update api doc

doc/requirements.txt

@@ -1,4 +1,5 @@
 ipython
+jinja2
 sphinx
 numpydoc
 sphinx_copybutton

doc/scripts/gendoc.sh

@@ -6,6 +6,7 @@ PYSCFAD_PATH=$(python -c "import pyscfad; print(pyscfad.__path__[0])")
 # Run sphinx
 DESTINATION=source/api_reference/apidoc
 LOGFILE=_api_docs.log
+TEMPLATEDIR=source/_templates
 
 mkdir -p $DESTINATION
-sphinx-apidoc -d 1 -T -e -f -o $DESTINATION $PYSCFAD_PATH "test" > ${LOGFILE}
+sphinx-apidoc -d 1 -T -e -f -t $TEMPLATEDIR -o $DESTINATION $PYSCFAD_PATH "test" > ${LOGFILE}

doc/source/_templates/autosummary/class.rst

@@ -0,0 +1,28 @@
+{{ fullname | escape | underline}}
+
+.. currentmodule:: {{ module }}
+
+.. autoclass:: {{ objname }}
+   :show-inheritance:
+
+   {% block attributes %}
+   {% if attributes %}
+
+   {% endif %}
+   {% endblock %}
+
+   {% block methods %}
+   {% if methods %}
+   .. rubric:: {{ _('Methods') }}
+
+   .. autosummary::
+      :toctree: methods/
+
+      {% for item in methods %}
+         {% if item not in inherited_members and (not item.startswith('_') or item in ['__call__']) %}
+           ~{{ name }}.{{ item }}
+         {% endif %}
+      {%- endfor %}
+
+   {% endif %}
+   {% endblock %}

doc/source/_templates/autosummary/module.rst

@@ -0,0 +1,64 @@
+{{ fullname | escape | underline}}
+
+.. automodule:: {{ fullname }}
+
+   {% block attributes %}
+   {% if attributes %}
+
+   {% endif %}
+   {% endblock %}
+
+   {% block classes %}
+   {% if classes %}
+   .. rubric:: {{ _('Classes') }}
+
+   .. autosummary::
+      :toctree: classes/
+
+   {% for item in classes %}
+      {{ item }}
+   {%- endfor %}
+
+   {% endif %}
+   {% endblock %}
+
+   {% block functions %}
+   {% if functions %}
+   .. rubric:: {{ _('Functions') }}
+
+   .. autosummary::
+      :toctree: functions/
+
+   {% for item in functions %}
+      {{ item }}
+   {%- endfor %}
+
+   {% endif %}
+   {% endblock %}
+
+
+   {% block exceptions %}
+   {% if exceptions %}
+   .. rubric:: {{ _('Exceptions') }}
+
+   .. autosummary::
+   {% for item in exceptions %}
+      {{ item }}
+   {%- endfor %}
+   {% endif %}
+   {% endblock %}
+
+{% block modules %}
+{% if modules %}
+.. rubric:: Modules
+
+.. autosummary::
+   :toctree:
+   :recursive:
+{% for item in modules %}
+   {% if not 'test' in item %}
+   {{ item }}
+   {% endif %}
+{%- endfor %}
+{% endif %}
+{% endblock %}

doc/source/api_reference/ao2mo.rst

@@ -0,0 +1,13 @@
+.. _ao2mo:
+
+======================
+Orbital transformation
+======================
+
+The :mod:`pyscfad.ao2mo` subpackage defines the orbital transformation methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.ao2mo

doc/source/api_reference/cc.rst

@@ -0,0 +1,13 @@
+.. _cc:
+
+=======================
+Coupled cluster methods
+=======================
+
+The :mod:`pyscfad.cc` subpackage defines the coupled cluster methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.cc

doc/source/api_reference/df.rst

@@ -0,0 +1,13 @@
+.. _scf:
+
+===============
+Density fitting
+===============
+
+The :mod:`pyscfad.df` subpackage defines the density fitting methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.df

