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| # Automated scholarly manuscripts on GitHub | ||
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| <!-- usage note: edit the H1 title above to personalize the manuscript --> | ||
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| [](https://plantbreeding.github.io/BrAPI-Manuscript2/) | ||
| [](https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf) | ||
| [](https://github.com/plantbreeding/BrAPI-Manuscript2/actions) | ||
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| ## Manuscript description | ||
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| <!-- usage note: edit this section. --> | ||
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| This repository is a template manuscript (a.k.a. rootstock). | ||
| Actual manuscript instances will clone this repository (see [`SETUP.md`](SETUP.md)) and replace this paragraph with a description of their manuscript. | ||
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| ## Manubot | ||
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| <!-- usage note: do not edit this section --> | ||
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| Manubot is a system for writing scholarly manuscripts via GitHub. | ||
| Manubot automates citations and references, versions manuscripts using git, and enables collaborative writing via GitHub. | ||
| An [overview manuscript](https://greenelab.github.io/meta-review/ "Open collaborative writing with Manubot") presents the benefits of collaborative writing with Manubot and its unique features. | ||
| The [rootstock repository](https://git.io/fhQH1) is a general purpose template for creating new Manubot instances, as detailed in [`SETUP.md`](SETUP.md). | ||
| See [`USAGE.md`](USAGE.md) for documentation how to write a manuscript. | ||
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| Please open [an issue](https://git.io/fhQHM) for questions related to Manubot usage, bug reports, or general inquiries. | ||
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| ### Repository directories & files | ||
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| The directories are as follows: | ||
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| + [`content`](content) contains the manuscript source, which includes markdown files as well as inputs for citations and references. | ||
| See [`USAGE.md`](USAGE.md) for more information. | ||
| + [`output`](output) contains the outputs (generated files) from Manubot including the resulting manuscripts. | ||
| You should not edit these files manually, because they will get overwritten. | ||
| + [`webpage`](webpage) is a directory meant to be rendered as a static webpage for viewing the HTML manuscript. | ||
| + [`build`](build) contains commands and tools for building the manuscript. | ||
| + [`ci`](ci) contains files necessary for deployment via continuous integration. | ||
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| ### Local execution | ||
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| The easiest way to run Manubot is to use [continuous integration](#continuous-integration) to rebuild the manuscript when the content changes. | ||
| If you want to build a Manubot manuscript locally, install the [conda](https://conda.io) environment as described in [`build`](build). | ||
| Then, you can build the manuscript on POSIX systems by running the following commands from this root directory. | ||
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| ```sh | ||
| # Activate the manubot conda environment (assumes conda version >= 4.4) | ||
| conda activate manubot | ||
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| # Build the manuscript, saving outputs to the output directory | ||
| bash build/build.sh | ||
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| # At this point, the HTML & PDF outputs will have been created. The remaining | ||
| # commands are for serving the webpage to view the HTML manuscript locally. | ||
| # This is required to view local images in the HTML output. | ||
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| # Configure the webpage directory | ||
| manubot webpage | ||
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| # You can now open the manuscript webpage/index.html in a web browser. | ||
| # Alternatively, open a local webserver at http://localhost:8000/ with the | ||
| # following commands. | ||
| cd webpage | ||
| python -m http.server | ||
| ``` | ||
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| Sometimes it's helpful to monitor the content directory and automatically rebuild the manuscript when a change is detected. | ||
| The following command, while running, will trigger both the `build.sh` script and `manubot webpage` command upon content changes: | ||
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| ```sh | ||
| bash build/autobuild.sh | ||
| ``` | ||
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| ### Continuous Integration | ||
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| Whenever a pull request is opened, CI (continuous integration) will test whether the changes break the build process to generate a formatted manuscript. | ||
| The build process aims to detect common errors, such as invalid citations. | ||
| If your pull request build fails, see the CI logs for the cause of failure and revise your pull request accordingly. | ||
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| When a commit to the `main` branch occurs (for example, when a pull request is merged), CI builds the manuscript and writes the results to the [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) and [`output`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/output) branches. | ||
| The `gh-pages` branch uses [GitHub Pages](https://pages.github.com/) to host the following URLs: | ||
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| + **HTML manuscript** at https://plantbreeding.github.io/BrAPI-Manuscript2/ | ||
| + **PDF manuscript** at https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf | ||
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| For continuous integration configuration details, see [`.github/workflows/manubot.yaml`](.github/workflows/manubot.yaml). | ||
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| ## License | ||
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| <!-- | ||
| usage note: edit this section to change the license of your manuscript or source code changes to this repository. | ||
| We encourage users to openly license their manuscripts, which is the default as specified below. | ||
| --> | ||
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| [](http://creativecommons.org/licenses/by/4.0/) | ||
| [](https://creativecommons.org/publicdomain/zero/1.0/) | ||
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| Except when noted otherwise, the entirety of this repository is licensed under a CC BY 4.0 License ([`LICENSE.md`](LICENSE.md)), which allows reuse with attribution. | ||
| Please attribute by linking to https://github.com/plantbreeding/BrAPI-Manuscript2. | ||
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| Since CC BY is not ideal for code and data, certain repository components are also released under the CC0 1.0 public domain dedication ([`LICENSE-CC0.md`](LICENSE-CC0.md)). | ||
| All files matched by the following glob patterns are dual licensed under CC BY 4.0 and CC0 1.0: | ||
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| + `*.sh` | ||
| + `*.py` | ||
| + `*.yml` / `*.yaml` | ||
| + `*.json` | ||
| + `*.bib` | ||
| + `*.tsv` | ||
| + `.gitignore` | ||
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| All other files are only available under CC BY 4.0, including: | ||
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| + `*.md` | ||
| + `*.html` | ||
| + `*.pdf` | ||
| + `*.docx` | ||
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| Please open [an issue](https://github.com/plantbreeding/BrAPI-Manuscript2/issues) for any question related to licensing. |
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