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In order to publish a new article (after acceptance), you'll need to have the
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article metadata file (YAML format) and the corresponding article (PDF
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format). The metadata file should be missing the article DOI, number and
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URL. The first step is thus to request this information from Zenodo. Before
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Congrats on accepting a ReScience article for publication! Follow the steps below to complete the metadata, submit to Zenodo, and get the final article published.
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### What you will need to begin
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- The article metadata file (`metadata.yaml`) from the author's repository. At this time the metadata file should **will be missing** the article DOI, number and URL. This is expected and something you will fix over the coming steps.
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- The final article itself (`article.pdf`)
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Have these two files ready before cloning this repository.
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### Publishing the article
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There are 5 parts to publishing the article.
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| Step | What it does |
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|:--|:--|
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| Set up credentials | Get setup to programmatically submit to Zenodo |
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| Pre-publish the paper | Reserves the DOI |
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| Update the metadata | Add volume, issue, page, doi to the paper & generate new pdf |
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| Publish the paper | Make the final Zenodo deposit |
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| Update the website | Enter bib information for the website |
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### 14 steps to publish a ReScience article
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1\. Clone this repository locally.
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2\. Copy the authors `metadata.yaml` and `article.pdf` into this folder
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### Set up Credentials
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3\. To submit the paper and metadata to Zenodo, you will need to set up access tokens. Setting up your Zenodo sandbox and production tokens is a one time step. If you have done this before, skip over to step 4.
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The first step is thus to request this information from Zenodo. Before
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proceeding further, you'll need a Zenodo token that can be requested from the
server](https://zenodo.org/account/settings/applications/tokens/new/). When creating tokens, be sure to check all three scopes.
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The sandbox token is expected to be stored in the environment variable
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`ZENODO_SANDBOX_TOKEN` while the true token must be stored in `ZENODO_TOKEN`, e.g.:
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```bash
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export ZENODO_SANDBOX_TOKEN="access token"
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export ZENODO_TOKEN="access token"
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```
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And to check it was set correctly:
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```bash
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echo$ZENODO_SANDBOX_TOKEN
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echo$ZENODO_TOKEN
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```
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We strongly advise you to **first test the procedure** on the sandbox server
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using the `--sandbox` switch.
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If you copy these in your bash profile you wont have to look for them again. We advise you to **first test the procedure** on the sandbox server using the `--sandbox` switch. More on this in the next step.
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### Pre-publish the paper
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#### 1. Pre-Publication (article DOI, URL and number)
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This step reserves the DOI for the paper, allowing you to update metadata before final publication.
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Run the [process.py](process.py) script using the provided metadata
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file. It requires Python 3 plus the libraries [PyYAML](https://pyyaml.org/), [Requests](https://requests.kennethreitz.org/), and [dateutil](https://dateutil.readthedocs.io/en/stable/).
Then use the actual server using the `--zenodo` switch instead of the
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`--sandbox` switch.
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Did this work? Were there any problems? If there were no problems, then use the production server using the `--zenodo` switch instead of the `--sandbox` switch.
You must also assign the issue, volume, and article numbers. Have a
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look on the published articles and assign the next available number in
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the same issue and same volume if your article is still in the same
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year. Otherwise, increment the volume number and start with
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issue 1. The issue number is only changed for accommodating special issues.
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Post your numbers to [this GitHub issue](https://github.com/ReScience/ReScience/issues/48)
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that serves to avoid that two editors assign the same numbers to two
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different articles.
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6\. If no errors were returned, you have successfully reserved a DOI! Next we’ll grab an issue, volume and article numbers.
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```
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NOTE: This DOI will not resolve anywhere. This behavior is expected
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```
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### Update the metadata
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#### 2. Metadata update and creation of the final PDF
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In this step, you'll update `metadata.yaml`, pull request the file back to the author, generate a new PDF (which will now contain the volume, issue, page, doi information), and copy that back here.
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The `metadata.yaml` has a section (at the end) for information added during
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the publication process. You should complete it and verify the whole file
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before moving on. The information you must add is:
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7\. Look at the last number on [this GitHub issue](https://github.com/ReScience/ReScience/issues/48) and choose the next one in the series. Post a comment to claim that issue for your article. This comment
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serves to avoid that two editors assign the same numbers to two
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different articles.
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8\. Then add these two bits of information (volume and article number) along with the Zenodo DOI and URL to `metadata.yaml`.
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You should complete the missing information and verify the whole file before moving on. The information you must add is:
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- DOI (from Zenodo)
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- article URL (from Zenodo)
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- contributors (reviewers and editors), with ORCIDs
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- acceptance and publication date
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- issue, volume, and article numbers.
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Next, there are two situations:
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- If the authors have used the [ReScience article template](http://github.com/rescience/template),
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you can fork their repository, copy the edited `metadata.yaml` to it, and create
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the final PDF by running `make`. Don't forget to submit a pull request to the
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authors' repository with the changes you made to `metadata.yaml`.
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- Otherwise, you give the authors the required information and
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ask them to update their article and produce the final PDF file. You should
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check that their PDF contains all the information you sent them.
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9\. Pull request just the `metadata.yaml` back to the author's repo (this will mean copying this file back to the author repo fork). Once the pull-request is merged, have them `Make` a new `article.pdf`. The PDF will now contain the volume, article number and DOI.
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You need to give this information back to author(s) such that they can update
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the metadata file as well as the article that display the DOI in the left
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margin (make sure they actually update this information). For the article
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number, you can have a look on the published articles and assign the next
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available number in the same issue and same volume.
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10\. Copy the newly updated `article.pdf` and `metadata.yaml` back to this repo.
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### Publish the paper
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#### 3. Publication (Zenodo and GitHub)
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In order to publish the **final** article, you'll need to run the
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11\. In order to publish the **final** article, you'll need to run the
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[publish.py](publish.py) script:
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```bash
@@ -113,19 +131,26 @@ A new git branch (10.5072_zenodo.xxxxx) has been created.
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```
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This example uses the sandbox, replace `--sandbox` by `--zenodo` for
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publishing to the Zenodo production site! This will create a new
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public record on Zenodo and also create a new local directory
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corresponding to the entry. This means you need to push this new
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branch on GitHub and make a pull request (the commit will have been
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created automatically).
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#### Website update
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To have the new article to appear on the website, you'll need to prepend the
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newly created bibtex entry (look into the local repository) to the
This will create a new folder and branch in `Rescience/articles` named after the article's DOI that contains three files:
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- The article (`article.pdf`)
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- metadata (`article.yaml`)
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- bib file (`article.bib`)
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- Now push this branch:
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```
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git push origin <DOI>
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```
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12\. Discard any changes on the master branch.
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### Website update
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To have the new article to appear on the website, you'll need to prepend the newly created bibtex entry.
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13\. Finally, copy the contents of `article.bib` from the doi folder for this paper into [rescience.github.io/_bibliography/published.bib](https://github.com/ReScience/rescience.github.io/blob/sources/_bibliography/published.bib) and send a final pull request (You can do this from the web).
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