Merge pull request #91 from biocore/fixv10bugs

v. 0.0.11 Fixes v. 0.0.10 bugs
biocore · Jun 13, 2024 · 7209fd3 · 7209fd3
2 parents 190f89e + a68b5a6
commit 7209fd3
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diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
@@ -22,21 +22,25 @@ jobs:
           fetch-depth: 0
 
       - name: Download Q2 file
-        run: wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py36-linux-conda.yml
+        run: wget -q https://raw.githubusercontent.com/qiime2/environment-files/master/latest/staging/qiime2-latest-py38-linux-conda.yml
 
       - uses: conda-incubator/setup-miniconda@v2
         with:
           activate-environment: q2
-          environment-file: qiime2-latest-py36-linux-conda.yml
+          environment-file: qiime2-latest-py38-linux-conda.yml
 
       - name: Install conda reqs
         shell: bash -l {0}
         run: conda install --file ci/conda_requirements.txt -c biocore
 
-      - name: Install auxillary CI packages
+      - name: Install auxillary conda CI packages
         shell: bash -l {0}
         run: conda install -c conda-forge coveralls flake8 nose
 
+      - name: Install auxillary pip CI packages
+        shell: bash -l {0}
+        run: pip install iow tax2tree
+
       - name: Install gemelli
         shell: bash -l {0}
         run: pip install -e .

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,4 +1,16 @@
 
+v0.0.11 (2024-06-24)
+
+### Bug fixes
+
+* Passes non-centered tables if non-centered flag is passed.
+    * see issue #82
+* setup.py packages html files so visualization commands works from pip install.
+    * see issue #83
+    * see issue #87
+* Passes no filtering to the QIIME2/API TEMPTED command since filtering and transformation should already be done.
+    * see issue #90
+
 v0.0.10 (2023-12-01)
 
 ### Bug fixes

diff --git a/gemelli/__init__.py b/gemelli/__init__.py
@@ -6,4 +6,4 @@
 # The full license is in the file COPYING.txt, distributed with this software.
 # ----------------------------------------------------------------------------
 
-__version__ = "0.0.10"
+__version__ = "0.0.11"
diff --git a/gemelli/rpca.py b/gemelli/rpca.py
@@ -579,15 +579,25 @@ def frequency_filter(val, id_, md):
         return (np.sum(val > 0) / n_samples) > (min_feature_frequency / 100)
 
     # filter and import table for each filter above
-    table = table.filter(observation_filter, axis='observation')
-    table = table.filter(frequency_filter, axis='observation')
-    table = table.filter(sample_filter, axis='sample')
-
+    if min_feature_count is not None:
+        table = table.filter(observation_filter,
+                             axis='observation',
+                             inplace=False)
+    if min_feature_frequency is not None:
+        table = table.filter(frequency_filter,
+                             axis='observation',
+                             inplace=False)
+    if min_sample_count is not None:
+        table = table.filter(sample_filter,
+                             axis='sample',
+                             inplace=False)
     # check the table after filtering
     if len(table.ids()) != len(set(table.ids())):
         raise ValueError('Data-table contains duplicate sample IDs')
     if len(table.ids('observation')) != len(set(table.ids('observation'))):
         raise ValueError('Data-table contains duplicate feature IDs')
+    # ensure empty samples / features are removed
+    table = table.remove_empty()
 
     return table
 

diff --git a/gemelli/tempted.py b/gemelli/tempted.py
@@ -264,9 +264,9 @@ def tempted_factorize(table: biom.Table,
                    individual_id_column,
                    state_column,
                    n_components=n_components,
-                   min_sample_count=0,
-                   min_feature_count=0,
-                   min_feature_frequency=0,
+                   min_sample_count=None,
+                   min_feature_count=None,
+                   min_feature_frequency=None,
                    transformation=lambda x: x,
                    pseudo_count=0,
                    replicate_handling=replicate_handling,
@@ -480,14 +480,24 @@ def tempted(table: biom.Table,
                      svd_centralized=svd_centralized,
                      n_components_centralize=n_components_centralize)
     # run TEMPTED
-    tempted_res = tempted_helper(tensor.individual_id_tables_centralized,
-                                 tensor.individual_id_state_orders,
-                                 tensor.feature_order,
-                                 n_components=n_components,
-                                 smooth=smooth,
-                                 resolution=resolution,
-                                 maxiter=max_iterations,
-                                 epsilon=epsilon)
+    if svd_centralized:
+        tempted_res = tempted_helper(tensor.individual_id_tables_centralized,
+                                     tensor.individual_id_state_orders,
+                                     tensor.feature_order,
+                                     n_components=n_components,
+                                     smooth=smooth,
+                                     resolution=resolution,
+                                     maxiter=max_iterations,
+                                     epsilon=epsilon)
+    else:
+        tempted_res = tempted_helper(tensor.individual_id_tables,
+                                     tensor.individual_id_state_orders,
+                                     tensor.feature_order,
+                                     n_components=n_components,
+                                     smooth=smooth,
+                                     resolution=resolution,
+                                     maxiter=max_iterations,
+                                     epsilon=epsilon)
     (individual_loadings,
      feature_loadings,
      state_loadings,

diff --git a/setup.py b/setup.py
@@ -116,7 +116,8 @@ def run(self):
                     'console_scripts': standalone},
       # Inclusion of citations.bib in package_data based on how this is done in
       # q2-emperor's setup.py file
-      package_data={'gemelli': ['citations.bib']},
+      package_data={'gemelli': ['citations.bib',
+                                'q2/qc_assests/*.html']},
       cmdclass={'install': CustomInstallCommand,
                 'develop': CustomDevelopCommand,
                 'egg_info': CustomEggInfoCommand, },