WIP: Refactor

.github/workflows/ci.yml

@@ -1,57 +1,12 @@
-name: Test and lint
-
+name: ci-q2-qsip2
 on:
     pull_request:
         branches: ["main"]
     push:
         branches: ["main"]
-
 jobs:
-    build-and-test-qiime2-amplicon-2024-5:
-        runs-on: ${{ matrix.os }}
-        strategy:
-            matrix:
-                os: [ubuntu-latest, macos-13]
-
-        steps:
-            - uses: actions/checkout@v2
-
-            - name: Set up Conda
-              uses: conda-incubator/setup-miniconda@v3
-              with:
-                  activate-environment: q2-qsip2-qiime2-amplicon-2025.4
-                  environment-file: environments/q2-qsip2-qiime2-amplicon-2025.4.yml
-                  auto-activate-base: false
-
-            - name: Install plugin
-              shell: bash -l {0}
-              run: make install
-              env:
-                  GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
-            - name: Run tests
-              shell: bash -l {0}
-              run: make test
-
-    lint:
-        runs-on: ubuntu-latest
-        steps:
-            - name: checkout source
-              uses: actions/checkout@v3
-
-            - name: set up python 3.11
-              uses: actions/setup-python@v4
-              with:
-                  python-version: 3.11
-
-            - name: install dependencies
-              run: |
-                  python -m pip install --upgrade pip
-                  pip install -q https://github.com/qiime2/q2lint/archive/master.zip
-                  pip install -q flake8
-
-            - name: run flake8
-              run: flake8
-
-            - name: run q2lint
-              run: q2lint
+    ci:
+        uses: caporaso-lab/q2-qsip2/.github/workflows/lib-community-ci-custom.yml
+        with:
+            github-repo: q2-qsip2
+            env-file-name: q2-qsip2-qiime2-amplicon-2026.1.yml

.github/workflows/lib-community-ci-custom.yml

@@ -0,0 +1,83 @@
+# # Example of workflow trigger for calling workflow (the client).
+# name: ci-vizard
+# on:
+#   pull_request:
+#     branches: ["dev"]
+#   push:
+#     branches: ["dev"]
+# jobs:
+#   ci:
+#     uses: qiime2/distributions/.github/workflows/lib-community-ci.yaml@dev
+#     with:
+#       github-repo: q2-vizard
+#       env-file-name: 2024.5-vizard-environment.yml
+
+on:
+    workflow_call:
+        inputs:
+            github-repo:
+                description: "Plugin repository name on Github"
+                type: string
+                required: true
+
+            env-file-name:
+                description: "Name of environment file to test with"
+                type: string
+                required: true
+
+env:
+    name: ${{ inputs.github-repo }}
+    filepath: environment-files/${{ inputs.env-file-name }}
+
+jobs:
+    install-env-and-test:
+        strategy:
+            matrix:
+                os: [ubuntu-latest, macos-15-intel]
+        runs-on: ${{ matrix.os }}
+        steps:
+            - name: "checkout source"
+              uses: actions/checkout@v4
+
+            - name: "set up python 3.9"
+              uses: actions/setup-python@v4
+              with:
+                  python-version: 3.9
+
+            - name: "Manually set up conda environment, install ${{ env.name }} locally and run tests"
+              shell: bash -el {0}
+              run: |
+                  if ! command -v conda >/dev/null 2>&1; then
+                    echo "Miniconda not found. Installing Miniconda..."
+                    if [[ "$(uname)" == "Darwin" ]]; then
+                      MINICONDA_INSTALLER_SCRIPT=Miniconda3-latest-MacOSX-x86_64.sh
+                    else
+                      MINICONDA_INSTALLER_SCRIPT=Miniconda3-latest-Linux-x86_64.sh
+                    fi
+                    curl -LO https://repo.anaconda.com/miniconda/$MINICONDA_INSTALLER_SCRIPT
+                    bash $MINICONDA_INSTALLER_SCRIPT -b -p $HOME/miniconda
+                    export PATH="$HOME/miniconda/bin:$PATH"
+                  fi
+
+                  echo "Creating environment '${{ env.name }}' from file '${{ env.filepath }}'"
+                  conda env create --file "${{ env.filepath }}" --name "${{ env.name }}"
+
+                  echo "Activating environment '${{ env.name }}'"
+                  set +e
+                  source "$(conda info --base)/etc/profile.d/conda.sh"
+                  conda activate "${{ env.name }}" || true
+
+                  echo "Installing '${{ env.name }}' locally..."
+                  set -e
+                  pip install .
+                  make install
+                  echo "Installation successful!"
+
+                  echo "Running 'qiime info' to check package versions..."
+                  qiime info
+
+                  echo "Installing pytest to run '${{ env.name }}'' test suite..."
+                  conda install -y pytest
+
+                  echo "Running tests for '${{ env.name }}'..."
+                  pytest

Makefile

@@ -12,7 +12,7 @@ test: all
 	py.test
 
 REPO = jeffkimbrel/qSIP2
-HASH = b867c96aa7b72b72f47942f11dbcd18319cae8bc
+HASH = af7e19757ae73c837507bbd672054bb9fdee74d5
 install: all
 	pip install .
 	Rscript -e 'devtools::install_github("$(REPO)", ref="$(HASH)")'

environments/q2-qsip2-qiime2-amplicon-2026.1.yml → environment-files/q2-qsip2-qiime2-amplicon-2026.1.yml

