MAINT: Rename package to q2-rgi (#110)

.coveragerc

@@ -1,16 +1,16 @@
 [run]
-source=q2_amr
+source=q2_rgi
 branch = True
 omit =
     */tests*
     */__init__.py
-    q2_amr/_version.py
+    q2_rgi/_version.py
     versioneer.py
 
 [report]
 fail_under = 90
 omit =
     */tests*
     */__init__.py
-    q2_amr/_version.py
+    q2_rgi/_version.py
     versioneer.py

.gitattributes

@@ -1 +1 @@
-q2_amr/_version.py export-subst
+q2_rgi/_version.py export-subst

.gitignore

@@ -131,6 +131,6 @@ dmypy.json
 
 # PyCharm configuration
 .idea/
-/q2_amr/charts_testing.py
+/q2_rgi/charts_testing.py
 /index.html
 /bwt_test_file.py

MANIFEST.in

@@ -1,2 +1,2 @@
 include versioneer.py
-include q2_amr/_version.py
+include q2_rgi/_version.py

README.md

@@ -1,27 +1,27 @@
-# q2-amr
-![CI](https://github.com/bokulich-lab/q2-amr/actions/workflows/ci-dev.yaml/badge.svg)
-[![codecov](https://codecov.io/gh/bokulich-lab/q2-amr/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-amr)
+# q2-rgi
+![CI](https://github.com/bokulich-lab/q2-rgi/actions/workflows/ci-dev.yaml/badge.svg)
+[![codecov](https://codecov.io/gh/bokulich-lab/q2-rgi/branch/main/graph/badge.svg?token=THMBOFUZR0)](https://codecov.io/gh/bokulich-lab/q2-rgi)
 [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 QIIME 2 plugin for antimicrobial resistance gene annotation of MAGs and metagenomic reads.
 
 ## Installation
-To install _q2-amr_, follow the steps described below.
+To install _q2-rgi_, follow the steps described below.
 
 <details>
 <summary><b>macOS (intel) / Linux</b></summary>
 
 ```shell
-mamba create -yn q2-amr \
+mamba create -yn q2-rgi \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
   qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
 
-conda activate q2-amr
+conda activate q2-rgi
 
 pip install --no-deps --force-reinstall \
   git+https://github.com/misialq/rgi.git@py38-fix \
-  git+https://github.com/bokulich-lab/q2-amr.git
+  git+https://github.com/bokulich-lab/q2-rgi.git
 ```
 
 Refresh cache and check that everything worked:
@@ -35,17 +35,17 @@ qiime info
 <summary><b>macOS (apple silicon)</b></summary>
 
 ```shell
-CONDA_SUBDIR=osx-64 mamba create -yn q2-amr \
+CONDA_SUBDIR=osx-64 mamba create -yn q2-rgi \
   -c https://packages.qiime2.org/qiime2/2024.2/shotgun/released/ \
   -c qiime2 -c conda-forge -c bioconda -c defaults \
   qiime2 q2cli q2templates q2-types q2-feature-table q2-demux rgi tqdm
 
-conda activate q2-amr
+conda activate q2-rgi
 conda config --env --set subdir osx-64
 
 pip install --no-deps --force-reinstall \
   git+https://github.com/misialq/rgi.git@py38-fix \
-  git+https://github.com/bokulich-lab/q2-amr.git
+  git+https://github.com/bokulich-lab/q2-rgi.git
 ```
 
 Refresh cache and check that everything worked:
@@ -58,18 +58,18 @@ qiime info
 ## Functionality
 This QIIME 2 plugin contains actions used to annotate short single/paired-end
 sequencing reads and MAGs with antimicrobial resistance genes. Currently, the [CARD](https://card.mcmaster.ca) database is supported  (for details on
-the implementation and usage, please refer to the [RGI](https://github.com/arpcard/rgi) documentation). Below you will
+the implementation and usage, please refer to the [rgi](https://github.com/arpcard/rgi) documentation). Below you will
 find an overview of actions available in the plugin.
 
