21cmSense 2.0.0__tar.gz

21cmSense-2.0.0/.coveragerc

@@ -0,0 +1,8 @@
+[run]
+omit = */tests/*
+
+[report]
+omit = */tests/*
+exclude_lines =
+    pragma: no cover
+    @abstract

21cmSense-2.0.0/.flake8

@@ -0,0 +1,40 @@
+[flake8]
+ignore =
+    E203
+    E266
+    E501
+    W503
+    F403
+    F401
+    # 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 =
+    class
+    func
+    mod
+    data
+    const
+    meth
+    attr
+    exc
+    obj
+rst-directives =
+    note
+    warning
+    versionadded
+    versionchanged
+    deprecated
+    seealso
+per-file-ignores =
+    tests/*:D
+    setup.py:D

21cmSense-2.0.0/.github/dependabot.yml

@@ -0,0 +1,21 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: "/"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/.github/workflows"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/docs"
+    schedule:
+      interval: monthly
+  - package-ecosystem: pip
+    directory: "/"
+    schedule:
+      interval: monthly
+    versioning-strategy: lockfile-only
+    allow:
+      - dependency-type: "all"

21cmSense-2.0.0/.github/labels.yml

@@ -0,0 +1,85 @@
+---
+# Labels names are important as they are used by Release Drafter to decide
+# regarding where to record them in changelog or if to skip them.
+#
+# The repository labels will be automatically configured using this file and
+# the GitHub Action https://github.com/marketplace/actions/github-labeler.
+- name: "API breaking"
+  description: Breaking Changes
+  color: e305fc
+- name: "good first issue"
+  description: Good for newcomers
+  color: 7057ff
+
+- name: "status: duplicate"
+  description: This issue or pull request already exists
+  color: d93f0b
+- name: "status: invalid"
+  description: Invalid issue or pull request
+  color: d93f0b
+- name: "status: requires discussion"
+  description: Issue requires further discussion before implementation
+  color: f71bd2
+- name: "status: requires research"
+  description: Issue requires further research before implementation
+  color: "d93f0b"
+- name: "status: wontfix"
+  description: Valid issue, but out of scope for future fixes
+  color: "d93f0b"
+
+- name: "type: maint: dependencies"
+  description: Pull requests that update a dependency file
+  color: "0366d6"
+- name: "type: maint: documentation"
+  description: Improvements or additions to documentation
+  color: "0075ca"
+- name: "type: maint: refactoring"
+  description: Refactoring
+  color: ef67c4
+- name: "type: maint: removal"
+  description: Removals and Deprecations
+  color: 9ae7ea
+- name: "type: maint: style"
+  description: Style
+  color: c120e5
+- name: "type: maint: build"
+  description: Build System and Dependencies
+  color: bfdadc
+
+- name: "type: accuracy"
+  description: "Enhancement that improves accuracy"
+  color: "bfd4f2"
+- name: "type: bug"
+  description: Something isn't working
+  color: d73a4a
+- name: "type: feature: ui"
+  description: New feature that adds functionality for the user
+  color: "0e8a16"
+- name: "type: feature: physical"
+  description: New feature that adds new analysis/physical model
+  color: "0e8a16"
+- name: "type: testing"
+  description: Testing improvements
+  color: b1fc6f
+- name: "type: performance: memory"
+  description: Performance improvements that reduce memory usage
+  color: "016175"
+- name: "type: performance: cpu"
+  description: Performance improvements that reduce walltime
+  color: "016175"
+- name: "type: ci"
+  description: Updates to CI (GH actions, RTD, etc.)
+  color: "000000"
+- name: "type: question"
+  description: A question about the code or documentation
+  color: d876e3
+
+- name: "priority: low"
+  description: Low priority
+  color: "BFD4F2"
+- name: "priority: medium"
+  description: Medium priority
+  color: "E99695"
+- name: "priority: high"
+  description: High priority
+  color: "B60205"

