Transition from setup.py & friends to pyproject.toml

Makefile

@@ -15,7 +15,7 @@ test-cov: all
 	py.test --cov=q2_usearch
 
 install: all
-	$(PYTHON) setup.py install
+	$(PYTHON) -m pip install -v .
 
 dev: all
 	pip install pre-commit

README.md

@@ -1,9 +1,3 @@
----
-editor_options: 
-  markdown: 
-    wrap: 72
----
-
 # q2-usearch
 
 QIIME2 plug-in for [USEARCH](https://github.com/rcedgar/usearch12/)
@@ -43,7 +37,7 @@ git clone https://github.com/magicprotoss/q2-usearch .
 Step 2: Activate the QIIME2 conda enviroment you wish to install to
 
 ``` bash
-# conda activate qiime2-amplicon-2024.5
+# conda activate qiime2-amplicon-2025.4
 conda activate <replace-with-your-q2-conda-env-name>
 ```
 
@@ -57,23 +51,26 @@ conda env list | grep qiime2
 The env's name should appear in your terminal
 
 ``` bash
-# qiime2-amplicon-2024.5     /home/navi/miniconda3/envs/qiime2-amplicon-2024.5
+# qiime2-amplicon-2025.4     /home/navi/miniconda3/envs/qiime2-amplicon-2025.4
 ```
 
 Step 3: Change directory to the project folder and execute the following
 command
 
 ``` bash
-cd q2-usearch && python ./setup.py install
+cd q2-usearch && pip install .
 qiime dev refresh-cache
 ```
 
 Step 4: Install [seqkit2](https://bioinf.shenwei.me/seqkit/) and
-[usearch12](https://github.com/rcedgar/usearch12) using mamba/conda
+[usearch12](https://github.com/rcedgar/usearch12) using conda
+
+Note: the q2-usearch plug-in is compatible with usearch11 as well. If you wish to use usearch11, just skip installing usearch using conda. You can manually download the binary file from [GitHub](https://github.com/rcedgar/usearch_old_binaries), rename it to "usearch", add execute permission to it and move it to one of the executable paths on your system.
 
 ``` bash
-mamba install -c bioconda seqkit">=2.0.0" usearch
-# conda install -c bioconda seqkit">=2.0.0" usearch
+conda install -c bioconda --no-deps seqkit">=2.0.0" usearch
+# if you were using an older version of conda and got stuck at the "solving environment" stage for too long, consider using mamba
+# mamba install -c bioconda seqkit">=2.0.0" usearch
 ```
 
 If every thing went smoothly, you should be seeing sth. like this
@@ -216,7 +213,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences fastq-seqs.qza \
+        --i-demultiplexed-seqs fastq-seqs.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \
@@ -231,7 +228,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences ddbj_dl.qza \
+        --i-demultiplexed-seqs ddbj_dl.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \
@@ -275,7 +272,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences demux.qza \
+        --i-demultiplexed-seqs demux.qza \
         --p-min-size 4 \
         --p-trunc-len 120 \
         --o-representative-sequences rep-seqs-unoise3.qza \
@@ -325,7 +322,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences merged.qza \
+        --i-demultiplexed-seqs merged.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \

README_ZH_CN.md

@@ -1,9 +1,3 @@
----
-editor_options: 
-  markdown: 
-    wrap: 72
----
-
 # q2-usearch
 
 这是一个把 [USEARCH](https://github.com/rcedgar/usearch12/) 装进
@@ -30,7 +24,7 @@ editor_options:
 第一步: 激活我们想要安装到的 QIIME2 conda 环境
 
 ``` bash
-# conda activate qiime2-amplicon-2024.5
+# conda activate qiime2-amplicon-2025.4
 conda activate <目标q2环境名称>
 ```
 
@@ -43,7 +37,7 @@ conda env list | grep qiime2
 这样当前conda下所有环境名中带有qiime2字符的虚拟环境都会被检索出来
 
 ``` bash
-# qiime2-amplicon-2024.5     /home/navi/miniconda3/envs/qiime2-amplicon-2024.5
+# qiime2-amplicon-2025.4     /home/navi/miniconda3/envs/qiime2-amplicon-2025.4
 ```
 
