Fix plugin verbosity

.github/workflows/run-pytest.yml

@@ -11,8 +11,8 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        python-version: [3.6, 3.9]
-        os: [ubuntu-latest, macos-latest]
+        python-version: ["3.8", "3.10"]
+        os: [ubuntu-latest]
 
     steps:
     - uses: actions/checkout@v2
@@ -26,10 +26,10 @@ jobs:
       with:
         python-version: ${{ matrix.python-version }}
 
-    - name: Install dev dependancies
+    - name: Install dev dependencies
       run: if [ -f requirements/requirements-dev.txt ]; then pip install -r requirements/requirements-dev.txt; fi
 
-    - name: Install test dependancies
+    - name: Install test dependencies
       run: if [ -f requirements/requirements-test.txt ]; then pip install -r requirements/requirements-test.txt; fi
 
     - name: Install package

docs/changelog.md

@@ -2,6 +2,12 @@
 
 This project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html) and [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) format.
 
+## [0.12.3] - 2024-10-10
+
+### Fixed
+- Reduce verbosity of refgenie plugin
+
+
 ## [0.12.2] - 2021-11-04
 
 ### Fixed

refgenconf/_version.py

@@ -1 +1 @@
-__version__ = "0.12.2"
+__version__ = "0.12.3"

refgenconf/populator.py

@@ -57,14 +57,14 @@ def get_asset_tag(genome, asset):
                 return namespaces["project"]["refgenie"]["tag_overrides"][genome][asset]
             except KeyError:
                 default_tag = rgc.get_default_tag(genome=genome, asset=asset)
-                _LOGGER.info(
+                _LOGGER.debug(
                     f"Refgenie asset ({genome}/{asset}) tag not specified in `refgenie.tag_overrides` section. "
                     f"Using the default tag: {default_tag}"
                 )
                 return default_tag
             except TypeError:
                 default_tag = rgc.get_default_tag(genome=genome, asset=asset)
-                _LOGGER.warn(f"tag_overrides section is malformed. Using default.")
+                _LOGGER.warning(f"tag_overrides section is malformed. Using default.")
                 return default_tag
 
         # Restructure the seek key paths to make them accessible with
@@ -78,7 +78,7 @@ def get_asset_tag(genome, asset):
                 try:
                     paths_dict[g][k] = v[tag]
                 except KeyError:
-                    _LOGGER.warn(
+                    _LOGGER.warning(
                         f"Can't find tag '{tag}' for asset '{g}/{k}', as specified in your project config. Using default."
                     )
                     paths_dict[g][k] = v[rgc.get_default_tag(genome=g, asset=k)]
@@ -97,7 +97,7 @@ def get_asset_tag(genome, asset):
             except KeyError:
                 _LOGGER.debug("Did not find path_overrides section")
             except TypeError:
-                _LOGGER.warn("Warning: path_overrides is not iterable")
+                _LOGGER.warning("Warning: path_overrides is not iterable")
 
         # print(paths_dict)
         # Provide these values under the 'refgenie' namespace

refgenconf/refgenconf.py

@@ -557,9 +557,11 @@ def get_symlink_paths(self, genome, asset=None, tag=None, all_aliases=False):
         if asset:
             tag = tag or self.get_default_tag(genome, asset)
         return {
-            a: os.path.join(self.alias_dir, a, asset, tag)
-            if asset
-            else os.path.join(self.alias_dir, a)
+            a: (
+                os.path.join(self.alias_dir, a, asset, tag)
+                if asset
+                else os.path.join(self.alias_dir, a)
+            )
             for a in alias
         }
 
