fileglancer 0.2.0__tar.gz

fileglancer-0.2.0/.copier-answers.yml

@@ -0,0 +1,13 @@
+# Changes here will be overwritten by Copier; NEVER EDIT MANUALLY
+_commit: v4.3.7
+_src_path: https://github.com/jupyterlab/extension-template
+author_email: ''
+author_name: allison-truhlar
+has_binder: true
+has_settings: false
+kind: server
+labextension_name: fileglancer
+project_short_description: Browse, share, and publish files on the Janelia file system
+python_name: fileglancer
+repository: https://github.com/JaneliaSciComp/fileglancer
+test: true

fileglancer-0.2.0/.gitattributes

@@ -0,0 +1,2 @@
+# GitHub syntax highlighting
+pixi.lock linguist-language=YAML linguist-generated=true

fileglancer-0.2.0/.gitignore

@@ -0,0 +1,141 @@
+*.bundle.*
+lib/
+node_modules/
+*.log
+.eslintcache
+.stylelintcache
+*.egg-info/
+.ipynb_checkpoints
+*.tsbuildinfo
+fileglancer/labextension
+fileglancer/ui
+# Version file is handled by hatchling
+fileglancer/_version.py
+
+# Integration tests
+ui-tests/test-results/
+ui-tests/playwright-report/
+junit.xml
+
+# Created by https://www.gitignore.io/api/python
+# Edit at https://www.gitignore.io/?templates=python
+
+### Python ###
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage/
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# End of https://www.gitignore.io/api/python
+
+# OSX files
+.DS_Store
+
+# Yarn cache
+.yarn/
+
+# pixi environments
+.pixi
+*.egg-info
+
+# lock files
+pixi.lock
+package-lock.json
+
+# Zarr files
+*.zarr
+
+# Converted Tailwind CSS
+style/tailwind_converted.css

fileglancer-0.2.0/.prettierignore

@@ -0,0 +1,8 @@
+node_modules
+**/node_modules
+**/lib
+**/package.json
+!/package.json
+fileglancer
+.github
+/style/tailwind_converted.css

fileglancer-0.2.0/CHANGELOG.md

@@ -0,0 +1,5 @@
+# Changelog
+
+<!-- <START NEW CHANGELOG ENTRY> -->
+
+<!-- <END NEW CHANGELOG ENTRY> -->

fileglancer-0.2.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2025, allison-truhlar
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

fileglancer-0.2.0/PKG-INFO

@@ -0,0 +1,177 @@
+Metadata-Version: 2.4
+Name: fileglancer
+Version: 0.2.0
+Summary: Browse, share, and publish files on the Janelia file system
+Project-URL: Homepage, https://github.com/JaneliaSciComp/fileglancer
+Project-URL: Bug Tracker, https://github.com/JaneliaSciComp/fileglancer/issues
+Project-URL: Repository, https://github.com/JaneliaSciComp/fileglancer.git
+Author: allison-truhlar
+License: BSD 3-Clause License
+        
+        Copyright (c) 2025, allison-truhlar
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+License-File: LICENSE
+Keywords: jupyter,jupyterlab,jupyterlab-extension
+Classifier: Framework :: Jupyter
+Classifier: Framework :: Jupyter :: JupyterLab
+Classifier: Framework :: Jupyter :: JupyterLab :: 4
+Classifier: Framework :: Jupyter :: JupyterLab :: Extensions
+Classifier: Framework :: Jupyter :: JupyterLab :: Extensions :: Prebuilt
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Requires-Python: >=3.10
+Requires-Dist: jupyter-server<3,>=2.4.0
+Requires-Dist: jupyterlab>=4.3.0
+Requires-Dist: pydantic<3,>=2.10.6
+Provides-Extra: test
+Requires-Dist: coverage; extra == 'test'
+Requires-Dist: pytest; extra == 'test'
+Requires-Dist: pytest-asyncio; extra == 'test'
+Requires-Dist: pytest-cov; extra == 'test'
+Requires-Dist: pytest-jupyter[server]>=0.6.0; extra == 'test'
+Description-Content-Type: text/markdown
+
+# Fileglancer frontend extension
+
+[![Github Actions Status](https://github.com/JaneliaSciComp/fileglancer/workflows/Build/badge.svg)](https://github.com/JaneliaSciComp/fileglancer/actions/workflows/build.yml)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/JaneliaSciComp/fileglancer/main?urlpath=lab)
+
+React-based frontend extension for the Fileglancer app.
+
+## Development install
+
+Clone the repo to your local environment and change directory to the new repo folder.
+
+```bash
+git clone git@github.com:JaneliaSciComp/fileglancer.git
+cd fileglancer
+```
+
+If this is your first time installing the extension in dev mode, install package in development mode.
+
+```bash
+pixi run dev-install
+```
+
+You can build the frontend extension in watch mode - it will automatically rebuild when there are file changes to the frontend:
+
+```bash
+pixi run dev-watch
+```
+
+In new terminal, run Jupyter Lab in autoreload mode - it will automatically rebuild when there are file changes to the backend:
+
+```bash
+pixi run dev-launch
+```
+
+Saved changes in your directory should now be automatically built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).
+
+If everything has worked so far, you should see the React Widget on the Launcher pane:
+
+![Screenshot of the JupyterLab Launcher panel. In the bottom section, titled "Other", the square tile with the title "React Widget" is circled](./assets/img/JupyterLab-launcher.png)
+
+### Troubleshooting the extension
+
+If you run into any build issues, the first thing to try is to clear the build directories and start from scratch:
+
+```bash
+./clean.sh
+```
+
+If you're still having issues, try manually deleting the symlink at `.pixi/envs/share/jupyter/labextensions/fileglancer` inside the fileglancer repo directory. Then, reinstall the extension using `pixi run dev-install`, and follow the steps above from there.
+
+## Configuration
+
+By default, no [Fileglancer Central](https://github.com/JaneliaSciComp/fileglancer-central) server will be used.
+You can configure the URL of a Fileglancer Central server with traitlets, in several ways:
+
+### Command line
+
+```bash
+pixi run dev-launch --Fileglancer.central_url=http://0.0.0.0:7878
+```
+
+### Config file
+
+You can create a file at `~/.jupyter/jupyter_server_config.py` (or in any of the paths reported by `pixi run jupyter --paths`) and add your configuration there, e.g.:
+
+```python
+c.Fileglancer.central_url='http://0.0.0.0:7878'
+```
+
+To configure "Dev Mode" which simulates many zones and file share paths, add this to your config:
+
+```python
+c.Fileglancer.dev_mode=True
+```
+
+## Development Uninstall
+
+```bash
+pixi run pip-uninstall
+```
+
+In development mode, you will also need to remove the symlink created by `jupyter labextension develop`
+command. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`
+folder is located. Then you can remove the symlink named `fileglancer` within that folder.
+
+## Testing
+
+### Backend tests
+
+To run backend tests using pytest:
+
+```bash
+pixi run test-backend
+```
+
+### Frontend tests
+
+This extension is using [Jest](https://jestjs.io/) for JavaScript code testing.
+
+To execute them, execute:
+
+```bash
+pixi run test-frontend
+```
+
+### Integration tests
+
+This extension uses [Playwright](https://playwright.dev/docs/intro) for the integration tests (aka user level tests).
+More precisely, the JupyterLab helper [Galata](https://github.com/jupyterlab/jupyterlab/tree/master/galata) is used to handle testing the extension in JupyterLab.
+More information are provided within the [ui-tests](./ui-tests/README.md) README.
+
+## Packaging and Releases
+
+See [RELEASE](RELEASE.md)

