protein-quest 0.10.0__tar.gz → 1.0.0__tar.gz

{protein_quest-0.10.0 → protein_quest-1.0.0}/.github/workflows/ci.yml

@@ -81,4 +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-1.0.0/.howfairis.yml

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

{protein_quest-0.10.0 → protein_quest-1.0.0}/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/).
 

{protein_quest-0.10.0 → protein_quest-1.0.0}/PKG-INFO

@@ -1,12 +1,27 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.10.0
+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
@@ -35,9 +50,14 @@ 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 +124,7 @@ 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 +322,7 @@ 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-0.10.0 → protein_quest-1.0.0}/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-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-0.10.0 → 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-0.10.0 → 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-0.10.0 → protein_quest-1.0.0}/src/protein_quest/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.10.0"
+__version__ = "1.0.0"
 """The version of the package."""

{protein_quest-0.10.0 → protein_quest-1.0.0}/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-0.10.0 → protein_quest-1.0.0}/src/protein_quest/parallel.py

@@ -2,13 +2,19 @@
 
 import logging
 import os
+import sys
+import warnings
 from collections.abc import Callable, Collection, Iterator
-from contextlib import contextmanager
+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__)
 
@@ -80,6 +86,72 @@ def _configure_cpu_dask_scheduler(nproc: int, name: str) -> LocalCluster:
     return LocalCluster(name=name, threads_per_worker=1, n_workers=n_workers)
 
 
+class MyProgressBar(ProgressBar):
+    """Show progress of Dask computations.
+
+    Copy of distributed.diagnostics.progressbar.TextProgressBar that:
+
+    - prints to stderr instead of stdout
+    - Can have its interval (in seconds) set with `TQDM_MININTERVAL` environment variable
+
+    """
+
+    __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)
+        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
+
+        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()
+
+
 # Generic type parameters used across helpers
 P = ParamSpec("P")
 
@@ -94,6 +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
@@ -109,6 +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)
-    progress(futures)
+    if not os.getenv("TQDM_DISABLE"):
+        MyProgressBar(futures)
     results = client.gather(futures)
     return cast("list[R]", results)

{protein_quest-0.10.0 → protein_quest-1.0.0}/src/protein_quest/structure.py

@@ -132,6 +132,18 @@ class ChainNotFoundError(IndexError):
         """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,

