Merge pull request #30 from the-virtual-brain/EBR-91

EBR-91: rename the python package to align with the default convention

.github/workflows/build.yml

@@ -41,13 +41,11 @@ jobs:
         CLB_AUTH: 'TEST_TOKEN'
       run: |
         set -eux
-        jlpm
-        jlpm run build
         python -m pip install .[test]
 
         jupyter server extension list
         
-        jupyter server extension list 2>&1 | grep -ie "tvbextunicore.*OK"
+        jupyter server extension list 2>&1 | grep -ie "tvb_ext_unicore.*OK"
         jupyter labextension list 2>&1 | grep -ie "tvb-ext-unicore.*OK"
         python -m jupyterlab.browser_check
 
@@ -57,7 +55,7 @@ jobs:
     - name: Run Python & JS tests
       run: |
         set -eux
-        pytest tvbextunicore -r ap
+        pytest tvb_ext_unicore -r ap
         yarn test
 
     - name: Package the extension
@@ -126,6 +124,6 @@ jobs:
 
         pip install "jupyterlab>=4.0.0,<5" tvb_ext_unicore*.whl
 
-        jupyter server extension list 2>&1 | grep -ie "tvbextunicore.*OK"
+        jupyter server extension list 2>&1 | grep -ie "tvb_ext_unicore.*OK"
         jupyter labextension list 2>&1 | grep -ie "tvb-ext-unicore.*OK"
         python -m jupyterlab.browser_check --no-browser-test

.gitignore

@@ -7,9 +7,9 @@ node_modules/
 *.egg-info/
 .ipynb_checkpoints
 *.tsbuildinfo
-tvbextunicore/labextension
+tvb_ext_unicore/labextension
 # Version file is handled by hatchling
-tvbextunicore/_version.py
+tvb_ext_unicore/_version.py
 
 # Created by https://www.gitignore.io/api/python
 # Edit at https://www.gitignore.io/?templates=python

.prettierignore

@@ -3,4 +3,4 @@ node_modules
 **/lib
 **/package.json
 !/package.json
-tvbextunicore
+tvb_ext_unicore

README.md

@@ -10,7 +10,7 @@ This jupyter extension offers a UI component to monitor HPC jobs through Unicore
 to easily switch between computing sites, retrieve details about the jobs, 
 and also cancel them.
 
-The package is composed of a Python module named `tvbextunicore`
+The package is composed of a Python module named `tvb_ext_unicore`
 for the server extension and a NPM package named `tvb-ext-unicore`
 for the frontend extension.
 
@@ -85,7 +85,7 @@ pip install -e .
 # Link your development version of the extension with JupyterLab
 jupyter labextension develop . --overwrite
 # Server extension must be manually installed in develop mode
-jupyter server extension enable tvbextunicore
+jupyter server extension enable tvb_ext_unicore
 
 # Define CLB_AUTH environment variable holding your EBRAINS token
 export CLB_AUTH=${ebrains_token}
@@ -115,7 +115,7 @@ jupyter lab build --minimize=False
 
 ```bash
 # Server extension must be manually disabled in develop mode
-jupyter server extension disable tvbextunicore
+jupyter server extension disable tvb_ext_unicore
 pip uninstall tvb-ext-unicore
 ```
 
@@ -141,7 +141,7 @@ jupyter labextension develop . --overwrite
 To execute them, run:
 
 ```sh
-pytest -vv -r ap --cov tvbextunicore
+pytest -vv -r ap --cov tvb_ext_unicore
 ```
 
 #### Frontend tests

conftest.py

@@ -5,4 +5,4 @@
 
 @pytest.fixture
 def jp_server_config(jp_server_config):
-    return {"ServerApp": {"jpserver_extensions": {"tvbextunicore": True}}}
+    return {"ServerApp": {"jpserver_extensions": {"tvb_ext_unicore": True}}}

jupyter-config/nb-config/tvbextunicore.json

@@ -1,7 +1,7 @@
 {
   "NotebookApp": {
     "nbserver_extensions": {
-      "tvbextunicore": true
+      "tvb_ext_unicore": true
     }
   }
 }

jupyter-config/server-config/tvbextunicore.json

@@ -1,7 +1,7 @@
 {
   "ServerApp": {
     "jpserver_extensions": {
-      "tvbextunicore": true
+      "tvb_ext_unicore": true
     }
   }
 }

