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remove poetry, fix typos
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yibeichan authored Dec 21, 2023
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Expand Up @@ -3,33 +3,25 @@ A [Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/) for [ReproSchem

## Prerequisites

The following are required and recommended tools for using this cookiecutter and the ReproSchema protocol that it generates. This is all a one-time setup, so if you have already done it, skip to the [next section](#creating-a-new-project)!
The following are required and recommended tools for using this cookiecutter and the ReproSchema protocol it generates. This is all a one-time setup, so if you have already done it, skip to the [next section](#creating-a-new-project)!

* **pipx**

pipx is a tool for managing isolated Python-based applications. It is the recommended way to install Poetry and cruft. To install pipx follow the instructions here: https://pypa.github.io/pipx/installation/

* **Poetry**

Poetry is a Python project management tool. You will use it in your generated project to manage dependencies and build distribution files. If you have pipx installed you can install Poetry by running:
```shell
pipx install poetry
```
For other installation methods see: https://python-poetry.org/docs/#installation
pipx is a tool for managing isolated Python-based applications. It is the recommended way to install Poetry and cruft. To install `pipx` follow the instructions here: https://pypa.github.io/pipx/installation/

* **cruft**

cruft is a tool for generating projects based on a cookiecutter (like this one!) as well as keeping those projects updated if the original cookiecutter changes. Install it with pipx by running:
cruft is a tool for generating projects based on a cookiecutter (like this one!) and keeping those projects updated if the original cookiecutter changes. Install it with `pipx` by running:
```shell
pipx install cruft
```
You may also choose to not have a persistent installation of cruft, in which case you would replace any calls to the `cruft` command below with `pipx run cruft`.

## Creating a new project
## Creating a new protocol

### Step 1: Generate the project files
### Step 1: Generate the protocol files

To generate a new LinkML project run the following:
To generate a new Reproschema protocol, run the following:

```bash
cruft create https://github.com/ReproNim/reproschema-protocol-cookiecutter
Expand All @@ -39,7 +31,7 @@ You will be prompted for a few values. The defaults are fine for most
protocols, but do name your protocol something that makes sense to you!
The interactive session will guide you through the process:

1. `protocol_name`: Name of the protocol, use kebab-case with no spaces.
1. `protocol_name`: Name of the protocol; use kebab-case with no spaces.
Suggestions:
- `reproschema-protocol`
- `mood-protocol`
Expand All @@ -49,7 +41,7 @@ Suggestions:
3. `protocol_description`: Description of the protocol.
- A single brief sentence is recommended
- Can easily be modified later
4. `number_of_activities`: How many activities/assessments do you want to create? Choose between 1 and 5; later, it will randomly generate the number of activities of your choice for your protocol.
4. `number_of_activities`: How many activities/assessments do you want to create? Choose between 1 and 5; later, it will randomly generate the number of activities you choose for your protocol.
5. `full_name`: Your name
6. `email`: Your email
7. `license`: Choose a license for the project. If your desired license is not listed, you can update or remove the `LICENSE` file in the generated project.
Expand All @@ -60,9 +52,9 @@ cd my-reproschema-protocol # using the folder example above
make setup
```

### Step 2: Create a GitHub project
### Step 2: Create a GitHub repository

1. Go to https://github.com/new and follow the instructions, being sure NOT to add a `README` or `.gitignore` file (this cookiecutter template will take care of those files for you). Be sure your GitHub project uses the same `protocol_name`
1. Go to https://github.com/new and follow the instructions, being sure NOT to add a `README` or `.gitignore` file (this cookiecutter template will take care of those files for you). Be sure your GitHub repo uses the same `protocol_name`

2. Add the remote to your local git repository

Expand All @@ -88,7 +80,7 @@ make setup

## Keeping your project up to date

In order to be up-to-date with the template, first check if there is a mismatch
To be up-to-date with the template, first check if there is a mismatch
between the project's boilerplate code and the template by running:
```bash
Expand All @@ -100,16 +92,16 @@ boilerplate code and the latest version of the project template. If the project
is up-to-date with the template:

```output
SUCCESS: Good work! Project's cruft is up to date and as clean as possible :).
SUCCESS: Good work! Protocol's cruft is up to date and as clean as possible :).
```
Otherwise, it will indicate that the project's boilerplate code is not
up-to-date by the following:
```output
FAILURE: Project's cruft is out of date! Run `cruft update` to clean this mess up.
FAILURE: Protocol's cruft is out of date! Run `cruft update` to clean this mess up.
```
## Credits
This cookiecutter was made with pieces from
[Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/) and [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).
[Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/) and [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).

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