move to staplescience.com

.github/CONTRIBUTING.md

@@ -8,7 +8,7 @@ If you want to get started contributing to STAPLE, we recommend you set up your
 
 Anyone can open a pull request to STAPLE, which will automatically run certain checks. This means you can focus more time on contributing and less time on testing. We may ask you to make some changes during the review process, to ensure everything fits nicely. But rest assured, we share the burden with you, and you are not on your own!
 
-Before you get started please make sure to read through our [code of conduct](add link). Then, a good place to start would be looking at the issues at https://github.com/STAPLE-verse/STAPLE/issues. Issues that are tagged as _good-first-issue_ are ready to be worked on. If noone else is working on that issue you can claim it by leaving a comment on the issue. If you have any questions feel free to ask in the issue by leaving a comment and someone from the team will help you out. We are happy that you spend your time making STAPLE better!
+Before you get started please make sure to read through our [code of conduct](https://github.com/STAPLE-verse/STAPLE/tree/dev?tab=coc-ov-file). Then, a good place to start would be looking at the [issues](https://github.com/STAPLE-verse/STAPLE/issues). Issues that are tagged as _good-first-issue_ are ready to be worked on. If noone else is working on that issue you can claim it by leaving a comment on the issue. If you have any questions feel free to ask in the issue by leaving a comment and someone from the team will help you out. We are happy that you spend your time making STAPLE better!
 
 If you would like to contribute to STAPLE long-term you can join our community on [Slack](https://join.slack.com/t/staple-talk/shared_invite/zt-2u8yd4n7n-0ehpV2UmA0ORUvM_qQcDcA).
 
@@ -18,7 +18,7 @@ In general, contributions we welcome are small unknown issues (see the list belo
 
 We always welcome certain contributions:
 
-- Documenting issues with STAPLE (maybe link to the issues guide?)
+- Documenting issues with STAPLE
 - Fixing typos or grammatical errors
 - Adding unit tests to components, mutations, queries, or hooks
 - Improving type casting to be more robust
@@ -30,9 +30,12 @@ We always welcome certain contributions:
 
 In general, we discourage adding large unknown contributions without talking to us.
 
-If your contribution falls outside those we welcome anytime, please get in touch with us first. We do this to ensure you do not waste your time. For example, if you are looking to make a substantial contribution to STAPLE, please open an issue first so we can discuss your approach. We want your effort to be successful, and getting feedback early helps ensure your contribution is aligned with the project.
+If your contribution falls outside those we welcome anytime, please get in touch with us first. We do this to ensure you do not waste your time.
+For example, if you are looking to make a substantial contribution to STAPLE, please open an issue first so we can discuss your approach. We want your
+effort to be successful, and getting feedback early helps ensure your contribution is aligned with the project.
 
-What we actively discourage is adding features and opening up pull requests for them without talking to us first. You do this at your own risk, and with no guarantee that your contribution gets included.
+What we actively discourage is adding features and opening up pull requests for them without talking to us first. You do this at your own risk, and with no
+guarantee that your contribution gets included.
 
 ## How to make a pull request
 
@@ -43,9 +46,12 @@ Use the five minute rule:
 
 Once you are ready to submit your code, please use the appropriate pull request template.
 
-Please note that STAPLE is a small team, and pull requests will be responded to as quickly as possible. Depending on the time of year, it may take a few weeks. Feel free to check in if we have not responded within that time frame.
+Please note that STAPLE is a small team, and pull requests will be responded to as quickly as possible. Depending on the time of year, it may take a few
+weeks. Feel free to check in if we have not responded within that time frame.
 
-All pull requests should be sent to the `dev` branch for initial review. We will respond with comments and/or requests for updates. After approval, we will test the update on our [development website](https://test.staple.science). Once we verify that the update is integrated appropriated within STAPLE, we will pull the changes in the `main` branch to put on the [production website](https://app.staple.science/).
+All pull requests should be sent to the `dev` branch for initial review. We will respond with comments and/or requests for updates. After approval, we
+will test the update on our [development website](https://test.staplescience.com). Once we verify that the update is integrated appropriated within
+STAPLE, we will pull the changes in the `main` branch to put on the [production website](https://app.staplescience.com/).
 
