Skip to content

Commit

Permalink
Merge pull request #139 from seqeralabs/update-setup
Browse files Browse the repository at this point in the history
docs: update README links, version for release in setup
  • Loading branch information
ejseqera authored Apr 26, 2024
2 parents dac72e5 + 306bcb5 commit cfcf9c2
Show file tree
Hide file tree
Showing 2 changed files with 22 additions and 17 deletions.
37 changes: 21 additions & 16 deletions README.md
Original file line number Diff line number Diff line change
@@ -1,4 +1,8 @@
# <img src="https://raw.githubusercontent.com/seqeralabs/seqera-kit/main/assets/seqerakit.svg" width=50 alt="seqerakit logo"> seqerakit
<div align="center">
<img src="https://raw.githubusercontent.com/seqeralabs/seqera-kit/main/assets/seqerakit.svg" width="50" alt="seqerakit logo" style="vertical-align: middle; margin-right: 10px">
<span style="vertical-align: middle; font-size: 40px;">seqerakit</span>
</div>
<br>

`seqerakit` is a Python wrapper for the [Seqera Platform CLI](https://github.com/seqeralabs/tower-cli). It can be leveraged to automate the creation of all of the entities in Seqera Platform via a simple configuration file in YAML format.

Expand Down Expand Up @@ -220,7 +224,7 @@ DEBUG:root: Running command: tw organizations add --name $SEQERA_ORGANIZATION_NA
### 3. Specifying JSON configuration files with `file-path`
The Seqera Platform CLI allows export and import of entities through JSON configuration files for pipelines and compute environments. To use these files to add a pipeline or compute environment to a workspace, use the `file-path` key to specify a path to a JSON configuration file.

An example of the `file-path` option is provided in the [compute-envs.yml](templates/compute-envs.yml) template:
An example of the `file-path` option is provided in the [compute-envs.yml](./templates/compute-envs.yml) template:

```yaml
compute-envs:
Expand Down Expand Up @@ -264,7 +268,7 @@ You will need to have an account on Seqera Platform (see [Plans and pricing](htt

You can also launch the same pipeline via a Python script. This will essentially allow you to extend the functionality on offer within the Seqera Platform CLI by leveraging the flexibility and customisation options available in Python.

1. Download the [`launch_hello_world.py`](https://github.com/seqeralabs/seqera-kit/blob/main/examples/python/launch_hello_world.py) Python script and customise the `<YOUR_WORKSPACE>` and `<YOUR_COMPUTE_ENVIRONMENT>` entries as required.
1. Download the [`launch_hello_world.py`](./examples/python/launch_hello_world.py) Python script and customise the `<YOUR_WORKSPACE>` and `<YOUR_COMPUTE_ENVIRONMENT>` entries as required.

2. Launch the pipeline with `seqerakit`:

Expand Down Expand Up @@ -331,24 +335,25 @@ In this example:
- Ensure that the indentation and structure of the YAML file are correct - YAML is sensitive to formatting.
- Use quotes around strings that contain special characters or spaces.
- When listing multiple values (`labels`, `instance-types`, `allow-buckets`, etc), separate them with commas as shown above.
- For complex configurations, refer to the [Templates](/templates/) provided in this repository.
- For complex configurations, refer to the [Templates](./templates/) provided in this repository.


## Templates

We have provided template YAML files for each of the entities that can be created on Seqera Platform. These can be found in the [`templates/`](https://github.com/seqeralabs/blob/main/seqera-kit/templates) directory and should form a good starting point for you to add your own customization:

- [organizations.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/organizations.yml)
- [teams.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/teams.yml)
- [workspaces.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/workspaces.yml)
- [participants.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/participants.yml)
- [credentials.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/credentials.yml)
- [secrets.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/secrets.yml)
- [compute-envs.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/compute-envs.yml)
- [actions.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/actions.yml)
- [datasets.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/datasets.yml)
- [pipelines.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/pipelines.yml)
- [launch.yml](https://github.com/seqeralabs/seqera-kit/blob/main/templates/launch.yml)
- [organizations.yml](./templates/organizations.yml)
- [teams.yml](./templates/teams.yml)
- [workspaces.yml](./templates/workspaces.yml)
- [participants.yml](./templates/participants.yml)
- [credentials.yml](./templates/credentials.yml)
- [secrets.yml](./templates/secrets.yml)
- [compute-envs.yml](./templates/compute-envs.yml)
- [actions.yml](./templates/actions.yml)
- [datasets.yml](./templates/datasets.yml)
- [labels.yml](./templates/labels.yml)
- [pipelines.yml](./templates/pipelines.yml)
- [launch.yml](./templates/launch.yml)

## Real world example

Expand All @@ -370,7 +375,7 @@ $SENTIEON_LICENSE_BASE64

## Contributions and Support

If you would like to contribute to `seqerakit`, please see the [contributing guidelines](https://github.com/seqeralabs/seqera-kit/blob/main/.github/CONTRIBUTING.md).
If you would like to contribute to `seqerakit`, please see the [contributing guidelines](./.github/CONTRIBUTING.md).

For further information or help, please don't hesitate to create an [issue](https://github.com/seqeralabs/seqera-kit/issues) in this repository.

Expand Down
2 changes: 1 addition & 1 deletion setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@

from setuptools import find_packages, setup

VERSION = "0.4.6"
VERSION = "0.4.7"

with open("README.md") as f:
readme = f.read()
Expand Down

0 comments on commit cfcf9c2

Please sign in to comment.