Merge branch 'master' into update_Rmax2

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 3.1.2
+current_version = 3.3.1
 commit = False
 tag = False
 

.flake8

@@ -6,10 +6,14 @@ ignore =
  W503
  F403
  F401
- N803 # Naming upper/lowercase -- too hard right now.
- N806 # Naming upper/lowercase -- too hard right now.
- N802 # Naming upper/lowercase -- too hard right now.
- D401 # Docstring in imperative mood. This should *not* be the case for @property's, but can't ignore them atm.
+ # Naming upper/lowercase -- too hard right now.
+ N803
+ # Naming upper/lowercase -- too hard right now.
+ N806
+ # Naming upper/lowercase -- too hard right now.
+ N802
+ # Docstring in imperative mood. This should *not* be the case for @property's, but can't ignore them atm.
+ D401
 max-line-length = 88
 max-complexity = 40
 docstring-convention=numpy

.github/workflows/publish-to-pypi.yaml

@@ -5,7 +5,7 @@ on: push
 jobs:
  build-n-publish:
  name: Deploy
- runs-on: ubuntu-18.04
+ runs-on: ubuntu-latest
  if: "!contains(github.event.pull_request.labels.*.name, 'auto-pr')"
  steps:
  - uses: actions/checkout@master
@@ -16,13 +16,13 @@ jobs:
  git fetch --depth=1 origin +refs/tags/*:refs/tags/*
  git describe --tags
  git describe --tags $(git rev-list --tags --max-count=1)
- - name: Set up Python 3.7
+ - name: Set up Python 3.10
  uses: actions/setup-python@v1
  with:
- python-version: 3.7
- - name: Install pep517
+ python-version: "3.10"
+ - name: Install build
  run: |
- python -m pip install pep517 --user
+ python -m pip install build
  python -m pip install setuptools_scm
  python setup.py --version
  - name: Create setuptools_scm env variable
@@ -33,19 +33,20 @@ jobs:
  version=$(bash ../make_dev_version.sh)
  echo "SETUPTOOLS_SCM_PRETEND_VERSION=$version" >> $GITHUB_ENV
  - name: Build a source tarball
- run: python -m pep517.build --source --out-dir dist .
+ run: python -m build --sdist .
+
  # deploy to Test PyPI on any push except when merging to production, since that will
  # already exist, and thus fail.
  - name: Publish distribution 📦 to Test PyPI
  if: ${{ !contains(github.ref, 'production') }}
- uses: pypa/gh-action-pypi-publish@master
+ uses: pypa/gh-action-pypi-publish@release/v1
  with:
  password: ${{ secrets.test_pypi_password }}
  repository_url: https://test.pypi.org/legacy/
  # deploy to actual PyPI only when a tag is pushed (which should happen only
  # automatically on production)
  - name: Publish distribution 📦 to PyPI
  if: startsWith(github.ref, 'refs/tags')
- uses: pypa/gh-action-pypi-publish@master
+ uses: pypa/gh-action-pypi-publish@release/v1
  with:
  password: ${{ secrets.pypi_password }}

