diff --git a/INSTALL.md b/INSTALL.md
deleted file mode 100644
index 6c5fca38013669b37b4e801ce4f583e3bb8ab759..0000000000000000000000000000000000000000
--- a/INSTALL.md
+++ /dev/null
@@ -1,53 +0,0 @@
-# Installation
-
-Tested on: Mac OSX Mojave
-
-## Requirements
-We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
-Make sure you are using python 3.
-
-An environment can be created with using the conda package manager:
-
- $ conda create --name <env>
- $ conda activate <env>
-
-Which you can deactivate with:
-
- $ conda deactivate
-
-Or using virtualenv:
-
- $ python -m virtualenv /path/to/venv/
- $ source /path/to/venv/bin/activate
-
-This will download all of your packages under `/path/to/venv` and then activate it.
-Deactivate using
-
- $ deactivate
-
-You will also need to make sure you have a recent version of pip.
-In your local environment, run:
-
- $ pip install --upgrade pip
-
-## Pipeline installation
-
-Once you have created your local environment, run:
-
- $ cd pipeline-core
- $ pip install -e ./
-
-You will be asked to put in your GitLab credentials for a couple of the packages installed as dependencies.
-The `-e` option will install in 'editable' mode: all of the changes that are made to the code in the repository will immediately be reflected in the installation.
-This is very useful to keep up with any changes and branching that we make.
-That way, if you want to keep up with the most recent updates, just run:
-
- $ git pull
-
-If you would rather be more in charge of which updates you install and which you don't, remove `-e` from your installation command.
-In this case (or if you run into a dependency error) in order to update your installed version you will have to run:
-
- $ cd pipeline-core
- $ git pull
- $ pip install ./
-
diff --git a/docs/INSTALL.md b/docs/INSTALL.md
new file mode 100644
index 0000000000000000000000000000000000000000..47dfb80d26f59fe3fec30d4ae8ed48f6586cf9a8
--- /dev/null
+++ b/docs/INSTALL.md
@@ -0,0 +1,64 @@
+# Installation
+
+Tested on: Mac OSX Mojave and Ubuntu 20.04
+
+## Requirements
+We strongly recommend installing within a python environment as there are many dependencies that you may not want polluting your regular python environment.
+Make sure you are using python 3.
+
+An environment can be created with using the conda package manager:
+
+ $ conda create --name <env>
+ $ conda activate <env>
+
+Which you can deactivate with:
+
+ $ conda deactivate
+
+Or using virtualenv:
+
+ $ python -m virtualenv /path/to/venv/
+ $ source /path/to/venv/bin/activate
+
+This will download all of your packages under `/path/to/venv` and then activate it.
+Deactivate using
+
+ $ deactivate
+
+You will also need to make sure you have a recent version of pip.
+In your local environment, run:
+
+ $ pip install --upgrade pip
+
+Or using [pyenv](https://github.com/pyenv/pyenv) with pyenv-virtualenv:
+
+ $ pyenv install 3.7.9
+ $ pyenv virtualenv 3.7.9 aliby
+ $ pyenv local aliby
+
+
+## Pipeline installation
+
+### Pip version
+Once you have created your local environment, run:
+
+ $ cd aliby
+ $ pip install -e ./
+
+
+### Git version
+
+We use [ poetry ](https://python-poetry.org/docs/#installation) for dependency management.
+
+
+In case you want to have local versions (usually for development) the main three aliby dependencies you must install them in a specific order:
+
+ $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/aliby.git
+ $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/postprocessor.git
+ $ git clone git@git.ecdf.ed.ac.uk:swain-lab/aliby/agora.git
+
+ $ cd aliby && poetry install
+ $ cd ../postprocessor && poetry install
+ $ cd ../agora && poetry install
+
+And that should install all three main dependencies in an editable mode. The same process can be used for [BABY](https://git.ecdf.ed.ac.uk/swain-lab/aliby/baby)
diff --git a/README.md b/docs/README.md
similarity index 100%
rename from README.md
rename to docs/README.md
diff --git a/poetry.lock b/poetry.lock
index 852598bc29d8c32b5638602c57496bf53afd3ac8..b4407e3fc8fb414bbae91508615f87c2c5fab9b3 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -78,7 +78,7 @@ python-versions = "*"
[[package]]
name = "aliby-agora"
-version = "0.2.25"
+version = "0.2.27"
description = "A gathering of shared utilities for the Swain Lab image processing pipeline."