package.json

@@ -37,7 +37,7 @@
     "build:prod": "jlpm clean && jlpm build:lib:prod && jlpm build:labextension",
     "clean": "jlpm clean:lib",
     "clean:all": "jlpm clean:lib && jlpm clean:labextension && jlpm clean:lintcache",
-    "clean:labextension": "rimraf tvbextunicore/labextension tvbextunicore/_version.py",
+    "clean:labextension": "rimraf tvb_ext_unicore/labextension tvb_ext_unicore/_version.py",
     "clean:lib": "rimraf lib tsconfig.tsbuildinfo",
     "clean:lintcache": "rimraf .eslintcache .stylelintcache",
     "eslint": "jlpm eslint:check --fix",
@@ -122,7 +122,7 @@
       }
     },
     "extension": true,
-    "outputDir": "tvbextunicore/labextension"
+    "outputDir": "tvb_ext_unicore/labextension"
   },
   "jupyter-releaser": {
     "hooks": {

pyproject.toml

@@ -44,25 +44,25 @@ source = "nodejs"
 fields = ["description", "authors", "urls", "keywords"]
 
 [tool.hatch.build.targets.sdist]
-artifacts = ["tvbextunicore/labextension"]
+artifacts = ["tvb_ext_unicore/labextension"]
 exclude = [".github", "binder"]
 
 [tool.hatch.build.targets.wheel.shared-data]
-"tvbextunicore/labextension" = "share/jupyter/labextensions/tvb-ext-unicore"
+"tvb_ext_unicore/labextension" = "share/jupyter/labextensions/tvb-ext-unicore"
 "install.json" = "share/jupyter/labextensions/tvb-ext-unicore/install.json"
 "jupyter-config/server-config" = "etc/jupyter/jupyter_server_config.d"
 
 [tool.hatch.build.hooks.version]
-path = "tvbextunicore/_version.py"
+path = "tvb_ext_unicore/_version.py"
 
 [tool.hatch.build.hooks.jupyter-builder]
 dependencies = ["hatch-jupyter-builder>=0.5"]
 build-function = "hatch_jupyter_builder.npm_builder"
 ensured-targets = [
-    "tvbextunicore/labextension/static/style.js",
-    "tvbextunicore/labextension/package.json",
+    "tvb_ext_unicore/labextension/static/style.js",
+    "tvb_ext_unicore/labextension/package.json",
 ]
-skip-if-exists = ["tvbextunicore/labextension/static/style.js"]
+skip-if-exists = ["tvb_ext_unicore/labextension/static/style.js"]
 
 [tool.hatch.build.hooks.jupyter-builder.build-kwargs]
 build_cmd = "build:prod"
@@ -72,7 +72,7 @@ npm = ["jlpm"]
 build_cmd = "install:extension"
 npm = ["jlpm"]
 source_dir = "src"
-build_dir = "tvbextunicore/labextension"
+build_dir = "tvb_ext_unicore/labextension"
 
 [tool.jupyter-releaser.options]
 version_cmd = "hatch version"

src/__tests__/constants.tests.tsx

@@ -2,15 +2,15 @@ import { getJobCode, getDownloadFileCode } from '../constants';
 
 describe('test getJobCode, getDownloadFileCode', () => {
   it('generates code to get a job', () => {
-    const expected = `from tvbextunicore.unicore_wrapper import unicore_wrapper
+    const expected = `from tvb_ext_unicore.unicore_wrapper import unicore_wrapper
 unicore = unicore_wrapper.UnicoreWrapper()
 job = unicore.get_job('url')
 job`;
     expect(getJobCode('url')).toBe(expected);
   });
 
   it('generates code to download a file', () => {
-    const expected = `from tvbextunicore.unicore_wrapper import unicore_wrapper
+    const expected = `from tvb_ext_unicore.unicore_wrapper import unicore_wrapper
 unicore = unicore_wrapper.UnicoreWrapper()
 download_result = unicore.download_file('test_url', 'test_file')
 download_result`;

src/constants.ts

@@ -30,7 +30,7 @@ export const RELOAD_CHECK_RATE_MS = 10000; //should check every 10sec
  * @param file
  */
 export function getDownloadFileCode(job_url: string, file: string): string {
-  return `from tvbextunicore.unicore_wrapper import unicore_wrapper
+  return `from tvb_ext_unicore.unicore_wrapper import unicore_wrapper
 unicore = unicore_wrapper.UnicoreWrapper()
 download_result = unicore.download_file('${job_url}', '${file}')
 download_result`;
@@ -41,7 +41,7 @@ download_result`;
  * @param job_url
  */
 export function getJobCode(job_url: string): string {
-  return `from tvbextunicore.unicore_wrapper import unicore_wrapper
+  return `from tvb_ext_unicore.unicore_wrapper import unicore_wrapper
 unicore = unicore_wrapper.UnicoreWrapper()
 job = unicore.get_job('${job_url}')
 job`;