 第二步: 下载插件
@@ -56,18 +50,20 @@ git clone https://github.com/magicprotoss/q2-usearch .
 
 ``` bash
 cd q2-usearch # 切换路径
-python ./setup.py install # 安装插件
+pip install . # 安装插件
 qiime dev refresh-cache # 刷新QIIME2命令行界面缓存
 ```
 
 第四步:
-使用mamba或者conda安装[seqkit2](https://mp.weixin.qq.com/s/ucCA4-eZINkppdyQFItXHw)和[usearch12](https://mp.weixin.qq.com/s/i0zzOP5IRNdY9PfqHbpDEQ)
+使用conda安装[seqkit2](https://mp.weixin.qq.com/s/ucCA4-eZINkppdyQFItXHw)和[usearch12](https://mp.weixin.qq.com/s/i0zzOP5IRNdY9PfqHbpDEQ)
+
+注意：
+本插件也支持usearch11，如果要用老版本的话跳过conda安装usearch，去[GitHub](https://github.com/rcedgar/usearch_old_binaries)上下载可执行文件，重命名成"usearch"后加权并放到$PATH的文件夹里.
 
 ``` bash
-# 建议使用mamba
-# 国内网络不稳conda圈圈转到一半容易报断连错误
-mamba install -c bioconda seqkit">=2.0.0" usearch
-# conda install -c bioconda seqkit">=2.0.0" usearch
+conda install -c bioconda --no-deps seqkit">=2.0.0" usearch
+# 如果电脑上conda版本太老卡“solving environment”的话，可以使用mamba
+# mamba install -c bioconda --no-deps seqkit">=2.0.0" usearch
 ```
 
 测试一下usearch是否可以被正常调用
@@ -199,7 +195,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences fastq-seqs.qza \
+        --i-demultiplexed-seqs fastq-seqs.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \
@@ -213,7 +209,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences ddbj_dl.qza \
+        --i-demultiplexed-seqs ddbj_dl.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \
@@ -253,7 +249,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences demux.qza \
+        --i-demultiplexed-seqs demux.qza \
         --p-min-size 4 \
         --p-trunc-len 120 \
         --o-representative-sequences rep-seqs-unoise3.qza \
@@ -298,7 +294,7 @@ cd .. && rm -rf q2-usearch
 
     ``` bash
     qiime usearch denoise-no-primer-pooled \
-        --i-demultiplexed-sequences merged.qza \
+        --i-demultiplexed-seqs merged.qza \
         --p-min-size 4 \
         --o-representative-sequences rep-seqs-unoise3.qza \
         --o-table table-unoise3.qza \

pyproject.toml

@@ -0,0 +1,50 @@
+[project]
+name = "q2-usearch"
+authors = [
+    { name = "RobertEdgar, magicprotoss and biodps", email = "magicprotoss@hotmail.com" }
+]
+description = "This is a plug-in for USEARCH integration into QIIME2."
+readme = {file = "README.md", content-type = "text/markdown"}
+license = {file = "LICENSE"}
+dynamic = ["version"]
+
+[project.urls]
+Homepage = "https://github.com/magicprotoss/q2-usearch"
+Repository = "https://github.com/magicprotoss/q2-usearch"
+
+[project.entry-points.'qiime2.plugins']
+"q2-usearch" = "q2_usearch.plugin_setup:plugin"
+
+[build-system]
+requires = [
+    "setuptools",
+    "versioningit",
+    "wheel"
+]
+build-backend = "setuptools.build_meta"
+
+[tool.versioningit.vcs]
+method = "git-archive"
+describe-subst = "$Format:%(describe)$"
+default-tag = "0.0.1"
+
+[tool.versioningit.next-version]
+method = "minor"
+
+[tool.versioningit.format]
+distance = "{base_version}+{distance}.{vcs}{rev}"
+dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+distance-dirty = "{base_version}+{distance}.{vcs}{rev}.dirty"
+
+[tool.versioningit.write]
+file = "q2_usearch/_version.py"
+
+[tool.setuptools]
+include-package-data = false
+
+[tool.setuptools.packages.find]
+where = ["."]
+include = ["q2_usearch*"]
+
+[tool.setuptools.package-data]
+q2_usearch = ["**/*"]

q2_usearch/__init__.py

@@ -12,10 +12,10 @@
 # modified from q2-vsearch
 from ._merge_pairs import merge_pairs
 