 Here is the current workflow for pull requests:
 

CODE_OF_CONDUCT.md

@@ -0,0 +1,128 @@
+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+We as members, contributors, and leaders pledge to make participation in our
+community a harassment-free experience for everyone, regardless of age, body
+size, visible or invisible disability, ethnicity, sex characteristics, gender
+identity and expression, level of experience, education, socio-economic status,
+nationality, personal appearance, race, religion, or sexual identity
+and orientation.
+
+We pledge to act and interact in ways that contribute to an open, welcoming,
+diverse, inclusive, and healthy community.
+
+## Our Standards
+
+Examples of behavior that contributes to a positive environment for our
+community include:
+
+* Demonstrating empathy and kindness toward other people
+* Being respectful of differing opinions, viewpoints, and experiences
+* Giving and gracefully accepting constructive feedback
+* Accepting responsibility and apologizing to those affected by our mistakes,
+  and learning from the experience
+* Focusing on what is best not just for us as individuals, but for the
+  overall community
+
+Examples of unacceptable behavior include:
+
+* The use of sexualized language or imagery, and sexual attention or
+  advances of any kind
+* Trolling, insulting or derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or email
+  address, without their explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Enforcement Responsibilities
+
+Community leaders are responsible for clarifying and enforcing our standards of
+acceptable behavior and will take appropriate and fair corrective action in
+response to any behavior that they deem inappropriate, threatening, offensive,
+or harmful.
+
+Community leaders have the right and responsibility to remove, edit, or reject
+comments, commits, code, wiki edits, issues, and other contributions that are
+not aligned to this Code of Conduct, and will communicate reasons for moderation
+decisions when appropriate.
+
+## Scope
+
+This Code of Conduct applies within all community spaces, and also applies when
+an individual is officially representing the community in public spaces.
+Examples of representing our community include using an official e-mail address,
+posting via an official social media account, or acting as an appointed
+representative at an online or offline event.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported to the community leaders responsible for enforcement at
+staple.helpdesk@gmail.com.
+All complaints will be reviewed and investigated promptly and fairly.
+
+All community leaders are obligated to respect the privacy and security of the
+reporter of any incident.
+
+## Enforcement Guidelines
+
+Community leaders will follow these Community Impact Guidelines in determining
+the consequences for any action they deem in violation of this Code of Conduct:
+
+### 1. Correction
+
+**Community Impact**: Use of inappropriate language or other behavior deemed
+unprofessional or unwelcome in the community.
+
+**Consequence**: A private, written warning from community leaders, providing
+clarity around the nature of the violation and an explanation of why the
+behavior was inappropriate. A public apology may be requested.
+
+### 2. Warning
+
+**Community Impact**: A violation through a single incident or series
+of actions.
+
+**Consequence**: A warning with consequences for continued behavior. No
+interaction with the people involved, including unsolicited interaction with
+those enforcing the Code of Conduct, for a specified period of time. This
+includes avoiding interactions in community spaces as well as external channels
+like social media. Violating these terms may lead to a temporary or
+permanent ban.
+
+### 3. Temporary Ban
+
+**Community Impact**: A serious violation of community standards, including
+sustained inappropriate behavior.
+
+**Consequence**: A temporary ban from any sort of interaction or public
+communication with the community for a specified period of time. No public or
+private interaction with the people involved, including unsolicited interaction
+with those enforcing the Code of Conduct, is allowed during this period.
+Violating these terms may lead to a permanent ban.
+
+### 4. Permanent Ban
+
+**Community Impact**: Demonstrating a pattern of violation of community
+standards, including sustained inappropriate behavior,  harassment of an
+individual, or aggression toward or disparagement of classes of individuals.
+
+**Consequence**: A permanent ban from any sort of public interaction within
+the community.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 2.0, available at
+https://www.contributor-covenant.org/version/2/0/code_of_conduct.html.
+
+Community Impact Guidelines were inspired by [Mozilla's code of conduct
+enforcement ladder](https://github.com/mozilla/diversity).
+
+[homepage]: https://www.contributor-covenant.org
+
+For answers to common questions about this code of conduct, see the FAQ at
+https://www.contributor-covenant.org/faq. Translations are available at
+https://www.contributor-covenant.org/translations.

