Merge pull request #55 from tkphd/linting

Linting
linkml · Mar 11, 2023 · 33f5511 · 33f5511
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diff --git a/README.md b/README.md
@@ -1,35 +1,43 @@
 # LinkML Project Cookiecutter
 
-A [Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/) template for projects using [`Linkml`](https://github.com/linkml/linkml).
-
+A [Cookiecutter](https://cookiecutter.readthedocs.io/en/stable/) template for
+projects using [LinkML](https://github.com/linkml/linkml).
 
 ## Standard Protocol
 
 ### Step 1: Create a virtual environment
 
-Create a Python virtual environment. You can read [this 
-guide](https://realpython.com/python-virtual-environments-a-primer/) to learn more about them and how to create one.
-We suggest using poetry, but you can use any tool you like.  Please note, most LinkML tools work best in Python 3.8 or higher.
+Create a Python virtual environment.
+You can read [this guide](https://realpython.com/python-virtual-environments-a-primer/)
+to learn more about them and how to create one. We suggest using poetry, but
+you can use any tool you like. Please note, most LinkML tools work best in
+Python 3.8 or higher.
 
 An example using poetry:
+
 ```bash
 curl -sSL https://install.python-poetry.org | python3 -
 ```
 
 ```bash
 mkdir linkml-projects
 cd linkml-projects
-poetry init # creates a new poetry project with pyproject.toml.  Note this is not a new linkml project, it is just a virtual environment to install cruft.
+poetry init # creates a new poetry project with pyproject.toml
+            # Note this is not a new linkml project,
+            # it is just a virtual environment to install cruft.
 poetry add click==8.1.3  # this creates your virtual environment.
 ```
 
 Add `poetry-dynamic-versioning` as a plugin
-```
+
+```bash
 poetry self add "poetry-dynamic-versioning[plugin]"
 ```
 
 ### Step 2: Install the cruft tool in your virtual environment
-This tool will help you keep your project up to date with the latest LinkML tools and best practices.
+
+This tool will help you keep your project up to date with the latest LinkML
+tools and best practices.
 
 In your poetry virtual environment:
 
@@ -38,61 +46,73 @@ poetry shell
 poetry add cruft
 ```
 
-### Step 3:  Use cruft to create your brand new LinkML project:
+### Step 3:  Use cruft to create your brand new LinkML project
 
 In your poetry virtual environment:
 
 ```bash
 cruft create https://github.com/linkml/linkml-project-cookiecutter
 ```
 
-You will be prompted for a few values.  The defaults are fine for most projects, but do name your project something 
-that makes sense to you!  The interactive session will guide you through the process:
+You will be prompted for a few values.  The defaults are fine for most
+projects, but do name your project something that makes sense to you!
+The interactive session will guide you through the process:
 
-- `project_name`: Name of the project, use kebab-case with no spaces. Suggestions:
-    - `patient-observation-schema`
-    - `sample-collection-metadata`
-    - `resume-standard`
+- `project_name`: Name of the project, use kebab-case with no spaces.
+  Suggestions:
+  - `patient-observation-schema`
+  - `sample-collection-metadata`
+  - `resume-standard`
 - `project_description`: Description of the project.
-    - A single brief sentence is recommended
-    - Can easily be modified later
+  - A single brief sentence is recommended
+  - Can easily be modified later
 - `full_name`: Your name
 - `email`: your email
 - `main_schema_class`:
-    - This is used to generate an example schema which you can edit
-    - The value of this field is ignored if this is a schemasheets project
-    - You can always change this later
+  - This is used to generate an example schema which you can edit
+  - The value of this field is ignored if this is a schemasheets project
+  - You can always change this later
     - Examples: `Person`, `Observation`, `Sample`, `Entry`, `Gene`, `Event`
 - `create_python_project`
-    - If "Yes", set this up as a python project
-    - Select Yes if you want to make data classes that can be used by developers
+  - If "Yes", set this up as a python project
+  - Select Yes if you want to make data classes that can be used by developers
 - `use_schemasheets`
-    - If "Yes", set this to obtain your schema from [schemasheets](https://linkml.io/schemasheets)
+  - If "Yes", set this to obtain your schema from
+    [schemasheets](https://linkml.io/schemasheets)
 - `google_sheet_id`
-    - Ignore/use default value if answer to previous question was "No"
-    - If you are using schemasheets then enter your google doc ID here
-    - If you like you can leave the default value, and this will use the demo schema
+  - Ignore/use default value if answer to previous question was "No"
+  - If you are using schemasheets then enter your google doc ID here
+  - If you like you can leave the default value, and this will use the demo
+    schema
 - `google_sheet_tabs`
-    - Ignore/use default value if not using schemasheets
-    - If you are using schemasheets, enter a space-separated list of tabs
-    - your tabs in your sheet MUST NOT have spaces in them
+  - Ignore/use default value if not using schemasheets
+  - If you are using schemasheets, enter a space-separated list of tabs
+  - your tabs in your sheet MUST NOT have spaces in them
 - `github_token_for_pypi_deployment`:
-   - The github token name which aligns with your autogenerated PyPI token for making releases.
-   - This helps automated releases to PyPI
-   - This should be ignored if this is not a python project
-   - Even if this is a python project, you can leave blank and fill in later
+  - The github token name which aligns with your autogenerated PyPI token for
+    making releases.
+  - This helps automated releases to PyPI
+  - This should be ignored if this is not a python project
+  - Even if this is a python project, you can leave blank and fill in later
 