@@ -1128,9 +1130,9 @@ def list_seek_keys_values(self, genomes=None, assets=None):
                     tag_mapping = asset_mapping[CFG_ASSET_TAGS_KEY][tag_name]
                     ret[genome_name][asset_name][tag_name] = {}
                     for seek_key_name in get_tag_seek_keys(tag_mapping):
-                        ret[genome_name][asset_name][tag_name][
-                            seek_key_name
-                        ] = self.seek(genome_name, asset_name, tag_name, seek_key_name)
+                        ret[genome_name][asset_name][tag_name][seek_key_name] = (
+                            self.seek(genome_name, asset_name, tag_name, seek_key_name)
+                        )
         return ret
 
     def get_local_data_str(self, genome=None, order=None):
@@ -1217,9 +1219,11 @@ def listr(
             genomes = genome if isinstance(genome, list) else [genome]
             if genome is not None:
                 genome_digests = [
-                    g
-                    if g in aliases_by_digest.keys()
-                    else digests_by_alias.get(g, None)
+                    (
+                        g
+                        if g in aliases_by_digest.keys()
+                        else digests_by_alias.get(g, None)
+                    )
                     for g in genomes
                 ]
                 if genome_digests is None:
@@ -3139,7 +3143,7 @@ def _str2float(x):
         size = "{0:f}GB".format(_str2float(size) / 1000)
     if size.endswith("KB"):
         # convert to gigs
-        size = "{0:f}GB".format(_str2float(size) / 1000 ** 2)
+        size = "{0:f}GB".format(_str2float(size) / 1000**2)
     return size.endswith("TB") or (size.endswith("GB") and _str2float(size) > cutoff)
 
 

refgenconf/refgenconf_v03.py

@@ -9,7 +9,7 @@
 import sys
 import urllib.request
 import warnings
-from collections import Iterable, Mapping, OrderedDict
+from collections.abc import Iterable, Mapping
 from functools import partial
 from inspect import getfullargspec as finspect
 from tempfile import TemporaryDirectory
@@ -223,7 +223,7 @@ def list(self, genome=None, order=None, include_tags=False):
         )
         if include_tags:
             self.run_plugins(POST_LIST_HOOK)
-            return OrderedDict(
+            return dict(
                 [
                     (
                         g,
@@ -238,7 +238,7 @@ def list(self, genome=None, order=None, include_tags=False):
                 ]
             )
         self.run_plugins(POST_LIST_HOOK)
-        return OrderedDict(
+        return dict(
             [
                 (
                     g,
@@ -677,7 +677,7 @@ def listr(
         :param list[str] | str genome: genomes that the assets should be found for
         :param function(str) -> object order: how to key genome IDs and asset
             names for sort
-        :return dict[OrderedDict[list]]: remotely available genomes and assets
+        :return dict[dict[list]]: remotely available genomes and assets
             keyed by genome keyed by source server endpoint
         """
         data_by_server = {}
@@ -1575,7 +1575,7 @@ def _invert_genomes(self, order=None):
         asset ID.
         :param function(str) -> object order: how to key genome IDs and asset
             names for sort
-        :return OrderedDict[str, Iterable[str]] binding between asset kind/key/name
+        :return dict[str, Iterable[str]] binding between asset kind/key/name
             and collection of reference genome assembly names for which the
             asset type is available
         """
@@ -1584,7 +1584,7 @@ def _invert_genomes(self, order=None):
             for a in am[CFG_ASSETS_KEY].keys():
                 genomes.setdefault(a, []).append(g)
         assets = sorted(genomes.keys(), key=order)
-        return OrderedDict([(a, sorted(genomes[a], key=order)) for a in assets])
+        return dict([(a, sorted(genomes[a], key=order)) for a in assets])
 
     def _chk_digest_if_avail(self, genome, remote_asset_name, server_url):
         """
@@ -1892,7 +1892,7 @@ def _str2float(x):
         size = "{0:f}GB".format(_str2float(size) / 1000)
     if size.endswith("KB"):
         # convert to gigs
-        size = "{0:f}GB".format(_str2float(size) / 1000 ** 2)
+        size = "{0:f}GB".format(_str2float(size) / 1000**2)
     return size.endswith("TB") or (size.endswith("GB") and _str2float(size) > cutoff)
 
