Merge pull request #88 from joezuntz/interactive-use to make CosmoSIS…

… 3.0

- Allow more configuration of the `run_cosmosis` and `run_postprocess` functions, for use from Jupyter or other interactive notebooks.
- Add the `cosmosis-campaign` tool to manage suites of related runs.
- Allow output in `astropy` table format in interactive mode.
- Extensive changes to logging - we now exclusively use cosmosis.logs for anything that is printed during main sampling
- - The `quiet` option is deprecated in favour of more fine-grained logging control.
- Tidy up the output in general
- Update the setup script to avoid the deprecated distutils.
- Deal with various deprecation warnings
- Modify the format of the tables output by the "statistics" postprocessor so they can be read in astropy.
- Fix corner plots so you can put multiple chains on the same axes.
- Allow using MPI pools with general communicator objects - should make it possible to run under MPI in jupyter eventually.

.github/workflows/ci.yml

@@ -17,28 +17,28 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9, "3.10", 3.11]
+        python-version: [3.7, 3.8, 3.9, "3.10", 3.11]
         os: [ubuntu-20.04, macos-latest]
         include:
           - os: ubuntu-20.04
             INSTALL_DEPS: sudo apt-get update && sudo apt-get -y install gfortran-7 swig libopenmpi-dev openmpi-bin libopenblas-dev && sudo ln -s `which gfortran-7` /usr/local/bin/gfortran
           - os: macos-latest
-            INSTALL_DEPS: brew update && HOMEBREW_NO_AUTO_UPDATE=1 SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=1 HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas && if [ ! -f /usr/local/bin/gfortran ]; then ln -s /usr/local/bin/gfortran-$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) /usr/local/bin/gfortran; fi
+            INSTALL_DEPS: brew update-reset && HOMEBREW_NO_AUTO_UPDATE=1  HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1 brew install gcc swig libomp open-mpi openblas && if [ ! -f /usr/local/bin/gfortran ]; then ln -s /usr/local/bin/gfortran-$(brew list --versions gcc | awk '{print $2}' | cut -d. -f1) /usr/local/bin/gfortran; fi
     steps:
     - name: Checkout repository
-      uses: actions/checkout@v2
+      uses: actions/checkout@v3
       with:
         submodules: true
 
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v2
+      uses: actions/setup-python@v4
       with:
         python-version: ${{ matrix.python-version }}
 
     - name: Install dependencies
       run: ${{ matrix.INSTALL_DEPS }}
 
-    - uses: actions/cache@v2
+    - uses: actions/cache@v3
       name: Load pip cache
       id: cache-pip
       with:
@@ -48,14 +48,18 @@ jobs:
 
     - name: Install python dependencies
       run: |
-        if  [ "${{ matrix.python-version }}" == "3.6" ]; then export SKLEARN_ALLOW_DEPRECATED_SKLEARN_PACKAGE_INSTALL=1; fi
         python -m pip install --upgrade pip
         pip install -v .
-        pip install --no-binary=mpi4py mpi4py
-        pip install pytest
-        if  [ "${{ matrix.python-version }}" != "3.6" ]; then pip install pocomc; fi
+        pip install --no-binary=mpi4py mpi4py astropy pocomc pytest pytest-cov
 
     - name: Test with pytest
       run: |
         cosmosis --version
-        mkdir tmp && cd tmp && pytest --pyargs cosmosis
+        mkdir tmp && cd tmp && pytest --pyargs cosmosis --cov cosmosis --cov-report=xml
+
+    - name: Upload coverage reports to Codecov
+      uses: codecov/codecov-action@v3
+      if: matrix.python-version == '3.9' && matrix.os == 'ubuntu-20.04'
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+

.gitignore

@@ -44,3 +44,4 @@ install-record.txt
 *.egg-info
 .DS_Store
 output/*
+cosmosis.code-workspace

bin/cosmosis-campaign

@@ -0,0 +1,4 @@
+#!/usr/bin/env python3
+import cosmosis.campaign
+args = cosmosis.campaign.parser.parse_args()
+cosmosis.campaign.main(args)

cosmosis/__init__.py

@@ -1,7 +1,7 @@
 from .main import run_cosmosis
 from .runtime import MPIPool, LikelihoodPipeline, FunctionModule, \
                      stdout_redirected, Inifile, CosmosisConfigurationError, \
-                     MPIPool, Module, FunctionModule, ClassModule
+                     MPIPool, Module, FunctionModule, ClassModule, logs
 from .samplers import Sampler
 from . import samplers
 from .version import __version__