fileglancer-0.2.0/README.md

@@ -0,0 +1,114 @@
+# Fileglancer frontend extension
+
+[![Github Actions Status](https://github.com/JaneliaSciComp/fileglancer/workflows/Build/badge.svg)](https://github.com/JaneliaSciComp/fileglancer/actions/workflows/build.yml)
+[![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/JaneliaSciComp/fileglancer/main?urlpath=lab)
+
+React-based frontend extension for the Fileglancer app.
+
+## Development install
+
+Clone the repo to your local environment and change directory to the new repo folder.
+
+```bash
+git clone git@github.com:JaneliaSciComp/fileglancer.git
+cd fileglancer
+```
+
+If this is your first time installing the extension in dev mode, install package in development mode.
+
+```bash
+pixi run dev-install
+```
+
+You can build the frontend extension in watch mode - it will automatically rebuild when there are file changes to the frontend:
+
+```bash
+pixi run dev-watch
+```
+
+In new terminal, run Jupyter Lab in autoreload mode - it will automatically rebuild when there are file changes to the backend:
+
+```bash
+pixi run dev-launch
+```
+
+Saved changes in your directory should now be automatically built locally and available in your running JupyterLab. Refresh JupyterLab to load the change in your browser (you may need to wait several seconds for the extension to be rebuilt).
+
+If everything has worked so far, you should see the React Widget on the Launcher pane:
+
+![Screenshot of the JupyterLab Launcher panel. In the bottom section, titled "Other", the square tile with the title "React Widget" is circled](./assets/img/JupyterLab-launcher.png)
+
+### Troubleshooting the extension
+
+If you run into any build issues, the first thing to try is to clear the build directories and start from scratch:
+
+```bash
+./clean.sh
+```
+
+If you're still having issues, try manually deleting the symlink at `.pixi/envs/share/jupyter/labextensions/fileglancer` inside the fileglancer repo directory. Then, reinstall the extension using `pixi run dev-install`, and follow the steps above from there.
+
+## Configuration
+
+By default, no [Fileglancer Central](https://github.com/JaneliaSciComp/fileglancer-central) server will be used.
+You can configure the URL of a Fileglancer Central server with traitlets, in several ways:
+
+### Command line
+
+```bash
+pixi run dev-launch --Fileglancer.central_url=http://0.0.0.0:7878
+```
+
+### Config file
+
+You can create a file at `~/.jupyter/jupyter_server_config.py` (or in any of the paths reported by `pixi run jupyter --paths`) and add your configuration there, e.g.:
+
+```python
+c.Fileglancer.central_url='http://0.0.0.0:7878'
+```
+
+To configure "Dev Mode" which simulates many zones and file share paths, add this to your config:
+
+```python
+c.Fileglancer.dev_mode=True
+```
+
+## Development Uninstall
+
+```bash
+pixi run pip-uninstall
+```
+
+In development mode, you will also need to remove the symlink created by `jupyter labextension develop`
+command. To find its location, you can run `jupyter labextension list` to figure out where the `labextensions`
+folder is located. Then you can remove the symlink named `fileglancer` within that folder.
+
+## Testing
+
+### Backend tests
+
+To run backend tests using pytest:
+
+```bash
+pixi run test-backend
+```
+
+### Frontend tests
+
+This extension is using [Jest](https://jestjs.io/) for JavaScript code testing.
+
+To execute them, execute:
+
+```bash
+pixi run test-frontend
+```
+
+### Integration tests
+
+This extension uses [Playwright](https://playwright.dev/docs/intro) for the integration tests (aka user level tests).
+More precisely, the JupyterLab helper [Galata](https://github.com/jupyterlab/jupyterlab/tree/master/galata) is used to handle testing the extension in JupyterLab.
+More information are provided within the [ui-tests](./ui-tests/README.md) README.
+
+## Packaging and Releases
+
+See [RELEASE](RELEASE.md)

