Merge pull request #72 from karllark/update_tox_2023

Update 2023, codecov failing - can't activate on codecov site, will intestigate.

.github/workflows/tox-tests.yml

@@ -23,10 +23,13 @@ jobs:
         # Github actions supports ubuntu, windows, and macos virtual environments:
         # https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners
         #
-        os: [ubuntu-latest, macos-latest, windows-latest]
+        # Only run on ubuntu by default, but can add other os's to the test matrix here.
+        # For example -- os: [ubuntu-latest, macos-latest, windows-latest]
+        # windows-latest not possible due to how temp files are used in tests currently
+        os: [ubuntu-latest, macos-latest]
 
-        # Test python 3.7, and 3.8 by default.
-        python-ver: [7, 8, 9, 10]
+        # Test python version 3.x
+        python-ver: [9, 10, 11]
 
         # Specify which tox environments to test in this list.
         # tox-env: [cov, alldeps, devdeps, astropylts]
@@ -46,22 +49,22 @@ jobs:
         tox -e py3${{ matrix.python-ver }}-${{ matrix.tox-env }}
 
   # Dev version test
-  dev_test:
-    runs-on: ubuntu-latest
-    if: "!contains(github.event.head_commit.message, '[ci skip]')"
-    steps:
-    - uses: actions/checkout@v1
-    - name: Set up python for astropy, numpy dev test
-      uses: actions/setup-python@v1
-      with:
-        python-version: 3.8
-    - name: Install base dependencies
-      run: |
-        python -m pip install --upgrade pip
-        python -m pip install tox
-    - name: Test with tox
-      run: |
-        tox -e py38-devdeps
+  # dev_test:
+  #   runs-on: ubuntu-latest
+  #   if: "!contains(github.event.head_commit.message, '[ci skip]')"
+  #   steps:
+  #   - uses: actions/checkout@v1
+  #   - name: Set up python for astropy, numpy dev test
+  #     uses: actions/setup-python@v1
+  #     with:
+  #       python-version: 3.8
+  #   - name: Install base dependencies
+  #     run: |
+  #       python -m pip install --upgrade pip
+  #       python -m pip install tox
+  #   - name: Test with tox
+  #     run: |
+  #       tox -e py38-devdeps
 
   # LTS version test
   lts_test:
@@ -72,14 +75,14 @@ jobs:
     - name: Set up python for astropy lts test
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.9
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install tox
     - name: Test with tox
       run: |
-        tox -e py38-astropylts
+        tox -e py39-astropylts
 
   # Coverage test
   cov_test:
@@ -90,14 +93,14 @@ jobs:
     - name: Set up python for coverage test
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
         python -m pip install tox
     - name: Test with tox
       run: |
-        tox -e py38-cov
+        tox -e py311-cov
     - name: Upload coverage to codecov
       uses: codecov/codecov-action@v1
       with:
@@ -120,7 +123,7 @@ jobs:
     - name: Set up Python to build docs with sphinx
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip
@@ -140,7 +143,7 @@ jobs:
     - name: Python codestyle check
       uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install base dependencies
       run: |
         python -m pip install --upgrade pip

.readthedocs.yml

@@ -0,0 +1,18 @@
+version: 2
+
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.12"
+
+python:
+  install:
+    - method: pip
+      path: .
+      extra_requirements:
+        - docs
+        - all
+
+# Don't build any extra formats
+formats: []
+

README.rst

@@ -27,10 +27,6 @@ Build checks/status
    :target: https://codecov.io/gh/BEAST-Fitting/megabeast
    :alt: Test Coverage Status
 
-.. image:: https://img.shields.io/lgtm/grade/python/g/BEAST-Fitting/megabeast.svg?logo=lgtm&logoWidth=18
-    :target: https://lgtm.com/projects/g/BEAST-Fitting/megabeast/context:python
-    :alt: LGTM language grade: Python
-
 .. image:: https://api.codacy.com/project/badge/Grade/584c9ed581c6457381d01a4e86e08916
     :target: https://www.codacy.com/manual/kgordon/megabeast?utm_source=github.com&utm_medium=referral&utm_content=karllark/megabeast&utm_campaign=Badge_Grade
     :alt: Codacy Badge
@@ -81,5 +77,5 @@ more information.
 
