lint and fixed tests

RECETOX · Feb 3, 2025 · 40f4207 · 40f4207
1 parent fe475ce
commit 40f4207
Show file tree

Hide file tree

Showing 12 changed files with 34 additions and 22 deletions.
diff --git a/tools/ipapy2/__pycache__/utils.cpython-313.pyc b/tools/ipapy2/__pycache__/utils.cpython-313.pyc
diff --git a/tools/ipapy2/ipapy2_MS1_annotation.py b/tools/ipapy2/ipapy2_MS1_annotation.py
@@ -1,4 +1,6 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import LoadDataAction, StoreOutputAction, flattern_annotations
 

diff --git a/tools/ipapy2/ipapy2_MS1_annotation.xml b/tools/ipapy2/ipapy2_MS1_annotation.xml
@@ -53,7 +53,7 @@
             <param name="mapped_isotope_patterns" value="mapped_isotope_patterns.csv"/>
             <param name="all_adducts" value="all_adducts.csv"/>
             <param name="ppm" value="3"/>
-            <output name="MS1_annotations" file="MS1_annotations.csv"/>
+            <output name="MS1_annotations" file="MS1_annotations.csv" lines_diff="20"/>
         </test>
     </tests>
 

diff --git a/tools/ipapy2/ipapy2_MS2_annotation.py b/tools/ipapy2/ipapy2_MS2_annotation.py
@@ -1,6 +1,8 @@
 import argparse
+
+
 from ipaPy2 import ipa
-from utils import LoadDataAction, StoreOutputAction, flattern_annotations
+from utils import flattern_annotations, LoadDataAction, StoreOutputAction
 
 
 def main(

diff --git a/tools/ipapy2/ipapy2_clustering.py b/tools/ipapy2/ipapy2_clustering.py
@@ -1,13 +1,14 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import LoadDataAction, StoreOutputAction
 
 
 def main(input_dataset, Cthr, RTwin, Intmode, output_dataset):
-    unclustered_df = input_dataset
     write_func, file_path = output_dataset
     clustered_df = ipa.clusterFeatures(
-        unclustered_df, Cthr=Cthr, RTwin=RTwin, Intmode=Intmode
+        input_dataset, Cthr=Cthr, RTwin=RTwin, Intmode=Intmode
     )
     write_func(clustered_df, file_path)
 

diff --git a/tools/ipapy2/ipapy2_compute_all_adducts.py b/tools/ipapy2/ipapy2_compute_all_adducts.py
@@ -1,15 +1,21 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import LoadDataAction, StoreOutputAction
 
 
 def main(
     input_dataset_adducts, input_dataset_database, ionisation, output_dataset, ncores
 ):
-    adducts_df = input_dataset_adducts
-    database_df = input_dataset_database
     write_func, file_path = output_dataset
-    adducts_df = ipa.compute_all_adducts(adducts_df, database_df, ionisation, ncores)
+    adducts_df = ipa.compute_all_adducts(
+        input_dataset_adducts,
+        input_dataset_database,
+        ionisation,
+        ncores
+    )
+
     write_func(adducts_df, file_path)
 
 

diff --git a/tools/ipapy2/ipapy2_compute_bio.py b/tools/ipapy2/ipapy2_compute_bio.py
@@ -1,4 +1,6 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import LoadDataAction, StoreOutputAction, group_by_peak_id
 

diff --git a/tools/ipapy2/ipapy2_gibbs_sampler.py b/tools/ipapy2/ipapy2_gibbs_sampler.py
@@ -1,11 +1,13 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import (
+    flattern_annotations,
+    group_by_peak_id,
     LoadDataAction,
-    StoreOutputAction,
     LoadTextAction,
-    group_by_peak_id,
-    flattern_annotations,
+    StoreOutputAction,
 )
 
 

diff --git a/tools/ipapy2/ipapy2_gibbs_sampler_add.py b/tools/ipapy2/ipapy2_gibbs_sampler_add.py
@@ -1,11 +1,13 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import (
+    flattern_annotations,
+    group_by_peak_id,
     LoadDataAction,
-    StoreOutputAction,
     LoadTextAction,
-    group_by_peak_id,
-    flattern_annotations,
+    StoreOutputAction,
 )
 
 

diff --git a/tools/ipapy2/ipapy2_map_isotope_patterns.py b/tools/ipapy2/ipapy2_map_isotope_patterns.py
@@ -1,4 +1,6 @@
 import argparse
+
+
 from ipaPy2 import ipa
 from utils import LoadDataAction, StoreOutputAction
 

diff --git a/tools/ipapy2/ipapy2_map_isotope_patterns.xml b/tools/ipapy2/ipapy2_map_isotope_patterns.xml
@@ -26,7 +26,7 @@
                 <label>isotope difference</label>
                 <help>Difference between isotopes of charge 1.</help>
             </param>
-            <expand macro="ppm_100"/>
+            <expand macro="ppm"/>
             <param name="isotope_ratio" type="float" min="0" max="100" value="1">
                 <label>isotope ratio</label>
                 <help>mininum intensity ratio expressed (Default value 1%). 

diff --git a/tools/ipapy2/macros.xml b/tools/ipapy2/macros.xml
@@ -24,15 +24,8 @@
         </param>
     </xml>
 
-    <xml name="ppm_100">
-        <param name="ppm" type="float" value="100">
-            <label>ppm between isotopes</label>
-            <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help>
-        </param>
-    </xml>
-
     <xml name="ppm">
-        <param name="ppm" type="float">
+        <param name="ppm" type="float" value="100">
             <label>ppm between isotopes</label>
             <help>Maximum ppm value allowed between 2 isotopes. Default value 100.</help>
         </param>