protein-quest 0.10.1__tar.gz → 1.0.0__tar.gz

{protein_quest-0.10.1 → protein_quest-1.0.0}/PKG-INFO

@@ -1,12 +1,27 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.10.1
+Version: 1.0.0
 Summary: Search/retrieve/filter proteins and protein structures
 Project-URL: Homepage, https://github.com/haddocking/protein-quest
 Project-URL: Issues, https://github.com/haddocking/protein-quest/issues
 Project-URL: Documentation, https://www.bonvinlab.org/protein-quest/
 Project-URL: Source, https://github.com/haddocking/protein-quest
 License-File: LICENSE
+Keywords: alphafold,mmcif,pdb,protein,protein structure,uniprot
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Environment :: Console
+Classifier: Framework :: AsyncIO
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: Apache Software License
+Classifier: Natural Language :: English
+Classifier: Operating System :: MacOS
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: POSIX :: Linux
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Typing :: Typed
 Requires-Python: >=3.13
 Requires-Dist: aiofiles>=24.1.0
 Requires-Dist: aiohttp-retry>=2.9.1

protein_quest-1.0.0/docs/faq.md

@@ -0,0 +1,17 @@
+# Frequently Asked Questions (FAQ)
+
+## My search is taking a long time. What can I do?
+
+Most likely your search is returning a lot of results.
+The search commands have several options to reduce the number of results returned, such as `--limit`.
+
+## My log is polluted with progress bar lines. How can I fix this?
+
+To reduce the number of lines printed by the progress bar, you can increase the minimum interval between updates with the `TQDM_MININTERVAL` environment variable.
+For example, setting it to `9` will update the progress bar every 9 seconds instead of every 0.1 seconds.
+
+To not have any progress bars at all, you can set `TQDM_DISABLE` environment variable to any value.
+
+## My protein-quest question is not answered here. Where can I get help?
+
+Please see the [Contributing](CONTRIBUTING.md#you-have-a-question) document for instructions on how to ask questions and report issues.

{protein_quest-0.10.1 → protein_quest-1.0.0}/mkdocs.yml

@@ -76,6 +76,7 @@ markdown_extensions:
 nav:
   - Home: index.md
   - CLI Reference: cli.md
+  - FAQ: faq.md
   - Notebooks:
     - notebooks/index.md
     - Search uniprot: notebooks/uniprot.ipynb

{protein_quest-0.10.1 → protein_quest-1.0.0}/pyproject.toml

@@ -4,6 +4,30 @@ dynamic = ["version"]
 description = "Search/retrieve/filter proteins and protein structures"
 readme = "README.md"
 requires-python = ">=3.13"
+keywords = [
+    "alphafold",
+    "mmcif",
+    "pdb",
+    "protein structure",
+    "protein",
+    "uniprot",
+]
+classifiers = [
+    "Development Status :: 5 - Production/Stable",
+    "Environment :: Console",
+    "Framework :: AsyncIO",
+    "Intended Audience :: Science/Research",
+    "License :: OSI Approved :: Apache Software License",
+    "Natural Language :: English",
+    "Operating System :: MacOS",
+    "Operating System :: POSIX :: Linux",
+    "Operating System :: POSIX",
+    "Programming Language :: Python :: 3.13",
+    "Programming Language :: Python :: 3.14",
+    "Topic :: Scientific/Engineering :: Bio-Informatics",
+    "Topic :: Scientific/Engineering :: Chemistry",
+    "Typing :: Typed",
+]
 dependencies = [
     "aiofiles>=24.1.0",
     "aiohttp[speedups]>=3.11.18",

{protein_quest-0.10.1 → protein_quest-1.0.0}/src/protein_quest/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.10.1"
+__version__ = "1.0.0"
 """The version of the package."""