 | Action                | Description                                                                          | Underlying tool                       | Used function                        |
 |-----------------------|--------------------------------------------------------------------------------------|---------------------------------------|--------------------------------------|
-| fetch-card-db         | Download and preprocess CARD and WildCARD data.                                      | [RGI](https://github.com/arpcard/rgi) | card_annotation, wildcard_annotation |
-| annotate-mags-card    | Annotate MAGs with antimicrobial resistance gene information from CARD.              | [RGI](https://github.com/arpcard/rgi) | main, load                           |
-| annotate-reads-card   | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [RGI](https://github.com/arpcard/rgi) | bwt, load                            |
-| heatmap               | Create a heatmap from annotate-mags-card output files.                               | [RGI](https://github.com/arpcard/rgi) | heatmap                              |
-| kmer-query-mags-card  | Pathogen-of-origin prediction for ARGs in MAGs.                                      | [RGI](https://github.com/arpcard/rgi) | kmer-query, load                     |
-| kmer-query-reads-card | Pathogen-of-origin prediction for ARGs in reads.                                     | [RGI](https://github.com/arpcard/rgi) | kmer-query, load                     |
-| kmer-build-card       | Build a kmer database with a custom kmer length.                                     | [RGI](https://github.com/arpcard/rgi) | kmer-build                           |
+| fetch-card-db         | Download and preprocess CARD and WildCARD data.                                      | [rgi](https://github.com/arpcard/rgi) | card_annotation, wildcard_annotation |
+| annotate-mags-card    | Annotate MAGs with antimicrobial resistance gene information from CARD.              | [rgi](https://github.com/arpcard/rgi) | main, load                           |
+| annotate-reads-card   | Annotate metagenomic reads with antimicrobial resistance gene information from CARD. | [rgi](https://github.com/arpcard/rgi) | bwt, load                            |
+| heatmap               | Create a heatmap from annotate-mags-card output files.                               | [rgi](https://github.com/arpcard/rgi) | heatmap                              |
+| kmer-query-mags-card  | Pathogen-of-origin prediction for ARGs in MAGs.                                      | [rgi](https://github.com/arpcard/rgi) | kmer-query, load                     |
+| kmer-query-reads-card | Pathogen-of-origin prediction for ARGs in reads.                                     | [rgi](https://github.com/arpcard/rgi) | kmer-query, load                     |
+| kmer-build-card       | Build a kmer database with a custom kmer length.                                     | [rgi](https://github.com/arpcard/rgi) | kmer-build                           |
 
 ## Dev environment
 This repository follows the _black_ code style. To make the development slightly easier

ci/recipe/meta.yaml

@@ -2,7 +2,7 @@
 {% set version = data.get('version') or 'placehold' %}
 
 package:
-  name: q2-amr
+  name: q2-rgi
   version: {{ version }}
 
 source:
@@ -32,12 +32,12 @@ test:
     - coverage
     - pytest-cov
   imports:
-    - q2_amr
+    - q2_rgi
     - qiime2.plugins.amr
   commands:
-    - pytest --cov q2_amr --cov-report xml:coverage.xml --pyargs q2_amr
+    - pytest --cov q2_rgi --cov-report xml:coverage.xml --pyargs q2_rgi
 
 about:
-  home: https://github.com/bokulich-lab/q2-amr
+  home: https://github.com/bokulich-lab/q2-rgi
   license: BSD-3-Clause
   license_family: BSD

q2_amr/__init__.py → q2_rgi/__init__.py

@@ -5,6 +5,10 @@
 #
 # The full license is in the file LICENSE, distributed with this software.
 # ----------------------------------------------------------------------------
+import importlib
+
 from . import _version
 
 __version__ = _version.get_versions()["version"]
+
+importlib.import_module("q2_rgi.types")

q2_amr/_version.py → q2_rgi/_version.py

@@ -45,8 +45,8 @@ def get_config():
     cfg.VCS = "git"
     cfg.style = "pep440"
     cfg.tag_prefix = ""
-    cfg.parentdir_prefix = "q2-amr-"
-    cfg.versionfile_source = "q2_amr/_version.py"
+    cfg.parentdir_prefix = "q2-rgi-"
+    cfg.versionfile_source = "q2_rgi/_version.py"
     cfg.verbose = False
     return cfg
 

q2_amr/card/database.py → q2_rgi/card/database.py

@@ -9,8 +9,8 @@
 import requests
 from tqdm import tqdm
 
-from q2_amr.card.utils import colorify, run_command
-from q2_amr.types._format import (
+from q2_rgi.card.utils import colorify, run_command
+from q2_rgi.types._format import (
     CARDDatabaseDirectoryFormat,
     CARDKmerDatabaseDirectoryFormat,
 )

q2_amr/card/heatmap.py → q2_rgi/card/heatmap.py

@@ -8,8 +8,8 @@
 import pkg_resources
 import q2templates
 
-from q2_amr.card.utils import run_command
-from q2_amr.types import CARDAnnotationDirectoryFormat
+from q2_rgi.card.utils import run_command
+from q2_rgi.types import CARDAnnotationDirectoryFormat
 
