diff --git a/docs/source/conf.py b/docs/source/conf.py index 1c7a0103..c7467919 100644 --- a/docs/source/conf.py +++ b/docs/source/conf.py @@ -55,6 +55,8 @@ "sphinxext.opengraph", 'myst_parser', 'autoapi.extension', + 'sphinx_click', + 'sphinxcontrib.mermaid', ] language = 'en' @@ -115,7 +117,7 @@ target='_blank'>Helmholtz Association in the framework of the \ Helmholtz Metadata \ Collaboration", - "repository_url": "https://github.com/hermes-hmc/project", + "repository_url": "https://github.com/hermes-hmc/workflow", "use_repository_button": True, } diff --git a/docs/source/index.md b/docs/source/index.md index b0c9efe8..bb06bb5a 100644 --- a/docs/source/index.md +++ b/docs/source/index.md @@ -34,6 +34,19 @@ automatic submission to publication repositories. ![](_static/img/workflow-overview.svg) ## Documentation + + + +```{toctree} +:glob: +:maxdepth: 1 +:caption: Tutorials +tutorials/* +``` ```{toctree} :maxdepth: 1 diff --git a/docs/source/tutorials/automated-publication-with-ci.md b/docs/source/tutorials/automated-publication-with-ci.md new file mode 100644 index 00000000..45d8d063 --- /dev/null +++ b/docs/source/tutorials/automated-publication-with-ci.md @@ -0,0 +1,168 @@ + + + + +# Set up automatic software publishing + +```{note} +This tutorial works for repositories hosted on GitHub, and shows how to automatically publish to Zenodo Sandbox. +Zenodo Sandbox is a "toy" repository that can be used to try things out. + +This tutorial should also work with the "real" Zenodo. +``` + +## Configure your .gitignore + +The HERMES workflow (`hermes`) uses temporary caches in `.hermes/`. +Ignore this directory in your git repository. + +Add `.hermes/` to your `.gitignore` file: + +```{code-block} bash +:caption: .gitignore + +.hermes/ +``` + +## Provide additional metadata using CITATION.cff + +To provide high-quality citation metadata for your project and your publication, +provide a `CITATION.cff` file in the [Citation File Format](https://citation-file-format.github.io/). + +If you don't have one yet, +use the [cffinit](https://citation-file-format.github.io/cff-initializer-javascript/) website +to create a `CITATION.cff` file. +Save it to the root directory of your repository, and add it to version control. + +```bash +git add CITATION.cff +git commit -m "Add citation file" +git push +``` + +## HERMES configuration + +The HERMES workflow is configured in a [TOML](https://toml.io) file: `hermes.toml`. +Each step in the publication workflow has its own section. + +Configure HERMES to: + +- harvest metadata from Git and `CITATION.cff` +- skip validation of `CITATION.cff` +- deposit on Zenodo Sandbox (which is built on the InvenioRDM) +- use Zenodo Sandbox as the target publication repository + +```{code-block} toml +:caption: hermes.toml +:name: hermes.toml + +[harvest] +from = [ "git", "cff" ] + +[harvest.cff] +validate = false + +[deposit] +mapping = "invenio" +target = "invenio" + +[deposit.invenio] +base_url = "https://sandbox.zenodo.org" + +[postprocess] +execute = [ "config_record_id" ] +``` + +Copy this file to your repository and add it to version control: + +```bash +git add hermes.toml +git commit -m "Configure HERMES to harvest git and CFF, and deposit on Zenodo Sandbox" +git push +``` + +## Get a personal access token for Zenodo Sandbox + +To allow GitHub Actions to publish our repository to Zenodo Sandbox for us, +we need a personal access token from Zenodo Sandbox. + +Log in at https://sandbox.zenodo.org (you may have to register first), +then [create a personal access token in your user profile](https://sandbox.zenodo.org/account/settings/applications/tokens/new/) +with the scopes `deposit:actions` and `deposit:write`. + +Copy the newly created token into a new [GitHub Secret](https://docs.github.com/en/actions/security-guides/encrypted-secrets#creating-encrypted-secrets-for-a-repository) called `ZENODO_SANDBOX` in your repository. + +## Configure a GitHub Action to automate publication + +The HERMES project provides templates for continous integration systems in a dedicated repository: +https://github.com/hermes-hmc/ci-templates. + +Copy the [template for GitHub to Zenodo Sandbox publication](https://github.com/hermes-hmc/ci-templates/blob/main/TEMPLATE_hermes_github_to_zenodo.yml) +into the `.github/workflows/` directory in your repository, and rename it as you like (e.g. `hermes_github_to_zenodo.yml`). + +Go through the file, and look for comments marked with `# ADAPT`. +Adapt the file to your needs. +If you need help with how GitHub Action workflows work in general, +have a look at the [documentation on GitHub](https://docs.github.com/actions). + +Add the workflow file to version control and push it. + +```{warning} +If you haven't adapted the workflow file, and push it to the branch `main`, you will create an automatic publication at this point. +``` + +```bash +git add .github/workflows/hermes_github_to_zenodo.yml +git commit -m "Configure automatic publication with HERMES" +git push +``` + +## Automatic publication workflow + +````{margin} +```{mermaid} +flowchart TD + t(("Trigger\nGitHub Action\n(e.g. push)")) + rh("Run hermes") + subgraph "hermes (harvest, process, curate)" + ci1("Harvest & process metadata") + pr1("Create curation pull request") + end + d{"Merge?"} + subgraph "hermes (deposit, postprocess)" + ci2("Publish software") + pp("Postprocessing") + pr2("Create pull request\nfrom postprocessing") + ci3("Cleanup") + end + e((("End"))) + t --> rh --> ci1 --> pr1 --> d -->|Merge| ci2 --> pp --> pr2 --> e + d -->|Close| ci3 --> e +``` +```` + +```{admonition} Congratulations! +You can now automatically publish your repository to Zenodo Sandbox! +``` + +Now, whenever the GitHub Actions workflow is triggered, it will publish a new version of your repository to Zenodo Sandbox. +If you haven't adapted the workflow file, this will happen whenever you push to your `main` branch. + +The diagram to the right shows the different steps that will happen each time. + +When the workflow runs, it harvests and processes the metadata from Git and your `CITATION.cff` file, +and creates a new pull request in your repository. +You then have the chance to curate the metadata, i.e., make sure that it looks the way you want. +If you merge the pull request, the actual publication is created, +and a new pull request is opened to update the HERMES configuration file +in your repository +with the ID of the publication. +This is needed so that future published versions are collected under the same [*concept DOI*](https://help.zenodo.org/#versioning). diff --git a/poetry.lock b/poetry.lock index cf7aa99e..abab7d6c 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,3 +1,5 @@ +# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. + [[package]] name = "alabaster" version = "0.7.13" @@ -5,6 +7,10 @@ description = "A configurable sidebar-enabled Sphinx theme" category = "dev" optional = false python-versions = ">=3.6" +files = [ + {file = "alabaster-0.7.13-py3-none-any.whl", hash = "sha256:1ee19aca801bbabb5ba3f5f258e4422dfa86f82f3e9cefb0859b283cdd7f62a3"}, + {file = "alabaster-0.7.13.tar.gz", hash = "sha256:a27a4a084d5e690e16e01e03ad2b2e552c61a65469419b907243193de1a84ae2"}, +] [[package]] name = "astroid" @@ -13,6 +19,10 @@ description = "An abstract syntax tree for Python with inference support." category = "dev" optional = false python-versions = ">=3.7.2" +files = [ + {file = "astroid-2.15.0-py3-none-any.whl", hash = "sha256:e3e4d0ffc2d15d954065579689c36aac57a339a4679a679579af6401db4d3fdb"}, + {file = "astroid-2.15.0.tar.gz", hash = "sha256:525f126d5dc1b8b0b6ee398b33159105615d92dc4a17f2cd064125d57f6186fa"}, +] [package.dependencies] lazy-object-proxy = ">=1.4.0" @@ -29,6 +39,10 @@ description = "Classes Without Boilerplate" category = "main" optional = false python-versions = ">=3.6" +files = [ + {file = "attrs-22.2.0-py3-none-any.whl", hash = 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