protein-quest 0.9.0__tar.gz → 0.10.1__tar.gz

{protein_quest-0.9.0 → protein_quest-0.10.1}/.github/workflows/ci.yml

@@ -24,6 +24,11 @@ jobs:
         run: uv sync --locked --dev --extra mcp
       - name: Install pocl
         run: uv pip install pocl-binary-distribution==3.0
+      - name: Cache downloaded test data
+        uses: actions/cache@v4
+        with:
+            path: ~/.cache/protein-quest-tests
+            key: cached-protein-quest-tests
       - name: Run tests
         run: |
           uv run pytest --cov --cov-report=xml
@@ -32,6 +37,7 @@ jobs:
         with:
           project-token: ${{ secrets.CODACY_PROJECT_TOKEN }}
           coverage-reports: coverage.xml
+
   build:
     name: build
     runs-on: ubuntu-latest
@@ -75,4 +81,13 @@ jobs:
           find docs/ -name "*.ipynb" -exec uv run --group docs-type marimo convert {} -o {}.py \;
       - name: Run type checkers on docs
         run: uv run --group docs-type pyrefly check docs/notebooks/*.ipynb.py
-
+  duplicated-code:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install NodeJS
+        uses: actions/setup-node@v6
+        with:
+          node-version: '24'
+      - name: Run jscpd to detect duplicated code
+        run: npx jscpd src

protein_quest-0.10.1/.howfairis.yml

@@ -0,0 +1 @@
+skip_checklist_checks_reason: "I'm using the fairsoftwarechecklist"

{protein_quest-0.9.0 → protein_quest-0.10.1}/CONTRIBUTING.md

@@ -38,7 +38,8 @@ The sections below outline the steps in each case.
 1. format your code with `uvx ruff format` and sort imports with `uvx ruff check --select I --fix`;
 1. lint your code with `uvx ruff check` (use `uvx ruff check --fix` to fix issues automatically);
 1. type check your code with `uv run pyrefly check src tests`;
-1. update or expand the documentation (see [Contributing with documentation](#contributing-with-documentation) section below);
+1. prevent code duplication, detect with `npx jscpd src`;
+1. update or expand the documentation (see [Contributing to documentation](#contributing-to-documentation) section below);
 1. [push](http://rogerdudler.github.io/git-guide/) your feature branch to (your fork of) the protein-quest repository on GitHub;
 1. create the pull request, e.g. following the instructions [here](https://help.github.com/articles/creating-a-pull-request/).
 
@@ -104,3 +105,5 @@ The search functions of the protein-quest package talk to web services on the In
 To have fast tests we use [pytest-recording](https://github.com/kiwicom/pytest-recording) to record and replay HTTP interactions.
 See [pytest-recording documentation](https://github.com/kiwicom/pytest-recording) for more details on how to use it.
 Like overwrite previous recordings in test/cassettes/**.yaml files with `--record-mode=rewrite`.
+
+The files downloaded for tests are cached in `~/.cache/protein-quest-tests`.

{protein_quest-0.9.0 → protein_quest-0.10.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.9.0
+Version: 0.10.1
 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
@@ -35,9 +35,14 @@ Description-Content-Type: text/markdown
 [![Documentation](https://img.shields.io/badge/Documentation-bonvinlab.org-blue?style=flat-square&logo=gitbook)](https://www.bonvinlab.org/protein-quest/)
 [![CI](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml)
 [![Research Software Directory Badge](https://img.shields.io/badge/rsd-00a3e3.svg)](https://www.research-software.nl/software/protein-quest)
+[![bio.tools](https://img.shields.io/badge/bio.tools-protein--quest-009fdf.svg)](https://bio.tools/protein-quest)
 [![PyPI](https://img.shields.io/pypi/v/protein-quest)](https://pypi.org/project/protein-quest/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16941288.svg)](https://doi.org/10.5281/zenodo.16941288)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/7a3f3f1fe64640d583a5e50fe7ba828e)](https://app.codacy.com/gh/haddocking/protein-quest/coverage?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32121&r=133)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![Copy/paste detector](https://raw.githubusercontent.com/kucherenko/jscpd/refs/tags/v3.5.10/assets/jscpd-badge.svg?sanitize=true)](https://github.com/kucherenko/jscpd/)
+
 
 Python package to search/retrieve/filter proteins and protein structures.
 