 
 def heatmap(
@@ -20,7 +20,7 @@ def heatmap(
     display: str = "plain",
     frequency: bool = False,
 ):
-    TEMPLATES = pkg_resources.resource_filename("q2_amr", "assets")
+    TEMPLATES = pkg_resources.resource_filename("q2_rgi", "assets")
     annotation_dir = str(amr_annotation)
     with tempfile.TemporaryDirectory() as tmp:
         # Create directories for the JSON annotation files and the heatmap output files

q2_amr/card/kmer.py → q2_rgi/card/kmer.py

@@ -7,8 +7,8 @@
 import warnings
 from pathlib import Path
 
-from q2_amr.card.utils import load_card_db, run_command
-from q2_amr.types import (
+from q2_rgi.card.utils import load_card_db, run_command
+from q2_rgi.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,

q2_amr/card/mags.py → q2_rgi/card/mags.py

@@ -6,8 +6,8 @@
 import pandas as pd
 from q2_types.per_sample_sequences import MultiMAGSequencesDirFmt
 
-from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
-from q2_amr.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
+from q2_rgi.card.utils import create_count_table, load_card_db, read_in_txt, run_command
+from q2_rgi.types import CARDAnnotationDirectoryFormat, CARDDatabaseDirectoryFormat
 
 
 def annotate_mags_card(

q2_amr/card/partition.py → q2_rgi/card/partition.py

@@ -5,8 +5,8 @@
 import numpy as np
 from qiime2.util import duplicate
 
-from q2_amr.card.utils import copy_files
-from q2_amr.types import (
+from q2_rgi.card.utils import copy_files
+from q2_rgi.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDAnnotationDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,

q2_amr/card/reads.py → q2_rgi/card/reads.py

@@ -13,8 +13,8 @@
 )
 from q2_types.sample_data import SampleData
 
-from q2_amr.card.utils import create_count_table, load_card_db, read_in_txt, run_command
-from q2_amr.types import (
+from q2_rgi.card.utils import create_count_table, load_card_db, read_in_txt, run_command
+from q2_rgi.types import (
     CARDAlleleAnnotationDirectoryFormat,
     CARDDatabaseDirectoryFormat,
     CARDGeneAnnotationDirectoryFormat,

q2_amr/card/tests/test_database.py → q2_rgi/card/tests/test_database.py

@@ -7,12 +7,12 @@
 import requests
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_amr.card.database import download_with_progress_bar, fetch_card_db, preprocess
-from q2_amr.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat
+from q2_rgi.card.database import download_with_progress_bar, fetch_card_db, preprocess
+from q2_rgi.types import CARDDatabaseDirectoryFormat, CARDKmerDatabaseDirectoryFormat
 
 
 class TestAnnotateMagsCard(TestPluginBase):
-    package = "q2_amr.card.tests"
+    package = "q2_rgi.card.tests"
 
     def mock_preprocess(self, dir, operation):
         if operation == "card":
@@ -36,8 +36,8 @@ def test_fetch_card_db(self):
         wildcard_tar = self.get_data_path("wildcard_data.tar.bz2")
 
         # Patch requests.get,
-        with patch("q2_amr.card.database.download_with_progress_bar"), patch(
-            "q2_amr.card.database.preprocess", side_effect=self.mock_preprocess
+        with patch("q2_rgi.card.database.download_with_progress_bar"), patch(
+            "q2_rgi.card.database.preprocess", side_effect=self.mock_preprocess
         ), patch(
             "tarfile.open",
             side_effect=[tarfile.open(card_tar), tarfile.open(wildcard_tar)],
@@ -74,7 +74,7 @@ def test_fetch_card_db(self):
     def test_connection_error(self):
         # Simulate a ConnectionError during requests.get
         with patch(
-            "q2_amr.card.database.download_with_progress_bar",
+            "q2_rgi.card.database.download_with_progress_bar",
             side_effect=requests.ConnectionError,
         ), self.assertRaisesRegex(
             requests.ConnectionError,
@@ -85,14 +85,14 @@ def test_connection_error(self):
     def test_tarfile_read_error(self):
         # Simulate a tarfile.ReadError during tarfile.open
         with patch("tarfile.open", side_effect=tarfile.ReadError), patch(
-            "q2_amr.card.database.download_with_progress_bar"
+            "q2_rgi.card.database.download_with_progress_bar"
         ), self.assertRaisesRegex(tarfile.ReadError, "Tarfile is invalid."):
             fetch_card_db()
 
