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app_runner/.buildinfo

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+# Sphinx build info version 1
+# This file records the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: 3b7c129bcacffd00dd24cc29b6c50999
+tags: 645f666f9bcd5a90fca523b33c5a78b7

app_runner/_sources/changelog.md

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+# Changelog
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.1.0/).
+
+## \[Unreleased\]
+
+## \[0.0.3\] - 2024-10-24
+
+### Added
+
+- Specify environment variables for docker container in spec.
+
+## \[0.0.2\] - 2024-10-23
+
+### Added
+
+- App spec supports changing docker entrypoint.
+- `bfabric-app-runner inputs check` to validate the local files
+
+### Fixed
+
+- `bfabric-app-runner inputs list` does not fail anymore if resources have no "name" field value.

app_runner/_sources/index.md

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+```{toctree}
+:glob:
+specs/input_specification
+specs/output_specification
+specs/app_specification
+changelog
+*
+```
+
+## Install App Runner
+
+```bash
+pipx install app_runner@git+https://github.com/fgcz/bfabricPy.git@main#egg=app_runner&subdirectory=app_runner
+```

app_runner/_sources/specs/app_specification.md

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+## App specification
+
+TODO: not clear if this same document should also explain the individual steps, or if it would make sense to first
+describe the app anatomy in a separate document with figures etc. and then list how to specify it

app_runner/_sources/specs/input_specification.md

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+## Input specification
+
+The inputs module provides a specification schema to define the inputs required by an app.
+You can also use this functionality interactively while prototyping.
+The file is usually called `inputs.yml` and lists the different inputs, with information and how to retrieve them and
+the filename to save them as.
+
+### General structure
+
+Generally the structure is a yaml file containing a key `inputs` which is a list of dictionaries, each representing an
+input file.
+Each input has a `type` key which identifies the input type.
+This will allow us to extend this logic to different sources in the future.
+
+In general the only other input key that will be available for all types is `filename`, which is the name of the file to
+save the input as.
+Fields like `id` might not be relevant for all types in the future, and depending on the type more specific options
+might exist.
+
+An example file could look like this:
+
+```yaml
+# file: inputs.yml
+inputs:
+  - type: bfabric_dataset
+    id: 53706
+    filename: test.csv
+  - type: bfabric_resource
+    id: 2700958
+    filename: test.zip
+```
+
+## Commands
+
+### Validation
+
+The input file can be validated with the command:
+
+```bash
+bfabric-app-runner validate inputs-spec inputs.yml
+```
+
+Which on success will output a pretty-printed version of the inputs file.
+Validation will also be performed by all other commands, so this is not strictly necessary.
+
+For instance, in the above case this would print:
+
+```
+InputsSpec(
+│   inputs=[
+│   │   DatasetSpec(type='bfabric_dataset', id=53706, filename='test.csv', separator=','),
+│   │   ResourceSpec(type='bfabric_resource', id=2700958, filename='test.zip', check_checksum=True)
+│   ]
+)
+```
+
+Here you can also see all the extra parameters which were implicitly set.
+
+### Prepare files
+
+The prepare command downloads your files and requires two arguments.
+The first is the input file, and the second is the directory to save the files to.
+In general to download to the current directory simply use `.` as the second argument:
+
+```bash
+bfabric-app-runner inputs prepare inputs.yml .
+```
+
+If your files already exist and are up-to-date, it will not download them again.
+
+### List files
+
+You can list the files that are present or will be downloaded:
+
+```bash
+bfabric-app-runner inputs list inputs.yml .
+```
+
+If you also want to check whether the files are up-to-date, you can pass the `--check` flag:
+
+```bash
+bfabric-app-runner inputs list --check inputs.yml .
+```
+
+## Reference
+
+```{eval-rst}
+.. automodule:: app_runner.input_preparation.spec
+    :members:
+    :undoc-members:
+    :show-inheritance:
+```

app_runner/_sources/specs/output_specification.md

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+## Output specification
+
+The outputs module provides a specification schema to define the outputs that were created by an app and should be registered.
+The file is usually called `outputs.yml` and lists the different output files, with information how to register them.
+
+### General structure
+
+To be described.

app_runner/_static/autodoc_pydantic.css

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+  padding-left: 8px;
+  }
+
+.autodoc_pydantic_collapsable_json {
+  cursor: pointer;
+  }
+
+.autodoc_pydantic_collapsable_erd {
+  cursor: pointer;
+  }