Merge branch 'main' into profiles

.flake8

@@ -6,9 +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
+    # 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/deploy.yaml

@@ -1,59 +1,37 @@
-name: Deploy
+name: Publish Python distributions to PyPI
+
 on:
   push:
-    branches:
-      - main
+    tags:
+      - '*'
 
 jobs:
-  bump-version:
-    name: SemVer Bump
+  build-n-publish:
+    name: Build and publish to PyPI
     runs-on: ubuntu-latest
-    outputs:
-      new_version: ${{ steps.bump.outputs.new_version }}
-      new_tag: ${{ steps.bump.outputs.new_tag }}
-      previous_tag: ${{ steps.bump.outputs.previous_tag }}
-      previous_version: ${{ steps.bump.outputs.previous_version }}
-      release_type: ${{ steps.bump.outputs.release_type }}
-      changelog: ${{ steps.bump.outputs.changelog }}
-
+    env:
+      ENV_NAME: publish
+      PYTHON: 3.8
     steps:
-      - uses: actions/checkout@v2
-        # Ensure full history is gotten.
+      - uses: actions/checkout@main
         with:
           fetch-depth: 0
-      - name: Get New Version
-        id: bump
-        uses: mathieudutour/[email protected]
-        with:
-          default_bump: false
-          github_token: ${{ secrets.GITHUB_TOKEN }}
 
-
-  deploy:
-    name: Deploy
-    runs-on: ubuntu-latest
-    needs: bump-version
-    if: needs.bump-version.outputs.new_version != null
-    steps:
-      - uses: actions/checkout@master
-      # https://github.com/ansible/pylibssh/blob/1e7b17f/.github/workflows/build-test-n-publish.yml#L146-L151
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v3
         with:
-          python-version: 3.x
-      - name: Create setuptools_scm env variable
-        shell: bash
-        run: |
-          version=${{ needs.bump-version.outputs.new_version }}
-          echo "SETUPTOOLS_SCM_PRETEND_VERSION=$version" >> $GITHUB_ENV
+          python-version: ${{ env.PYTHON }}
+
       - name: Install build
-        run: |
-          python -m pip install build
-          python -m pip install setuptools_scm
-          python setup.py --version
+        run: pip install build
+
       - name: Build a binary wheel and a source tarball
-        run: python -m build
-      - name: Publish distribution 📦 to PyPI
+        run: |
+          python -m build
+
+      - name: Publish to PyPI
+        if: startsWith(github.event.ref, 'refs/tags')
         uses: pypa/gh-action-pypi-publish@master
         with:
+          user: __token__
           password: ${{ secrets.pypi_password }}

.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/[email protected]
+        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@v3
+        if: always()
+        with:
+          name: ${{ matrix.demo }}
+          path: output-${{ matrix.demo }}.ipynb

.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/[email protected]
+        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

.github/workflows/testsuite.yaml

@@ -25,7 +25,7 @@ jobs:
         uses: conda-incubator/[email protected]
         with:
           auto-update-conda: true
-#          mamba-version: "*"
+          mamba-version: "*"
           channels: conda-forge,defaults
           channel-priority: true
           python-version: ${{ matrix.python-version }}

.gitignore

@@ -1,24 +1,105 @@
+__pycache__/
+*.py[cod]
+*$py.class
 
-\.idea/
+# C extensions
+*.so
 
-__pycache__/
+# 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
 
-py21cmsense\.egg-info/
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
 
-*.pyc
-docs/_build/
-.ipynb_checkpoints/
-pip-wheel-metadata/
+# Unit test / coverage reports
+htmlcov/
 .tox/
-*.pkl
-*.npz
-*.png
+.nox/
 .coverage
 .coverage.*
 .cache
+nosetests.xml
 coverage.xml
-*,cover
-.pytest_cache
+*.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

.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: v4.5.0
   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: 6.1.0
   hooks:
   - id: flake8
     additional_dependencies:
@@ -39,22 +39,22 @@ repos:
 
 
 - repo: https://github.com/psf/black
-  rev: 22.3.0
+  rev: 23.11.0
   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: v3.15.0
   hooks:
   -   id: pyupgrade
       args: [--py38-plus]