{protein_quest-0.10.1 → protein_quest-1.0.0}/src/protein_quest/parallel.py

@@ -86,12 +86,15 @@ def _configure_cpu_dask_scheduler(nproc: int, name: str) -> LocalCluster:
     return LocalCluster(name=name, threads_per_worker=1, n_workers=n_workers)
 
 
-# Generic type parameters used across helpers
-P = ParamSpec("P")
+class MyProgressBar(ProgressBar):
+    """Show progress of Dask computations.
 
+    Copy of distributed.diagnostics.progressbar.TextProgressBar that:
 
-class _StderrTextProgressBar(ProgressBar):
-    """Copy of distributed.diagnostics.progressbar.TextProgressBar that prints to stderr instead of stdout."""
+    - prints to stderr instead of stdout
+    - Can have its interval (in seconds) set with `TQDM_MININTERVAL` environment variable
+
+    """
 
     __loop: IOLoop | None = None
 
@@ -107,6 +110,11 @@ class _StderrTextProgressBar(ProgressBar):
         **kwargs,  # noqa: ARG002
     ):
         self._loop_runner = loop_runner = LoopRunner(loop=loop)
+        if interval == "100ms":
+            interval_env = os.getenv("TQDM_MININTERVAL")
+            if interval_env is not None:
+                interval = interval_env + "s"
+
         super().__init__(keys, scheduler, interval, complete)
         self.width = width
 
@@ -144,6 +152,10 @@ class _StderrTextProgressBar(ProgressBar):
         sys.stderr.flush()
 
 
+# Generic type parameters used across helpers
+P = ParamSpec("P")
+
+
 def dask_map_with_progress[T, R, **P](
     client: Client,
     func: Callable[Concatenate[T, P], R],
@@ -154,6 +166,10 @@ def dask_map_with_progress[T, R, **P](
     """
     Wrapper for map, progress, and gather of Dask that returns a correctly typed list.
 
+    Environment variables:
+        - Set interval (in seconds) of progress updates with `TQDM_MININTERVAL`
+        - Disabled by setting `TQDM_DISABLE` to any value
+
     Args:
         client: Dask client.
         func: Function to map; first parameter comes from ``iterable`` and any
@@ -169,6 +185,7 @@ def dask_map_with_progress[T, R, **P](
     if client.dashboard_link:
         logger.info(f"Follow progress on dask dashboard at: {client.dashboard_link}")
     futures = client.map(func, iterable, *args, **kwargs)
-    _StderrTextProgressBar(futures)
+    if not os.getenv("TQDM_DISABLE"):
+        MyProgressBar(futures)
     results = client.gather(futures)
     return cast("list[R]", results)

protein_quest-1.0.0/tests/test_parallel.py

@@ -0,0 +1,45 @@
+import pytest
+from distributed import Client
+
+from protein_quest.parallel import MyProgressBar, dask_map_with_progress
+
+
+def test_MyProgressBar_interval_env(monkeypatch):
+    monkeypatch.setenv("TQDM_MININTERVAL", "1234")
+
+    with Client():
+        progress_bar = MyProgressBar([])
+        assert progress_bar.interval == 1234
+
+
+def run_dask_map_with_progress():
+    def square(x: int) -> int:
+        return x**2
+
+    with Client() as client:
+        result = dask_map_with_progress(
+            client,
+            square,
+            range(5),
+        )
+    assert result == [0, 1, 4, 9, 16]
+
+
+def test_dask_map_with_progress(capsys: pytest.CaptureFixture, caplog: pytest.LogCaptureFixture):
+    caplog.set_level("INFO")
+
+    run_dask_map_with_progress()
+
+    captured = capsys.readouterr()
+    assert "Completed" in captured.err
+
+    assert "Follow progress on dask dashboard at" in caplog.text
+
+
+def test_dask_map_with_progress_disabled(monkeypatch: pytest.MonkeyPatch, capsys: pytest.CaptureFixture):
+    monkeypatch.setenv("TQDM_DISABLE", "1")
+
+    run_dask_map_with_progress()
+
+    captured = capsys.readouterr()
+    assert "Completed" not in captured.err