fix: 🐛 Codefair v2.0.1

CHANGELOG.md

@@ -5,10 +5,55 @@ All notable changes the Codefair App will be documented in this file.
 The format is based on [Keep a Changelog](http://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.html).
 
+## v.2.0.1 - 2024-09-03
+
+### Identifier
+
+https://doi.org/10.5281/zenodo.13651177
+
+### Added
+
+- Added a migration script to update the database for users who may try to access the dashboard before the v2.0.0 bot has ran on all their repositories.
+- Added badges to the CWL card on the dashboard to show the overall status of the CWL validations.
+
+### Fixed
+
+- Fixed a bug where the bot would updated the overall status of the CWL validation on the database.
+- Link generator for Codefair repository settings was fixed to correctly generate the link for a user or repository.
+
+### Removed
+
+- Removed references to the action key in the database as it was not being used.
+
+## v.2.0.0 - 2024-08-29
+
+### Identifier
+
+https://doi.org/10.5281/zenodo.13544387
+
+### Added
+
+- Full CWL Validation to entire repositories and an user interface to view the validation reports.
+- UI Dashboard has been added for beta testing. The dashboard will provide a central location of the repositories being managed by Codefair. Users will have the ability to update their FAIR compliance items along with rerunning CWL validations and/or enture FAIR compliance checks.
+- Single instance database was created for the bot to remove the need for the database to be passed as a parameter in most of the bot functions.
+- An action queue was created for users who install Codefair to a large number of repositories in one installation. This will prevent an organization/user account from being spammed with alerts on issues being opened for each repository. The action queue will require 5 actions on said repository before the bot will begin to open a Fair Compliance Dashboard issue.
+
+### Changed
+
+- Workflow on the bot has been optimzed to reduce the number of database calls and improving the overall performance/readability of the bot.
+- File restructuring was done on the bot to improve maintainability and readability.
+- Logging has been updated on the bot side to use Consola for better tracking of bot errors and runtime details.
+
+### Removed
+
+- Mention of the FAIR-BioRS Guidelines have been removed to prevent users from thinking Codefair is solely for biomedical research software.
+
 ## v1.0.0 - 2024-08-26
 
 ### Identifier
+
 https://doi.org/10.5281/zenodo.13376617
 
 ### Added
+
 - First release with license file and metadata files generating features

CITATION.cff

@@ -17,7 +17,7 @@ message: If you use this software, please cite it using the metadata from this f
 type: software
 identifiers:
   - type: doi
-    value: https://doi.org/10.5281/zenodo.13376617
+    value: https://doi.org/10.5281/zenodo.13651177
 abstract: "Codefair is a free and open source GitHub app that acts as your
   personal assistant when it comes to making your research software reusable and
   especially complying with the Findable, Accessible, Interoperable, Reusable
@@ -33,5 +33,5 @@ keywords:
   - software
 license: MIT
 repository-code: https://github.com/fairdataihub/codefair-app
-version: 1.0.0
-date-released: 2024-08-26
+version: 2.0.1
+date-released: 2024-09-03

README.md

@@ -32,8 +32,8 @@ Your coding assistant to make research software reusable without breaking a swea
   <a href="https://github.com/fairdataihub/codefair-app/blob/main/LICENSE">
     <img src="https://img.shields.io/github/license/fairdataihub/codefair-app.svg?style=flat-square" alt="license" />
   </a>
-  <a href="https://doi.org/10.5281/zenodo.13376617">
-    <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13376617.svg" alt="Zenodo DOI" />
+  <a href="https://doi.org/10.5281/zenodo.13376616">
+    <img src="https://zenodo.org/badge/DOI/10.5281/zenodo.13376616.svg" alt="Zenodo DOI" />
   </a>
   <a href="https://archive.softwareheritage.org/browse/origin/https://github.com/fairdataihub/codefair-app/">
     <img src="https://archive.softwareheritage.org/badge/origin/https://github.com/fairdataihub/codefair-app/" alt="Software Heritage archive" />
@@ -65,46 +65,17 @@ Codefair is your personal assistant when it comes to making your research softwa
 > While Codefair is free, installing it via the GitHub Marketplace may still require a credit card to be associated with your (or your organization’s) GitHub account. To circumvent this requirement, you can alternatively install Codefair directly from the [app page](https://github.com/apps/codefair-app).
 
 ### Documentation
-See the our [dedicated webpage](https://docs.codefair.io) for the full documentation, including details about each features and how to use them.
 