protein_quest-1.0.0/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

protein_quest-1.0.0/tests/test_cli.py

@@ -0,0 +1,305 @@
+import csv
+from pathlib import Path
+from textwrap import dedent
+
+import pytest
+
+from protein_quest.cli import main, make_parser
+
+
+def test_make_parser_help(capsys: pytest.CaptureFixture[str]):
+    in_args = ["--help"]
+    parser = make_parser()
+    with pytest.raises(SystemExit):
+        parser.parse_args(in_args)
+
+    captured = capsys.readouterr()
+    assert "Protein Quest CLI" in captured.out
+
+
+@pytest.mark.vcr
+def test_search_uniprot(capsys: pytest.CaptureFixture[str], caplog: pytest.LogCaptureFixture):
+    argv = [
+        "search",
+        "uniprot",
+        "--taxon-id",
+        "9606",
+        "--reviewed",
+        "--limit",
+        "1",
+        "-",
+    ]
+
+    main(argv)
+
+    captured = capsys.readouterr()
+    expected = "A0A024R1R8\n"
+    assert captured.out == expected
+    assert "Searching for UniProt accessions" in captured.err
+    assert "Found 1 UniProt accessions, written to <stdout>" in captured.err
+    assert "There may be more results available" in caplog.text
+
+
+@pytest.mark.vcr
+def test_search_pdbe(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    input_text = tmp_path / "uniprot_accessions.txt"
+    input_text.write_text("P00811\n")
+    output_file = tmp_path / "pdbe_results.csv"
+    argv = [
+        "search",
+        "pdbe",
+        "--limit",
+        "150",
+        "--min-residues",
+        "360",  # P00811 has 377 residues and 5 full PDB entries
+        str(input_text),
+        str(output_file),
+    ]
+
+    main(argv)
+
+    result = output_file.read_text()
+    expected = dedent("""\
+        uniprot_accession,pdb_id,method,resolution,uniprot_chains,chain,chain_length
+        P00811,9C6P,X-Ray_Crystallography,1.66,A/B=1-377,A,377
+        P00811,9C81,X-Ray_Crystallography,1.7,A/B=1-377,A,377
+        P00811,9C83,X-Ray_Crystallography,2.9,A/B=1-377,A,377
+        P00811,9C84,X-Ray_Crystallography,1.7,A/B=1-377,A,377
+        P00811,9DHL,X-Ray_Crystallography,1.88,A/B=1-377,A,377
+        """)
+    assert result == expected
+
+    captured = capsys.readouterr()
+    assert "Finding PDB entries for 1 uniprot accessions" in captured.err
+    assert "Before filtering found 120 PDB entries for 1 uniprot accessions." in captured.err
+    assert "After filtering on chain length (360, None) remained 5 PDB entries for 1 uniprot" in captured.err
+    assert "Written to " in captured.err
+
+
+@pytest.mark.vcr
+def test_search_uniprot_details(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    input_text = tmp_path / "uniprot_accessions.txt"
+    input_text.write_text("P05067\nA0A0B5AC95\n")
+    output_csv = tmp_path / "uniprot_details.csv"
+    argv = [
+        "search",
+        "uniprot-details",
+        str(input_text),
+        str(output_csv),
+    ]
+
+    main(argv)
+
+    result = output_csv.read_text()
+    expected = dedent("""\
+        uniprot_accession,uniprot_id,sequence_length,reviewed,protein_name,taxon_id,taxon_name
+        A0A0B5AC95,INS1A_CONGE,115,True,Con-Ins G1a,6491,Conus geographus
+        P05067,A4_HUMAN,770,True,Amyloid-beta precursor protein,9606,Homo sapiens
+        """)
+    assert result == expected
+    captured = capsys.readouterr()
+    assert "Retrieving UniProt entry details for 2 uniprot accessions" in captured.err
+    assert "Retrieved details for 2 UniProt entries, written to " in captured.err
+
+
+@pytest.mark.vcr
+def test_search_alphafold(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    input_text = tmp_path / "uniprot_accessions.txt"
+    input_text.write_text("P00811\n")
+    output_file = tmp_path / "af_results.csv"
+
+    argv = [
+        "search",
+        "alphafold",
+        str(input_text),
+        str(output_file),
+    ]
+
+    main(argv)
+
+    result = output_file.read_text()
+
+    expected = dedent("""\
+        uniprot_accession,af_id
+        P00811,P00811
+        """)
+    assert result == expected
+
+    captured = capsys.readouterr()
+    assert "Finding AlphaFold entries for 1 uniprot accessions" in captured.err
+    assert "Found 1 AlphaFold entries, written to " in captured.err
+
+
+def test_filter_chain_happy_path(sample2_cif: Path, tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    chains_fn = tmp_path / "chains.csv"
+    chains_fn.write_text("pdb_id,chain\n2Y29,A\n")
+
+    argv = [
+        "filter",
+        "chain",
+        str(chains_fn),
+        str(sample2_cif.parent),
+        str(tmp_path),
+    ]
+
+    main(argv)
+
+    output_file = tmp_path / "2Y29_A2A.cif.gz"
+    assert output_file.exists()
+
+    captured = capsys.readouterr()
+    assert "Wrote 1 single-chain PDB/mmCIF files to" in captured.err
+
+
+def test_filter_chain_input_file_notfound(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    input_dir = tmp_path / "input"
+    input_dir.mkdir()
+    output_dir = tmp_path / "output"
+    output_dir.mkdir()
+    chains_fn = tmp_path / "chains.csv"
+    chains_fn.write_text("pdb_id,chain\n2Y29,A\n")
+
+    argv = [
+        "filter",
+        "chain",
+        str(chains_fn),
+        str(input_dir),
+        str(output_dir),
+    ]
+
+    with pytest.raises(SystemExit):
+        main(argv)
+
+    assert not any(output_dir.iterdir())
+
+    captured = capsys.readouterr()
+    assert "No structure file found for 2Y29" in captured.err
+
+
+def test_filter_residue(sample_cif: Path, sample2_cif: Path, tmp_path: Path, capsys: pytest.CaptureFixture[str]):
+    input_dir = tmp_path / "input"
+    input_dir.mkdir()
+    local_sample = input_dir / sample_cif.name
+    local_sample.symlink_to(sample_cif)
+    local_sample2 = input_dir / sample2_cif.name
+    local_sample2.symlink_to(sample2_cif)
+    output_dir = tmp_path / "output"
+    output_dir.mkdir()
+    stats_fn = tmp_path / "stats.csv"
+
+    argv = [
+        "filter",
+        "residue",
+        str(input_dir),
+        str(output_dir),
+        "--min-residues",
+        "100",
+        "--max-residues",
+        "200",
+        "--copy-method",
+        "symlink",
+        "--write-stats",
+        str(stats_fn),
+    ]
+
+    main(argv)
+
+    # Check output files
+    output_files = list(output_dir.iterdir())
+    assert len(output_files) == 1
+    expected_passed_file = output_dir / sample_cif.name
+    assert expected_passed_file in output_files
+
+    # Check stats file
+    with stats_fn.open() as f:
+        rows = list(csv.DictReader(f))
+    # Input files processed in alphabetical order
+    expected_stats = [
+        {
+            "input_file": str(local_sample2),
+            "residue_count": "8",
+            "passed": "False",
+            "output_file": "",
+        },
+        {
+            "input_file": str(local_sample),
+            "residue_count": "173",
+            "passed": "True",
+            "output_file": str(expected_passed_file),
+        },
+    ]
+    assert rows == expected_stats
+
+    # Check captured output
+    captured = capsys.readouterr()
+    assert "by number of residues in chain A" in captured.err
+    assert "Wrote 1 files to" in captured.err
+    assert "Statistics written to" in captured.err
+
+
+def test_filter_secondary_structure(
+    sample_cif: Path, sample2_cif: Path, tmp_path: Path, capsys: pytest.CaptureFixture[str]
+):
+    input_dir = tmp_path / "input"
+    input_dir.mkdir()
+    local_sample = input_dir / sample_cif.name
+    local_sample.symlink_to(sample_cif)
+    local_sample2 = input_dir / sample2_cif.name
+    local_sample2.symlink_to(sample2_cif)
+    output_dir = tmp_path / "output"
+    output_dir.mkdir()
+    stats_fn = tmp_path / "ss_stats.csv"
+
+    argv = [
+        "filter",
+        "secondary-structure",
+        str(input_dir),
+        str(output_dir),
+        "--abs-min-helix-residues",
+        "10",
+        "--copy-method",
+        "symlink",
+        "--write-stats",
+        str(stats_fn),
+    ]
+
+    main(argv)
+
+    # Check output files
+    output_files = list(output_dir.iterdir())
+    assert len(output_files) == 1
+    expected_passed_file = output_dir / sample_cif.name
+    assert expected_passed_file in output_files
+
+    # Check stats file
+    with stats_fn.open() as f:
+        rows = list(csv.DictReader(f))
+    expected_stats = [
+        {
+            "helix_ratio": "0.0",
+            "input_file": str(local_sample2),
+            "nr_helix_residues": "0",
+            "nr_residues": "8",
+            "nr_sheet_residues": "0",
+            "output_file": "",
+            "passed": "False",
+            "sheet_ratio": "0.0",
+        },
+        {
+            "input_file": str(local_sample),
+            "nr_residues": "173",
+            "nr_helix_residues": "58",
+            "nr_sheet_residues": "59",
+            "helix_ratio": f"{58 / 173:.3f}",
+            "sheet_ratio": f"{59 / 173:.3f}",
+            "passed": "True",
+            "output_file": str(expected_passed_file),
+        },
+    ]
+    assert rows == expected_stats
+
+    # Check captured output
+    captured = capsys.readouterr()
+    assert "by secondary structure" in captured.err
+    assert "Wrote 1 files to" in captured.err
+    assert "Statistics written to" in captured.err

