fix scripts (#9)

* fix scripts

* qiime2-2019.1-py36-linux-conda.yml

.travis.yml

@@ -10,10 +10,10 @@ before_install:
   - ./miniconda.sh -b
   - export PATH=/home/travis/miniconda3/bin:$PATH
 install:
-  - wget https://data.qiime2.org/distro/core/qiime2-2018.11-py35-linux-conda.yml
-  - travis_retry conda env create -n qiime2-2018.11 -q --file qiime2-2018.11-py35-linux-conda.yml
-  - rm qiime2-2018.11-py35-linux-conda.yml
-  - source activate qiime2-2018.11
+  - wget https://data.qiime2.org/distro/core/qiime2-2019.1-py36-linux-conda.yml
+  - travis_retry conda env create -n qiime2 -q --file qiime2-2019.1-py36-linux-conda.yml
+  - rm qiime2-2019.1-py36-linux-conda.yml
+  - source activate qiime2
   - pip install flake8
   - pip install joblib
   - pip install .

evident/summarize_mdfdr.py

@@ -66,7 +66,7 @@ def summarize(input_fp, output_fp, check_pval):
                 all_effect_sizes.append((1, (
                     row.column_name, max_effect_size[0],
                     np.square(max_effect_size[0]), max_effect_size[1],
-                    pval_corrected, max_effect_size[2])))
+                    pval_corrected, pval)))
 
         if bool(all_effect_sizes):
             effect_sizes = pd.DataFrame.from_items(
@@ -101,6 +101,10 @@ def summarize(input_fp, output_fp, check_pval):
                             "%s-effect_size_square.pdf" % '.'.join(name)),
                             bbox_inches='tight')
                 fig.clf()
+        else:
+            raise ValueError("Nothing was found significant. The corrected "
+                             "pvalue should be under %f. For more details "
+                             "try --no-pval-check" % pval_corrected)
 
 
 if __name__ == '__main__':

evident/tests/test-effect-size.py

@@ -73,8 +73,15 @@ def test_effect_size_alpha(self):
                                  na_values=na_values,
                                  overwrite=True)
 
+        # this should raise a value error
+        with self.assertRaisesRegex(ValueError, 'Nothing was found '
+                                    'significant. The corrected pvalue should '
+                                    'be under '):
+            _mdfdr.summarize(
+                input_fp=output, output_fp=output, check_pval=True)
+
         # adjusted p-values
-        _mdfdr.summarize(input_fp=output, output_fp=output, check_pval=True)
+        _mdfdr.summarize(input_fp=output, output_fp=output, check_pval=False)
 
         # check effect size calculation for gender (two-group categorical)
         pfp = partial(join, output)

scripts/evident

@@ -66,38 +66,13 @@ def summarize_group():
               help='output filepath')
 @click.option('--check-pval/--no-pval-check', default=True)
 @summarize_group.command()
-def summarize(input_fp, output_fp, alpha_files, check_pval):
-    pass
-    _summarize(input_fp, output_fp, alpha_files, check_pval)
-
-
-@click.group()
-def beta_group():
-    pass
-
-
-@click.option('--metadata-fp', type=click.Path(exists=True),
-              help='metadata filepath')
-@click.option('--subject-column', type=str, help='the metadata column that '
-              'has the subject information')
-@click.option('--input_biom', type=click.Path(exists=True),
-              help='the biom file to process')
-@click.option('--rarefaction-level', type=click.Path(exists=True),
-              help='the biom file to process')
-@click.option('--samples-per-subject', type=click.IntRange(1, 1000), default=3,
-              help='how many samples per subject we should use')
-@click.option('--iterations', type=click.IntRange(1, 1000), default=10,
-              help='how many iterations we should run')
-@click.option('--output_folder', type=click.Path(exists=False),
-              help='output folder')
-@beta_group.command()
-def beta(metadata_fp, subject_column, input_biom, rarefaction_level,
-         samples_per_subject, iterations, output_folder):
-    pass
+def summarize(input_fp, output_fp, check_pval):
+    _summarize(input_fp, output_fp, check_pval)
 
 
 commands = click.CommandCollection(sources=[
-    effect_size_group, summarize_group, beta_group])
+    effect_size_group, summarize_group])
+
 
 if __name__ == '__main__':
     commands()