.version_info[0] < 3:
-    from itertools import izip as zip
-
-    string = lambda s: s
-    string_dtype = 'S'
-else:
-    # what is the default encoding here?
-    string = lambda s: s.decode()
-    string_dtype = 'U'
-
-# get zip-as-iterator behavior in Python 2
-try:
-    import itertools.izip as zip
-except ImportError:
-    pass
 
 from libc cimport stdlib, stdio
 from libc.string cimport strncpy, memset
@@ -81,6 +63,12 @@ from functools import wraps
 
 from . import utils
 
+# set long double format for ARM64 compatibility
+try:
+    NP_LONG_DOUBLE_FORMAT = numpy.float128
+except AttributeError:
+    NP_LONG_DOUBLE_FORMAT = numpy.double
+
 # return numpy array as astropy table with unit
 def dimensionfy(unit):
     def dimensionfy_decorator(func):
@@ -902,12 +890,12 @@ cdef class tempopulsar:
         toas = self.__input_toas
 
         if toas is not None:
-            if isinstance(toas, (list, numpy.ndarray, tuple, float, numpy.float128)):
-                toamjd = numpy.atleast_1d(toas).astype(numpy.float128)
+            if isinstance(toas, (list, numpy.ndarray, tuple, float, NP_LONG_DOUBLE_FORMAT)):
+                toamjd = numpy.atleast_1d(toas).astype(NP_LONG_DOUBLE_FORMAT)
             else:
                 # check if using an astropy time object
                 try:
-                    toamjd = numpy.atleast_1d(toas.mjd).astype(numpy.float128)  # make sure in MJD
+                    toamjd = numpy.atleast_1d(toas.mjd).astype(NP_LONG_DOUBLE_FORMAT)  # make sure in MJD
                 except Exception as e:
                     raise TypeError("Input TOAs are not of an allowed type: {}".format(e))
 
@@ -957,7 +945,7 @@ cdef class tempopulsar:
         npjump = numpy.asarray(_jump)
         npfdjump = numpy.asarray(_fdjump)
 
-        days = numpy.floor(toas).astype(numpy.float128)
+        days = numpy.floor(toas).astype(NP_LONG_DOUBLE_FORMAT)
         npsatday[:] = days
         npsatsec[:] = toas - days
 

libstempo/libstempo.pyx

@@ -120,7 +120,7 @@ def plothist(
 
     for i in range(p):
         # figure out how big the multiplot needs to be
-        if type(append) == int:  # need this since isinstance(False,int) == True
+        if type(append) is int:  # need this since isinstance(False,int) == True
             q = append
         elif isinstance(append, (list, tuple)):
             q = len(append)

libstempo/plot.py

@@ -63,7 +63,6 @@ def add_dipole_gwb(
     dipoledir=None,
     dipolemag=None,
 ):
-
     """Add a stochastic background from inspiraling binaries distributed
     according to a pure dipole distribution, using the tempo2
     code that underlies the GWdipolebkgrd plugin.
@@ -502,7 +501,6 @@ def add_cgw(
 
     # evolution
     if evolve:
-
         # calculate time dependent frequency at earth and pulsar
         omega = w0 * (1 - fac1 * toas) ** (-3 / 8)
         omega_p = w0 * (1 - fac1 * tp) ** (-3 / 8)
@@ -513,7 +511,6 @@ def add_cgw(
 
     # use approximation that frequency does not evlolve over observation time
     elif phase_approx:
-
         # frequencies
         omega = w0
         omega_p = w0 * (1 + fac1 * pd * (1 - cosMu)) ** (-3 / 8)
@@ -524,7 +521,6 @@ def add_cgw(
 
     # no evolution
     else:
-
         # monochromatic
         omega = w0
         omega_p = omega
@@ -681,7 +677,6 @@ def add_ecc_cgw(
 