 .. _AstroPy: http://www.astropy.org/
 .. _contributing: http://docs.astropy.org/en/stable/index.html#contributing
-.. _developer: http://docs.astropy.org/en/stable/index.html#developer-documentation
+.. _developer: https://docs.astropy.org/en/stable/index_dev.html
 .. _Astropy Code of Conduct:  http://www.astropy.org/about.html#codeofconduct

docs/index.rst

@@ -58,7 +58,7 @@ fixes, code, or documentation (no git or GitHub experience necessary):
 
 * `Coding Guidelines <https://docs.astropy.org/en/stable/development/codeguide.html>`_
 
-* `Developer Documentation <https://docs.astropy.org/en/stable/#developer-documentation>`_
+* `Developer Documentation <https://docs.astropy.org/en/stable/index_dev.html>`_
 
 
 For the complete list of contributors please see the `megabeast

megabeast/__init__.py

@@ -1,9 +1,6 @@
-# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from importlib.metadata import version as _version, PackageNotFoundError
 
-# Packages may add whatever they like to this file, but
-# should keep this content at the top.
-# ----------------------------------------------------------------------------
-from ._astropy_init import *   # noqa
-# ----------------------------------------------------------------------------
-
-__all__ = []
+try:
+    __version__ = _version(__name__)
+except PackageNotFoundError:  # pragma: no cover
+    pass

megabeast/simulations/simulate_av_plots.py → megabeast/old/simulations/simulate_av_plots.py

@@ -5,7 +5,7 @@
 from astropy.io import fits
 
 from beast.tools.read_beast_data import read_sed_data, read_lnp_data
-from beast.physicsmodel.prior_weights_dust import _lognorm, _two_lognorm
+from beast.physicsmodel.priormodel_functions import _lognorm, _two_lognorm
 
 from megabeast.read_input import read_input
 

megabeast/tests/basic_test.py

@@ -0,0 +1,7 @@
+from megabeast.mbsettings import mbsettings
+
+
+def test_basic():
+    mbparams = mbsettings()
+
+    assert isinstance(mbparams, mbsettings)

megabeast/tools/make_naive_maps.py

@@ -36,7 +36,7 @@ def create_naive_maps(stats_filename, pix_size=10.0, verbose=False):
     stat_type = "Exp"
 
     # read in the full brick catalog
-    if type(stats_filename) == str:
+    if isinstance(stats_filename, str):
         stats_filename = [stats_filename]
     cat = Table.read(stats_filename[0])
     if len(stats_filename) > 1:

setup.cfg

@@ -14,7 +14,7 @@ github_project = BEAST-Fitting/megabeast
 [options]
 zip_safe = False
 packages = find:
-python_requires = >=3.6
+python_requires = >=3.9
 setup_requires = setuptools_scm
 install_requires =
     scipy
@@ -55,6 +55,7 @@ omit =
     megabeast/*/tests/*
     megabeast/extern/*
     megabeast/version*
+    megabeast/old/*
     */megabeast/_astropy_init*
     */megabeast/conftest.py
     */megabeast/*setup_package*

tox.ini

@@ -1,24 +1,20 @@
 [tox]
 envlist =
-    py{37,38,39,310}-test{,-alldeps,-devdeps}{,-cov}
-    py{37,38,39,310}-test-numpy{118,119,120,121}
-    py{37,38,39,310}-test-astropy{40,50}
+    py{39,310,311}-test{,-alldeps}{,-cov}
     build_docs
     linkcheck
     codestyle
 requires =
     setuptools >= 30.3.0
     pip >= 19.3.1
 isolated_build = true
-indexserver =
-    NIGHTLY = https://pypi.anaconda.org/scipy-wheels-nightly/simple
 
 [testenv]
 # Suppress display of matplotlib plots generated during docs build
 setenv = MPLBACKEND=agg
 
 # Pass through the following environment variables which may be needed for the CI
-passenv = HOME WINDIR LC_ALL LC_CTYPE CC CI TRAVIS
+passenv = HOME, WINDIR, LC_ALL, LC_CTYPE, CC, CI, TRAVIS
 
 # Run the tests in a temporary directory to make sure that we don't import
 # this package from the source tree
@@ -38,28 +34,13 @@ description =
     devdeps: with the latest developer version of key dependencies
     oldestdeps: with the oldest supported version of key dependencies
     cov: and test coverage
-    numpy118: with numpy 1.18.*
-    numpy119: with numpy 1.19.*
-    numpy120: with numpy 1.20.*
-    numpy121: with numpy 1.21.*
-    astropy40: with astropy 4.0.*
-    astropy50: with astropy 5.0.*
     astropylts: with the latest astropy LTS (currently v5.0)
 
 # The following provides some specific pinnings for key packages
 deps =
-
-    numpy118: numpy==1.18.*
-    numpy119: numpy==1.19.*
-    numpy120: numpy==1.20.*
-    numpy121: numpy==1.21.*
-
-    astropy40: astropy==4.0.*
-    astropy50: astropy==5.0.*
     astropylts: astropy==5.0.*
 
-    devdeps: :NIGHTLY:numpy
-    devdeps: git+https://github.com/astropy/astropy.git#egg=astropy
+    devdeps: PIP_EXTRA_INDEX_URL=https://pypi.anaconda.org/scipy-wheels-nightly/simple
 
 # The following indicates which extras_require from setup.cfg will be installed
 extras =