merging and fixing test

.github/workflows/main.yml

@@ -1,4 +1,4 @@
-name: Run unittests
+name: Tests
 
 on: [push]
 
@@ -47,6 +47,7 @@ jobs:
             echo "Branch $BRANCH did not exist in $PACKAGE"
           else
             echo "Branch $BRANCH did exist in $PACKAGE"
+            git fetch
             git checkout $BRANCH
           fi
           popd
@@ -57,7 +58,7 @@ jobs:
         pip3 install --upgrade pip
         pip3 install setuptools
         pip3 install wheel
-        pip3 install pytest
+        pip3 install pytest coverage pytest-cov
         pip3 install -r PyAutoConf/requirements.txt
         pip3 install -r PyAutoFit/requirements.txt
         pip3 install -r PyAutoFit/build_requirements.txt
@@ -67,7 +68,9 @@ jobs:
         export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoConf
         export PYTHONPATH=$PYTHONPATH:$ROOT_DIR/PyAutoFit
         pushd PyAutoFit
-        pytest
+        pytest --cov autofit --cov-report xml:coverage.xml
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v3
     - name: Slack send
       if: ${{ failure() }}
       id: slack

CITATIONS.rst

@@ -0,0 +1,13 @@
+.. _references:
+
+Citations & References
+======================
+
+The bibtex entries for **PyAutoFit** and its affiliated software packages can be found
+`here <https://github.com/rhayes777/PyAutoFit/blob/main/files/citations.bib>`_, with example text for citing **PyAutoFit**
+in `.tex format here <https://github.com/rhayes777/PyAutoFit/blob/main/files/citation.tex>`_ format here and
+`.md format here <https://github.com/rhayes777/PyAutoFit/blob/main/files/citations.md>`_. As shown in the examples, we
+would greatly appreciate it if you mention **PyAutoFit** by name and include a link to our GitHub page!
+
+**PyAutoFit** is published in the `Journal of Open Source Software <https://joss.theoj.org/papers/10.21105/joss.02550#>`_ and its
+entry in the above .bib file is under the key ``pyautofit``.

CODE_OF_CONDUCT.md

@@ -302,7 +302,7 @@ the situation is not yet resolved.
 
 ## License
 
-This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/master/manual/numfocus-coc.md#the-short-version),
-which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Fiterence_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/master/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/master/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
+This code of conduct has been adapted from [*NUMFOCUS code of conduct*](https://github.com/numfocus/numfocus/blob/main/manual/numfocus-coc.md#the-short-version),
+which is adapted from numerous sources, including the [*Geek Feminism wiki, created by the Ada Initiative and other volunteers, which is under a Creative Commons Zero license*](http://geekfeminism.wikia.com/wiki/Fiterence_anti-harassment/Policy), the [*Contributor Covenant version 1.2.0*](http://contributor-covenant.org/version/1/2/0/), the [*Bokeh Code of Conduct*](https://github.com/bokeh/bokeh/blob/main/CODE_OF_CONDUCT.md), the [*SciPy Code of Conduct*](https://github.com/jupyter/governance/blob/main/conduct/enforcement.md), the [*Carpentries Code of Conduct*](https://docs.carpentries.org/topic_folders/policies/code-of-conduct.html#enforcement-manual), and the [*NeurIPS Code of Conduct*](https://neurips.cc/public/CodeOfConduct).
 
 **PyAutoFit Code of Conduct is licensed under the [Creative Commons Attribution 3.0 Unported License](https://creativecommons.org/licenses/by/3.0/).**

MANIFEST.in

@@ -1,19 +1,22 @@
 # MANIFEST.in
 exclude .gitignore
-exclude .coverage
-exclude .travis.yml
-exclude docs
 include README.rst
 include setup.cfg
-recursive-include autofit/config *
+include CITATIONS.rst
+include LICENSE
+include requirements.txt
+include optional_requirements.txt
+
 prune .cache
 prune .git
 prune build
 prune dist
+
 recursive-exclude *.egg-info *
-recursive-include tests *
-include requirements.txt
-recursive-include data *
+
+recursive-include autofit/config *
+
+exclude docs
 
 global-exclude test_autofit
 recursive-exclude test_autofit *

README.rst

@@ -4,16 +4,30 @@ PyAutoFit: Classy Probabilistic Programming
 .. |binder| image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/Jammy2211/autofit_workspace/HEAD
 
