diff --git a/CHANGELOG.html b/CHANGELOG.html index 17c7c3f..a1428b8 100644 --- a/CHANGELOG.html +++ b/CHANGELOG.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/_images/social_previews/summary_user_guide_templates_45ad33ac.png b/_images/social_previews/summary_user_guide_templates_45ad33ac.png deleted file mode 100644 index f4e08d3..0000000 Binary files a/_images/social_previews/summary_user_guide_templates_45ad33ac.png and /dev/null differ diff --git a/_images/social_previews/summary_user_guide_templates_fb98484a.png b/_images/social_previews/summary_user_guide_templates_fb98484a.png new file mode 100644 index 0000000..c0cb5d1 Binary files /dev/null and b/_images/social_previews/summary_user_guide_templates_fb98484a.png differ diff --git a/_sources/user_guide/templates.md b/_sources/user_guide/templates.md index c52753a..514c37c 100644 --- a/_sources/user_guide/templates.md +++ b/_sources/user_guide/templates.md @@ -1,3 +1,64 @@ # Project and stage templates -TODO +DSO provides a templating engine that allows to quickly bootrstap a project (`dso init`), folder, or stages (`dso create`). +Templates are based on [jinja2](https://jinja.palletsprojects.com/en/stable/templates/). + +## Available templates + +DSO currently comes with the following templates: + +Project templates: + +- [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/init/default) - Default template, with + integration of `git`, `dvc`, `uv`, `pre-commit`, and `editorconfig`. + +Folder templates: + +- [default](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/folder/default) - This one is very minimal, just a folder with `dvc.yaml` and `params.in.yaml` files. + +Stage templates: + +- [quarto](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/quarto) - Template for quarto notebook in R +- [bash](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates/stage/bash) - Template for executing a bash snippet + +The source code of the templates can be [inspected on GitHub](https://github.com/Boehringer-Ingelheim/dso/tree/main/src/dso/templates). +Templates shipped with DSO are [licensed](https://github.com/Boehringer-Ingelheim/dso/blob/main/src/dso/templates/LICENSE) under the Creative Commons Zero v1.0 +Universal license. + +## Using custom template libraries + +Currently, dso only supports the internal templates mentioned above. However, we plan to add support to custom +stage templates soon. This enables some interesting use-cases: + +- Organization-specific templates: Use templates that make it easier to comply with internal processes or apply + corporate design. +- Best-practice codebases: Start off common analysis types off a predefined template. We believe that some analyses + require more flexibility than predefined worflows such as nf-core, but can still benefit from a structured + "base" document to get started with. + +## Writing templates + +Template directories are recursively copied to their destination and files are rendered with [jinja2](https://jinja.palletsprojects.com/en/stable/templates/). +You can use all features of jinja2 such as `if/else` blocks or loops. Additionally, you have access to the +following variables: + +Available variables for **project** templates: + +| variable | content | +| ------------------- | ----------------------------------------------------- | +| project_name | project/folder name as provided to the `dso init` CLI | +| project_description | description as provided to the `dso init` CLI | + +Available variables for **folder** templates: + +| variable | content | +| ----------- | ------------------------------------------------------ | +| folder_name | folder name as provided to the `dso create folder` CLI | + +Available variables for **stage** templates: + +| variable | content | +| ----------------- | ----------------------------------------------------- | +| stage_name | folder name as provided to the `dso create stage` CLI | +| stage_description | description as provided to the `dso create stage` CLI | +| stage_path | Path to the stage relative to the project root | diff --git a/_static/documentation_options.js b/_static/documentation_options.js index 5e60357..dd5756b 100644 --- a/_static/documentation_options.js +++ b/_static/documentation_options.js @@ -1,5 +1,5 @@ const DOCUMENTATION_OPTIONS = { - VERSION: '0.1.dev1+gf67c66b', + VERSION: '0.1.dev1+g92ce961', LANGUAGE: 'en', COLLAPSE_INDEX: false, BUILDER: 'html', diff --git a/cli_command_reference.html b/cli_command_reference.html index 76188ff..0c6dd0b 100644 --- a/cli_command_reference.html +++ b/cli_command_reference.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/cli_configuration.html b/cli_configuration.html index 2bab451..bbe4c8d 100644 --- a/cli_configuration.html +++ b/cli_configuration.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/cli_installation.html b/cli_installation.html index 7236e8a..7f96578 100644 --- a/cli_installation.html +++ b/cli_installation.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + @@ -367,7 +367,7 @@

Installationdso binary:

