**kwargs input and anesthetic.NestedSamples output (#90)

* neighbor spelling (assuming we're sticking to American spelling!)

* updated run_poypolychord to use **kwargs rather than PolyChordSettings

* return anesthetic.NestedSamples output if installed

* added kwargs to run_pypolychord() docstring

* changed examples to use **kwargs

* accidental rename of run_polychord()

* set kwarg defaults separately to run_pypolychord so that they can be given to resume file

* run_polychord creates the paramnames file

* changed other examples paramnames are passed to run_pypolychord

* mention anesthetic output in docstring (incomplete)

* tidied up grade_dims and nlives argument processing

* logx should be logc

* missing comma

* removed settings argument

* Restored old interface

* run_polychord -> run

* reverted Python_Functions/ (apart from logx->logc correction

* put PolyChordSettings back in __init__.py

* run() uses make_resume_file_kwargs_interface

* added run to __init__.py

* update nDerived, prior and dumper to kwargs

* nDims is not a kwarg

* add nDerived, prior and dumper to kwargs

* use default_kwargs to set the defaults, then use this to see if kwargs has any excess keys

* separate default_kwargs that refer to other default_kwargs

* wrong brackets - think it's time to leave this for a moment

* removed accidental commas

* pass kwargs directly rather than creating dict

* added anesthetic to install_requires

* anesthetic now assumed to be installed, so new interface always returns an anesthetic output

* tidy up plotting to just use anesthetic output

* simplified to _make_resume_file(), plus wrapper _legacy_make_resume_file which translates from a settings object

* added run_pypolychord_legacy_interface.py

* update run() docstring to anesthetic output

* removed unused sqrt from run_pypolychord.py

* updated run_pypolychord.ipynb with py2nb

* change requirement to anesthetic==2.0.0b11

* removed creation of .paramnames file from run(), added to run_pypolychord.py

* corrected kwargs error message

* exception handling if chains/ already exists

* update to anesthetic 2.0.0b12

* rather than repeating PolyChordOutput.make_paramnames_file(), make it a static method and reuse it

* changed setup.py to point to github anesthetic as 2.0.0b12 hasn't been released

* remove unecessary os import

* removed commented out/empty lines around paramname creation

* removed unnecessary kwargs = kwargs.copy()

* double quotes to be more civilised

* change to single quotes to make Lucas happy

* update for more recent anesthetic

* line spacing and remove todo (see pr 110

* get anesthetic from pypi instead of gh

* might as well do some formatting

* also fix wrap_loglikelihood for new interface (#110)

* anesthetic back to optional, return None if not installed

* version bump to 1.22.0

* py2nb run_pypolychord.py

* Fix names of run scripts/notebooks

* remove testing print statement

* remove sqrt import, who knows where this came from

* Updated with new recommended interface

* anesthetic root is deprecated

* Update README.rst

* more anesthetic 2 madness

* update notebooks

* remove () from dict

* play around with tests

* add anesthetic to CI install step

* only run tests on python>=3.8

* test likelihood without derived parameters

* some test housekeeping

* use or between the two loglikelihood return options

* use pathlib.Path to save OSError nonsense

* explain paramnames more clearly

* check that grade_dims add up to nDims and test

* update run docstring anesthetic stuff

* correct run_pypolychord return

* correct missing blank lines in run() docstring

* add cluster_dir to kwargs, since technically it could be changed in PolyChordSettings (with difficulty)

* remove os entirely in favour of pathlib

* fix line too long

* update date

* fix default grade_frac

* remove pytest-mpi requirement from CI

* remove unecessary cast to set

* don't use ac shorthand, but also don't clutter the namespace with log and pi

* Revert "don't use ac shorthand, but also don't clutter the namespace with log and pi"

This reverts commit cc807f5.

* from anesthetic import make_2d_axes

---------

Co-authored-by: Adam Ormondroyd <52655393+Ormorod@users.noreply.github.com>
Co-authored-by: Will Handley <wh260@cam.ac.uk>

.github/workflows/CI.yml

@@ -57,10 +57,7 @@ jobs:
     strategy:
       matrix:
         os: [ubuntu-latest]
-        python-version: ['3.7', '3.8', '3.9', '3.10', '3.11']
-        include:
-          - os: ubuntu-20.04
-            python-version: '3.6'
+        python-version: ['3.8', '3.9', '3.10', '3.11']
 
     steps:
     - uses: actions/checkout@v3
@@ -75,7 +72,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        python -m pip install mpi4py pytest pytest-mpi fortranformat
+        python -m pip install mpi4py pytest fortranformat anesthetic
 
     - name: Install pypolychord
       run: pip install -v '.[test]'
@@ -84,4 +81,4 @@ jobs:
       run: python -m pytest tests
 
     - name: Test pypolychord (MPI)
-      run: mpirun --oversubscribe -np 3 python -m pytest tests --only-mpi 
+      run: mpirun --oversubscribe -np 3 python -m pytest tests

README.rst

@@ -5,17 +5,17 @@
    :target: https://arxiv.org/abs/1506.00171
    :alt: Open-access paper
 
-PolyChord v 1.21.4
+PolyChord v 1.22.0
 
 Will Handley, Mike Hobson & Anthony Lasenby
 
 wh260@mrao.cam.ac.uk
 
-arXiv:1502.01856
+`arXiv:1502.01856 <https://arxiv.org/abs/1502.01856>`_
 
-arXiv:1506.00171
+`arXiv:1506.00171 <https://arxiv.org/abs/1506.00171>`_
 
-Latest version Released Apr 2020
+Latest version Released Jan 2024
 
 
 PolyChord Licence
@@ -26,11 +26,12 @@ file. PolyChord is free for academic usage
 
 Users are also required to cite the PolyChord papers: 
 
-- arXiv:1502.01856
-- arXiv:1506.00171
+- `arXiv:1502.01856 <https://arxiv.org/abs/1502.01856>`_
+- `arXiv:1506.00171 <https://arxiv.org/abs/1506.00171>`_
 
 in their publications.
 
