Merge branch 'master' into readme

.github/workflows/CI.yml

@@ -43,10 +43,42 @@ jobs:
       run: python run_pypolychord.py
 
     - name: Test pypolychord (MPI)
-      run: mpirun -np 2 python run_pypolychord.py
+      run: mpirun --oversubscribe -np 3 python run_pypolychord.py
 
     - name: Test pypolychord (anesthetic)
       if: ${{ ! contains( '3.6, 3.7', matrix.python-version ) }}
       run: |
         pip install -r requirements.txt
         python run_pypolychord.py
+
+
+  tests:
+    runs-on: ${{ matrix.os }}
+    strategy:
+      matrix:
+        os: [ubuntu-latest]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v4
+      with:
+        python-version: ${{ matrix.python-version }}
+
+    - name: Install dependencies (Linux)
+      run: sudo apt-get install gfortran libopenmpi-dev
+
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        python -m pip install mpi4py pytest fortranformat anesthetic
+
+    - name: Install pypolychord
+      run: pip install -v '.[test]'
+
+    - name: Test pypolychord (no MPI)
+      run: python -m pytest tests
+
+    - name: Test pypolychord (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 1.20.2
+PolyChord v 1.22.1
 
 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
 =================
 
@@ -39,30 +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/williamjameshandley/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
 
+    pip install anesthetic
 
-https://github.com/williamjameshandley/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
 ===========
@@ -215,7 +230,6 @@ 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
@@ -236,26 +250,27 @@ 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__ = "1.20.2"
+__version__ = "1.22.1"
 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))
@@ -215,7 +216,7 @@ def _dataframes_for_printing(self):
         for paramname in self._samples_table.columns[2:]:
             mean = np.mean(np.array( self._samples_table[paramname]) )
             std = np.std(np.array( self._samples_table[paramname]) )
-            stats_dict[paramname] = '%.3E +\- %.3E' % (mean, std)
+            stats_dict[paramname] = '%.3E +/- %.3E' % (mean, std)
 
         lst.append(pd.Series(stats_dict))
         return lst