Pre commit autoformat (#846)

* Removed unused imports using autoflake.

* Ordered imports using isort.

* Reformatted using black.

* Setting up pre-commits.

* Ran pre-commit an all files.

* Working on creating openapi.json without running backend to be used with codegen.

* Fixed `MUI: The Tabs component doesn't accept a Fragment as a child.`

* Fixed runtime error due to replacing `== None` with 'is None'.

* Fixed runtime error due to replacing `== None` with 'is None'.

* Automatically generate openapi json file using pre-commit hook.

* Added codegen precommit hook.

* Setting up prettier and eslint.

* First run of prettier.

* Runnin eslint and prettier as hooks.

* Skip codegen directories when running eslint and prettier.

* Flake8 E711 exception. Required for Beanie query to work.

* Fixed search_users_prefix codegen stub.

* Fixed beanie query for get_dataset_folders.

* Ignore Flake8 E711 since beanie query do not support `is None`.

.flake8

@@ -0,0 +1,5 @@
+[flake8]
+max-line-length = 180
+extend-ignore = E203, E266, E501, W503, E741, E711
+exclude = .svn,CVS,.bzr,.hg,.git,__pycache__,venv/*,src/*,.rst,build
+max-complexity=16

.github/workflows/backend.yaml

@@ -111,4 +111,4 @@ jobs:
           push: ${{ github.event_name != 'pull_request' }}
           tags: ${{ steps.messagesMeta.outputs.tags }}
           file: ./backend/messages.Dockerfile
-          labels: ${{ steps.messagesMeta.outputs.labels }}
+          labels: ${{ steps.messagesMeta.outputs.labels }}

.github/workflows/codegen.yaml

@@ -57,7 +57,7 @@ jobs:
       - name: Run Codegen
         working-directory: frontend
         run: npm run codegen:v2:test
-        
+
       - name: Verify Changed files
         uses: tj-actions/verify-changed-files@v14
         id: verify-changed-files

.github/workflows/helm-release.yaml

@@ -50,7 +50,7 @@ jobs:
 
       - name: Publish to NCSA OpenSource
         if: |
-          github.event_name != 'pull_request' 
+          github.event_name != 'pull_request'
           && github.repository == env.MAIN_REPO
         uses: bsord/[email protected]
         with:

.pre-commit-config.yaml

@@ -0,0 +1,53 @@
+repos:
+  - repo: local
+    hooks:
+      - id: extract-openapi
+        name: extract-openapi
+        entry: pipenv run extract-openapi
+        language: system
+        pass_filenames: false
+  - repo: local
+    hooks:
+      - id: generate-frontend-api-client
+        name: generate-frontend-api-client
+        entry: bash -c 'cd frontend && npm run codegen:v2:file'
+        language: system
+        pass_filenames: false
+  - repo: local
+    hooks:
+      - id: eslint
+        name: eslint
+        entry: bash -c "cd frontend && npx eslint --fix src"
+        language: system
+  - repo: local
+    hooks:
+      - id: prettier
+        name: prettier
+        entry: bash -c "cd frontend && npx prettier src --write"
+        language: system
+  - repo: https://github.com/psf/black
+    rev: 23.11.0
+    hooks:
+      - id: black
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: [ "--profile=black" ]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.5.0
+    hooks:
+      - id: check-yaml
+        exclude: deployments/kubernetes/charts
+      - id: end-of-file-fixer
+        exclude: 'openapi.json|frontend/src/openapi/v2/'
+      - id: trailing-whitespace
+        exclude: 'openapi.json|frontend/src/openapi/v2/'
+  - repo: https://github.com/shellcheck-py/shellcheck-py
+    rev: v0.9.0.6
+    hooks:
+      - id: shellcheck
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.1.0
+    hooks:
+      - id: flake8

.run/Clowder2 Dev.run.xml

@@ -5,4 +5,4 @@
     <toRun name="uvicorn" type="PythonConfigurationType" />
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/Debug.run.xml

@@ -2,4 +2,4 @@
   <configuration default="false" name="Debug" type="JavascriptDebugType" uri="http://localhost:3000">
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/Docker Dev.run.xml

@@ -10,4 +10,4 @@
     </deployment>
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/Python tests in tests.run.xml

@@ -14,4 +14,4 @@
     <option name="_new_targetType" value="&quot;PATH&quot;" />
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/start.run.xml

@@ -9,4 +9,4 @@
     <envs />
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/start_dev.run.xml

@@ -9,4 +9,4 @@
     <envs />
     <method v="2" />
   </configuration>
-</component>
+</component>

.run/uvicorn.run.xml

@@ -21,4 +21,4 @@
     <option name="INPUT_FILE" value="" />
     <method v="2" />
   </configuration>
-</component>
+</component>

Pipfile

@@ -40,3 +40,6 @@ sphinx-material = "*"
 