@@ -1,6 +1,6 @@
 name: q2-qsip2-qiime2-amplicon-2026.1
 channels:
-    - https://packages.qiime2.org/qiime2/2026.1/amplicon/passed
+    - https://packages.qiime2.org/qiime2/2026.1/amplicon/released
     - conda-forge
     - bioconda
 dependencies:
@@ -14,3 +14,5 @@ dependencies:
     - r-clock
     - rpy2
     - pip
+    - pip:
+          - q2-qsip2@git+https://github.com/caporaso-lab/q2-qsip2.git

q2_qsip2/_constructors.py

@@ -0,0 +1,148 @@
+# ----------------------------------------------------------------------------
+# Copyright (c) 2024-2026, 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.
+# ----------------------------------------------------------------------------
+
+import biom
+import pandas as pd
+import rpy2.robjects as ro
+from rpy2.robjects.packages import importr
+from rpy2.robjects.methods import RS4
+from rpy2.robjects import pandas2ri
+
+import rachis
+
+from q2_qsip2.metadata import (
+    standardize_metadata, _extract_source_metadata, _get_source_vectors
+)
+
+qsip2 = importr('qSIP2')
+base = importr('base')
+importr('S7')
+
+
+def _create_qsip_data(
+    table: biom.Table, metadata: rachis.Metadata, relative: bool = False
+) -> RS4:
+    '''
+    Create a `qsip_data` R object from a feature table and standardized
+    metadata.
+
+    Parameters
+    ----------
+    table : biom.Table
+        The feature table containing sample ids on one axis and feature ids
+        on the other.
+    metadata : rachis.Metadata
+        The standardized sample-level metadata containing all required
+        sample-level and source-level variables.
+    relative : bool
+        Whether `table` is in relative frequency format.
+
+    Returns
+    -------
+    RObject
+        The qSIP2 data object as created by the qSIP2 R package. This wraps the
+        sample metadata, the source metadata, and the feature table.
+    '''
+    # validate metadata by restandardizing
+    sample_metadata = standardize_metadata(sample_metadata=metadata)
+
+    # split standardized metadata into sample- & source-level
+    source_metadata = _extract_source_metadata(metadata)
+
+    # convert to dataframes
+    sample_df = sample_metadata.to_dataframe()
+    sample_index_name = sample_df.index.name
+    sample_df.reset_index(inplace=True)
+
+    source_df = source_metadata.to_dataframe()
+    source_index_name = source_df.index.name
+    source_df.reset_index(inplace=True)
+
+    table_df = table.to_dataframe(dense=True)
+    table_df.index.name = 'ASV'
+    table_df.reset_index(inplace=True)
+
+    # construct qsip object
+    with (ro.default_converter + pandas2ri.converter).context():
+        R_source_obj = qsip2.qsip_source_data(
+            source_df, source_mat_id=source_index_name
+        )
+        R_sample_obj = qsip2.qsip_sample_data(
+            sample_df, sample_id=sample_index_name,
+        )
+        R_feature_obj = qsip2.qsip_feature_data(
+           table_df,
+           feature_id='ASV',
+           type='relative' if relative else 'counts'
+        )
+        R_qsip_obj = qsip2.qsip_data(
+            source_data=R_source_obj,
+            sample_data=R_sample_obj,
+            feature_data=R_feature_obj
+        )
+
+    return R_qsip_obj
+
+
+def _create_filtered_qsip_data(
+    table: biom.Table,
+    feature_wads: pd.DataFrame,
+    metadata: rachis.Metadata,
+    unlabeled_isotope: str,
+    labeled_isotope: str,
+) -> RS4:
+    '''
+    Parameters
+    ----------
+    table : biom.Table
+        The feature table.
+    feature_wads : pd.DataFrame
+        The per-feature weighted average density values.
+    metadata : rachis.Metadata
+        The standardized qSIP2 metadata.
+    unlabeled_isotope : str
+        The metadata value corresponding to the unlabeled isotope.
+    labeled_isotope : str
+        The metadata value corresponding to the labeled isotope.
+
+    Returns
+    -------
+    RS4
+        A qSIP2 data object with the necessary state to be considered to have
+        gone through filtering.
+    '''
+    R_qsip_object = _create_qsip_data(table, metadata, relative=True)
+
+    R_qsip_object.slots['filtered_feature_data'] = R_qsip_object.slots[
+        'feature_data'
+    ]
+
+    with (ro.default_converter + pandas2ri.converter).context():
+        R_qsip_object.slots['filtered_wad_data'] = feature_wads
+
+    R_feature_wads = R_qsip_object.slots['filtered_wad_data']
+    R_feature_wads.rownames = ro.NULL
+    R_qsip_object.slots['filtered_wad_data'] = R_feature_wads
+
+    status = R_qsip_object.slots['status']
+    status.rx2['filtered'] = True
+    R_qsip_object.slots['status'] = status
+
+    unlabeled_sources, labeled_sources = _get_source_vectors(
+        table, metadata, unlabeled_isotope, labeled_isotope
+    )
+    retained_features = ro.vectors.StrVector(
+        list(table.ids(axis='observation'))
+    )
+    R_filter_results = R_qsip_object.slots['filter_results']
+    R_filter_results.rx2['unlabeled_source_mat_ids'] = unlabeled_sources
+    R_filter_results.rx2['labeled_source_mat_ids'] = labeled_sources
+    R_filter_results.rx2['retained_features'] = retained_features
+    R_qsip_object.slots['filter_results'] = R_filter_results
+
+    return R_qsip_object