Merge pull request #241 from zblz/remove-stale-files

Remove stale files

Author: zblz

.landscape.yaml

@@ -28,7 +28,9 @@
 import datetime
 import os
 import sys
+from pathlib import Path
 
+import tomllib
 from pkg_resources import get_distribution
 
 try:
@@ -39,12 +41,9 @@
     )
     sys.exit(1)
 
-# Get configuration information from setup.cfg
-from configparser import ConfigParser
-
-conf = ConfigParser()
-conf.read([os.path.join(os.path.dirname(__file__), "..", "setup.cfg")])
-setup_cfg = dict(conf.items("metadata"))
+# Grab minversion from pyproject.toml
+with (Path(__file__).parents[1] / "pyproject.toml").open("rb") as f:
+    pyproject = tomllib.load(f)
 
 # -- General configuration ----------------------------------------------------
 
@@ -54,7 +53,6 @@
 # If your documentation needs a minimal Sphinx version, state it here.
 needs_sphinx = "1.3"
 
-
 intersphinx_mapping["emcee"] = (
     "https://emcee.readthedocs.io/en/stable/",
     None,
@@ -73,15 +71,15 @@
 # -- Project information ------------------------------------------------------
 
 # This does not *have* to match the package name, but typically does
-project = setup_cfg["name"]
-author = setup_cfg["author"]
-copyright = "{0}, {1}".format(datetime.datetime.now().year, setup_cfg["author"])
+project = pyproject["project"]["name"]
+author = pyproject["project"]["authors"][0]["name"]
+copyright = "{0}, {1}".format(datetime.datetime.now().year, author)
 
 # The version info for the project you're documenting, acts as replacement for
 # |version| and |release|, also used in various other places throughout the
 # built documents.
 
-package_version = get_distribution(setup_cfg["name"]).version
+package_version = get_distribution(project).version
 
 # The short X.Y version.
 version = package_version.split("-", 1)[0]
@@ -91,13 +89,6 @@
 
 # -- Options for HTML output ---------------------------------------------------
 
-# A NOTE ON HTML THEMES
-# The global astropy configuration uses a custom theme, 'bootstrap-astropy',
-# which is installed along with astropy. A different theme can be used or
-# the options for this theme can be modified by overriding some of the
-# variables set in the global configuration. The variables set in the
-# global configuration are listed below, commented out.
-
 # Add any paths that contain custom themes here, relative to this directory.
 # To use a different custom theme, add the directory containing the theme.
 # html_theme_path = []
@@ -160,19 +151,3 @@
 # One entry per manual page. List of tuples
 # (source start file, name, description, authors, manual section).
 man_pages = [("index", project.lower(), project + " Documentation", [author], 1)]
-
-
-## -- Options for the edit_on_github extension ----------------------------------------
-
-if eval(setup_cfg.get("edit_on_github")):
-    extensions += ["sphinx_astropy.ext.edit_on_github"]
-
-    versionmod = __import__(setup_cfg["name"] + ".version")
-    edit_on_github_project = setup_cfg["github_project"]
-    if versionmod.version.release:
-        edit_on_github_branch = "v" + versionmod.version.version
-    else:
-        edit_on_github_branch = "master"
-
-    edit_on_github_source_root = ""
-    edit_on_github_doc_root = "docs"

docs/conf.py

@@ -2,20 +2,24 @@
 name = "naima"
 description = "Derivation of non-thermal particle distributions through MCMC spectral fitting"
 readme = "README.rst"
+authors = [{ name = "Víctor Zabalza", email = "[email protected]" }]
 license = "MIT"
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
         "astropy>=6.1",
-        "emcee",
-        "corner",
-        "matplotlib>=1.4.0",
-        "scipy",
+        "corner>=2.0",
+        "emcee>=3.0",
+        "h5py>=3.14.0",
+        "matplotlib>=3.10.0",
         "numpy>=2.0",
-        "h5py",
-        "pyyaml",
+        "pyyaml>=6.0.2",
+        "scipy>=1.15.3",
 ]
 
+[dependency-groups]
+dev = ["pytest>=8.3.5", "sphinx>=8.0", "sphinx-astropy>=1.9.1"]
+
 [tool.hatch.version]
 source = "vcs"
 

pyproject.toml

@@ -1,4 +1,5 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
+
 """
 `naima` is a Python package for computation of non-thermal radiation from
 relativistic particle populations. It includes tools to perform MCMC fitting of

setup.cfg

@@ -1,7 +1,7 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-from pathlib import Path
 import warnings
 from importlib.util import find_spec
+from pathlib import Path
 
 import astropy.units as u
 import numpy as np

setup.py

@@ -1,13 +1,13 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
-import importlib
+from importlib.util import find_spec
+
 import numpy as np
 from astropy import units as u
 from astropy.constants import c, hbar, m_e, sigma_sb
 from astropy.modeling.physical_models import BlackBody
 from astropy.table import QTable, Table
 from astropy.tests.helper import pytest
 from numpy.testing import assert_allclose
-from importlib.util import find_spec
 
 from naima.models import (
     Bremsstrahlung,

src/naima/__init__.py

@@ -1,18 +1,17 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
 import os
+from pathlib import Path
 
 import astropy.units as u
 import numpy as np
 from astropy.io import ascii
 from astropy.tests.helper import pytest
-from pathlib import Path
 
 from naima.analysis import read_run, save_run
 from naima.model_fitter import InteractiveModelFitter
 from naima.plot import plot_chain, plot_data, plot_fit
 from naima.utils import validate_data_table
 
-
 try:
     import matplotlib
 
@@ -53,9 +52,9 @@ def test_roundtrip(simple_sampler, tmp_path):
     new_blobs = nresult.get_blobs()
     assert sampler_blobs.shape == new_blobs.shape
     j, k = nwalkers // 2, nsteps // 2
-    for l in range(len(sampler_blobs[j][k])):
-        b0 = sampler_blobs[j][k][l]
-        b1 = new_blobs[j][k][l]
+    for l_index in range(len(sampler_blobs[j][k])):
+        b0 = sampler_blobs[j][k][l_index]
+        b1 = new_blobs[j][k][l_index]
         if isinstance(b0, tuple) or isinstance(b0, list):
             for b0m, b1m in zip(b0, b1):
                 assert np.allclose(b0m, b1m)

tests/test_functionfit.py

@@ -1,9 +1,10 @@
 # Licensed under a 3-clause BSD style license - see LICENSE.rst
+from pathlib import Path
+
 import astropy.units as u
 import numpy as np
 from astropy.io import ascii
 from astropy.tests.helper import pytest
-from pathlib import Path
 from numpy.testing import assert_allclose
 
 from naima.utils import (