     # pulsar term #####
     if psrTerm:
-
         # convert units
         pd *= eu.KPC2S  # convert from kpc to seconds
 
@@ -855,7 +850,6 @@ def createGWB(
 
     # strain amplitude
     if userSpec is None:
-
         f1yr = 1 / 3.16e7
         alpha = -0.5 * (gam - 3)
         hcf = Amp * (f / f1yr) ** (alpha)
@@ -864,7 +858,6 @@ def createGWB(
             hcf /= (1 + (f / f0) ** (power * si)) ** (1 / power)
 
     elif userSpec is not None:
-
         freqs = userSpec[:, 0]
         if len(userSpec[:, 0]) != len(freqs):
             raise ValueError("Number of supplied spectral points does not match number of frequencies!")

libstempo/toasim.py

@@ -1,31 +1,124 @@
+# to create a new release, do the following:
+# install the build and twine packages
+# $ pip install build twine
+# create a git tag with the new version number, e.g.,
+# $ git tag -a v3.5.0 -m "Version 3.5.0"
+# build the source distribution
+# $ python -m build --sdist --outdir .
+# Upload to PyPI with:
+# $ twine upload --repository libstempo libstempo-*.tar.gz
+
+[build-system]
+requires = [
+    "setuptools>=61",
+    "setuptools_scm[toml]>=6.2",
+    "wheel", # ephem package likes to have wheel installed
+    "cython",
+    'numpy>=2.0.0; python_version > "3.8"',
+    'numpy<2.0; python_version == "3.8"',
+]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "libstempo"
+description = "A Python wrapper for tempo2"
+authors = [{name = "Michele Vallisneri", email = "[email protected]"}]
+urls = { Homepage = "https://github.com/vallis/libstempo" }
+readme = "README.md"
+license = { text = "MIT" }
+classifiers=[
+    "Intended Audience :: Developers",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: MIT License",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.8",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+dynamic = [
+    "version",
+]
+
+requires-python = ">=3.8, <4"
+dependencies = [
+    'numpy<2.0; python_version == "3.8"',
+    'numpy; python_version > "3.8"',
+    "scipy",
+    "matplotlib",
+    "ephem",
+]
+
+[project.optional-dependencies]
+astropy = [
+    "astropy",
+]
+dev = [
+    "black",
+    "flake8",
+    "Flake8-pyproject",
+    "pre-commit",
+    "wheel",
+    "coverage",
+    "pytest",
+    "pytest-cov",
+    "jupyter",
+]
+
+[tool.setuptools]
+include-package-data = true
+
+[tool.setuptools.packages.find]
+include = [
+    "libstempo*",
+]
+
+[tool.setuptools_scm]
+write_to = "libstempo/_version.py"
+
 [tool.black]
 line-length = 120
-target_version = ['py38']
-include = '\.pyi?$'
+target_version = ['py39']
+include = '\\.pyi?$'
 exclude = '''
-
 (
   /(
-      \.eggs         # exclude a few common directories in the
-    | \.git          # root of the project
-    | \.hg
-    | \.mypy_cache
-    | \.tox
+      \\.eggs         # exclude a few common directories in the
+    | \\.git          # root of the project
+    | \\.hg
+    | \\.mypy_cache
+    | \\.tox
     | _build
     | buck-out
     | build
     | dist
     | docs
     | .libstempo
+    | libstempo/_version\.py
   )/
 )
 '''
 
-[build-system]
-requires = [
-    "setuptools>=40.8.0",
-    "wheel", # ephem package likes to have wheel installed
-    "Cython>=0.22",
-    "oldest-supported-numpy",
+[tool.flake8]
+max-line-length = 120
+max-complexity = 45
+ignore = [
+    "E203",
+    "W503",      # line break before binary operator; conflicts with black
+    "E722",      # bare except ok
+    "E731",      # lambda expressions ok
+    "E741",      # undescriptive variable ok
+]
+exclude = [
+    ".git",
+    ".tox",
+    "__pycache__",
+    "build",
+    "dist",
+    "docs",
+    ".libstempo",
 ]
-build-backend = "setuptools.build_meta"