$ dso --version
-dso, version 0.1.dev1+gf67c66b
+dso, version 0.1.dev1+g92ce961

If you prefer to manage the Python environment yourself, you can use pip as usual:

diff --git a/contributing.html b/contributing.html index b59f69d..e851a43 100644 --- a/contributing.html +++ b/contributing.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/faq.html b/faq.html index a3ae819..38e70a5 100644 --- a/faq.html +++ b/faq.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/genindex.html b/genindex.html index e5853e3..438f00e 100644 --- a/genindex.html +++ b/genindex.html @@ -41,7 +41,7 @@ - + @@ -52,7 +52,7 @@ - + diff --git a/getting_started.html b/getting_started.html index f3e3ced..e23b528 100644 --- a/getting_started.html +++ b/getting_started.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/index.html b/index.html index 2d8f214..4f16e86 100644 --- a/index.html +++ b/index.html @@ -53,7 +53,7 @@ - + @@ -65,7 +65,7 @@ - + diff --git a/objects.inv b/objects.inv index ef37c6f..94fd9d8 100644 Binary files a/objects.inv and b/objects.inv differ diff --git a/py-modindex.html b/py-modindex.html index 6b3bd21..2fb3763 100644 --- a/py-modindex.html +++ b/py-modindex.html @@ -41,7 +41,7 @@ - + @@ -53,7 +53,7 @@ - + + @@ -63,7 +63,7 @@ - + diff --git a/python_usage.html b/python_usage.html index b267ef7..f9067b0 100644 --- a/python_usage.html +++ b/python_usage.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/search.html b/search.html index 33063fc..97a4a56 100644 --- a/search.html +++ b/search.html @@ -40,7 +40,7 @@ - + @@ -54,7 +54,7 @@ - + diff --git a/searchindex.js b/searchindex.js index 79ce892..608e30f 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"API reference": [[8, null]], "Accessing files and parameters from R or Python": [[6, "accessing-files-and-parameters-from-r-or-python"]], "Accessing stage config": [[10, null]], "Bash Stage": [[6, "bash-stage"]], "Building the docs locally": [[4, "building-the-docs-locally"]], "Can I use dvc to track files that are outside the repository?": [[5, 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b/user_guide/dvc.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/user_guide/linting.html b/user_guide/linting.html index d65192d..4d4f7cd 100644 --- a/user_guide/linting.html +++ b/user_guide/linting.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/user_guide/params_files.html b/user_guide/params_files.html index 8fadd45..78da9fc 100644 --- a/user_guide/params_files.html +++ b/user_guide/params_files.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/user_guide/pre_commit.html b/user_guide/pre_commit.html index 8b6f1e2..c66297b 100644 --- a/user_guide/pre_commit.html +++ b/user_guide/pre_commit.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/user_guide/quarto.html b/user_guide/quarto.html index 800a166..ce05528 100644 --- a/user_guide/quarto.html +++ b/user_guide/quarto.html @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + diff --git a/user_guide/templates.html b/user_guide/templates.html index 2228acf..b58a5b5 100644 --- a/user_guide/templates.html +++ b/user_guide/templates.html @@ -11,12 +11,12 @@ - + - - - + + + Project and stage templates — dso-core @@ -53,7 +53,7 @@ - + @@ -66,7 +66,7 @@ - + @@ -321,7 +321,9 @@ - + @@ -337,6 +339,16 @@

Project and stage templates

@@ -348,7 +360,98 @@

Project and stage templates

Project and stage templates#

-

TODO

+

DSO provides a templating engine that allows to quickly bootrstap a project (dso init), folder, or stages (dso create). +Templates are based on jinja2.

+
+

Available templates#

+

DSO currently comes with the following templates:

+

Project templates:

+ +

Folder templates:

+ +

Stage templates:

+ +

The source code of the templates can be inspected on GitHub. +Templates shipped with DSO are licensed under the Creative Commons Zero v1.0 +Universal license.

+
+
+

Using custom template libraries#

+

Currently, dso only supports the internal templates mentioned above. However, we plan to add support to custom +stage templates soon. This enables some interesting use-cases:

+ +
+
+

Writing templates#

+

Template directories are recursively copied to their destination and files are rendered with jinja2. +You can use all features of jinja2 such as if/else blocks or loops. Additionally, you have access to the +following variables:

+

Available variables for project templates:

+
+ + + + + + + + + + + + + +

variable

content

project_name

project/folder name as provided to the dso init CLI

project_description

description as provided to the dso init CLI

+
+

Available variables for folder templates:

+
+ + + + + + + + + + +

variable

content

folder_name

folder name as provided to the dso create folder CLI

+
+

Available variables for stage templates:

+
+ + + + + + + + + + + + + + + + +

variable

content

stage_name

folder name as provided to the dso create stage CLI

stage_description

description as provided to the dso create stage CLI

stage_path

Path to the stage relative to the project root

+
+
@@ -387,6 +490,24 @@

Project and stage templates +
+ + +
+
+ Contents +
+
+ +
+