 
@@ -1910,7 +1910,7 @@ def _list_remote(url, genome, order=None, as_str=True):
     )
     if not refgens:
         return None, None if as_str else dict()
-    filtered_genomes_data = OrderedDict(
+    filtered_genomes_data = dict(
         [(rg, sorted(genomes_data[rg], key=order)) for rg in refgens]
     )
     if not as_str:

refgenconf/seqcol.py

@@ -19,17 +19,17 @@ def _schema_path(name):
     return os.path.join(SCHEMA_FILEPATH, name)
 
 
-CONTENT_ALL_A_IN_B = 2 ** 0
-CONTENT_ALL_B_IN_A = 2 ** 1
-LENGTHS_ALL_A_IN_B = 2 ** 2
-LENGTHS_ALL_B_IN_A = 2 ** 3
-NAMES_ALL_A_IN_B = 2 ** 4
-NAMES_ALL_B_IN_A = 2 ** 5
-CONTENT_A_ORDER = 2 ** 6
-CONTENT_B_ORDER = 2 ** 7
-CONTENT_ANY_SHARED = 2 ** 8
-LENGTHS_ANY_SHARED = 2 ** 9
-NAMES_ANY_SHARED = 2 ** 10
+CONTENT_ALL_A_IN_B = 2**0
+CONTENT_ALL_B_IN_A = 2**1
+LENGTHS_ALL_A_IN_B = 2**2
+LENGTHS_ALL_B_IN_A = 2**3
+NAMES_ALL_A_IN_B = 2**4
+NAMES_ALL_B_IN_A = 2**5
+CONTENT_A_ORDER = 2**6
+CONTENT_B_ORDER = 2**7
+CONTENT_ANY_SHARED = 2**8
+LENGTHS_ANY_SHARED = 2**9
+NAMES_ANY_SHARED = 2**10
 
 FLAGS = {
     CONTENT_ALL_A_IN_B: "CONTENT_ALL_A_IN_B",
@@ -244,5 +244,5 @@ def explain_flag(flag):
     """Explains a compare flag"""
     print(f"Flag: {flag}\nBinary: {bin(flag)}\n")
     for e in range(0, 13):
-        if flag & 2 ** e:
-            print(FLAGS[2 ** e])
+        if flag & 2**e:
+            print(FLAGS[2**e])

requirements/requirements-test.txt

@@ -2,6 +2,5 @@ mock
 pytest
 pytest-cov
 pytest-remotedata
-git+git://github.com/databio/refgenie_myplugin@master#egg=refgenie_myplugin
 tqdm
 veracitools

setup.py

@@ -33,10 +33,9 @@
     classifiers=[
         "Development Status :: 4 - Beta",
         "License :: OSI Approved :: BSD License",
-        "Programming Language :: Python :: 3.5",
-        "Programming Language :: Python :: 3.6",
-        "Programming Language :: Python :: 3.7",
         "Programming Language :: Python :: 3.8",
+        "Programming Language :: Python :: 3.9",
+        "Programming Language :: Python :: 3.10",
         "Topic :: Scientific/Engineering :: Bio-Informatics",
     ],
     license="BSD2",
@@ -48,6 +47,6 @@
         ["pytest-runner"] if {"test", "pytest", "ptr"} & set(sys.argv) else []
     ),
     url="https://refgenie.databio.org",
-    author=u"Nathan Sheffield, Vince Reuter, Michal Stolarczyk",
+    author="Nathan Sheffield, Vince Reuter, Michal Stolarczyk",
     **extra
 )

tests/conftest.py

@@ -1,4 +1,5 @@
 """ Test suite shared objects and setup """
+
 import os
 import random
 import shutil

tests/test_utils.py

@@ -1,4 +1,4 @@
-from collections import Mapping
+from collections.abc import Mapping
 
 import pytest