@@ -104,7 +109,7 @@ pip install git+https://github.com/haddocking/protein-quest.git
 
 The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
 
-To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/protein_quest/).
 
 While downloading or copying files it uses a global cache (located at `~/.cache/protein-quest`) and hardlinks to save disk space and improve speed.
 This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--copy-method` command line arguments.
@@ -302,7 +307,7 @@ The mcp server contains an prompt template to search/retrieve/filter candidate s
 
 ## Shell autocompletion
 
-The `protein-quest` command line tool supports shell autocompletion using [shtab](https://shtab.readthedocs.io/).
+The `protein-quest` command line tool supports shell autocompletion using [shtab](https://docs.iterative.ai/shtab).
 
 Initialize for bash shell with:
 

{protein_quest-0.9.0 → protein_quest-0.10.1}/README.md

@@ -3,9 +3,14 @@
 [![Documentation](https://img.shields.io/badge/Documentation-bonvinlab.org-blue?style=flat-square&logo=gitbook)](https://www.bonvinlab.org/protein-quest/)
 [![CI](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml)
 [![Research Software Directory Badge](https://img.shields.io/badge/rsd-00a3e3.svg)](https://www.research-software.nl/software/protein-quest)
+[![bio.tools](https://img.shields.io/badge/bio.tools-protein--quest-009fdf.svg)](https://bio.tools/protein-quest)
 [![PyPI](https://img.shields.io/pypi/v/protein-quest)](https://pypi.org/project/protein-quest/)
 [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16941288.svg)](https://doi.org/10.5281/zenodo.16941288)
 [![Codacy Badge](https://app.codacy.com/project/badge/Coverage/7a3f3f1fe64640d583a5e50fe7ba828e)](https://app.codacy.com/gh/haddocking/protein-quest/coverage?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
+[![FAIR checklist badge](https://fairsoftwarechecklist.net/badge.svg)](https://fairsoftwarechecklist.net/v0.2?f=31&a=32113&i=32121&r=133)
+[![fair-software.eu](https://img.shields.io/badge/fair--software.eu-%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F%20%20%E2%97%8F-green)](https://fair-software.eu)
+[![Copy/paste detector](https://raw.githubusercontent.com/kucherenko/jscpd/refs/tags/v3.5.10/assets/jscpd-badge.svg?sanitize=true)](https://github.com/kucherenko/jscpd/)
+
 
 Python package to search/retrieve/filter proteins and protein structures.
 
@@ -72,7 +77,7 @@ pip install git+https://github.com/haddocking/protein-quest.git
 
 The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
 
-To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/protein_quest/).
 
 While downloading or copying files it uses a global cache (located at `~/.cache/protein-quest`) and hardlinks to save disk space and improve speed.
 This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--copy-method` command line arguments.
@@ -270,7 +275,7 @@ The mcp server contains an prompt template to search/retrieve/filter candidate s
 
 ## Shell autocompletion
 
-The `protein-quest` command line tool supports shell autocompletion using [shtab](https://shtab.readthedocs.io/).
+The `protein-quest` command line tool supports shell autocompletion using [shtab](https://docs.iterative.ai/shtab).
 
 Initialize for bash shell with:
 

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.9.0"
+__version__ = "0.10.1"
 """The version of the package."""

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/alphafold/confidence.py

@@ -209,12 +209,7 @@ def filter_files_on_confidence(
             copy_method=copy_method,
         )
 
-    scheduler_address = configure_dask_scheduler(
-        scheduler_address,
-        name="filter-confidence",
-    )
-
-    with Client(scheduler_address) as client:
+    with configure_dask_scheduler(scheduler_address, name="filter-confidence") as cluster, Client(cluster) as client:
         client.forward_logging()
         return dask_map_with_progress(
             client,

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/alphafold/fetch.py

@@ -114,7 +114,6 @@ class AlphaFoldEntry:
         """Convert paths in an AlphaFoldEntry to be relative to the session directory.
 
         Args:
-            entry: An AlphaFoldEntry instance with absolute paths.
             session_dir: The session directory to which the paths should be made relative.
 