doc/source/api_reference/dft.rst

@@ -0,0 +1,13 @@
+.. _dft:
+
+===========
+DFT methods
+===========
+
+The :mod:`pyscfad.dft` subpackage defines the DFT methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.dft

doc/source/api_reference/fci.rst

@@ -0,0 +1,13 @@
+.. _fci:
+
+=======
+Full CI
+=======
+
+The :mod:`pyscfad.fci` subpackage defines the full CI methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.fci

doc/source/api_reference/geomopt.rst

@@ -0,0 +1,13 @@
+.. _geomopt:
+
+=====================
+Geometry optimization
+=====================
+
+The :mod:`pyscfad.geomopt` subpackage defines the geometry optimization methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.geomopt

doc/source/api_reference/gto.rst

@@ -0,0 +1,14 @@
+.. _gto:
+
+=====================
+Molecular information
+=====================
+
+The :mod:`pyscfad.gto` subpackage defines the molecular information
+and ERI methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.gto

doc/source/api_reference/gw.rst

@@ -0,0 +1,13 @@
+.. _gw:
+
+==========
+GW methods
+==========
+
+The :mod:`pyscfad.gw` subpackage defines the GW methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.gw

doc/source/api_reference/index.rst

@@ -3,8 +3,26 @@
 =============
 API reference
 =============
+.. currentmodule:: pyscfad
+
+This page gives an overview of all public pyscfad objects, functions and methods.
+All classes and functions exposed in pyscfad.* namespace are public.
 
 .. toctree::
    :maxdepth: 1
 
-   apidoc/pyscfad
+   ao2mo
+   cc
+   df
+   dft
+   fci
+   geomopt
+   gto
+   gw
+   mp
+   pbc
+   prop
+   scf
+   tdscf
+   tools
+   util

doc/source/api_reference/mp.rst

@@ -0,0 +1,13 @@
+.. _mp:
+
+===========
+MP2 methods
+===========
+
+The :mod:`pyscfad.mp` subpackage defines the MP2 methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.mp

doc/source/api_reference/pbc.rst

@@ -0,0 +1,13 @@
+.. _pbc:
+
+==================
+Methods for Solids
+==================
+
+The :mod:`pyscfad.pbc` subpackage defines the methods for solid calculations.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.pbc

doc/source/api_reference/prop.rst

@@ -0,0 +1,13 @@
+.. _prop:
+
+================
+Property methods
+================
+
+The :mod:`pyscfad.prop` subpackage defines the property calculation methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.prop

doc/source/api_reference/scf.rst

@@ -0,0 +1,13 @@
+.. _scf:
+
+====================
+Hartree-Fock methods
+====================
+
+The :mod:`pyscfad.scf` subpackage defines the Hartree-Fock methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.scf

doc/source/api_reference/tdscf.rst

@@ -0,0 +1,13 @@
+.. _tdscf:
+
+=============
+TDSCF methods
+=============
+
+The :mod:`pyscfad.tdscf` subpackage defines the linear-response mean-field methods.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.tdscf

doc/source/api_reference/tools.rst

@@ -0,0 +1,13 @@
+.. _tools:
+
+=====
+Tools
+=====
+
+The :mod:`pyscfad.tools` subpackage provides useful tools.
+
+.. autosummary::
+   :toctree: api/
+   :recursive:
+
+   pyscfad.tools

doc/source/api_reference/util.rst

@@ -0,0 +1,13 @@
+.. _util:
+
+=================
+Utility functions
+=================
+.. currentmodule:: pyscfad
+
+The :mod:`pyscfad.util` module provides useful utility functions.
+
+.. autosummary::
+   :toctree: api/
+
+   util.pytree_node

doc/source/conf.py

@@ -161,7 +161,7 @@ def linkcode_resolve(domain, info) -> str | None:
 
     return (
         f"https://github.com/fishjojo/pyscfad/blob/"
-        f"v{pyscfad.__version__}/pyscfad/{fn}{linespec}"
+        f"doc/pyscfad/{fn}{linespec}"  # direct to the doc branch for now
     )
 
 def rstjinja(app, docname, source) -> None: