From 6485e867c175de1efda14592b3194bf81e6fb64b Mon Sep 17 00:00:00 2001
From: Arin Wongprommoon <arin.wongprommoon@ed.ac.uk>
Date: Thu, 26 Jan 2023 16:24:49 +0000
Subject: [PATCH] docs: update repo references
---
.gitlab-ci.yml | 1 -
CONTRIBUTING.md | 4 ++--
README.md | 6 +++---
docs/source/INSTALL.md | 4 ++--
4 files changed, 7 insertions(+), 8 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8597d35a..5059b9ce 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -42,7 +42,6 @@ Local Tests:
- poetry run coverage report -m
- poetry run coverage xml
coverage: '/(?i)total.*? (100(?:\.0+)?\%|[1-9]?\d(?:\.\d+)?\%)$/'
-# Legacy because we use GitLab 14.2.6
artifacts:
reports:
coverage_report:
diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
index 5b051ca2..b62a8f46 100644
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -1,9 +1,9 @@
# Contributing
-We focus our work on python 3.7 due to the current neural network being developed on tensorflow 1. In the near future we will migrate the networ to pytorch to support more recent versions of all packages.
+We focus our work on python 3.8 due to the current neural network being developed on tensorflow 1. In the near future we will migrate the network to pytorch to support more recent versions of all packages.
## Issues
-All issues are managed within the gitlab [ repository ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/issues), if you don't have an account on the University of Edinburgh's gitlab instance and would like to submit issues please get in touch with [Prof. Peter Swain](mailto:peter.swain@ed.ac.uk ).
+All issues are managed within the gitlab [ repository ](https://gitlab.com/aliby/aliby/-/issues), if you don't have an account on the University of Edinburgh's gitlab instance and would like to submit issues please get in touch with [Prof. Peter Swain](mailto:peter.swain@ed.ac.uk ).
## Data aggregation
diff --git a/README.md b/README.md
index 2e66c2e8..0837e85a 100644
--- a/README.md
+++ b/README.md
@@ -2,9 +2,9 @@
[](https://aliby.readthedocs.io/en/latest)
[](https://badge.fury.io/py/aliby)
-[](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/pipelines)
-[](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/commits/dev)
-[](https://git.ecdf.ed.ac.uk/swain-lab/aliby/aliby/-/commits/dev)
+[](https://gitlab.com/aliby/aliby/-/pipelines)
+[](https://gitlab.com/aliby/aliby/-/commits/dev)
+[](https://gitlab.com/aliby/aliby/-/commits/dev)
End-to-end processing of cell microscopy time-lapses. ALIBY automates segmentation, tracking, lineage predictions, post-processing and report production. It leverages the existing Python ecosystem and open-source scientific software available to produce seamless and standardised pipelines.
diff --git a/docs/source/INSTALL.md b/docs/source/INSTALL.md
index 73ec4b10..94abc570 100644
--- a/docs/source/INSTALL.md
+++ b/docs/source/INSTALL.md
@@ -70,10 +70,10 @@ Install [ poetry ](https://python-poetry.org/docs/#installation) for dependency
In case you want to have local version:
- $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/aliby.git
+ $ git clone git@gitlab.com/aliby/aliby.git
$ cd aliby && poetry install --all-extras
-This will automatically install the [ BABY ](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
+This will automatically install the [ BABY ](https://gitlab.com/aliby/baby) segmentation software. Support for additional segmentation and tracking algorithms is under development.
## Omero Server
--
GitLab