         Returns:
@@ -483,6 +482,7 @@ def fetch_many_async(
     )
 
 
+# jscpd:ignore-start  # noqa: ERA001
 def fetch_many(
     uniprot_accessions: Iterable[str],
     save_dir: Path,
@@ -492,6 +492,7 @@ def fetch_many(
     cacher: Cacher | None = None,
     gzip_files: bool = False,
     all_isoforms: bool = False,
+    # jscpd:ignore-end  # noqa: ERA001
 ) -> list[AlphaFoldEntry]:
     """Synchronously fetches summaries and/or files like cif from AlphaFold Protein Structure Database.
 

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/filters.py

@@ -96,12 +96,13 @@ def filter_files_on_chain(
 
     # TODO make logger.debug in filter_file_on_chain show to user when --log
     # GPT-5 generated a fairly difficult setup with a WorkerPlugin, need to find a simpler approach
-    scheduler_address = configure_dask_scheduler(
-        scheduler_address,
-        name="filter-chain",
-    )
-
-    with Client(scheduler_address) as client:
+    with (
+        configure_dask_scheduler(
+            scheduler_address,
+            name="filter-chain",
+        ) as cluster,
+        Client(cluster) as client,
+    ):
         client.forward_logging()
         return dask_map_with_progress(
             client,

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/parallel.py

@@ -2,36 +2,52 @@
 
 import logging
 import os
-from collections.abc import Callable, Collection
+import sys
+import warnings
+from collections.abc import Callable, Collection, Iterator
+from contextlib import contextmanager, suppress
 from typing import Concatenate, ParamSpec, cast
 
-from dask.distributed import Client, LocalCluster, progress
+from dask.distributed import Client, LocalCluster
 from distributed.deploy.cluster import Cluster
+from distributed.diagnostics.progress import format_time
+from distributed.diagnostics.progressbar import ProgressBar
+from distributed.utils import LoopRunner
 from psutil import cpu_count
+from tornado.ioloop import IOLoop
 
 logger = logging.getLogger(__name__)
 
 
+@contextmanager
 def configure_dask_scheduler(
     scheduler_address: str | Cluster | None,
     name: str,
     nproc: int = 1,
-) -> str | Cluster:
-    """Configure the Dask scheduler by reusing existing or creating a new cluster.
+) -> Iterator[str | Cluster]:
+    """Context manager that offers a Dask cluster.
+
+    If scheduler_address is None then creates a local Dask cluster
+    else returns scheduler_address unchanged and the callee is responsible for cluster cleanup.
 
     Args:
         scheduler_address: Address of the Dask scheduler to connect to, or None for local cluster.
         name: Name for the Dask cluster.
         nproc: Number of processes to use per worker for CPU support.
 
-    Returns:
-        A Dask Cluster instance or a string address for the scheduler.
+    Yields:
+        The scheduler address as a string or a cluster.
     """
-    if scheduler_address is None:
-        scheduler_address = _configure_cpu_dask_scheduler(nproc, name)
-        logger.info(f"Using local Dask cluster: {scheduler_address}")
-
-    return scheduler_address
+    if scheduler_address is not None:
+        # Pass through existing scheduler address or cluster
+        yield scheduler_address
+        return
+    cluster = _configure_cpu_dask_scheduler(nproc, name)
+    logger.info(f"Using local Dask cluster: {cluster}")
+    try:
+        yield cluster
+    finally:
+        cluster.close()
 
 
 def nr_cpus() -> int:
@@ -74,6 +90,60 @@ def _configure_cpu_dask_scheduler(nproc: int, name: str) -> LocalCluster:
 P = ParamSpec("P")
 