-from ._version import get_versions
-
-__version__ = get_versions()["version"]
-del get_versions
+try:
+    from ._version import __version__
+except ModuleNotFoundError:
+    __version__ = '0.0.0+notfound'
 
 __all__ = ['denoise_no_primer_pooled', 'cluster_no_primer_pooled',
            'denoise_then_cluster_no_primer_pooled', 'merge_pairs', 'sintax']

q2_usearch/_examples.py

@@ -0,0 +1,97 @@
+# ----------------------------------------------------------------------------
+# Modified from q2-dada2
+#
+# Copyright (c) 2016-2024, QIIME 2 development team.
+#
+# Distributed under the terms of the Modified BSD License.
+#
+# The full license is in the file LICENSE, distributed with this software.
+# ----------------------------------------------------------------------------
+
+
+demux_single_url = \
+    'https://data.qiime2.org/usage-examples/moving-pictures/demux.qza'
+demux_paired_url = \
+    'https://data.qiime2.org/usage-examples/atacama-soils/demux-full.qza'
+
+
+def denoise_no_primer_pooled(use):
+    demux_single = use.init_artifact_from_url('demux_single', demux_single_url)
+
+    rep_seqs, table_unoise3, denoise_stats = use.action(
+        use.UsageAction('usearch', 'denoise_no_primer_pooled'),
+        use.UsageInputs(
+            demultiplexed_seqs=demux_single,
+            trunc_len=120
+        ),
+        use.UsageOutputNames(
+            representative_sequences='zOTUs',
+            table='zOTU_Table',
+            denoising_stats='denoising_stats'
+        )
+    )
+
+    rep_seqs.assert_output_type('FeatureData[Sequence]')
+    table_unoise3.assert_output_type('FeatureTable[Frequency]')
+    denoise_stats.assert_output_type('SampleData[USEARCHStats]')
+
+
+def denoise_then_cluster_no_primer_pooled(use):
+    demux_single = use.init_artifact_from_url('demux_single', demux_single_url)
+
+    rep_seqs, table_uclust, denoise_uclust_stats = use.action(
+        use.UsageAction('usearch', 'denoise_then_cluster_no_primer_pooled'),
+        use.UsageInputs(
+            demultiplexed_seqs=demux_single,
+            trunc_len=120,
+            min_size=4
+        ),
+        use.UsageOutputNames(
+            representative_sequences='99_OTUs',
+            table='OTU_Table',
+            stats='denoising_and_uclusting_stats'
+        )
+    )
+
+    rep_seqs.assert_output_type('FeatureData[Sequence]')
+    table_uclust.assert_output_type('FeatureTable[Frequency]')
+    denoise_uclust_stats.assert_output_type('SampleData[USEARCHStats]')
+
+
+def cluster_no_primer_pooled(use):
+    demux_single = use.init_artifact_from_url('demux_single', demux_single_url)
+
+    rep_seqs, table_uparse, cluster_stats = use.action(
+        use.UsageAction('usearch', 'cluster_no_primer_pooled'),
+        use.UsageInputs(
+            demultiplexed_seqs=demux_single,
+            trunc_len=120
+        ),
+        use.UsageOutputNames(
+            representative_sequences='97_OTUs',
+            table='OTU_Table',
+            stats='clustering_stats'
+        )
+    )
+
+    rep_seqs.assert_output_type('FeatureData[Sequence]')
+    table_uparse.assert_output_type('FeatureTable[Frequency]')
+    cluster_stats.assert_output_type('SampleData[USEARCHStats]')
+
+
+def merge_pairs(use):
+    demux_paired = use.init_artifact_from_url('demux_paired', demux_paired_url)
+
+    merged_sequences, unmerged_sequences = use.action(
+        use.UsageAction('usearch', 'merge_pairs'),
+        use.UsageInputs(
+            demultiplexed_seqs=demux_paired
+        ),
+        use.UsageOutputNames(
+            merged_sequences='merged_seqs',
+            unmerged_sequences='unmerged_seqs'
+        )
+    )
+
+    merged_sequences.assert_output_type('SampleData[JoinedSequencesWithQuality]')
+    unmerged_sequences.assert_output_type('SampleData[PairedEndSequencesWithQuality]')