diff --git a/cytominer_eval/__init__.py b/cytominer_eval/__init__.py index df46a0c..bef2bb3 100644 --- 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 index 7600a62..822739e 100644 --- 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 index bbca1d5..c3f1850 100644 --- 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 index d0fcdca..0b4f26b 100644 --- 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 deleted file mode 100644 index 97bc3c2..0000000 --- a/docs/cytominer_eval.transform.rst +++ /dev/null @@ -1,28 +0,0 @@ -Transform functions -=================== - -Helper functions to process profile data. - -cytominer\_eval.transform.transform ------------------------------------ - -.. automodule:: cytominer_eval.transform.transform - :members: - :undoc-members: - :show-inheritance: - -cytominer\_eval.transform.util ------------------------------- - -.. automodule:: cytominer_eval.transform.util - :members: - :undoc-members: - :show-inheritance: - -Module contents ---------------- - -.. automodule:: cytominer_eval.transform - :members: - :undoc-members: - :show-inheritance: diff --git a/docs/index.rst b/docs/index.rst index 55ce623..8a042d2 100644 --- 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