rework the priors API

docs/_templates/autosummary/class.rst

@@ -4,7 +4,9 @@
 
 .. add toctree option to make autodoc generate the pages
 
-.. autoclass:: {{ objname }}
+.. autoclass:: {{ fullname }}
+
+{% set methods = methods | select("ne", "__init__") | list %}
 
 {% block attributes %}
 {% if attributes %}
@@ -25,10 +27,8 @@ Methods table
 
 .. autosummary::
 {% for item in methods %}
-    {%- if item != '__init__' %}
     ~{{ name }}.{{ item }}
-    {%- endif -%}
-{%- endfor %}
+{% endfor %}
 {% endif %}
 {% endblock %}
 
@@ -51,10 +51,8 @@ Methods
 ~~~~~~~
 
 {% for item in methods %}
-{%- if item != '__init__' %}
 
 .. automethod:: {{ [objname, item] | join(".") }}
-{%- endif -%}
 {%- endfor %}
 
 {% endif %}

docs/_templates/autosummary/module.rst

@@ -0,0 +1,62 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+    {% block attributes %}
+    {% if attributes %}
+    .. rubric:: {{ _('Module Attributes') }}
+
+    .. autosummary::
+    {% for item in attributes %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block functions %}
+    {% if functions %}
+    .. rubric:: {{ _('Functions') }}
+
+    .. autosummary::
+        :toctree:
+    {% for item in functions %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block classes %}
+    {% if classes %}
+    .. rubric:: {{ _('Classes') }}
+
+    .. autosummary::
+        :toctree:
+    {% for item in classes %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+    {% block exceptions %}
+    {% if exceptions %}
+    .. rubric:: {{ _('Exceptions') }}
+
+    .. autosummary::
+        :toctree:
+    {% for item in exceptions %}
+        {{ item }}
+    {%- endfor %}
+    {% endif %}
+    {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+{% for item in modules %}
+   {{ item }}
+{%- endfor %}
+{% endif %}
+{% endblock %}

docs/api/index.md → docs/api.md

@@ -1,24 +1,14 @@
 # API
 
-```{eval-rst}
-.. module:: mofaflex
-```
-
 ```{eval-rst}
 .. currentmodule:: mofaflex
-
 .. toctree::
-    :hidden:
-
-    core.md
-    tools.md
-    plotting.md
 ```
-
 ## Core
 
 ```{eval-rst}
 .. autosummary::
+    :toctree: generated
 
     DataOptions
     ModelOptions
@@ -29,11 +19,13 @@
     FeatureSets
 ```
 
-### Presets
-
+### Priors
 ```{eval-rst}
-.. automodule:: mofaflex.presets
-   :no-index:
+.. autosummary::
+    :toctree: generated
+    :recursive:
+
+    priors
 ```
 
 ### Settings
@@ -43,18 +35,27 @@ An instance of the [](#_core.settings.Settings) class is available as `mofaflex.
 ```{eval-rst}
 .. currentmodule:: mofaflex
 .. autosummary::
+    :toctree: generated
 
     _core.settings.Settings
 ```
 
 ## Tools
 
 ```{eval-rst}
-.. automodsumm:: mofaflex.tl
+.. autosummary::
+    :toctree: generated
+    :recursive:
+
+    tl
 ```
 
 ## Plotting
 