src/handler.ts

@@ -17,7 +17,7 @@ export async function requestAPI<T>(
   const settings = ServerConnection.makeSettings();
   const requestUrl = URLExt.join(
     settings.baseUrl,
-    'tvbextunicore', // API Namespace
+    'tvb_ext_unicore', // API Namespace
     endPoint
   );
   let response: Response;
@@ -60,7 +60,7 @@ export async function requestStream<T>(
   const settings = ServerConnection.makeSettings();
   const requestUrl = URLExt.join(
     settings.baseUrl,
-    'tvbextunicore', // API Namespace
+    'tvb_ext_unicore', // API Namespace
     endPoint
   );
   let response: Response;

src/index.ts

@@ -51,7 +51,7 @@ export type NullableIKernelConnection =
  * Initialization data for the tvb-ext-unicore extension.
  */
 const plugin: JupyterFrontEndPlugin<void> = {
-  id: 'tvbextunicore:plugin',
+  id: 'tvb_ext_unicore:plugin',
   autoStart: true,
   requires: [
     ICommandPalette,
@@ -73,7 +73,7 @@ const plugin: JupyterFrontEndPlugin<void> = {
     console.log('JupyterLab extension tvb-ext-unicore is activated!');
     let widget: MainAreaWidget<PyunicoreWidget>;
     const columns = ['id', 'name', 'owner', 'site', 'status', 'start_time'];
-    const command = 'tvbextunicore:open';
+    const command = 'tvb_ext_unicore:open';
     app.commands.addCommand(command, {
       label: 'PyUnicore Task Stream',
       execute: async (args = { defaultSite: NO_SITE }): Promise<any> => {
@@ -125,7 +125,7 @@ const plugin: JupyterFrontEndPlugin<void> = {
           });
 
           widget = new MainAreaWidget({ content });
-          widget.id = 'tvbextunicore';
+          widget.id = 'tvb_ext_unicore';
           widget.title.label = 'PyUnicore Task Stream';
           widget.title.closable = true;
         }

tvbextunicore/__init__.py → tvb_ext_unicore/__init__.py

@@ -6,14 +6,14 @@
 def _jupyter_labextension_paths():
     return [{
         "src": "labextension",
-        "dest": "tvbextunicore"
+        "dest": "tvb_ext_unicore"
     }]
 
 
 
 def _jupyter_server_extension_points():
     return [{
-        "module": "tvbextunicore"
+        "module": "tvb_ext_unicore"
     }]
 
 
@@ -26,7 +26,7 @@ def _load_jupyter_server_extension(server_app):
         JupyterLab application instance
     """
     setup_handlers(server_app.web_app)
-    server_app.log.info("Registered tvbextunicore server extension")
+    server_app.log.info("Registered tvb_ext_unicore server extension")
 
 
 # For backward compatibility with notebook server - useful for Binder/JupyterHub

tvbextunicore/handlers.py → tvb_ext_unicore/handlers.py

@@ -13,10 +13,10 @@
 import tornado
 from tornado.web import MissingArgumentError
 
-from tvbextunicore.exceptions import SitesDownException, FileNotExistsException, JobRunningException
-from tvbextunicore.unicore_wrapper.unicore_wrapper import UnicoreWrapper
-from tvbextunicore.logger.builder import get_logger
-from tvbextunicore.utils import build_response, DownloadStatus
+from tvb_ext_unicore.exceptions import SitesDownException, FileNotExistsException, JobRunningException
+from tvb_ext_unicore.unicore_wrapper.unicore_wrapper import UnicoreWrapper
+from tvb_ext_unicore.logger.builder import get_logger
+from tvb_ext_unicore.utils import build_response, DownloadStatus
 
 LOGGER = get_logger(__name__)
 
@@ -135,10 +135,10 @@ def setup_handlers(web_app):
     host_pattern = ".*$"
 
     base_url = web_app.settings["base_url"]
-    sites_pattern = url_path_join(base_url, "tvbextunicore", "sites")
-    jobs_pattern = url_path_join(base_url, "tvbextunicore", "jobs")
-    output_pattern = url_path_join(base_url, "tvbextunicore", "job_output")
-    drive_pattern = url_path_join(base_url, "tvbextunicore", r"drive/([^/]+)?/([^/]+)?")
+    sites_pattern = url_path_join(base_url, "tvb_ext_unicore", "sites")
+    jobs_pattern = url_path_join(base_url, "tvb_ext_unicore", "jobs")
+    output_pattern = url_path_join(base_url, "tvb_ext_unicore", "job_output")
+    drive_pattern = url_path_join(base_url, "tvb_ext_unicore", r"drive/([^/]+)?/([^/]+)?")
     handlers = [
         (jobs_pattern, JobsHandler),
         (sites_pattern, SitesHandler),

tvbextunicore/logger/logging.conf → tvb_ext_unicore/logger/logging.conf

@@ -2,7 +2,7 @@
 ## TVB-EXT-UNICORE - logging configuration.   ##
 ############################################
 [loggers]
-keys=root, tvbextunicore
+keys=root, tvb_ext_unicore
 