protein_quest-1.0.0/tests/test_filters.py

@@ -0,0 +1,78 @@
+from pathlib import Path
+
+import pytest
+
+from protein_quest.filters import (
+    ChainFilterStatistics,
+    ResidueFilterStatistics,
+    filter_files_on_chain,
+    filter_files_on_residues,
+)
+from protein_quest.structure import ChainNotFoundError
+
+
+@pytest.mark.parametrize(
+    "scheduler_address,expected_progress_bar",
+    [
+        (None, "Completed"),  # creates a local cluster
+        ("sequential", "file/s"),
+    ],
+)
+def test_filter_files_on_chain_local_cluster(
+    sample2_cif: Path,
+    tmp_path: Path,
+    capsys: pytest.CaptureFixture[str],
+    scheduler_address: str | None,
+    expected_progress_bar: str,
+):
+    file2chains = [
+        (sample2_cif, "A"),  # should pass
+        (sample2_cif, "B"),  # should be discarded
+    ]
+
+    results = filter_files_on_chain(file2chains, tmp_path, scheduler_address=scheduler_address)
+
+    expected_passed = ChainFilterStatistics(
+        input_file=sample2_cif,
+        chain_id="A",
+        passed=True,
+        output_file=tmp_path / "2Y29_A2A.cif.gz",
+    )
+    assert expected_passed.output_file and expected_passed.output_file.exists()
+    expected_discarded = ChainFilterStatistics(
+        input_file=sample2_cif,
+        chain_id="B",
+        passed=False,
+        output_file=None,
+        discard_reason=ChainNotFoundError("B", sample2_cif, {"A"}),
+    )
+    assert results == [expected_passed, expected_discarded]
+
+    _, stderr = capsys.readouterr()
+    assert expected_progress_bar in stderr
+
+
+def test_filter_files_on_residues(sample_cif: Path, sample2_cif: Path, tmp_path: Path):
+    results = list(
+        filter_files_on_residues(
+            input_files=[sample_cif, sample2_cif],
+            output_dir=tmp_path,
+            min_residues=100,
+            max_residues=200,
+        )
+    )
+    expected_passed = ResidueFilterStatistics(
+        input_file=sample_cif,
+        residue_count=173,
+        passed=True,
+        output_file=tmp_path / sample_cif.name,
+    )
+    assert expected_passed.output_file and expected_passed.output_file.exists()
+    expected_discarded = ResidueFilterStatistics(
+        input_file=sample2_cif,
+        residue_count=8,
+        passed=False,
+        output_file=None,
+    )
+
+    assert results == [expected_passed, expected_discarded]

