Update Jupyter API

README.md

@@ -44,7 +44,7 @@ Example usage in the code:
 
 ```python
 from time import sleep
-from r2dt_client import setup, submit, update_status_for, fetch_results_for, clear_job_cache
+from r2dt_client import setup, submit, update_status_for, fetch_results_for
 
 setup(email="YOUR_EMAIL")
 
@@ -58,6 +58,18 @@ fetch_results_for(job)
 print(job.results['fasta'])
 ```
 
+Using the widget via Jupyter Notebook:
+
+```jupyter
+!pip install r2dt_client[widget]
+
+from r2dt_client import setup, draw
+
+setup(email="YOUR_EMAIL")
+draw(
+    ">S box leader))\nCTCTTATCGAGAGTTGGGCGAGGGATTTGGCCTTTTGACCCCAAAAGCAACCGACCGTAATTCCATTGTGAAATGGGGCGCATTTTTTTCGCGCCGAGACGCTGGTCTCTTAAGGCACGGTGCTAATTCCATTCAGATCTGATCTGAGAGATAAGAG")
+```
+
 ## Contributing
 
 Contributions are very welcome.

pyproject.toml

@@ -17,24 +17,22 @@ Changelog = "https://github.com/anayden/r2dt-client/releases"
 
 [tool.poetry.dependencies]
 python = "^3.9"
-click = ">=8.0.1"
-ipython = "*"
-typer = {extras = ["all"], version = "^0.9.0"}
 rich = "^13.7.0"
 diskcache = "^5.6.3"
-httpx = "^0.25.2"
+httpx = "^0.26.0"
 yarl = "^1.9.4"
-anywidget = {extras = ["dev"], version = "^0.8.0"}
+ipython = { version = "^8.18.0", optional = true }
+ipywidgets = { version = "^8.1.1", optional = true }
 
-[tool.poetry.scripts]
-r2dt-client = "r2dt_client.__main__:main"
+[tool.poetry.extras]
+widgets = ["ipython", "ipywidget"]
 
 [tool.poetry.group.dev.dependencies]
 jupyter = "^1.0.0"
 poetry-plugin-export = "^1.6.0"
 Pygments = ">=2.10.0"
 black = ">=21.10b0"
-coverage = {extras = ["toml"], version = ">=6.2"}
+coverage = { extras = ["toml"], version = ">=6.2" }
 darglint = ">=1.8.1"
 flake8 = ">=4.0.1"
 flake8-bandit = ">=2.1.2"
@@ -54,8 +52,8 @@ sphinx = ">=4.3.2"
 sphinx-autobuild = ">=2021.3.14"
 sphinx-click = ">=3.0.2"
 typeguard = ">=2.13.3"
-xdoctest = {extras = ["colors"], version = ">=0.15.10"}
-myst-parser = {version = ">=0.16.1"}
+xdoctest = { extras = ["colors"], version = ">=0.15.10" }
+myst-parser = { version = ">=0.16.1" }
 
 [tool.coverage.paths]
 source = ["src", "*/site-packages"]

src/r2dt_client/__init__.py

@@ -5,6 +5,7 @@
 from r2dt_client.client.client import setup
 from r2dt_client.client.client import submit
 from r2dt_client.client.client import update_status_for
+from r2dt_client.widgets.widget import draw
 
 
 __all__ = [
@@ -13,4 +14,5 @@
     "update_status_for",
     "fetch_results_for",
     "clear_job_cache",
+    "draw",
 ]

src/r2dt_client/widgets/widget.py

@@ -0,0 +1,67 @@
+import threading
+import time
+
+
+try:
+    from IPython.display import clear_output
+    from IPython.display import display
+    from ipywidgets import ValueWidget
+
+    _HAS_IPYWIDGETS = True
+except ImportError:
+    _HAS_IPYWIDGETS = False
+
+from r2dt_client import fetch_results_for
+from r2dt_client import submit
+from r2dt_client import update_status_for
+
+
+def _display_spinner() -> ValueWidget:
+    from ipywidgets import HTML
+
+    spinner = HTML(value="<i>Waiting for results from R2DT...</i>")
+    display(spinner)
+    return spinner
+
+
+def _update_spinner(spinner, elapsed_time):
+    spinner.value = (
+        f"<i>Waiting for results from R2DT... {elapsed_time} seconds elapsed</i>"
+    )
+
+
+def _display_svg(svg_content):
+    from IPython.display import HTML
+
+    display(HTML(svg_content))
+
+
+def draw(sequence: str) -> None:
+    if not _HAS_IPYWIDGETS:
+        print(
+            "This function is only available in Jupyter notebooks and "
+            "after installing the library with 'pip install "
+            "r2dt_client[widgets]'\nConsider using standard API - submit, "
+            "update_status_for, fetch_results_for - instead."
+        )
+        return
+
+    job = submit(sequence)
+
+    spinner = _display_spinner()
+    start_time = time.time()
+
+    def job_monitor():
+        while not job.done:
+            time.sleep(2)
+            update_status_for(job)
+            elapsed_time = int(time.time() - start_time)
+            _update_spinner(spinner, elapsed_time)
+        fetch_results_for(job)
+        svg_content = job.results["svg"]
+        clear_output(wait=True)  # Clear the spinner
+        _display_svg(svg_content)
+
+    # Run the monitoring in a separate thread, so it doesn't block the notebook
+    thread = threading.Thread(target=job_monitor)
+    thread.start()

tests/test_main.py

@@ -1,14 +1,2 @@
-import pytest
-from typer.testing import CliRunner
-
-from r2dt_client.__main__ import app
-
-
-@pytest.fixture
-def runner() -> CliRunner:
-    return CliRunner()
-
-
-def test_main_succeeds(runner: CliRunner) -> None:
-    result = runner.invoke(app, ["--help"])
-    assert result.exit_code == 0
+def test_fake() -> None:
+    pass