21cmSense-2.0.0/.github/release-drafter.yml

@@ -0,0 +1,66 @@
+# See https://github.com/marketplace/actions/release-drafter for configuration
+categories:
+  - title: ":boom: Breaking Changes"
+    label: "breaking"
+  - title: ":rocket: Features"
+    label: "enhancement"
+  - title: ":fire: Removals and Deprecations"
+    label: "removal"
+  - title: ":beetle: Fixes"
+    label: "bug"
+  - title: ":racehorse: Performance"
+    label: "performance"
+  - title: ":rotating_light: Testing"
+    label: "testing"
+  - title: ":construction_worker: Continuous Integration"
+    label: "ci"
+  - title: ":books: Documentation"
+    label: "documentation"
+  - title: ":hammer: Refactoring"
+    label: "refactoring"
+  - title: ":lipstick: Style"
+    label: "style"
+  - title: ":package: Dependencies"
+    labels:
+      - "dependencies"
+      - "build"
+name-template: 'v$RESOLVED_VERSION'
+tag-template: 'v$RESOLVED_VERSION'
+autolabeler:
+  - label: 'documentation'
+    files:
+      - '*.md'
+    branch:
+      - '/.*docs{0,1}.*/'
+  - label: 'bug'
+    branch:
+      - '/fix.*/'
+    title:
+      - '/fix/i'
+  - label: 'enhancement'
+    branch:
+      - '/feature.*|add-.+/'
+    title:
+      - '/feat:.+|feature:.+/i'
+  - label: "removal"
+    title:
+      - "/remove .*/i"
+  - label: "performance"
+    title:
+      - "/.* performance .*/i"
+  - label: "ci"
+    files:
+      - '.github/*'
+      - '.pre-commit-config.yaml'
+      - '.coveragrc'
+  - label: "style"
+    files:
+      - ".flake8"
+  - label: "refactoring"
+    title:
+      - "/.* refactor.*/i"
+
+template: |
+  ## Changes
+
+  $CHANGES

21cmSense-2.0.0/.github/workflows/auto-merge-deps.yml

@@ -0,0 +1,14 @@
+name: auto-merge
+
+on:
+  pull_request:
+
+jobs:
+  auto-merge:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: ahmadnassri/action-dependabot-auto-merge@v2
+        with:
+          target: minor
+          github-token: ${{ secrets.AUTO_MERGE }}

21cmSense-2.0.0/.github/workflows/check-build.yml

@@ -0,0 +1,27 @@
+name: Check Distribution Build
+
+on: push
+
+jobs:
+  check-build:
+    name: Twine Check
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Install Build Tools
+        run: pip install build twine
+
+      - name: Build a binary wheel
+        run: |
+          python -m build .
+
+      - name: Check Distribution
+        run: |
+          twine check dist/*

21cmSense-2.0.0/.github/workflows/deploy.yaml

@@ -0,0 +1,34 @@
+name: Publish Python distributions to PyPI
+
+on:
+  release:
+    types: [published]
+
+jobs:
+  build-n-publish:
+    name: Build and publish to PyPI
+    runs-on: ubuntu-latest
+    env:
+      ENV_NAME: publish
+      PYTHON: "3.10"
+    permissions:
+      id-token: write  # IMPORTANT: this permission is mandatory for trusted publishing
+    steps:
+      - uses: actions/checkout@main
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ env.PYTHON }}
+
+      - name: Install build
+        run: pip install build
+
+      - name: Build a binary wheel and a source tarball
+        run: |
+          python -m build
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@v1.8.11

21cmSense-2.0.0/.github/workflows/labeler.yaml

@@ -0,0 +1,18 @@
+name: Labeler
+
+on:
+  push:
+    branches:
+      - main
+
+jobs:
+  labeler:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the repository
+        uses: actions/checkout@v4
+
+      - name: Run Labeler
+        uses: crazy-max/ghaction-github-labeler@v5.0.0
+        with:
+          skip-delete: false

21cmSense-2.0.0/.github/workflows/release-draft.yml

@@ -0,0 +1,23 @@
+name: Update Draft Release
+
+on:
+  push:
+    branches: main
+
+jobs:
+  draft-release:
+    name: Update Draft Release
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.10"
+
+      - name: Publish the release notes
+        uses: release-drafter/release-drafter@v5.25.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

21cmSense-2.0.0/.github/workflows/run-docs-code.yaml

@@ -0,0 +1,56 @@
+name: Run Demo
+on: [push, pull_request]
+
+
+jobs:
+  tests:
+    name: Run Demo
+    runs-on: ubuntu-latest
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      ENV_NAME: testing
+    strategy:
+      fail-fast: false
+      matrix:
+        demo: ["getting_started", "understanding_21cmsense", "reproducing_pober_2015"]
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 1
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3.0.1
+        with:
+          auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          python-version: "3.10"
+          environment-file: ci/${{ env.ENV_NAME }}.yaml
+          activate-environment: ${{ env.ENV_NAME }}
+
+      - name: Conda Info
+        run: |
+          conda info
+          python --version
+
+      - name: Install Deps
+        run: |
+          pip install .
+          pip install papermill ipykernel
+          conda list
+
+      - name: Install ipykernel
+        run: python -m ipykernel install --user --name sense --display-name "sense"
+
+      - name: Run Notebook
+        run: |
+          papermill -k sense docs/tutorials/${{ matrix.demo }}.ipynb output-${{ matrix.demo }}.ipynb
+
+      - uses: actions/upload-artifact@v4
+        if: always()
+        with:
+          name: ${{ matrix.demo }}
+          path: output-${{ matrix.demo }}.ipynb