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

protein_quest-0.10.0/tests/test_cli.py

@@ -1,101 +0,0 @@
-from pathlib import Path
-from textwrap import dedent
-
-import pytest
-
-from protein_quest.cli import main, make_parser
-
-
-def test_make_parser_help(capsys: pytest.CaptureFixture[str]):
-    in_args = ["--help"]
-    parser = make_parser()
-    with pytest.raises(SystemExit):
-        parser.parse_args(in_args)
-
-    captured = capsys.readouterr()
-    assert "Protein Quest CLI" in captured.out
-
-
-@pytest.mark.vcr
-def test_search_uniprot(capsys: pytest.CaptureFixture[str], caplog: pytest.LogCaptureFixture):
-    argv = [
-        "search",
-        "uniprot",
-        "--taxon-id",
-        "9606",
-        "--reviewed",
-        "--limit",
-        "1",
-        "-",
-    ]
-
-    main(argv)
-
-    captured = capsys.readouterr()
-    expected = "A0A024R1R8\n"
-    assert captured.out == expected
-    assert "Searching for UniProt accessions" in captured.err
-    assert "Found 1 UniProt accessions, written to <stdout>" in captured.err
-    assert "There may be more results available" in caplog.text
-
-
-@pytest.mark.vcr
-def test_search_pdbe(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
-    input_text = tmp_path / "uniprot_accessions.txt"
-    input_text.write_text("P00811\n")
-    output_file = tmp_path / "pdbe_results.csv"
-    argv = [
-        "search",
-        "pdbe",
-        "--limit",
-        "150",
-        "--min-residues",
-        "360",  # P00811 has 377 residues and 5 full PDB entries
-        str(input_text),
-        str(output_file),
-    ]
-
-    main(argv)
-
-    result = output_file.read_text()
-    expected = dedent("""\
-        uniprot_accession,pdb_id,method,resolution,uniprot_chains,chain,chain_length
-        P00811,9C6P,X-Ray_Crystallography,1.66,A/B=1-377,A,377
-        P00811,9C81,X-Ray_Crystallography,1.7,A/B=1-377,A,377
-        P00811,9C83,X-Ray_Crystallography,2.9,A/B=1-377,A,377
-        P00811,9C84,X-Ray_Crystallography,1.7,A/B=1-377,A,377
-        P00811,9DHL,X-Ray_Crystallography,1.88,A/B=1-377,A,377
-        """)
-    assert result == expected
-
-    captured = capsys.readouterr()
-    assert "Finding PDB entries for 1 uniprot accessions" in captured.err
-    assert "Before filtering found 120 PDB entries for 1 uniprot accessions." in captured.err
-    assert "After filtering on chain length (360, None) remained 5 PDB entries for 1 uniprot" in captured.err
-    assert "Written to " in captured.err
-
-
-@pytest.mark.vcr
-def test_search_uniprot_details(tmp_path: Path, capsys: pytest.CaptureFixture[str]):
-    input_text = tmp_path / "uniprot_accessions.txt"
-    input_text.write_text("P05067\nA0A0B5AC95\n")
-    output_csv = tmp_path / "uniprot_details.csv"
-    argv = [
-        "search",
-        "uniprot-details",
-        str(input_text),
-        str(output_csv),
-    ]
-
-    main(argv)
-
-    result = output_csv.read_text()
-    expected = dedent("""\
-        uniprot_accession,uniprot_id,sequence_length,reviewed,protein_name,taxon_id,taxon_name
-        A0A0B5AC95,INS1A_CONGE,115,True,Con-Ins G1a,6491,Conus geographus
-        P05067,A4_HUMAN,770,True,Amyloid-beta precursor protein,9606,Homo sapiens
-        """)
-    assert result == expected
-    captured = capsys.readouterr()
-    assert "Retrieving UniProt entry details for 2 uniprot accessions" in captured.err
-    assert "Retrieved details for 2 UniProt entries, written to " in captured.err