-This will generate the project folder abiding by the template configuration specified by `linkml-project-cookiecutter` in the [`cookiecutter.json`](https://github.com/linkml/linkml-project-cookiecutter/blob/main/cookiecutter.json) file. 
+This will generate the project folder abiding by the template configuration
+specified by `linkml-project-cookiecutter` in the
+[`cookiecutter.json`](https://github.com/linkml/linkml-project-cookiecutter/blob/main/cookiecutter.json)
+file.
 
-This will generate the project folder very similar to what is mentioned in the [linkml-project-template](https://github.com/linkml/linkml-project-template) project.
+This will generate the project folder very similar to what is mentioned in the
+[linkml-project-template](https://github.com/linkml/linkml-project-template)
+project.
 
-See [linkml/linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter) for more docs.
+For more docs, see
+[linkml/linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter).
 
 ### Step 4: Setup the LinkML project
 
-Optionally set project generation environment variables (see `gen-doc --help` and `gen-project --help`):
+Optionally set project generation environment variables
+(see `gen-doc --help` and `gen-project --help`):
 
-```
+```bash
 export LINKML_COOKIECUTTER_GEN_DOC_ARGS=--no-mergeimports      # example
 export LINKML_COOKIECUTTER_GEN_PROJECT_ARGS=--no-mergeimports  # example
 ```
@@ -106,7 +126,9 @@ make setup
 
 ### Step 5: Edit the schema
 
-Edit the schema (the .yaml file) in the linkml-projects/my-awesome-schema/src/my_awesome_schema/schema folder
+Edit the schema (the .yaml file) in the
+`linkml-projects/my-awesome-schema/src/my_awesome_schema/schema` folder
+
 ```bash
 nano src/my_awesome_schema/schema/my_awesome_schema.yaml
 ```
@@ -117,28 +139,31 @@ nano src/my_awesome_schema/schema/my_awesome_schema.yaml
 make test
 ```
 
-### Step 7: Auto-generate your documentation locally.
-LinkML generates schema documenation automatically.  Step 7 here, allows you to preview the documentation
-that LinkML generates before pushing to GitHub.  Note, this template comes with GitHub
-Actions that autogenerate this documentation on release of your schema repository at a URL like this one:
-https://my-user-or-organization.github.io/my-awesome-schema/ 
+### Step 7: Auto-generate your documentation locally
+
+LinkML generates schema documenation automatically. Step 7 here, allows you to
+preview the documentation that LinkML generates before pushing to GitHub.
+Note, this template comes with GitHub Actions that autogenerate this
+documentation on release of your schema repository at a URL like this one:
+[https://my-user-or-organization.github.io/my-awesome-schema/]
 
 ```bash
 make serve
 ```
 
 ### Step 8: Create a github project
 
-8a: Go to https://github.com/new and follow the instructions, being sure to NOT add a README or .gitignore file (this
-cookiecutter template will take care of this for you)
+1. Go to [https://github.com/new] and follow the instructions, being sure to
+   NOT add a README or .gitignore file (this cookiecutter template will take
+   care of this for you)
 
-8b: Add the remote to your local git repository`
+2. Add the remote to your local git repository
 
-```bash
-git remote add origin https://github.com/my-user-or-organization/my-awesome-schema.git
-git branch -M main
-git push -u origin main
-```
+   ```bash
+   git remote add origin https://github.com/my-user-or-organization/my-awesome-schema.git
+   git branch -M main
+   git push -u origin main
+   ```
 
 ### Step 9: Deploy documentation
 
@@ -150,29 +175,31 @@ See [How to register a schema](../faq/contributing)
 