+.. |RTD| image:: https://readthedocs.org/projects/pyautofit/badge/?version=latest
+    :target: https://pyautofit.readthedocs.io/en/latest/?badge=latest
+    :alt: Documentation Status
+
+.. |Tests| image:: https://github.com/rhayes777/PyAutoFit/actions/workflows/main.yml/badge.svg
+   :target: https://github.com/rhayes777/PyAutoFit/actions
+
+.. |Build| image:: https://github.com/rhayes777/PyAutoBuild/actions/workflows/release.yml/badge.svg
+   :target: https://github.com/rhayes777/PyAutoBuild/actions
+
 .. |JOSS| image:: https://joss.theoj.org/papers/10.21105/joss.02550/status.svg
    :target: https://doi.org/10.21105/joss.02550
 
-|binder| |JOSS|
+|binder| |Tests| |Build| |RTD| |JOSS|
 
 `Installation Guide <https://pyautofit.readthedocs.io/en/latest/installation/overview.html>`_ |
 `readthedocs <https://pyautofit.readthedocs.io/en/latest/index.html>`_ |
 `Introduction on Binder <https://mybinder.org/v2/gh/Jammy2211/autofit_workspace/release?filepath=introduction.ipynb>`_ |
 `HowToFit <https://pyautofit.readthedocs.io/en/latest/howtofit/howtofit.html>`_
 
+
+..
+   _ One day make these BOLD with a colon like my fellowsahip proposa,s where the first is Model Composition & Fitting: Tools for composing a complex model and fitting it with dynesty...
+
 PyAutoFit is a Python based probabilistic programming language for the fully Bayesian analysis of extremely large
 datasets which:
 
@@ -59,7 +73,6 @@ noisy 1D data. Here's the ``data`` (black) and the model (red) we'll fit:
 
 .. image:: https://raw.githubusercontent.com/rhayes777/PyAutoFit/master/files/toy_model_fit.png
   :width: 400
-  :alt: Alternative text
 
 We define our model, a 1D Gaussian by writing a Python class using the format below:
 

autofit/__init__.py

@@ -55,14 +55,14 @@
 from .mapper.prior_model.attribute_pair import InstanceNameValue
 from .mapper.prior_model.attribute_pair import PriorNameValue
 from .mapper.prior_model.attribute_pair import cast_collection
-from .mapper.prior_model.collection import CollectionPriorModel
-from .mapper.prior_model.collection import CollectionPriorModel as Collection
-from .mapper.prior_model.prior_model import PriorModel
-from .mapper.prior_model.prior_model import PriorModel as Model
+from .mapper.prior_model.collection import Collection
+from .mapper.prior_model.prior_model import Model
+from .mapper.prior_model.prior_model import Model
 from .mapper.prior_model.util import PriorModelNameValue
 from .non_linear.abstract_search import NonLinearSearch
 from .non_linear.abstract_search import PriorPasser
 from .non_linear.analysis.analysis import Analysis
+from .non_linear.analysis.combined import CombinedAnalysis
 from .non_linear.grid.grid_search import GridSearchResult
 from .non_linear.initializer import InitializerBall
 from .non_linear.initializer import InitializerPrior
@@ -86,6 +86,7 @@
 from .example.model import Gaussian
 from .text import formatter
 from .text import samples_text
+from .interpolator import LinearInterpolator, SplineInterpolator
 from .tools import util
 
 
@@ -109,4 +110,4 @@ def save_abc(pickler, obj):
 
 conf.instance.register(__file__)
 