21cmSense-2.0.0/.github/workflows/test-deploy.yaml

@@ -0,0 +1,39 @@
+name: Test Deploy
+on: push
+
+jobs:
+  test-deploy:
+    name: Test Deploy
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@master
+      # https://github.com/ansible/pylibssh/blob/1e7b17f/.github/workflows/build-test-n-publish.yml#L146-L151
+      - name: Get history and tags for SCM versioning to work
+        run: |
+          git fetch --prune --unshallow
+          git fetch --depth=1 origin +refs/tags/*:refs/tags/*
+          git describe --tags
+          git describe --tags $(git rev-list --tags --max-count=1)
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: 3.x
+      - name: Install build
+        run: |
+          python -m pip install build
+          python -m pip install setuptools_scm
+          python setup.py --version
+      - name: Create setuptools_scm env variable
+        shell: bash
+        run: |
+          wget https://gist.github.com/plaplant/0902f09e59166bac742bbd554f3cd2f9/raw/make_dev_version.sh -O ../make_dev_version.sh
+          version=$(bash ../make_dev_version.sh)
+          echo "SETUPTOOLS_SCM_PRETEND_VERSION=$version" >> $GITHUB_ENV
+      - name: Build a binary wheel and a source tarball
+        run: python -m build
+      - name: Publish distribution 📦 to Test PyPI
+        if: github.event_name == 'push' && github.ref == 'refs/heads/main'
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.test_pypi_password }}
+          repository_url: https://test.pypi.org/legacy/

21cmSense-2.0.0/.github/workflows/test-with-warnings.yaml

@@ -0,0 +1,47 @@
+name: Warnings Test
+on: [pull_request]
+
+
+jobs:
+  tests:
+    name: Test With Warnings
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      ENV_NAME: testing
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.10"]
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 1
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3.0.1
+        with:
+          auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/${{ env.ENV_NAME }}.yaml
+          activate-environment: ${{ env.ENV_NAME }}
+
+      - name: Conda Info
+        run: |
+          conda info
+          python --version
+
+      - name: Install Test Deps
+        run: |
+          pip install .[test]
+          conda list
+
+      - name: Run Tests
+        run: |
+          python -m pytest -W error

21cmSense-2.0.0/.github/workflows/testsuite.yaml

@@ -0,0 +1,53 @@
+name: Test Suite
+on: [push, pull_request]
+
+
+jobs:
+  tests:
+    name: Test Suite
+    runs-on: ${{ matrix.os }}
+    defaults:
+      run:
+        shell: bash -l {0}
+    env:
+      ENV_NAME: testing
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-latest, macos-latest]
+        python-version: [3.9, "3.10"]
+    steps:
+      - uses: actions/checkout@master
+        with:
+          fetch-depth: 1
+
+      - name: Setup Miniconda
+        uses: conda-incubator/setup-miniconda@v3.0.1
+        with:
+          auto-update-conda: true
+          mamba-version: "*"
+          channels: conda-forge,defaults
+          channel-priority: true
+          python-version: ${{ matrix.python-version }}
+          environment-file: ci/${{ env.ENV_NAME }}.yaml
+          activate-environment: ${{ env.ENV_NAME }}
+
+      - name: Conda Info
+        run: |
+          conda info
+          python --version
+
+      - name: Install Test Deps
+        run: |
+          pip install .[test]
+          conda list
+
+      - name: Run Tests
+        run: |
+          python -m pytest --cov=py21cmsense --cov-config=.coveragerc --cov-report xml:./coverage.xml --junitxml=test-reports/xunit.xml
+
+      - uses: codecov/codecov-action@v3
+        if: success()
+        with:
+          file: ./coverage.xml #optional
+          token: ${{ secrets.CODECOV_TOKEN }} #required

21cmSense-2.0.0/.gitignore

@@ -0,0 +1,106 @@
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Sphinx documentation
+docs/_build/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+.idea/
+
+
+
+pip-wheel-metadata/
+.tox/
+*.pkl
+*.png
+.vscode/
+*MHz.h5
+docs/reference/_autosummary
+*.egg-info/

21cmSense-2.0.0/.isort.cfg

@@ -0,0 +1,11 @@
+[settings]
+line_length=88
+indent='    '
+skip=.tox,.venv,build,dist
+known_standard_library=setuptools,pkg_resources
+known_test=pytest
+known_first_party=21cmSense
+sections=FUTURE,STDLIB,TEST,THIRDPARTY,FIRSTPARTY,LOCALFOLDER
+default_section=THIRDPARTY
+multi_line_output=3
+profile=black