 
+class _StderrTextProgressBar(ProgressBar):
+    """Copy of distributed.diagnostics.progressbar.TextProgressBar that prints to stderr instead of stdout."""
+
+    __loop: IOLoop | None = None
+
+    def __init__(
+        self,
+        keys,
+        scheduler=None,
+        interval="100ms",
+        width=40,
+        loop=None,
+        complete=True,
+        start=True,
+        **kwargs,  # noqa: ARG002
+    ):
+        self._loop_runner = loop_runner = LoopRunner(loop=loop)
+        super().__init__(keys, scheduler, interval, complete)
+        self.width = width
+
+        if start:
+            loop_runner.run_sync(self.listen)
+
+    @property
+    def loop(self) -> IOLoop | None:
+        loop = self.__loop
+        if loop is None:
+            # If the loop is not running when this is called, the LoopRunner.loop
+            # property will raise a DeprecationWarning
+            # However subsequent calls might occur - eg atexit, where a stopped
+            # loop is still acceptable - so we cache access to the loop.
+            self.__loop = loop = self._loop_runner.loop
+        return loop
+
+    @loop.setter
+    def loop(self, value: IOLoop) -> None:
+        warnings.warn("setting the loop property is deprecated", DeprecationWarning, stacklevel=2)
+        self.__loop = value
+
+    def _draw_bar(self, remaining, all, **kwargs):  # noqa: A002, ARG002
+        frac = (1 - remaining / all) if all else 1.0
+        bar = "#" * int(self.width * frac)
+        percent = int(100 * frac)
+        elapsed = format_time(self.elapsed)
+        msg = "\r[{0:<{1}}] | {2}% Completed | {3}".format(bar, self.width, percent, elapsed)
+        with suppress(ValueError):
+            sys.stderr.write(msg)
+            sys.stderr.flush()
+
+    def _draw_stop(self, **kwargs):  # noqa: ARG002
+        sys.stderr.write("\33[2K\r")
+        sys.stderr.flush()
+
+
 def dask_map_with_progress[T, R, **P](
     client: Client,
     func: Callable[Concatenate[T, P], R],
@@ -99,6 +169,6 @@ 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)
-    progress(futures)
+    _StderrTextProgressBar(futures)
     results = client.gather(futures)
     return cast("list[R]", results)

{protein_quest-0.9.0 → protein_quest-0.10.1}/src/protein_quest/structure.py

@@ -1,7 +1,6 @@
 """Module for querying and modifying [gemmi structures][gemmi.Structure]."""
 
 import logging
-from collections.abc import Iterable
 from datetime import UTC, datetime
 from pathlib import Path
 
@@ -123,11 +122,28 @@ def chains_in_structure(structure: gemmi.Structure) -> set[gemmi.Chain]:
 class ChainNotFoundError(IndexError):
     """Exception raised when a chain is not found in a structure."""
 
-    def __init__(self, chain: str, file: Path | str, available_chains: Iterable[str]):
-        super().__init__(f"Chain {chain} not found in {file}. Available chains are: {available_chains}")
-        self.chain_id = chain
+    def __init__(self, chain_id: str, file: Path | str, available_chains: set[str]):
+        super().__init__(f"Chain {chain_id} not found in {file}. Available chains are: {available_chains}")
+        self.available_chains = available_chains
+        self.chain_id = chain_id
         self.file = file
 
+    def __reduce__(self):
+        """Helper for pickling the exception."""
+        return (self.__class__, (self.chain_id, self.file, self.available_chains))
+
+    def __eq__(self, other):
+        if not isinstance(other, ChainNotFoundError):
+            return NotImplemented
+        return (
+            self.chain_id == other.chain_id
+            and self.file == other.file
+            and self.available_chains == other.available_chains
+        )
+
+    def __hash__(self):
+        return hash((self.chain_id, str(self.file), frozenset(self.available_chains)))
+
 
 def write_single_chain_structure_file(
     input_file: Path,
@@ -194,7 +210,7 @@ def write_single_chain_structure_file(
         copyfile(input_file, output_file, copy_method)
         return output_file
 
-    gemmi.Selection(chain_name).remove_not_selected(structure)
+    gemmi.Selection(f"/1/{chain_name}").remove_not_selected(structure)
     for m in structure:
         m.remove_ligands_and_waters()
     structure.setup_entities()
@@ -203,6 +219,14 @@ def write_single_chain_structure_file(
     _dedup_sheets(structure, out_chain)
     _add_provenance_info(structure, chain_name, out_chain)
 