-__version__ = "2022.11.26.11"
+__version__ = "2023.3.27.1"

autofit/aggregator/aggregator.py

@@ -48,12 +48,7 @@ def filter(self, *predicates) -> "AggregatorGroup":
         -------
         A collection of groups of the same length with each group having the same or fewer members.
         """
-        return AggregatorGroup(
-            [
-                group.filter(*predicates)
-                for group in self.groups
-            ]
-        )
+        return AggregatorGroup([group.filter(*predicates) for group in self.groups])
 
     def __getitem__(self, item):
         return self.groups[item]
@@ -75,10 +70,7 @@ def values(self, name: str) -> List[List]:
         -------
         A list of lists of values.
         """
-        return [
-            group.values(name)
-            for group in self.groups
-        ]
+        return [group.values(name) for group in self.groups]
 
 
 class AbstractAggregator:
@@ -98,23 +90,15 @@ def remove_unzipped(self):
         Removes the unzipped output directory for each phase.
         """
         for phase in self.search_outputs:
-
             split_path = path.split(phase.directory)[0]
 
             unzipped_path = path.join(split_path)
 
-            rmtree(
-                unzipped_path,
-                ignore_errors=True
-            )
+            rmtree(unzipped_path, ignore_errors=True)
 
     def __getitem__(
-            self,
-            item: Union[slice, int]
-    ) -> Union[
-        "AbstractAggregator",
-        SearchOutput
-    ]:
+        self, item: Union[slice, int]
+    ) -> Union["AbstractAggregator", SearchOutput]:
         """
         If an index is passed in then a specific phase output is returned.
 
@@ -130,9 +114,7 @@ def __getitem__(
         An aggregator or phase
         """
         if isinstance(item, slice):
-            return AbstractAggregator(
-                self.search_outputs[item]
-            )
+            return AbstractAggregator(self.search_outputs[item])
         return self.search_outputs[item]
 
     def __len__(self):
@@ -184,12 +166,26 @@ def values(self, name: str) -> Iterator:
         -------
         A generator of values for the attribute
         """
-        return map(
-            lambda phase: getattr(
-                phase, name
-            ),
-            self.search_outputs
-        )
+        return map(lambda phase: getattr(phase, name), self.search_outputs)
+
+    def child_values(self, name: str) -> Iterator[List]:
+        """
+        Get values with a given name from the child analyses of each search in
+        this aggregator.
+
+        Parameters
+        ----------
+        name
+            The name of an attribute expected to be associated with
+            child analysis output. If a pickle file with this name
+            is in the child analysis output directory then that pickle
+            will be loaded.
+
+        Returns
+        -------
+        A generator of values for the attribute
+        """
+        return (phase.child_values(name) for phase in self.search_outputs)
 
     def map(self, func):
         """
@@ -204,10 +200,7 @@ def map(self, func):
         -------
         A generator of results
         """
-        return map(
-            func,
-            self.search_outputs
-        )
+        return map(func, self.search_outputs)
 
     def group_by(self, field: str) -> AggregatorGroup:
         """
@@ -241,11 +234,7 @@ def model_results(self) -> str:
 
 
 class Aggregator(AbstractAggregator):
-    def __init__(
-            self,
-            directory: Union[str, os.PathLike],
-            completed_only=False
-    ):
+    def __init__(self, directory: Union[str, os.PathLike], completed_only=False):
         """
         Class to aggregate phase results for all subdirectories in a given directory.
 
@@ -276,9 +265,7 @@ def __init__(
                             f.extractall(path.join(root, filename[:-4]))
                     except zipfile.BadZipFile:
                         raise zipfile.BadZipFile(
-                            f"File is not a zip file: \n "
-                            f"{root} \n"
-                            f"{filename}"
+                            f"File is not a zip file: \n " f"{root} \n" f"{filename}"
                         )
 
         for root, _, filenames in os.walk(directory):
@@ -289,5 +276,7 @@ def __init__(
         if len(search_outputs) == 0:
             print(f"\nNo search_outputs found in {directory}\n")
         else:
-            print(f"\n A total of {str(len(search_outputs))} search_outputs and results were found.")
+            print(
+                f"\n A total of {str(len(search_outputs))} search_outputs and results were found."
+            )
         super().__init__(search_outputs)