     def test_subprocess_error(self):
         # Simulate a subprocess.CalledProcessError during run_command
         with patch(
-            "q2_amr.card.database.run_command",
+            "q2_rgi.card.database.run_command",
             side_effect=subprocess.CalledProcessError(1, "cmd"),
         ), self.assertRaisesRegex(
             Exception,
@@ -104,7 +104,7 @@ def test_subprocess_error(self):
     def test_preprocess_card(self):
         # Ensure preprocess calls run_command with the correct arguments for "card"
         # operation
-        with patch("q2_amr.card.database.run_command") as mock_run_command:
+        with patch("q2_rgi.card.database.run_command") as mock_run_command:
             preprocess("path_tmp", "card")
             mock_run_command.assert_called_once_with(
                 ["rgi", "card_annotation", "-i", "card/card.json"],
@@ -115,7 +115,7 @@ def test_preprocess_card(self):
     def test_preprocess_wildcard(self):
         # Ensure preprocess calls run_command with the correct arguments for "wildcard"
         # operation
-        with patch("q2_amr.card.database.run_command") as mock_run_command:
+        with patch("q2_rgi.card.database.run_command") as mock_run_command:
             preprocess("path_tmp", "wildcard")
             mock_run_command.assert_called_once_with(
                 [
@@ -138,7 +138,7 @@ def test_download_with_progressbar(self):
         tar_path = "/path/to/downloaded/file.tar"
 
         with patch("requests.get") as mock_get, patch(
-            "q2_amr.card.database.tqdm"
+            "q2_rgi.card.database.tqdm"
         ) as mock_tqdm, patch("builtins.open") as mock_open:
             # Mock response object
             response_mock = MagicMock()

q2_amr/card/tests/test_heatmap.py → q2_rgi/card/tests/test_heatmap.py

@@ -4,17 +4,17 @@
 
 from qiime2.plugin.testing import TestPluginBase
 
-from q2_amr.card.heatmap import (
+from q2_rgi.card.heatmap import (
     InvalidParameterCombinationError,
     change_names,
     heatmap,
     run_rgi_heatmap,
 )
-from q2_amr.types import CARDAnnotationDirectoryFormat
+from q2_rgi.types import CARDAnnotationDirectoryFormat
 
 
 class TestHeatmap(TestPluginBase):
-    package = "q2_amr.card.tests"
+    package = "q2_rgi.card.tests"
 
     def test_heatmap(self):
         amr_annotation = CARDAnnotationDirectoryFormat()
@@ -28,7 +28,7 @@ def mock_run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency):
                     file.write(file_type)
 
         with patch(
-            "q2_amr.card.heatmap.run_rgi_heatmap", side_effect=mock_run_rgi_heatmap
+            "q2_rgi.card.heatmap.run_rgi_heatmap", side_effect=mock_run_rgi_heatmap
         ), tempfile.TemporaryDirectory() as tmp:
             os.makedirs(os.path.join(tmp, "results"))
             heatmap(tmp, amr_annotation)
@@ -45,7 +45,7 @@ def mock_run_rgi_heatmap(tmp, json_files_dir, clus, cat, display, frequency):
             self.assertTrue(os.path.exists(os.path.join(tmp, "q2templateassets")))
 
     def test_run_rgi_heatmap(self):
-        with patch("q2_amr.card.heatmap.run_command") as mock_run_command:
+        with patch("q2_rgi.card.heatmap.run_command") as mock_run_command:
             run_rgi_heatmap(
                 "path_tmp", "json_files_dir_path", "samples", "drug_class", "fill", True
             )
@@ -71,9 +71,9 @@ def test_run_rgi_heatmap(self):
 
     def test_change_names(self):
         with patch(
-            "q2_amr.card.heatmap.os.listdir",
+            "q2_rgi.card.heatmap.os.listdir",
             return_value=["heatmap-7.eps", "heatmap-7.png", "heatmap-7.csv"],
-        ), patch("q2_amr.card.heatmap.os.rename") as mock_rename:
+        ), patch("q2_rgi.card.heatmap.os.rename") as mock_rename:
             results_dir = "/path/to/results"
             change_names(results_dir)
             expected_calls = [
@@ -85,8 +85,8 @@ def test_change_names(self):
             self.assertEqual(expected_calls, actual_calls)
 
     def test_change_names_empty(self):
-        with patch("q2_amr.card.heatmap.os.listdir", return_value=[]), patch(
-            "q2_amr.card.heatmap.os.rename"
+        with patch("q2_rgi.card.heatmap.os.listdir", return_value=[]), patch(
+            "q2_rgi.card.heatmap.os.rename"
         ) as mock_rename:
             results_dir = "/path/to/results"
             change_names(results_dir)