Merge pull request #59 from gwaygenomics/docs-update

Autodoc update
cytomining · Jun 1, 2021 · 779cea1 · 779cea1
2 parents b3f8000 + b921262
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diff --git a/cytominer_eval/__init__.py b/cytominer_eval/__init__.py
@@ -1 +1,3 @@
 from .evaluate import evaluate
+from cytominer_eval import __about__
+from cytominer_eval.__about__ import __version__
diff --git a/docs/conf.py b/docs/conf.py
@@ -12,18 +12,23 @@
 
 import os
 import sys
+from datetime import date
 
 sys.path.insert(0, os.path.abspath(".."))
 
+import cytominer_eval
 
 # -- Project information -----------------------------------------------------
 
-project = "cytominer-eval"
-copyright = "2021, Gregory P. Way"
-author = "Gregory P. Way"
+project = cytominer_eval.__about__.__project__
+author = cytominer_eval.__about__.__author__
+copyright = "Copyright 2019 - {date} {author}".format(
+    date=date.today().year, author=author
+)
 
 # The full version, including alpha/beta/rc tags
-release = "0.1"
+version = cytominer_eval.__about__.__version__
+release = version
 
 
 # -- General configuration ---------------------------------------------------

diff --git a/docs/cytominer_eval.operations.rst b/docs/cytominer_eval.operations.rst
@@ -1,55 +1,47 @@
-Metric operations
-=================
+Metrics
+=======
 
 Implementations of various profile evaluation metrics.
-These can be used directly, but we recommend usage through cytominer_eval.evaluate().
+These can be used directly, but we recommend usage through `cytominer_eval.evaluate()``.
 
-cytominer_eval.evaluate() contains several checks to confirm metrics are properly implemented.
+`cytominer_eval.evaluate()` contains several checks to confirm metrics are properly implemented.
 
-cytominer\_eval.operations.grit
--------------------------------
+Grit
+----
 
 .. automodule:: cytominer_eval.operations.grit
    :members:
    :undoc-members:
    :show-inheritance:
 
-cytominer\_eval.operations.mp\_value
-------------------------------------
+mp-value
+--------
 
 .. automodule:: cytominer_eval.operations.mp_value
    :members:
    :undoc-members:
    :show-inheritance:
 
-cytominer\_eval.operations.replicate\_reproducibility
------------------------------------------------------
+Replicate reproducibility
+-------------------------
 
 .. automodule:: cytominer_eval.operations.replicate_reproducibility
    :members:
    :undoc-members:
    :show-inheritance:
 
-cytominer\_eval.operations.precision\_recall
---------------------------------------------
+Precision and recall
+--------------------
 
 .. automodule:: cytominer_eval.operations.precision_recall
    :members:
    :undoc-members:
    :show-inheritance:
 
-cytominer\_eval.operations.util
--------------------------------
+Enrichment
+----------
 
-.. automodule:: cytominer_eval.operations.util
-   :members:
-   :undoc-members:
-   :show-inheritance:
-
-Module contents
----------------
-
-.. automodule:: cytominer_eval.operations
-   :members:
-   :undoc-members:
-   :show-inheritance:
+.. automodule:: cytominer_eval.operations.enrichment
+  :members:
+  :undoc-members:
+  :show-inheritance:
diff --git a/docs/cytominer_eval.rst b/docs/cytominer_eval.rst
@@ -1,6 +1,9 @@
 cytominer_eval
 ==============
 
+The primary way to use cytominer-eval is through `evaluate.py`.
+The `operation` argument controls which metric to calculate.
+
 evaluate.py
 -----------
 
@@ -9,19 +12,10 @@ evaluate.py
    :undoc-members:
    :show-inheritance:
 
-Other functions
----------------
+cytominer_eval.operations
+-------------------------
 
 .. toctree::
   :maxdepth: 4
 
   cytominer_eval.operations
-  cytominer_eval.transform
-
-Module contents
----------------
-
-.. automodule:: cytominer_eval
-   :members:
-   :undoc-members:
-   :show-inheritance:
diff --git a/docs/cytominer_eval.transform.rst b/docs/cytominer_eval.transform.rst
diff --git a/docs/index.rst b/docs/index.rst
@@ -11,7 +11,7 @@ Profiles are high dimensional readouts from high-throughput experiments represen
 This python package implements common metrics used to evaluate profile quality and strength.
 
 .. toctree::
-   :maxdepth: 2
+   :maxdepth: 3
    :caption: Contents:
 
    install