Cleaning package for release

.github/workflows/pr_standards.yml → .github/workflows/check_standards.yml

@@ -2,10 +2,10 @@ name: Check Code Standard Adherence
 env:
   CLONE_PATH: ${{ github.workspace }}
 on:
+  push:
+    branches: [main, develop]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [main, develop]
 
 jobs:
   build:

.github/workflows/pr_test.yml → .github/workflows/run_tests.yml

@@ -1,10 +1,9 @@
-name: Test PRs into develop & main
-
+name: Test package & measure coverage
 on:
+  push:
+    branches: [main, develop]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [main, develop]
 
 jobs:
   tests:
@@ -13,7 +12,7 @@ jobs:
     # packaging.
     strategy:
       matrix:
-        os: [ubuntu-20.04, ubuntu-22.04, macos-12, macos-13, macos-latest]
+        os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04, macos-12, macos-13, macos-14]
         python-version: ["3.9", "3.10", "3.11", "3.12"]
     runs-on: ${{ matrix.os }}
     env:

.github/workflows/test_book.yml

@@ -3,10 +3,10 @@ env:
   CLONE_PATH:    ${{ github.workspace }}
   EXAMPLES_BOOK: ${{ github.workspace }}/book/_build/html
 on:
+  push:
+    branches: [main, develop]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [main, develop]
 
 jobs:
   build:

.github/workflows/pr_docs.yml → .github/workflows/test_docs.yml

@@ -1,16 +1,13 @@
-# TODO: Remove pandoc installation after example notebooks moved out of sphinx
-# docs?  Check with tox and setup.py as well.
-
-name: Test PR doc builds in develop & main
+name: Test sphinx docs build
 env:
   CLONE_PATH: ${{ github.workspace }}
   HTML_DOCS:  ${{ github.workspace }}/docs/build_html
   PDF_DOCS:   ${{ github.workspace }}/docs/build_pdf
 on:
+  push:
+    branches: [main, develop]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [main, develop]
 
 jobs:
   build:

.github/workflows/test_tools.yml

@@ -1,10 +1,10 @@
 name: Test Taweret tools
 
 on:
+  push:
+    branches: [main, develop]
   pull_request:
-    branches:
-      - main
-      - develop
+    branches: [main, develop]
 
 jobs:
   test_tools:

.readthedocs.yaml

@@ -1,9 +1,5 @@
 # Read the Docs configuration file for Sphinx projects
 # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
-#
-# TODO: Set fail_on_warning to true once the example notebooks are moved out of
-# the sphinx docs.  The only remaining errors/warnings on doc builds is from
-# those.
 
 version: 2
 
@@ -14,7 +10,7 @@ build:
 
 sphinx:
   configuration: docs/source/conf.py
-  fail_on_warning: false
+  fail_on_warning: true
 
 formats:
   - pdf

docs/source/conf.py

@@ -34,8 +34,7 @@
 extensions = [
     'sphinx.ext.autodoc',
     'sphinx.ext.viewcode',
-    'sphinx.ext.napoleon',
-    'nbsphinx'
+    'sphinx.ext.napoleon'
 ]
 
 # Add any paths that contain templates here, relative to this directory.

docs/source/installation.rst

@@ -27,6 +27,14 @@ Prerequisites
 
 The Trees module depends on OpenMPI. Please ensure OpenMPI is installed with shared/built libraries prior to using the Trees module.
 
+The list of dependences is as short as possible to keep the installation process streamlined and allow for minimal, clean installations; however, if a user would like to run 
+the Jupyter notebooks in the associated Jupyter Book, dependences for the notebooks will need to be installed in the relevant environment.
+These dependences are commented out in the Jupyter notebooks, but can be uncommented and quickly installed.
+
+The `bilby` sampler comes with the ability to use a suite of samplers---in the case of Taweret, we also have not listed all
+samplers as dependences. However, the user can (and should) install any samplers that they wish to use and `bilby` will be able
+to use them through its wrapper in the Taweret package.
+
 
 Windows Users
 --------------

pyproject.toml

@@ -18,25 +18,14 @@ description = "A python package for Bayesian model mixing"
 readme = "README.md"
 license = {file = "LICENSE"}
 requires-python = ">=3.9"
+# We request that users who want to use non-default bilby samplers (e.g.,
+# ptemcee) manually install the related packages first.
 dependencies = [
     "numpy>=1.20.3",
     "matplotlib",
     "scipy>=1.7.0",
-    "seaborn",
-    "emcee",
-    "corner",
-    "scikit-learn",
-    "cycler",
-    "statistics",
     "bilby",
-    "ptemcee",
-    "sphinx_rtd_theme",
-    "sphinxcontrib-bibtex",
-    "nbsphinx",
-    "pandoc",
     "pytest",
-    "pytest-cov",
-    "Pyarrow",
     "openbtmixing",
 ]
 classifiers = [

tox.ini

@@ -76,6 +76,8 @@ commands =
 # be used for official builds and testing.
 description = Generate Taweret examples in jupyterbook
 deps =
+    ptemcee
+    seaborn
     jupyter-book
 commands = 
     jupyter-book build --all --warningiserror {env:BOOK_ROOT}
@@ -87,6 +89,8 @@ commands =
 # through the cracks.
 description = Regenerate Taweret jupyterbook as it is developed
 deps =
+    ptemcee
+    seaborn
     jupyter-book
 commands = 
     jupyter-book build {env:BOOK_ROOT}