-## Run the GitHub app locally
-
-### Setup
-
-This repository uses a pnpm workspace to handle both the bot and the frontend UI. You will need to install pnpm globally to run the app locally. You will also need to be on Node.js version 20 or higher.
-
-```bash
-npm install -g pnpm
-```
-
-To start both the bot and the frontend UI, run the following command at the root of the repository:
-
-```bash
-pnpm dev
-```
+See our [dedicated webpage](https://docs.codefair.io/docs/installation.html) for full details on what permissions are used and the features Codefair provides.
 
-This will start the bot and the frontend UI in development mode. The bot will be available at `http://localhost:3001` and the frontend UI will be available at `http://localhost:3000`.
-
-The .env files for each package are located in the respective package directories. You will need to create a `.env` file in the `bot` and `ui` directories. Use the .env.example files in each directory as a template.
-
-To run the bot only, run the following command at the root of the repository:
-
-```bash
-cd bot
-pnpm dev
-```
-
-To run the frontend UI only, run the following command at the root of the repository:
+## Run the GitHub app locally
 
-```bash
-cd ui
-pnpm dev
-```
+For detailed instructions on setting up running the application locally, please refer to our [documentation site](https://docs.codefair.io/dev/running-locally.html).
 
 ## How Codefair is developed
 
-Codefair is developed using Probot and is deployed on a server as a serverless function. The GitHub app is configured to receive webhooks for important actions such as pushing code, opening or closing issues, opening or merging pull requests and commenting on discussions.
-By leveraging a serverless environment on a server, Codefair can automatically scale to handle the workload of the GitHub app. The app is written in Node.js and utilizes the Octokit library to interact with the GitHub APIenabling seamless integration with GitHub's features and functionality.
+Codefair is developed using [Probot](https://probot.github.io/docs/) and is deployed on a server as a serverless function. The GitHub app is configured to receive webhooks for important actions such as pushing code, opening or closing issues, opening or merging pull requests and commenting on discussions.
+By leveraging a serverless environment on a server, Codefair can automatically scale to handle the workload of the GitHub app. The app is written in [Node.js](https://nodejs.org/en) and utilizes the [Octokit library](https://github.com/octokit) to interact with the GitHub API enabling seamless integration with GitHub's features and functionality.
 
 ## Contributing
 
@@ -127,11 +98,8 @@ This work is licensed under
 
 ## How to cite
 
-If you are using this package or reusing the source code from this repository for any purpose, please cite:
+If you are using this package or reusing the source code from this repository for any purpose, please cite the corresponding Zenodo record. If you are using the latest version, you can see the citation instruction in the GitHub Citation panel or in the CITATION.cff file. You can also find the citation instruction on the Zenodo page 10.5281/zenodo.13376616 (especially if you would like to cite an older version). 
 
-```text
-   Portillo, D., Soundarajan, S., & Patel, B., (2024). Codefair App. Zenodo. 10.5281/zenodo.13376617
-```
 <br />
 
 ---

bot/.npmrc

@@ -0,0 +1 @@
+package-manager-strict=false

bot/utils/citation/index.js → bot/citation/index.js

@@ -1,4 +1,4 @@
-import { gatherRepoAuthors } from "../tools/index.js";
+import { gatherRepoAuthors } from "../utils/tools/index.js";
 
 export async function checkForCitation(context, owner, repo) {
   try {
@@ -14,7 +14,6 @@ export async function checkForCitation(context, owner, repo) {
   }
 }
 
-
 // TODO: Verify if this is still needed
 export async function gatherCitationInfo(context, owner, repo) {
   // Verify there is no PR open already for the CITATION.cff file
@@ -86,9 +85,7 @@ export async function gatherCitationInfo(context, owner, repo) {
   // Get the keywords of the repo
   let keywords = [];
   if (repoData.data.topics != null && repoData.data.topics.length > 0) {
-    // console.log(repoData.data.topics);
     keywords = repoData.data.topics;
-    // console.log(keywords);
   }
 
   // Begin creating json for CITATION.cff file

bot/utils/codemeta/index.js → bot/codemeta/index.js

@@ -1,4 +1,4 @@
-import { gatherRepoAuthors } from "../tools/index.js";
+import { gatherRepoAuthors } from "../utils/tools/index.js";
 
 export async function checkForCodeMeta(context, owner, repo) {
   try {
@@ -23,8 +23,6 @@ export async function gatherCodeMetaInfo(context, owner, repo) {
   });
 
   // Get the languages used in the repo
-  console.log(repoData.data);
-
   const languagesUsed = await gatherLanguagesUsed(context, owner, repo);
   const authors = await gatherRepoAuthors(context, owner, repo, "codemeta");
   const codeRepository = repoData.data.html_url;