.github/workflows/test_suite.yaml

@@ -20,86 +20,92 @@ jobs:
  ENV_NAME: tests
  PYTHON: ${{ matrix.python-version }}
  OS: ${{ matrix.os }}
+ CC: gcc
  name: Testing
- # needs: [linter]
  runs-on: ${{ matrix.os }}
  strategy:
  fail-fast: false
  matrix:
  os: [ubuntu-latest, macos-latest]
- python-version: [3.6, 3.7, 3.8]
+ python-version: [3.7, 3.8, 3.9, "3.10"]
+ defaults:
+ run:
+ # Adding -l {0} ensures conda can be found properly in each step
+ shell: bash -l {0}
  steps:
  - uses: actions/checkout@master
  with:
+ ref: ${{ github.event.pull_request.head.sha }}
  fetch-depth: 0
- - name: Get Miniconda MacOSX
- if: matrix.os == 'macos-latest'
- run: |
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O $HOME/miniconda.sh;
- bash $HOME/miniconda.sh -b -p $HOME/miniconda
- - name: Get Miniconda Linux
- if: matrix.os == 'ubuntu-latest'
- run: |
- wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O $HOME/miniconda.sh;
- bash $HOME/miniconda.sh -b -p $HOME/miniconda
- - name: Logging
+
+ - name: Print head git commit message
+ id: get_head_commit_message
+ run: echo "commit_message=$(git show -s --format=%s)" >> "$GITHUB_ENV"
+
+ - name: Setup Miniconda
+ uses: conda-incubator/[email protected]
+ with:
+ # auto-update-conda: true
+ miniconda-version: "latest"
+ python-version: ${{ matrix.python-version }}
+ environment-file: ci/${{ matrix.os }}-env.yml
+ activate-environment: tests
+ channel-priority: strict
+ use-only-tar-bz2: true
+
+ - name: Conda Info
  run: |
- echo ${{ github.event.commits }}
- echo ${{ github.event.commits[0] }}
+ conda info -a
+ conda list
+ conda config --show-sources
+ conda config --show
+ printenv | sort
+
  - name: Make it a Debug Run
- if: "contains(github.event.payload.commits[0].message, 'ci debug')"
+ if: "contains(env.commit_message, 'ci debug')"
  run: |
  echo "log_level=ULTRA_DEBUG" >> $GITHUB_ENV
- echo "extra_pytest_args='-s -k test_perturb_field_data --log-level-21=DEBUG'" >> $GITHUB_ENV
- - name: 'Log Commit Message'
- run: echo ${{ github.event.commits[0].message }}
+ echo "extra_pytest_args=-s -k "test_power_spectra_lightcone[mdz_tsfluct_nthreads]" --log-level-21=DEBUG" >> $GITHUB_ENV
+
  - name: Make it a Normal Run
- if: "!contains(github.event.commits[0].message, 'ci debug')"
+ if: "!contains(env.commit_message, 'ci debug')"
  run: |
  echo "log_level=INFO" >> $GITHUB_ENV
  echo "extra_pytest_args=" >> $GITHUB_ENV
- - name: Setup Environment
- run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- ./ci/install_conda.sh
- - name: Install Dependencies
- run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- source activate ${ENV_NAME}
- conda env update -f ci/test-env.yml
+
  - name: Get C Libraries Linux
  if: matrix.os == 'ubuntu-latest'
  run: |
  sudo apt-get install libfftw3-dev
  sudo apt-get install libgsl0-dev
- - name: Get C Libraries MacOSX
- if: matrix.os == 'macos-latest'
- run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- source activate $ENV_NAME
- conda install gsl
- conda install -c conda-forge fftw
- conda install -c conda-forge/label/cf201901 gcc
+
  - name: Install 21cmFAST Linux
  if: matrix.os == 'ubuntu-latest'
  run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- source activate $ENV_NAME
  LOG_LEVEL=${{ env.log_level }} pip install .
+
  - name: Install 21cmFAST MacOS
  if: matrix.os == 'macos-latest'
  run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- source activate $ENV_NAME
  LOG_LEVEL=${{ env.log_level }} CFLAGS="-isysroot /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk" pip install .
+
  - name: Run Tests
  run: |
- export PATH="$HOME/miniconda/bin:$PATH"
- source activate $ENV_NAME
- python -m pytest -l --cov=py21cmfast --cov-config=.coveragerc -vv --cov-report xml:./coverage.xml --durations=25 ${{ env.extra_pytest_args }}
- - uses: codecov/[email protected]
+ python -m pytest -n 2 -l ${{ env.extra_pytest_args }} --cov=py21cmfast --cov-config=.coveragerc -vv --cov-report xml:./coverage.xml --durations=25 --plots=testplots
+
+ - name: Archive Integration Test Plots
+ if: always() && contains(env.commit_message, 'ci debug')
+ uses: actions/upload-artifact@v3
+ with:
+ name: integration-test-plots-${{ matrix.os }}-${{ matrix.python-version }}
+ path: |
+ testplots/*.pdf
+
+ - uses: codecov/codecov-action@v3
  if: matrix.os == 'ubuntu-latest' && success() && !contains(github.event.pull_request.labels.*.name, 'auto-pr')
  with:
- file: ./coverage.xml # optional
  fail_ci_if_error: true
  verbose: true
+ token: ${{ secrets.CODECOV_TOKEN }}
+
+# CC=$HOME/miniconda/envs/$ENV_NAME/bin/gcc

.gitignore

@@ -52,3 +52,5 @@ c2r*
 r2c*
 plots/
 .vscode/
+src/21cmfast/_version.py
+src/py21cmfast/_version.py

.pre-commit-config.yaml

@@ -1,8 +1,8 @@
 exclude: '(^docs/conf.py|^src/py21cmfast/_data/|changethelog.py)'
 
 repos:
- - repo: git://github.com/pre-commit/pre-commit-hooks
- rev: v4.0.1
+ - repo: https://github.com/pre-commit/pre-commit-hooks
+ rev: v4.4.0
  hooks:
  - id: trailing-whitespace
  - id: check-added-large-files
@@ -16,43 +16,42 @@ repos:
  - id: requirements-txt-fixer
  - id: mixed-line-ending
  args: ['--fix=no']
- - repo: https://gitlab.com/pycqa/flake8
- rev: 3.9.2 # pick a git hash / tag to point to
+ - repo: https://github.com/pycqa/flake8
+ rev: 6.1.0 # pick a git hash / tag to point to
  hooks:
  - id: flake8
  additional_dependencies:
  - flake8-quotes
- - flake8-comprehensions
+# - flake8-comprehensions # no support for flake8 v6
  - flake8-builtins
- - flake8-eradicate
+ # - flake8-eradicate # no support for flake8 v6
  - pep8-naming
  - flake8-pytest
  - flake8-docstrings
  - flake8-rst-docstrings
  - flake8-rst
- - flake8-copyright
- - flake8-ownership
+ # - flake8-copyright # no support flor flake8 v6
  - flake8-print
 
  - repo: https://github.com/psf/black
- rev: 21.6b0
+ rev: 23.9.1
  hooks:
  - id: black
 
- - repo: https://github.com/pre-commit/mirrors-isort
- rev: v5.9.2
+ - repo: https://github.com/PyCQA/isort
+ 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
  - id: rst-directive-colons
  - id: rst-inline-touching-normal
 
  - repo: https://github.com/asottile/pyupgrade
- rev: v2.21.0
+ rev: v3.11.0
  hooks:
  - id: pyupgrade
  args: [--py36-plus]

.readthedocs.yml

@@ -14,10 +14,3 @@ formats: all
 
 conda:
  environment: docs/environment.yaml
-
-# Optionally set the version of Python and requirements required to build the docs
-# We don't install 21cmFAST -- we just load it into the path in conf.py, and mock
-# out the C stuff.
-python:
- version: 3.7
- system_packages: true