update documentation

Author: jhrmnn

docs/api.rst

@@ -45,7 +45,7 @@ FHI-aims
 .. autofunction:: parse_aims
 
 LaTeX
-^^^^^^^^
+^^^^^
 
 .. automodule:: mona.sci.tex
     :members:

docs/conf.py

@@ -34,7 +34,8 @@ def __getattr__(cls, name):
     'textx',
     'textx.metamodel',
     'numpy',
-    'contextvars',  # for python 3.6 (readthedocs)
+    # for python 3.6 (readthedocs)
+    'contextvars',
     'contextlib',
     'importlib.resources',
 ]
@@ -85,3 +86,4 @@ def __getattr__(cls, name):
     '**': ['about.html', 'navigation.html', 'relations.html', 'searchbox.html']
 }
 htmlhelp_basename = f'{project}doc'
+autodoc_default_options = {'special-members': '__call__'}

docs/glossary.rst

@@ -0,0 +1,26 @@
+Glossary
+========
+
+.. glossary::
+
+    task
+        The basic building block of a calculation. A task consists of a Python
+        function and the arguments passed into it (inputs). The result of
+        a task is the return value of the function (output). A task depends on
+        other tasks when its inputs reference outputs of other tasks. When
+        run, a task can create new tasks, and its output may reference outputs
+        of those tasks.
+
+    rule
+        Recipe for creating tasks. Calling a rule with soem arguments creates
+        a task with those arguments as inputs.
+
+    task factory
+        Generalization of a rule that returns a task when called, but may first
+        preprocess the arguments before assigning them as inputs to the task.
+
+    directory task
+        A special kind of file-based :term:`task` which has an executable instead of
+        a Python function and files instead of arguments, and the output is
+        a collection of files generated by the executable when run in
+        a temporary directory with the input files present.

docs/index.rst

@@ -10,6 +10,7 @@ User guide
     :maxdepth: 2
 
     quickstart
+    glossary
 
 API reference
 -------------

mona/sci/aims/__init__.py

@@ -1,4 +1,12 @@
-from .aims import Aims, SpeciesDefaults
+from .aims import Aims, Atoms, Control, Geom, Script, SpeciesDefaults
 from .parse import parse_aims
 
-__all__ = ['Aims', 'SpeciesDefaults', 'parse_aims']
+__all__ = [
+    'Aims',
+    'Atoms',
+    'SpeciesDefaults',
+    'Control',
+    'Geom',
+    'Script',
+    'parse_aims',
+]

pyproject.toml

@@ -4,7 +4,7 @@ skip-string-normalization = true
 
 [tool.poetry]
 name = "mona"
-version = "0.2.5"
+version = "0.2.6"
 description = "Calculation framework"
 readme = "README.md"
 authors = ["Jan Hermann <dev@janhermann.cz>"]