test: reproduce Pober+2014 results

.flake8

@@ -6,11 +6,16 @@ ignore =
  W503
  F403
  F401
- D401 # Imperative mood -- doesn't work for cached-property.
- N802 # TODO: remove this (function name should be lower-case)
- B019 # no using lru_cache on methods
- G004 # logging uses f-string
- D107 # no docstring in __init__
+ # Imperative mood -- doesn't work for cached-property.
+ D401
+ # TODO: remove this (function name should be lower-case)
+ N802
+ # no using lru_cache on methods
+ B019
+ # logging uses f-string
+ G004
+ # no docstring in __init__
+ D107
 max-line-length = 88
 max-complexity = 18
 rst-roles =

.github/workflows/run-docs-code.yaml

@@ -14,7 +14,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- demo: ["getting_started", "understanding_21cmsense"]
+ demo: ["getting_started", "understanding_21cmsense", "reproducing_pober_2015"]
  steps:
  - uses: actions/checkout@master
  with:
@@ -27,7 +27,7 @@ jobs:
  mamba-version: "*"
  channels: conda-forge,defaults
  channel-priority: true
- python-version: ${{ matrix.python-version }}
+ python-version: "3.10"
  environment-file: ci/${{ env.ENV_NAME }}.yaml
  activate-environment: ${{ env.ENV_NAME }}
 
@@ -50,6 +50,7 @@ jobs:
  papermill -k sense docs/tutorials/${{ matrix.demo }}.ipynb output-${{ matrix.demo }}.ipynb
 
  - uses: actions/upload-artifact@v3
+ if: always()
  with:
  name: ${{ matrix.demo }}
  path: output-${{ matrix.demo }}.ipynb

.github/workflows/test-with-warnings.yaml

@@ -14,7 +14,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- os: [ubuntu-latest, macos-latest, windows-latest]
+ os: [ubuntu-latest, macos-latest]
  python-version: ["3.10"]
  steps:
  - uses: actions/checkout@master

.github/workflows/testsuite.yaml

@@ -14,7 +14,7 @@ jobs:
  strategy:
  fail-fast: false
  matrix:
- os: [ubuntu-latest, macos-latest, windows-latest]
+ os: [ubuntu-latest, macos-latest]
  python-version: [3.9, "3.10"]
  steps:
  - uses: actions/checkout@master

.gitignore

@@ -99,7 +99,6 @@ cython_debug/
 pip-wheel-metadata/
 .tox/
 *.pkl
-*.npz
 *.png
 .vscode/
 *MHz.h5

.pre-commit-config.yaml

@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
 
 repos:
 - repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v4.2.0
+ rev: v4.4.0
  hooks:
  - id: trailing-whitespace
  - id: check-added-large-files
@@ -17,7 +17,7 @@ repos:
  args: ['--fix=no']
 
 - repo: https://github.com/PyCQA/flake8
- rev: 4.0.1
+ rev: 6.0.0
  hooks:
  - id: flake8
  additional_dependencies:
@@ -39,22 +39,22 @@ repos:
 
 
 - repo: https://github.com/psf/black
- rev: 22.3.0
+ rev: 23.7.0
  hooks:
  - id: black
 
 - repo: https://github.com/PyCQA/isort
- rev: 5.10.1
+ rev: 5.12.0
  hooks:
  - id: isort
 
 - repo: https://github.com/pre-commit/pygrep-hooks
- rev: v1.9.0
+ rev: v1.10.0
  hooks:
  - id: rst-backticks
 
 - repo: https://github.com/asottile/pyupgrade
- rev: v2.32.0
+ rev: v3.9.0
  hooks:
  - id: pyupgrade
  args: [--py38-plus]

docs/conf.py

@@ -45,11 +45,8 @@
  "issue": ("https://github.com/steven-murray/21cmSense/issues/%s", "#"),
  "pr": ("https://github.com/steven-murray/21cmSense/pull/%s", "PR #"),
 }
-# on_rtd is whether we are on readthedocs.org
-on_rtd = os.environ.get("READTHEDOCS", None) == "True"
 
-if not on_rtd: # only set the theme if we're building docs locally
- html_theme = "sphinx_rtd_theme"
+html_theme = "furo"
 
 html_use_smartypants = True
 html_last_updated_fmt = "%b %d, %Y"

docs/environment.yml

@@ -21,5 +21,6 @@ dependencies:
  - pandoc
  - pip
  - python=3.10
- - sphinx_rtd_theme
  - setuptools_scm
+ - pip:
+ - furo

docs/tutorials.rst

@@ -9,3 +9,4 @@ The following introductory tutorials will help you get started with ``21cmSense`
  tutorials/getting_started
  tutorials/understanding_21cmsense
  tutorials/cli_tutorial
+ tutorials/reproducing_pober_2015