README.md

@@ -6,16 +6,16 @@
 [![License: MIT](https://img.shields.io/badge/License-MIT-blue.svg)](LICENSE)
 [![Build Status](https://github.com/STAPLE-verse/STAPLE/actions/workflows/dry-run.yml/badge.svg)](https://github.com/STAPLE-verse/STAPLE/actions/workflows/dry-run.yml)
 [![Contributions Welcome](https://img.shields.io/badge/contributions-welcome-brightgreen.svg)](https://github.com/STAPLE-verse/STAPLE?tab=contributing-ov-file)
-[![Slack](https://img.shields.io/badge/chat-on%20Slack-purple.svg?logo=slack)]([https://your-slack-invite-link](https://join.slack.com/t/staple-talk/shared_invite/zt-25c08jrdt-f66do2kbIZExpAou5ZQYew))  
+[![Slack](https://img.shields.io/badge/chat-on%20Slack-purple.svg?logo=slack)]([https://your-slack-invite-link](https://join.slack.com/t/staple-talk/shared_invite/zt-25c08jrdt-f66do2kbIZExpAou5ZQYew))
 
-### 📖 Documentation: 
+### 📖 Documentation:
 
-👉 [Full installation and usage guide](https://staple.science/documentation/)
+👉 [Full installation and usage guide](https://staplescience.com/documentation/)
 
 ### 📦 Citation
 
 If you use STAPLE in your work, please cite it using the concept DOI or a release-specific DOI:
-	
+
 - Concept DOI: https://doi.org/10.5281/zenodo.13916969
 - For specific releases, use the DOI associated with that release (badge above links to the latest).
 

cron/cronJobDailyMailer.mjs

@@ -25,8 +25,8 @@ function createDailyNotification(email, notificationContent, overdueContent) {
 
         <p>
           This email is to notify you about overdue tasks and recent updates to your project(s).
-          You can view all notifications on the <a href="https://app.staple.science/auth/login?next=%2Fnotifications">Notifications page</a>.
-          You change the frequency of these emails on your <a href="https://app.staple.science/auth/login?next=%2Fprofile">Profile page</a>.
+          You can view all notifications on the <a href="https://app.staplescience.com/auth/login?next=%2Fnotifications">Notifications page</a>.
+          You change the frequency of these emails on your <a href="https://app.staplescience.com/auth/login?next=%2Fprofile">Profile page</a>.
           </p>
 
         <h3>⏰ Overdue Tasks</h3>
@@ -39,7 +39,7 @@ function createDailyNotification(email, notificationContent, overdueContent) {
   `
 
   return {
-    from: "STAPLE <app@staple.science>",
+    from: "STAPLE <app@staplescience.com>",
     to: email,
     subject: "STAPLE Daily Notifications",
     replyTo: "STAPLE Help <staple.helpdesk@gmail.com>",
@@ -286,7 +286,7 @@ export async function sendGroupedNotifications(groupedNotifications, groupedOver
 
     // Send email
     try {
-      const response = await fetch("https://app.staple.science/api/send-email", {
+      const response = await fetch("https://app.staplescience.com/api/send-email", {
         method: "POST",
         headers: { "Content-Type": "application/json" },
         body: JSON.stringify(emailContent),

cron/cronJobWeeklyMailer.mjs

@@ -25,8 +25,8 @@ function createWeeklyNotification(email, notificationContent, overdueContent) {
 
         <p>
           This email is to notify you about overdue tasks and updates to your project(s) from the last week.
-          You can view all notifications on the <a href="https://app.staple.science/auth/login?next=%2Fnotifications">Notifications page</a>.
-          You change the frequency of these emails on your <a href="https://app.staple.science/auth/login?next=%2Fprofile">Profile page</a>.
+          You can view all notifications on the <a href="https://app.staplescience.com/auth/login?next=%2Fnotifications">Notifications page</a>.
+          You change the frequency of these emails on your <a href="https://app.staplescience.com/auth/login?next=%2Fprofile">Profile page</a>.
           </p>
 
         <h3>⏰ Overdue Tasks</h3>
@@ -39,7 +39,7 @@ function createWeeklyNotification(email, notificationContent, overdueContent) {
   `
 
   return {
-    from: "STAPLE <app@staple.science>",
+    from: "STAPLE <app@staplescience.com>",
     to: email,
     subject: "STAPLE Weekly Notifications",
     replyTo: "STAPLE Help <staple.helpdesk@gmail.com>",
@@ -275,7 +275,7 @@ export async function sendGroupedNotifications(groupedNotifications, groupedOver
 
     // Send email
     try {
-      const response = await fetch("https://app.staple.science/api/send-email", {
+      const response = await fetch("https://app.staplescience.com/api/send-email", {
         method: "POST",
         headers: { "Content-Type": "application/json" },
         body: JSON.stringify(emailContent),