 [requires]
 python_version = "3.9"
+
+[scripts]
+extract-openapi = "python backend/extract-openapi.py app.main:app"

README.md

@@ -1,4 +1,4 @@
-![](docs/source/img/logo_full.png) 
+![](docs/source/img/logo_full.png)
 
 # Clowder v2 (In active development)
 [![Build Status](https://github.com/clowder-framework/clowder2/actions/workflows/pytest.yml/badge.svg?branch=main)](https://github.com/clowder-framework/clowder2/actions?query=branch%3Amain)
@@ -9,8 +9,8 @@
 *For the previous version of Clowder, please see [Clowder v1](https://github.com/clowder-framework/clowder).*
 
 Clowder v2 is a reimagining of the [Clowder research data management system](https://clowderframework.org/)
-using a different and newer technology stack. Clowder is a cloud native data management framework to support any 
-research domain. Clowder was developed to help researchers and scientists in data intensive domains manage raw data, 
+using a different and newer technology stack. Clowder is a cloud native data management framework to support any
+research domain. Clowder was developed to help researchers and scientists in data intensive domains manage raw data,
 complex metadata, and automatic data pipelines.
 
 While the Clowder v1 has worked well over the years, many of the underlying
@@ -31,36 +31,36 @@ The v2 documentation is still work in progress. It's available at https://clowde
 
 The v1 documentation is not fully compatible with v2, but it does provide some still relevant information.
 It is available at https://clowder-framework.readthedocs.io.
-There is a few other documentation links available on the [website](https://clowderframework.org/documentation.html). 
+There is a few other documentation links available on the [website](https://clowderframework.org/documentation.html).
 
 ## Installation
 
-The easiest way of running Clowder v2 is checking out the [code](https://github.com/clowder-framework/clowder2) 
+The easiest way of running Clowder v2 is checking out the [code](https://github.com/clowder-framework/clowder2)
 and running `docker compose up` in the main directory.
 
 Helm charts are available for running Clowder v2 on Kubernetes. See the [helm](https://github.com/clowder-framework/clowder2/tree/main/deployments/kubernetes/charts) directory for more information.
 
 ## Contributing
 
-We are always looking for contributors. This could be anything from fixing bugs, adding new features, providing new 
-feature requests, reccomending UI/UX improvements, helping with the documentation, or just testing the system and 
+We are always looking for contributors. This could be anything from fixing bugs, adding new features, providing new
+feature requests, reccomending UI/UX improvements, helping with the documentation, or just testing the system and
 providing feedback. Here are a few ways to get started:
 
-- Join our [Slack](https://join.slack.com/t/clowder-software/shared_invite/zt-4e0vo0sh-YNndJEuLtPGRa7~uIlpcNA) 
+- Join our [Slack](https://join.slack.com/t/clowder-software/shared_invite/zt-4e0vo0sh-YNndJEuLtPGRa7~uIlpcNA)
   channel, introduce yourself, and ask questions about the specific aspects of the system you are interested in.
 - Submit an issue (bug or feature request) on the [issue tracker](https://github.com/clowder-framework/clowder2/issues).
-- Submit a [pull request](https://github.com/clowder-framework/clowder2/pulls) with a bug fix or new feature. For 
+- Submit a [pull request](https://github.com/clowder-framework/clowder2/pulls) with a bug fix or new feature. For
   larger changes, it's best to open an issue first or ask on Slack to discuss the changes.
 - Develop new [information extractors](https://github.com/clowder-framework/pyclowder) and/or visualizations.
 
-Please follow our [code of conduct](https://github.com/clowder-framework/clowder/blob/develop/CODE_OF_CONDUCT.md) when 
+Please follow our [code of conduct](https://github.com/clowder-framework/clowder/blob/develop/CODE_OF_CONDUCT.md) when
 interacting with the community.
 
 ## Support & Contacts
 
 The easiest way to get in touch with us is [Slack](https://join.slack.com/t/clowder-software/shared_invite/zt-4e0vo0sh-YNndJEuLtPGRa7~uIlpcNA).
-This is a public forum. If you prefer email, you can contact us at [[email protected]](mailto:[email protected]). 
+This is a public forum. If you prefer email, you can contact us at [[email protected]](mailto:[email protected]).
 
 ## License
 
-Clowder v2 is licensed under the [Apache 2.0 license](https://github.com/clowder-framework/clowder2/blob/main/LICENSE). 
+Clowder v2 is licensed under the [Apache 2.0 license](https://github.com/clowder-framework/clowder2/blob/main/LICENSE).

backend/Pipfile

@@ -26,6 +26,12 @@ rocrate = "0.7.0"
 httpx = "0.24.0"
 packaging = "23.1"
 itsdangerous = "2.1.2"
+flake8 = "*"
+pyflakes = "*"
+autoflake = "*"
+isort = "*"
+shellcheck-py = "*"
+pre-commit = "*"
 
 [dev-packages]
 requests = "2.28.2"