+
 Python quickstart
 =================
 
@@ -39,34 +40,44 @@ For Python users in a hurry:
 .. code:: bash
 
     pip install git+https://github.com/PolyChord/PolyChordLite@master
-    wget https://raw.githubusercontent.com/PolyChord/PolyChordLite/master/run_pypolychord.py
-    python run_pypolychord.py
+    wget https://raw.githubusercontent.com/PolyChord/PolyChordLite/master/quickstart.py
+    python quickstart.py
 
-You can then modify the file run_pypolychord.py to your needs. If you have mpi compilers available, this version can be run in parallel with mpi.
+You should make sure that you have gfortran/gcc (or equivalent) fortran compilers installed. 
 
-You should make sure that you have gfortran (or equivalent) fortran compilers installed. 
+You can then modify the file quickstart.py to your needs. If you have mpi compilers available, this version can be run in parallel with mpi.
 
-If any of the above steps fail (this can in general happen for certain Mac OSX versions), then try installing without pip:
+If any of the above steps fail (this can in general happen for certain macOS versions), then try installing without pip:
 
 .. code:: bash
 
     git clone https://github.com/PolyChord/PolyChordLite.git
     cd PolyChordLite
     python setup.py install
 
+or perhaps:
+
+.. code:: bash
+
+    git clone https://github.com/PolyChord/PolyChordLite.git
+    cd PolyChordLite
+    make
+    pip install .
+
+our apologies -- the shifting sands that are macOS do not play well with the delicate dance of fortran, C and Python that is (py)PolyChordLite.
+
 If you do not have sudo access/virtual environments/anaconda, then appending `--user` to the install command may be necessary.
 
 Post Processing
 ===============
 
-We recommend the tool `anesthetic <https://github.com/handley-lab/anesthetic>`_ for post-processing your nested sampling runs. A plot gallery can be found `here <http://htmlpreview.github.io/?https://github.com/williamjameshandley/cosmo_example/blob/master/demos/demo.html>`_
+We recommend the pip-installable tool `anesthetic <https://github.com/handley-lab/anesthetic>`_ for post-processing your nested sampling runs. A plot gallery can be found `here <https://anesthetic.readthedocs.io/en/latest/plotting.html>`_
 
+.. code:: bash
 
-https://github.com/handley-lab/anesthetic
+    pip install anesthetic
 
-```
-pip install anesthetic
-```
+If `anesthetic` is already installed, then `pypolychord.run()` will return an `anesthetic.NestedSamples` object, which can be used directly for post-processing.
 
 MPI Support
 ===========
@@ -211,7 +222,6 @@ You can install direct from the git repository using:
 
     pip install https://github.com/PolyChord/PolyChordLite/archive/master.zip
 
-(N.B. PyPi coming soon)
 or you can install locally with the command:
 
 .. code:: bash
@@ -232,26 +242,27 @@ and check that it's working by running:
 
 .. code:: bash
 
-    $  python run_pypolychord.py
+    $  python quickstart.py
 
 or in MPI:
 
 .. code:: bash
 
-    $  mpirun -np 4 python run_pypolychord.py
+    $  mpirun -np 4 python quickstart.py
 
 If so, the rest of the interface is relatively painless. Follow the example in
-run_pypolychord.py, and consult the docstring if you need help:
+quickstart.py, and consult the docstring if you need help:
 
 .. code:: python
 
-    import pypolychord
-    from pypolychord.settings import PolyChordSettings
+    >>> import pypolychord
+    >>> help(pypolychord.run)
+
+There is also a demo `python notebook <https://github.com/PolyChord/PolyChordLite/blob/master/quickstart.ipynb>`_.
+
+To post-process nested sampling runs we recommend the pip-installable tool `anesthetic <https://github.com/handley-lab/anesthetic>`_. A plot gallery can be found `here <https://anesthetic.readthedocs.io/en/latest/plotting.html>`_ 
 
-    help(pypolychord.run_polychord)
-    help(PolyChordSettings)
 
-There is also a demo `python notebook <https://github.com/PolyChord/PolyChordLite/blob/master/run_pypolychord.ipynb>`_.
 
 Output files 
 =============

pypolychord/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "1.21.4"
+__version__ = "1.22.0"
 from pypolychord.settings import PolyChordSettings
-from pypolychord.polychord import run_polychord
+from pypolychord.polychord import run_polychord, run

pypolychord/output.py

@@ -170,7 +170,8 @@ def make_paramnames_files(self, paramnames):
             self._create_pandas_table(paramnames = paramnames)
 
 
-    def make_paramnames_file(self, paramnames, filename):
+    @staticmethod
+    def make_paramnames_file(paramnames, filename):
         with open(filename, 'w') as f:
             for name, latex in paramnames:
                 f.write('%s   %s\n' % (name, latex))