 ## Keeping your project up to date
 
-In order 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:
+In order 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
 poetry shell
 cruft check
 ```
 
-This indicates if there is a difference between the current project's boilerplate code and the latest version of the 
-project template. If the project is up-to-date with the template:
+This indicates if there is a difference between the current project's
+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 :).
 ```
 
-Otherwise, it will indicate that the project's boilerplate code is not up-to-date by the following:
+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.
 ```
 
-For viewing the difference, run `cruft diff`. This shows the difference between the project's boilerplate code and the 
-template's latest version.
-
-After running `cruft update`, the project's boilerplate code will be updated to the latest version of the template.
+For viewing the difference, run `cruft diff`. This shows the difference between
+the project's boilerplate code and the template's latest version.
 
+After running `cruft update`, the project's boilerplate code will be updated to
+the latest version of the template.
diff --git a/hooks/post_gen_project.py b/hooks/post_gen_project.py
@@ -1,9 +1,6 @@
 """Code to run after generating the project."""
 
-import re
-import sys
 import shutil
-from pathlib import Path
 
 shutil.rmtree("licenses")
 

diff --git a/hooks/pre_gen_project.py b/hooks/pre_gen_project.py
@@ -2,7 +2,6 @@
 
 import re
 import sys
-from pathlib import Path
 
 MODULE_REGEX = re.compile(r'^[_a-zA-Z][_a-zA-Z0-9\-]+$')
 project_name = '{{ cookiecutter.project_name }}'

diff --git a/{{cookiecutter.project_name}}/.github/workflows/deploy-docs.yaml b/{{cookiecutter.project_name}}/.github/workflows/deploy-docs.yaml
@@ -1,31 +1,32 @@
+---
 name: Auto-deployment of {{cookiecutter.__project_slug}} Documentation
 on:
   push:
-    branches: [ main ]
+    branches: [main]
 
 jobs:
   build-docs:
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout
-      uses: actions/checkout@main
-      with:
-        fetch-depth: 0 # otherwise, you will failed to push refs to dest repo
-
-    - name: Set up Python 3.
-      uses: actions/setup-python@v3
-      with:
-        python-version: 3.9
+      - name: Checkout
+        uses: actions/checkout@main
+        with:
+          fetch-depth: 0  # otherwise, you will failed to push refs to dest repo
 
-    - name: Install Poetry.
-      uses: snok/[email protected]
+      - name: Set up Python 3.
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.9
 
-    - name: Install dependencies.
-      run: poetry install -E docs
-
-    - name: Build documentation.
-      run: |
-        mkdir -p docs
-        touch docs/.nojekyll
-        poetry run gen-doc -d docs src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
-        poetry run mkdocs gh-deploy
+      - name: Install Poetry.
+        uses: snok/[email protected]
+
+      - name: Install dependencies.
+        run: poetry install -E docs
+
+      - name: Build documentation.
+        run: |
+          mkdir -p docs
+          touch docs/.nojekyll
+          poetry run gen-doc -d docs src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
+          poetry run mkdocs gh-deploy
diff --git a/{{cookiecutter.project_name}}/.github/workflows/main.yaml b/{{cookiecutter.project_name}}/.github/workflows/main.yaml
@@ -1,7 +1,7 @@
 # Built from:
 # https://docs.github.com/en/actions/guides/building-and-testing-python
 # https://github.com/snok/install-poetry#workflows-and-tips
-
+---
 name: Build and test {{cookiecutter.__project_slug}}
 
 on: [pull_request]
@@ -16,9 +16,6 @@ jobs:
 
     steps:
 
-      #----------------------------------------------
-      #       check-out repo and set-up python
-      #----------------------------------------------
       - name: Check out repository
         uses: actions/checkout@v2
 
@@ -27,27 +24,14 @@ jobs:
         with:
           python-version: ${{ "{{" }} matrix.python-version {{ "}}" }}
 
-      #----------------------------------------------
-      #          install & configure poetry
-      #----------------------------------------------
       - name: Install Poetry
         uses: snok/[email protected]
 
-      #----------------------------------------------
-      # install dependencies if cache does not exist 
-      #----------------------------------------------
       - name: Install dependencies
         run: poetry install --no-interaction --no-root
 
-      #----------------------------------------------
-      #    install your root project, if required 
-      #----------------------------------------------      
-      - name: Install library
+      - name: Install project
         run: poetry install --no-interaction
 
-      #----------------------------------------------
-      #              run test suite   
-      #----------------------------------------------
-      - name: Run tests
+      - name: Run test suite
         run: make test
-