+    if not (len(structure) == 1 and len(structure[0]) == 1 and len(structure[0][out_chain]) > 0):
+        msg = (
+            f"After processing, structure does not have exactly one model ({len(structure)}) "
+            f"with one chain (found {len(structure[0])}) called {out_chain} "
+            f"with some residues ({len(structure[0][out_chain])})."
+        )
+        raise ValueError(msg)
+
     write_structure(structure, output_file)
 
     return output_file

protein_quest-0.10.1/tests/cassettes/test_cli/test_search_alphafold.yaml

@@ -0,0 +1,66 @@
+interactions:
+- request:
+    body: null
+    headers:
+      Accept:
+      - application/sparql-results+json,application/json,text/javascript,application/javascript
+      Connection:
+      - close
+      Host:
+      - sparql.uniprot.org
+      User-Agent:
+      - sparqlwrapper 2.0.0 (rdflib.github.io/sparqlwrapper)
+    method: GET
+    uri: https://sparql.uniprot.org/sparql?query=%0A++++++++PREFIX+up%3A+%3Chttp%3A//purl.uniprot.org/core/%3E%0A++++++++PREFIX+taxon%3A+%3Chttp%3A//purl.uniprot.org/taxonomy/%3E%0A++++++++PREFIX+rdf%3A+%3Chttp%3A//www.w3.org/1999/02/22-rdf-syntax-ns%23%3E%0A++++++++PREFIX+rdfs%3A+%3Chttp%3A//www.w3.org/2000/01/rdf-schema%23%3E%0A++++++++PREFIX+skos%3A+%3Chttp%3A//www.w3.org/2004/02/skos/core%23%3E%0A++++++++PREFIX+GO%3A%3Chttp%3A//purl.obolibrary.org/obo/GO_%3E%0A%0A++++++++SELECT+%3Fprotein+%3Faf_db%0A++++++++WHERE+%7B%0A%0A++++++++%23+---+Protein+Selection+---%0A++++++++VALUES+%28%3Fac%29+%7B+%28%22P00811%22%29%7D%0A++++++++BIND+%28IRI%28CONCAT%28%22http%3A//purl.uniprot.org/uniprot/%22%2C%3Fac%29%29+AS+%3Fprotein%29%0A++++++++%3Fprotein+a+up%3AProtein+.%0A%0A%0A%23+---+Protein+Selection+---%0A%3Fprotein+a+up%3AProtein+.%0A%0A%23+---+AlphaFoldDB+Info+---%0A%3Fprotein+rdfs%3AseeAlso+%3Faf_db+.%0A%3Faf_db+up%3Adatabase+%3Chttp%3A//purl.uniprot.org/database/AlphaFoldDB%3E+.%0A%0A%0A++++++++%7D%0A%0A++++++++LIMIT+10000%0A&format=json&output=json&results=json
+  response:
+    body:
+      string: "{\n  \"head\" : {\n    \"vars\" : [\n      \"protein\",\n      \"af_db\"\n
+        \   ]\n  },\n  \"results\" : {\n    \"bindings\" : [\n      {\n        \"protein\"
+        : {\n          \"type\" : \"uri\",\n          \"value\" : \"http://purl.uniprot.org/uniprot/P00811\"\n
+        \       },\n        \"af_db\" : {\n          \"type\" : \"uri\",\n          \"value\"
+        : \"http://purl.uniprot.org/alphafolddb/P00811\"\n        }\n      }\n    ]\n
+        \ }\n}"
+    headers:
+      Access-Control-Allow-Headers:
+      - origin, x-requested-with, content-type, X-Release, queryid
+      Access-Control-Allow-Origin:
+      - '*'
+      Access-Control-Expose-Headers:
+      - X-Total-Results, X-Release, queryid, content-type, user-agent, cache-control,
+        etag, range
+      Cache-Control:
+      - public
+      Connection:
+      - close
+      Content-Disposition:
+      - attachment; filename="sparql-CA32A0B92DC5589CE5CD9BF33CF492F9.srj"
+      Content-Length:
+      - '375'
+      Content-Type:
+      - application/sparql-results+json
+      Date:
+      - Mon, 17 Nov 2025 11:45:48 GMT
+      ETag:
+      - W/"2025_04"
+      Expires:
+      - Tue, 18 Nov 2025 11:45:48 GMT
+      Server:
+      - Apache
+      Strict-Transport-Security:
+      - max-age=31536001; includeSubDomains
+      Vary:
+      - Negotiate,Accept,Accept-Encoding,Content-Type
+      X-Content-Type-Options:
+      - nosniff
+      X-Frame-Options:
+      - SAMEORIGIN
+      X-Powered-By:
+      - sib.swiss
+      X-Release:
+      - '2025_04'
+      queryid:
+      - '770887'
+    status:
+      code: 200
+      message: ''
+version: 1