protein-quest 0.10.1__py3-none-any.whl → 1.0.0__py3-none-any.whl

protein_quest/__version__.py

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

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-0.10.1.dist-info → protein_quest-1.0.0.dist-info}/METADATA

@@ -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-0.10.1.dist-info → protein_quest-1.0.0.dist-info}/RECORD

@@ -1,5 +1,5 @@
 protein_quest/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-protein_quest/__version__.py,sha256=qCmLtq4uktEgR1D3vZFBaO_0UsYFvPWt7gmxqgWwku0,57
+protein_quest/__version__.py,sha256=fb4tmcrpQ8DpX5nyj0S9YU6dOsGM0L_N3rGiboRYQ-8,56
 protein_quest/cli.py,sha256=aWqdAeseUm7s8UGmrPFNfJPW6W83RmpJAsEy4sZscQY,57506
 protein_quest/converter.py,sha256=Y-Oxf7lDNbEicL6GS-IpNWDwaAiHgIgs5bFAcEHCKdQ,1441
 protein_quest/emdb.py,sha256=641c6RwNYnu-0GBFyCFBiI58fNc0jMkd0ZZ9MW9-Jmc,1501
@@ -7,7 +7,7 @@ protein_quest/filters.py,sha256=em1FYD7Y9z98ZSaJGYCv1VCGRADLbat8FfSOlNJNAJM,5663
 protein_quest/go.py,sha256=lZNEcw8nTc9wpV3cl4y2FG9Lsj8wsXQ6zemmAQs_DWE,5650
 protein_quest/io.py,sha256=ngV_HU2HIQFO-bP2xQj_fhgv0MYjW4puqz_9CxGpBv8,13017
 protein_quest/mcp_server.py,sha256=ZmEs18crS_Ce1-b_PM4m5kmS5C8lLlcrgpocTt7GVrg,8551
-protein_quest/parallel.py,sha256=uf26nD5l1Gp4Z5AFgb0K3vNBUlzvfFh8NSDbGzePSr0,5856
+protein_quest/parallel.py,sha256=hmwjv-KeiC7qSs5xApAvh3ZKkJ9HDW5zmr1zuwOzFpg,6367
 protein_quest/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 protein_quest/ss.py,sha256=4ZGIHfjTlodYTXqGUKhMnGbgaStYOGaWg2oYrWIjdgo,10118
 protein_quest/structure.py,sha256=3TdzrXbGpmnskp3gjwVevwD1tfhKfAUPOHWi9ViaheM,9101
@@ -20,8 +20,8 @@ protein_quest/alphafold/entry_summary.py,sha256=Qhnw75RXFaoOU332g7axg_jYbbdZbUps
 protein_quest/alphafold/fetch.py,sha256=D-RWKWo5kWpCko_LNT_sslzrpeR3HX9nu5F4MUOFRtI,21979
 protein_quest/pdbe/__init__.py,sha256=eNNHtN60NAGea7gvRkIzkoTXsYPK99s-ldIcKWYO6So,61
 protein_quest/pdbe/fetch.py,sha256=e8CHWDX2QzWnVLmYXCfNrscw1UcN1lI9Uz6Z5HmEOEQ,2510
-protein_quest-0.10.1.dist-info/METADATA,sha256=Mz2JLKRAqBvcbMsr1I1rdeYlJK8lTUXCX3AwBpSywxI,11939
-protein_quest-0.10.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-protein_quest-0.10.1.dist-info/entry_points.txt,sha256=f1RtOxv9TFBO3w01EMEuFXBTMsqKsQcKlkxmj9zE-0g,57
-protein_quest-0.10.1.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-protein_quest-0.10.1.dist-info/RECORD,,
+protein_quest-1.0.0.dist-info/METADATA,sha256=6BeMJwGMFaHE03fo_Eqc-fGAz3NeX8SiLQb6tsJwz5I,12652
+protein_quest-1.0.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+protein_quest-1.0.0.dist-info/entry_points.txt,sha256=f1RtOxv9TFBO3w01EMEuFXBTMsqKsQcKlkxmj9zE-0g,57
+protein_quest-1.0.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+protein_quest-1.0.0.dist-info/RECORD,,