 ```{eval-rst}
-.. automodsumm:: mofaflex.pl
+.. autosummary::
+    :toctree: generated
+    :recursive:
+
+    pl
 ```

docs/conf.py

@@ -64,6 +64,7 @@
 ]
 
 autosummary_generate = True
+autosummary_imported_members = True
 autodoc_member_order = "groupwise"
 default_role = "literal"
 napoleon_google_docstring = True

docs/index.md

@@ -9,7 +9,7 @@
 notebooks/getting_started.ipynb
 tutorials.md
 modeldescription.md
-api/index
+api.md
 changelog.md
 contributing.md
 references.md

src/mofaflex/__init__.py

@@ -1,17 +1,8 @@
 import logging
 
 from . import pl, tl
-from ._core import (
-    MOFAFLEX,
-    DataOptions,
-    FeatureSet,
-    FeatureSets,
-    ModelOptions,
-    SmoothOptions,
-    TrainingOptions,
-    presets,
-    settings,
-)
+from ._core import MOFAFLEX, DataOptions, FeatureSet, FeatureSets, ModelOptions, TrainingOptions, settings
+from ._core.api import priors
 from ._version import __version__, __version_tuple__
 
 _logger = logging.getLogger(__name__)

src/mofaflex/_core/__init__.py

@@ -1,6 +1,5 @@
-from . import presets
 from .datasets import MofaFlexDataset
 from .feature_sets import FeatureSet, FeatureSets
-from .mofaflex import MOFAFLEX, DataOptions, ModelOptions, SmoothOptions, TrainingOptions
+from .mofaflex import MOFAFLEX, DataOptions, ModelOptions, TrainingOptions
 from .pcgse import pcgse_test
 from .settings import settings

src/mofaflex/_core/api/__init__.py

@@ -0,0 +1 @@
+from . import priors

src/mofaflex/_core/api/priors.py

@@ -0,0 +1,76 @@
+from abc import ABC, abstractmethod
+from collections.abc import Sequence
+from inspect import Parameter, signature
+from types import MappingProxyType
+from typing import Literal
+
+from ..priors import Prior as PriorCore
+
+
+class Prior(ABC):
+    @abstractmethod
+    def __call__(self, axis, names):
+        pass
+
+    def __init__(self, *args, **kwargs):
+        self._args = args
+        self._kwargs = MappingProxyType(kwargs)
+
+    def __eq__(self, other):
+        if not isinstance(other, __class__):
+            return NotImplemented
+        elif other.__class__ != self.__class__:
+            return False
+        else:
+            return self._args == other._args and self._kwargs == other._kwargs
+
+    def __hash__(self):
+        return hash((self.__class__, self._args, tuple(sorted(self._kwargs.items()))))
+
+
+__all__ = []
+
+
+def _init_priors():
+    for priorname in PriorCore.known_priors():
+        priorcls = PriorCore.class_(priorname)
+        sig = signature(priorcls.__init__)
+        params = [param for param in sig.parameters.values() if param.name not in ("axis", "names")]
+        sig = sig.replace(parameters=params)
+
+        def init(self, *args, **kwargs):
+            self.__init__.__signature__.bind(self, *args, **kwargs)  # check for argument compatibility
+            super(self.__class__, self).__init__(*args, **kwargs)
+
+        if priorcls is not PriorCore:
+
+            def call(self, axis: Literal[0, 1, "samples", "features"], names: str | Sequence[str]):
+                return self._cls(axis, names, *self._args, **self._kwargs)
+        else:
+
+            def call(self, axis: Literal[0, 1, "samples", "features"], names: str | Sequence[str]):
+                return PriorCore(self.__class__.__name__, axis, names, *self._args, **self._kwargs)
+
+        init.__signature__ = sig
+        init.__annotations__ = {
+            param.name: param.annotation for param in params if param.annotation is not Parameter.empty
+        }
+        init.__name__ = "__init__"
+        init.__qualname__ = f"{priorname}.__init__"
+        call.__name__ = "__call__"
+        call.__qualname__ = f"{priorname}.__call__"
+        apicls = type(
+            priorname, (Prior,), {"_cls": priorcls, "__init__": init, "__call__": call, "__module__": __name__}
+        )
+        if priorcls is not PriorCore:
+            apicls.__doc__ = priorcls.__doc__
+
+        globals()[priorname] = apicls
+        __all__.append(priorname)
+
+
+_init_priors()
+
+
+def __dir__():
+    return __all__