From 7a9380ac581bf4f321c192a956f381fba307dbd1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Al=C3=A1n=20Mu=C3=B1oz?= <alan.munoz@ed.ac.uk>
Date: Fri, 17 Mar 2023 19:56:19 +0000
Subject: [PATCH] docs(index): Include pipeline in index
---
README.md | 7 ++++---
docs/source/index.rst | 1 -
src/aliby/bin/__init__.py | 4 +++-
src/aliby/lineage/__init__.py | 4 +++-
src/aliby/lineage/bud_tracker.py | 6 +++++-
src/postprocessor/core/lineageprocess.py | 2 +-
6 files changed, 16 insertions(+), 8 deletions(-)
diff --git a/README.md b/README.md
index 4c4e84c7..2e8c40ad 100644
--- a/README.md
+++ b/README.md
@@ -11,11 +11,12 @@ End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentati
## Quickstart Documentation
Installation of [VS Studio](https://visualstudio.microsoft.com/downloads/#microsoft-visual-c-redistributable-for-visual-studio-2022) Native MacOS support for is under work, but you can use containers (e.g., Docker, Podman) in the meantime.
-For analysing local data
+To analyse local data
```bash
-pip install aliby # aliby[network] if you want to access an OMERO server
+pip install aliby
```
-
+ Add any of the optional flags `omero` and `utils` (e.g., `pip install aliby[omero, utils]`). `omero` provides tools to connect with an OMERO server and `utils` provides visualisation, user interface and additional deep learning tools.
+
See our [installation instructions]( https://aliby.readthedocs.io/en/latest/INSTALL.html ) for more details.
### CLI
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 6d3af3b5..d415b3f3 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -4,7 +4,6 @@
contain the root `toctree` directive.
.. toctree::
- :hidden:
Home page <self>
Installation <INSTALL.md>
diff --git a/src/aliby/bin/__init__.py b/src/aliby/bin/__init__.py
index a051bb08..916e9528 100644
--- a/src/aliby/bin/__init__.py
+++ b/src/aliby/bin/__init__.py
@@ -1 +1,3 @@
-#!/usr/bin/env jupyter
+"""
+Command Line Interface utilities.
+"""
diff --git a/src/aliby/lineage/__init__.py b/src/aliby/lineage/__init__.py
index a051bb08..7105ba35 100644
--- a/src/aliby/lineage/__init__.py
+++ b/src/aliby/lineage/__init__.py
@@ -1 +1,3 @@
-#!/usr/bin/env jupyter
+"""
+Models that link regions of interest, such as mothers and buds.
+"""
diff --git a/src/aliby/lineage/bud_tracker.py b/src/aliby/lineage/bud_tracker.py
index ef6a2e46..659e690d 100644
--- a/src/aliby/lineage/bud_tracker.py
+++ b/src/aliby/lineage/bud_tracker.py
@@ -1,4 +1,8 @@
-#!/usr/bin/env jupyter
+"""
+Extracted from the baby repository. Bud Tracker algorithm to link
+cell outlines as mothers and buds.
+"""
+# /usr/bin/env jupyter
import pickle
from os.path import join
diff --git a/src/postprocessor/core/lineageprocess.py b/src/postprocessor/core/lineageprocess.py
index 856d0791..8c2874e2 100644
--- a/src/postprocessor/core/lineageprocess.py
+++ b/src/postprocessor/core/lineageprocess.py
@@ -21,7 +21,7 @@ class LineageProcessParameters(ParametersABC):
class LineageProcess(PostProcessABC):
"""
- Lineage process that must be passed a (N,3) lineage matrix (where the coliumns are trap, mother, daughter respectively)
+ Lineage process that must be passed a (N,3) lineage matrix (where the columns are trap, mother, daughter respectively)
"""
def __init__(self, parameters: LineageProcessParameters):
--
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