fileglancer-0.2.0/RELEASE.md

@@ -0,0 +1,82 @@
+# Making a new release of fileglancer_server
+
+The extension can be published to `PyPI` and `npm` manually or using the [Jupyter Releaser](https://github.com/jupyter-server/jupyter_releaser).
+
+## Manual release
+
+### Python package
+
+This extension can be distributed as Python packages. All of the Python
+packaging instructions are in the `pyproject.toml` file to wrap your extension in a
+Python package. 
+
+Make sure to clean up all the development files before building the package:
+
+```bash
+pixi run npm run clean:all
+```
+
+You could also clean up the local git repository:
+
+```bash
+git clean -dfX
+```
+
+Before generating a package, you first need to install some tools:
+
+```bash
+pixi run pip install build twine hatch
+```
+
+Bump the version using `hatch`. By default this will create a tag.
+See the docs on [hatch-nodejs-version](https://github.com/agoose77/hatch-nodejs-version#semver) for details.
+
+```bash
+pixi run hatch version <new-version>
+```
+
+To create a Python source package (`.tar.gz`) and the binary package (`.whl`) in the `dist/` directory, do:
+
+```bash
+pixi run pypi-build
+```
+
+> `python setup.py sdist bdist_wheel` is deprecated and will not work for this package.
+
+Then to upload the package to PyPI, do:
+
+```bash
+twine upload dist/*
+```
+
+### NPM package
+
+To publish the frontend part of the extension as a NPM package, do:
+
+```bash
+npm login
+npm publish --access public
+```
+
+## Automated releases with the Jupyter Releaser
+
+The extension repository should already be compatible with the Jupyter Releaser. But
+the GitHub repository and the package managers need to be properly set up. Please
+follow the instructions of the Jupyter Releaser [checklist](https://jupyter-releaser.readthedocs.io/en/latest/how_to_guides/convert_repo_from_repo.html).
+
+Here is a summary of the steps to cut a new release:
+
+- Go to the Actions panel
+- Run the "Step 1: Prep Release" workflow
+- Check the draft changelog
+- Run the "Step 2: Publish Release" workflow
+
+> [!NOTE]
+> Check out the [workflow documentation](https://jupyter-releaser.readthedocs.io/en/latest/get_started/making_release_from_repo.html)
+> for more information.
+
+## Publishing to `conda-forge`
+
+If the package is not on conda forge yet, check the documentation to learn how to add it: https://conda-forge.org/docs/maintainer/adding_pkgs.html
+
+Otherwise a bot should pick up the new version publish to PyPI, and open a new PR on the feedstock repository automatically.

fileglancer-0.2.0/clean.sh

@@ -0,0 +1,24 @@
+#!/usr/bin/env bash
+
+clean_dir() {
+    local dir=$1
+    local random_num=$RANDOM
+    local temp_dir="${dir}_${random_num}_deleting"
+    
+    # Rename directory if it exists
+    if [ -d "$dir" ]; then
+        mv "$dir" "$temp_dir"
+        if [ $? -ne 0 ]; then
+            echo "Failed to rename $dir to $temp_dir"
+            return 1
+        fi
+        rm -rf "$temp_dir" &
+    fi
+}
+
+rm -f fileglancer/_version.py || true
+clean_dir ".pixi/envs" || true
+clean_dir ".pixi/solve-group-envs" || true
+clean_dir "fileglancer/labextension" || true
+clean_dir "node_modules" || true
+echo "Cleaned up dev environment."

fileglancer-0.2.0/conftest.py

@@ -0,0 +1,8 @@
+import pytest
+
+pytest_plugins = ("pytest_jupyter.jupyter_server", )
+
+
+@pytest.fixture
+def jp_server_config(jp_server_config):
+    return {"ServerApp": {"jpserver_extensions": {"fileglancer": True}}}