Merge pull request #3 from bokulich-lab/2024.10

update to q2 2024.10

README.md

@@ -6,7 +6,26 @@ Note: this plugin is under active development during pre-release. The code shoul
 
 ## Installation instructions
 
-### Installation of stable release (QIIME 2 version 2024.5)
+The easiest way to install q2-kmerizer is to install it directly into an existing installation of [QIIME 2](https://qiime2.org/) (amplicon distribution version 2024.10 or later). If you have the QIIME 2 amplicon distribution installed, activate your environment and run the following to install q2-kmerizer into this environment:
+```
+pip install q2_kmerizer@git+https://github.com/bokulich-lab/q2-kmerizer.git@main
+```
+
+And refresh your cache:
+```
+qiime dev refresh-cache
+```
+
+If the installation worked correctly, the following command should display a description of the plugin in your terminal:
+```
+qiime kmerizer --help
+```
+
+
+
+### Installation of stable release
+
+If you do not already have QIIME 2 installed, you can follow these instructions to install the QIIME 2 amplicon distribution as well as the latest stable version of q2-kmerizer.
 
 [Miniconda](https://conda.io/miniconda.html) provides the `conda` environment and package manager, and is currently the only supported way to install QIIME 2.
 Follow the instructions for downloading and installing Miniconda.
@@ -17,27 +36,19 @@ After installing Miniconda and opening a new terminal, make sure you're running
 conda update conda
 ```
 
-Now install q2-kmerizer and QIIME 2:
+Now ue conda to install q2-kmerizer and QIIME 2:
 
 ```shell
-conda env create -n q2-kmerizer2 --file https://raw.githubusercontent.com/bokulich-lab/q2-kmerizer/main/environments/q2-kmerizer-qiime2-amplicon-2024.10.yml
+conda env create -n kmerizer-stable --file https://raw.githubusercontent.com/bokulich-lab/q2-kmerizer/main/environments/q2-kmerizer-qiime2-amplicon-2024.10.yml
 ```
 
 After this completes, activate the new environment you created by running:
 
 ```shell
-conda activate q2-kmerizer-dev
+conda activate kmerizer-stable
 ```
 
-And refresh your cache:
-```
-qiime dev refresh-cache
-```
-
-If the installation worked correctly, the following command should display a description of the plugin in your terminal:
-```
-qiime kmerizer --help
-```
+Then refresh your cache and test as shown above.
 
 
 ### Install development version of `q2-kmerizer`
@@ -71,6 +82,8 @@ Finally, run:
 make install
 ```
 
+Then refresh your cache and test as shown above.
+
 
 
 ## Examples
@@ -80,9 +93,9 @@ As an example test, we will use data from [Sampson et al, 2016](https://www.ncbi
 First we will download the test data:
 
 ```
-wget https://data.qiime2.org/2024.5/tutorials/pd-mice/sample_metadata.tsv
-wget https://docs.qiime2.org/2024.5/data/tutorials/pd-mice/dada2_table.qza
-wget https://docs.qiime2.org/2024.5/data/tutorials/pd-mice/dada2_rep_set.qza
+wget https://data.qiime2.org/2024.10/tutorials/pd-mice/sample_metadata.tsv
+wget https://docs.qiime2.org/2024.10/data/tutorials/pd-mice/dada2_table.qza
+wget https://docs.qiime2.org/2024.10/data/tutorials/pd-mice/dada2_rep_set.qza
 ```
 
 We can count kmer frequencies per sample with this command:

environments/q2-kmerizer-qiime2-amplicon-2024.10.yml

@@ -1,15 +1,12 @@
 name: q2-kmerizer-qiime2-amplicon-2024.10
 channels:
-- https://packages.qiime2.org/qiime2/2024.10/amplicon/passed
+- https://packages.qiime2.org/qiime2/2024.10/amplicon/released
 - conda-forge
 - bioconda
 dependencies:
   - qiime2-amplicon
   - numpy
   - scikit-learn
-  - frictionless 
   - pip
   - pip:
      - "q2_kmerizer@git+https://github.com/bokulich-lab/q2-kmerizer.git@main"
-     - "q2_vizard@git+https://github.com/qiime2/q2-vizard.git@dev"
-     - "q2_stats@git+https://github.com/qiime2/q2-stats.git@dev"

q2_kmerizer/_methods.py

@@ -56,7 +56,7 @@ def seqs_to_kmers(sequences: pd.Series, table: pd.DataFrame,
 def core_metrics(ctx, sequences, table, sampling_depth, metadata,
                  kmer_size=16, tfidf=False, max_df=1.0, min_df=1,
                  max_features=None, with_replacement=False, n_jobs=1,
-                 pc_dimensions=3, color_by_group=None):
+                 pc_dimensions=3, color_by=None):
 
     rarefy = ctx.get_action('feature_table', 'rarefy')
     kmerize = ctx.get_action('kmerizer', 'seqs_to_kmers')
@@ -104,6 +104,6 @@ def core_metrics(ctx, sequences, table, sampling_depth, metadata,
     results += scatter(metadata=metadata,
                        # x_measure=pc_result.columns[0],
                        # y_measure=pc_result.columns[1],
-                       color_by_group=color_by_group)
+                       color_by=color_by)
 
     return tuple(results)

q2_kmerizer/plugin_setup.py

@@ -94,7 +94,7 @@
                 'with_replacement': Bool,
                 'n_jobs': Int % Range(1, None) | Str % Choices(['auto']),
                 'pc_dimensions': Int,
-                'color_by_group': Str},
+                'color_by': Str},
     outputs=[
         ('rarefied_table', FeatureTable[Frequency]),
         ('kmer_table', FeatureTable[Frequency]),
@@ -118,8 +118,8 @@
         'n_jobs': '[beta methods only] - %s' % n_jobs_description,
         'pc_dimensions': 'Number of principal coordinate dimensions to keep '
                          'for plotting.',
-        'color_by_group': 'Categorical measure from the input Metadata that '
-                          'should be used for color-coding the scatterplot.'},
+        'color_by': 'Categorical measure from the input Metadata that '
+                    'should be used for color-coding the scatterplot.'},
     output_descriptions={
         'rarefied_table': 'The resulting rarefied feature table.',
         'kmer_table': 'Frequencies of kmers per sample.',

q2_kmerizer/tests/test_methods.py

@@ -101,4 +101,4 @@ def test_core_metrics(self):
         table = Artifact.import_data('FeatureTable[Frequency]', self.table)
         self.core_metrics(seqs, table, metadata=metadata,
                           sampling_depth=1, kmer_size=7,
-                          color_by_group='color')
+                          color_by='color')