 [handlers]
 keys=consoleHandler, fileHandler
@@ -16,12 +16,12 @@ handlers=consoleHandler, fileHandler
 propagate=0
 
 ############################################
-## tvbextunicore specific logging            ##
+## tvb_ext_unicore specific logging            ##
 ############################################
-[logger_tvbextunicore]
+[logger_tvb_ext_unicore]
 level=INFO
 handlers=consoleHandler, fileHandler
-qualname=tvbextunicore
+qualname=tvb_ext_unicore
 propagate=0
 
 ############################################

tvbextunicore/tests/test_unicore_wrapper.py → tvb_ext_unicore/tests/test_unicore_wrapper.py

@@ -10,15 +10,15 @@
 import pytest
 from datetime import datetime
 
-from tvbextunicore.exceptions import TVBExtUnicoreException, SitesDownException, \
+from tvb_ext_unicore.exceptions import TVBExtUnicoreException, SitesDownException, \
     FileNotExistsException, JobRunningException
-from tvbextunicore.unicore_wrapper.unicore_wrapper import UnicoreWrapper, DOWNLOAD_MESSAGE
-from tvbextunicore.unicore_wrapper.job_dto import JobDTO, NAME, OWNER, SITE_NAME, STATUS, SUBMISSION_TIME, \
+from tvb_ext_unicore.unicore_wrapper.unicore_wrapper import UnicoreWrapper, DOWNLOAD_MESSAGE
+from tvb_ext_unicore.unicore_wrapper.job_dto import JobDTO, NAME, OWNER, SITE_NAME, STATUS, SUBMISSION_TIME, \
     TERMINATION_TIME, \
     MOUNT_POINT
-from tvbextunicore.utils import build_response, DownloadStatus
+from tvb_ext_unicore.utils import build_response, DownloadStatus
 
-GET_JOB = 'tvbextunicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper.get_job'
+GET_JOB = 'tvb_ext_unicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper.get_job'
 SHUTIL_MOVE = 'shutil.move'
 
 
@@ -135,7 +135,7 @@ def test_get_jobs(mocker):
     def mockk(self, site=''):
         return MockPyUnicoreClient()
 
-    mocker.patch('tvbextunicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper._UnicoreWrapper__build_client', mockk)
+    mocker.patch('tvb_ext_unicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper._UnicoreWrapper__build_client', mockk)
     unicore_wrapper = UnicoreWrapper()
     jobs, msg = unicore_wrapper.get_jobs('TEST_SITE')
 
@@ -153,7 +153,7 @@ def test_get_jobs_exception_at_sites(mocker):
     def mockk(self, site=''):
         raise SitesDownException(exception_msg)
 
-    mocker.patch('tvbextunicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper._UnicoreWrapper__build_client', mockk)
+    mocker.patch('tvb_ext_unicore.unicore_wrapper.unicore_wrapper.UnicoreWrapper._UnicoreWrapper__build_client', mockk)
     unicore_wrapper = UnicoreWrapper()
     jobs, msg = unicore_wrapper.get_jobs('TEST_SITE')
 

tvbextunicore/unicore_wrapper/unicore_wrapper.py → tvb_ext_unicore/unicore_wrapper/unicore_wrapper.py

@@ -10,10 +10,10 @@
 import pyunicore.client as unicore_client
 from pyunicore.credentials import OIDCToken
 from requests.exceptions import ConnectionError
-from tvbextunicore.exceptions import TVBExtUnicoreException, ClientAuthException, SitesDownException
-from tvbextunicore.exceptions import FileNotExistsException, JobRunningException
-from tvbextunicore.logger.builder import get_logger
-from tvbextunicore.unicore_wrapper.job_dto import JobDTO
+from tvb_ext_unicore.exceptions import TVBExtUnicoreException, ClientAuthException, SitesDownException
+from tvb_ext_unicore.exceptions import FileNotExistsException, JobRunningException
+from tvb_ext_unicore.logger.builder import get_logger
+from tvb_ext_unicore.unicore_wrapper.job_dto import JobDTO
 
 LOGGER = get_logger(__name__)
 DOWNLOAD_MESSAGE = 'Downloaded successfully!'

tvbextunicore/utils.py → tvb_ext_unicore/utils.py

@@ -7,7 +7,7 @@
 
 import json
 import enum
-from tvbextunicore.logger.builder import get_logger
+from tvb_ext_unicore.logger.builder import get_logger
 
 LOGGER = get_logger(__name__)