category = "main"
optional = false
@@ -91,6 +91,7 @@ opencv-python = "*"
pandas = ">=1.1.4,<2.0.0"
py-find-1st = ">=1.1.5,<2.0.0"
PyYAML = ">=6.0,<7.0"
+scipy = ">=1.7.3"
[[package]]
name = "aliby-baby"
@@ -118,14 +119,14 @@ xgboost = "1.4.2"
[[package]]
name = "aliby-post"
-version = "0.1.25"
+version = "0.1.26"
description = "Post-processing tools for aliby pipeline."
category = "main"
optional = false
python-versions = ">=3.7.1,<3.11"
[package.dependencies]
-aliby-agora = ">=0.2.25,<0.3.0"
+aliby-agora = ">=0.2.27,<0.3.0"
catch22 = ">=0.2.0,<0.3.0"
gaussianprocessderivatives = ">=0.1.2,<0.2.0"
leidenalg = ">=0.8.8,<0.9.0"
@@ -2008,7 +2009,7 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
[metadata]
lock-version = "1.1"
python-versions = ">=3.7.1,<3.11"
-content-hash = "f9ee341dcb5c812f3112752cb5234c62a73c320a20a048b2e000d45efd5c6a7d"
+content-hash = "ebcffe1a9437b624306cf70a29e431bbdce98596f844a9453757564a7a3035c4"
[metadata.files]
absl-py = [
@@ -2106,16 +2107,16 @@ alabaster = [
{file = "alabaster-0.7.12.tar.gz", hash = "sha256:a661d72d58e6ea8a57f7a86e37d86716863ee5e92788398526d58b26a4e4dc02"},
]
aliby-agora = [
- {file = "aliby-agora-0.2.25.tar.gz", hash = "sha256:bb1a32e3f7c0dc1c7c745174a4d13e09a07375d9f5a655783b532a7473b3f962"},
- {file = "aliby_agora-0.2.25-py3-none-any.whl", hash = "sha256:43ef2103685b544669032792f651d75c7cc33cfd3fdc0774dfc919a44b93cd22"},
+ {file = "aliby-agora-0.2.27.tar.gz", hash = "sha256:04509d86348ccfa758672eb236714a663c07f5321058f3247e53ca41463db08f"},
+ {file = "aliby_agora-0.2.27-py3-none-any.whl", hash = "sha256:17499f4d76ca97950859747dc96e3d35560c0386bc4af7b019ce1453c7175f8a"},
]
aliby-baby = [
{file = "aliby-baby-0.1.8.tar.gz", hash = "sha256:edd9773040bc80640dd1aab0ec87e1f2eb043232beb1b819274f2f915958520a"},
{file = "aliby_baby-0.1.8-py3-none-any.whl", hash = "sha256:21c7c46f5da719f03f3657b31e6112953e97236a9e5e69537cdde75a4be338f4"},
]
aliby-post = [
- {file = "aliby-post-0.1.25.tar.gz", hash = "sha256:dffd3c77d400df4adb610a5ec2fd7bb6833cb277018e0f0d696c18a79bd2150e"},
- {file = "aliby_post-0.1.25-py3-none-any.whl", hash = "sha256:2cf93978e35f39d80a1e8be9687414b041a4f88a1ca004b5f04f6a2f7fdda2ef"},
+ {file = "aliby-post-0.1.26.tar.gz", hash = "sha256:13ad2df77b28a5ecfb5a8f15e318593b505cfce70a4b41b805a071f08f22c60f"},
+ {file = "aliby_post-0.1.26-py3-none-any.whl", hash = "sha256:7d710794c446c63fdb79b9f5515b894eb3c458bd129b4610d789dd6bcfe447a9"},
]
appdirs = [
{file = "appdirs-1.4.4-py2.py3-none-any.whl", hash = "sha256:a841dacd6b99318a741b166adb07e19ee71a274450e68237b4650ca1055ab128"},
diff --git a/pyproject.toml b/pyproject.toml
index 5b9b5cc482b3a8cc824888bd0846a87e16abcc98..6f978dcd6bcc82e68fc307ea68c3f01dc3ed46e5 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,6 +1,6 @@
[tool.poetry]
name = "aliby"
-version = "0.1.26"
+version = "0.1.27"
description = "Process and analyse live-cell imaging data"
authors = ["Alan Munoz <alan.munoz@ed.ac.uk>"]
packages = [
@@ -26,7 +26,7 @@ omero-py = ">=5.6.2"
zeroc-ice = "3.6.5"
aliby-agora = "^0.2.23"
aliby-baby = "^0.1.7"
-aliby-post = "^0.1.25"
+aliby-post = "^0.1.26"
p-tqdm = "^1.3.3"
xmltodict = "^0.13.0"