Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Install via conda environment file #7

Merged
merged 2 commits into from
Oct 19, 2023
Merged

Install via conda environment file #7

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
45837ad
added conda environment file
niksirbi Oct 18, 2023
8fe2aea
updated installation instructions in README
niksirbi Oct 18, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion MANIFEST.in
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
include LICENSE
include README.md
exclude .pre-commit-config.yaml
exclude *.yaml
exclude cruft.json

recursive-exclude * __pycache__
Expand Down
17 changes: 12 additions & 5 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,25 +26,32 @@ Build unbiased anatomical templates from individual images
- Support 3D volumetric microscopy images, such as STPT and LSM.
- Generate templates compatible with the [BrainGlobe ecosystem](https://brainglobe.info/), especially the [BrainGlobe Atlas API](https://brainglobe.info/documentation/bg-atlasapi/index.html).

> **Warning** 🏗️
> **Warning**
> - Early development phase. Stay tuned
> - Interface may undergo changes.

## Installation

> **Warning**
> - [ANTs](http://stnava.github.io/ANTs/), which [we depend on](#template-construction-with-ants), is a large package. The installation may take a while.
> - ANTs is only available for Linux and macOS. If you are on Windows, you can use [WSL](https://learn.microsoft.com/en-us/windows/wsl/install)

We recommend installing `brainglobe-template-builder` within a [conda](https://docs.conda.io/en/latest/) or [mamba](https://mamba.readthedocs.io/en/latest/index.html) environment. Instructions assume `conda` usage, but `mamba`/`micromamba` are interchangeable.

Use the provided `environment.yaml` file to create a new environment.

```sh
conda create -n template-builder -c aramislab -c conda-forge python=3.10 ants parallel
git clone https://github.com/brainglobe/brainglobe-template-builder
cd brainglobe-template-builder
conda env create -f environment.yaml -n template-builder
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

I started from scratch: removed the existing environment, cloned the repo and manually downloaded the environment.yaml file. The environment was not created. I got this message:
Collecting package metadata (repodata.json): done Solving environment: \ Killed

conda activate template-builder
```

To get the latest development version of `brainglobe-template-builder`, clone this repository and pip install the package, including all the extra "dev" dependencies:
We have called the environment `template-builder`, but you can choose any name you like.

To install the latest development version of `brainglobe-template-builder`,

```sh
git clone https://github.com/brainglobe/brainglobe-template-builder
cd brainglobe-template-builder
pip install -e .[dev]
```
For zsh users (default shell on macOS):
Expand Down
11 changes: 11 additions & 0 deletions environment.yaml
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
channels:
- aramislab
- conda-forge
- defaults
dependencies:
- python=3.10
- conda-forge::parallel
- conda-forge::napari
- conda-forge::pyqt
- aramislab::ants
- pip