Iss60 (#62)

* verified changes realted to issue 60 and updated docs

* fixed spelling in main

README.rst

@@ -71,34 +71,34 @@ QIIME2 is being used.
 Installing ITSxpress for use as a QIIME2 Plugin
 ----------------------------------------------------
 
-To install ITSxpress as a plugin for QIIME 2 first install QIIME 2 as a separate Conda/Mamba environemnt using thier instructions 
-https://docs.qiime2.org/2024.5/install/ then add ITSxress to the QIIME 2 Conda environment. The examples below are for QIIME2 2 
-version 2024.2 an so please update the commands if you want a newer release.
+To install ITSxpress as a plugin for QIIME 2, first install QIIME 2 Amplicon Distribution as a separate Conda/Mamba environemnt using their instructions 
+https://docs.qiime2.org/2024.10/install/native then add ITSxpress to the QIIME 2 Conda environment. The examples below are for QIIME2 
+version 2024.10 an so please update the commands if you want a newer release.
 
 
 For Linux:
 
 .. code-block:: bash
 
-    conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-linux-conda.yml
-    conda activate qiime2-amplicon-2024.5
+    conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-linux-conda.yml
+    conda activate qiime2-amplicon-2024.10
     conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
 
 For maxOS (Intel) and OS X:
 
 .. code-block:: bash
 
-    conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
-     conda activate qiime2-amplicon-2024.5
+    conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
+    conda activate qiime2-amplicon-2024.10
     conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
 
 For macOS (Arm / Apple Silicon):
 
 .. code-block:: bash
-    CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.5 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.5-py39-osx-conda.yml
-    conda activate qiime2-amplicon-2024.5
+    CONDA_SUBDIR=osx-64 conda env create -n qiime2-amplicon-2024.10 --file https://data.qiime2.org/distro/amplicon/qiime2-amplicon-2024.10-py310-osx-conda.yml
+    conda activate qiime2-amplicon-2024.10
     conda config --env --set subdir osx-64
     CONDA_SUBDIR=osx-64 conda install -c bioconda -c conda-forge ITSxpress
     qiime dev refresh-cache
@@ -111,16 +111,16 @@ For Linux, maxOS (Intel), and OS X:
 
 .. code-block:: bash
 
-    mamba create -n itsxpressenv -c bioconda -c conda-forge itsxpress
-    mamba activate itsxpressenv 
+    conda create -n itsxpressenv -c bioconda -c conda-forge itsxpress
+    conda activate itsxpressenv 
 
 
 For macOS (Arm/Apple Silicon):
 
 .. code-block:: bash
 
-    CONDA_SUBDIR=osx-64 mamba create -n itsxpressenv -c bioconda -c conda-forge itsxpress
-    mamba activate itsxpressenv
+    CONDA_SUBDIR=osx-64 conda create -n itsxpressenv -c bioconda -c conda-forge itsxpress
+    conda activate itsxpressenv
     conda  config --env --set subdir osx-64
 
 
@@ -210,7 +210,7 @@ ITSxpress can take uncompressed, gzipped or zstd compressed FASTQ files and it c
 zstd compressed FASTQ files. It expects FASTQ files to end in: .fq, .fastq, .fq.gz, fastq.gz, .fq.zst or fastq.zst.
 
 Use case 2: Trimming the ITS2 region from a fungal amplicon sequencing dataset with
-forward and reverse gzipped FASTQ files using two cpu threads. Return a forward
+forward and reverse gzipped FASTQ files using two cpu threads. Return forward
 and reverse read files for use in Dada2.
 
 .. code-block:: bash

changelog.md

@@ -1,6 +1,13 @@
+# 2.1.4 (2025-01-13)
+
+- Fixed a bug in [Issue 60](https://github.com/USDA-ARS-GBRU/itsxpress/issues/60) That caused the QIIME 2 plugin of ITSXpress to crash when running `.qza` files with more than one sample (thanks @hyphaltip). This bug was introduced in v2.1.2 or v2.1.3.
+- Verified that the version will work with HMMER 3.4 and Vsearch 2.22.1 the current dependencies in QIIME 2 2024.11  Bioconda recipe was updated to allow later versions of HMMER.
+- cleanup of setuptools-scm version file. 
+- Updates to the install instructions in the readme file.
+
 # 2.1.3 (2024-11-14)
 
-- fixed bug in [Issue 56](https://github.com/USDA-ARS-GBRU/itsxpress/issues/56) that caused some FASTQ files generated by PacBio to raise an error during validation.
+- Fixed a bug in [Issue 56](https://github.com/USDA-ARS-GBRU/itsxpress/issues/56) that caused some FASTQ files generated by PacBio to raise an error during validation.
   these files now pass validation and the interleave check has been modified from raise a warning not an error. 
 - Updated the citations.bib file to include the new Microbiology Spectrum article for ITSxpress
 

itsxpress/main.py

@@ -140,7 +140,7 @@ def read_file(filename: str, mode: str ='r') -> contextlib.contextmanager:
 
         Args:
             filename: the filename to open
-            mode: 'r' for read 'w' for write. 't' will be adeed automacially for compressed files.
+            mode: 'r' for read 'w' for write. 't' will be added automatically for compressed files.
         
         Returns a context manager so the file can be opened using 'with'
     """