deploy v0.1

ssi-dk · Nov 15, 2024 · d9347c7 · d9347c7
1 parent 2ff1ec6
commit d9347c7
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Showing 32 changed files with 14,001 additions and 177 deletions.
diff --git a/bifrost_bridge/_modidx.py b/bifrost_bridge/_modidx.py
@@ -5,13 +5,31 @@
                 'doc_host': 'https://$GIT_USER_NAME.github.io',
                 'git_url': 'https://github.com/$GIT_USER_NAME/bifrost_bridge',
                 'lib_path': 'bifrost_bridge'},
-  'syms': { 'bifrost_bridge.core': { 'bifrost_bridge.core.cli': ('core.html#cli', 'bifrost_bridge/core.py'),
+  'syms': { 'bifrost_bridge.cli': {'bifrost_bridge.cli.cli': ('cli.html#cli', 'bifrost_bridge/cli.py')},
+            'bifrost_bridge.core': { 'bifrost_bridge.core.DataFrame': ('core.html#dataframe', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.DataFrame.__init__': ('core.html#dataframe.__init__', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.cli': ('core.html#cli', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.export_data': ('core.html#export_data', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.export_nested_json_data': ( 'core.html#export_nested_json_data',
+                                                                                      'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.export_nested_xml_data': ( 'core.html#export_nested_xml_data',
+                                                                                     'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.filter_columns': ('core.html#filter_columns', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.filter_rows': ('core.html#filter_rows', 'bifrost_bridge/core.py'),
                                      'bifrost_bridge.core.get_config': ('core.html#get_config', 'bifrost_bridge/core.py'),
                                      'bifrost_bridge.core.get_samplesheet': ('core.html#get_samplesheet', 'bifrost_bridge/core.py'),
                                      'bifrost_bridge.core.hello_world': ('core.html#hello_world', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.import_data': ('core.html#import_data', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.import_nested_json_data': ( 'core.html#import_nested_json_data',
+                                                                                      'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.import_nested_xml_data': ( 'core.html#import_nested_xml_data',
+                                                                                     'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.print_header': ('core.html#print_header', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.rename_header': ('core.html#rename_header', 'bifrost_bridge/core.py'),
                                      'bifrost_bridge.core.set_env_variables': ('core.html#set_env_variables', 'bifrost_bridge/core.py'),
+                                     'bifrost_bridge.core.show': ('core.html#show', 'bifrost_bridge/core.py'),
                                      'bifrost_bridge.core.show_project_env_vars': ( 'core.html#show_project_env_vars',
                                                                                     'bifrost_bridge/core.py')},
-            'bifrost_bridge.hello_world': { 'bifrost_bridge.hello_world.cli': ('hello_world.html#cli', 'bifrost_bridge/hello_world.py'),
-                                            'bifrost_bridge.hello_world.hello_two_world': ( 'hello_world.html#hello_two_world',
-                                                                                            'bifrost_bridge/hello_world.py')}}}
+            'bifrost_bridge.fastp': { 'bifrost_bridge.fastp.process_fastp_data': ( 'fastp.html#process_fastp_data',
+                                                                                   'bifrost_bridge/fastp.py')},
+            'bifrost_bridge.mlst': {'bifrost_bridge.mlst.process_mlst_data': ('mlst.html#process_mlst_data', 'bifrost_bridge/mlst.py')}}}
diff --git a/bifrost_bridge/hello_world.py → bifrost_bridge/cli.py b/bifrost_bridge/hello_world.py → bifrost_bridge/cli.py
@@ -1,9 +1,9 @@
-# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/01_hello_world.ipynb.
+# AUTOGENERATED! DO NOT EDIT! File to edit: ../nbs/01_cli.ipynb.
 
 # %% auto 0
-__all__ = ['hello_two_world', 'cli']
+__all__ = ['cli']
 
-# %% ../nbs/01_hello_world.ipynb 6
+# %% ../nbs/01_cli.ipynb 2
 # That export there, it makes sure this code goes into the module.
 
 # standard libs
@@ -24,18 +24,12 @@
 import json  # for nicely printing json and yaml
 from fastcore import test
 
-# Project specific libraries
-
-# %% ../nbs/01_hello_world.ipynb 8
+# %% ../nbs/01_cli.ipynb 4
 from bifrost_bridge import (
     core,
 )
 
-# %% ../nbs/01_hello_world.ipynb 17
-def hello_two_world(name1: str, name2: str) -> str:
-    return f"Hello {name1} and {name2}!"
-
-# %% ../nbs/01_hello_world.ipynb 19
+# %% ../nbs/01_cli.ipynb 8
 from fastcore.script import call_parse
 
 
@@ -53,10 +47,4 @@ def cli(
         config["example"]["input"]["name"] = name
     if alternative_name is not None:
         config["example"]["input"]["alternative_name"] = alternative_name
-
-    print(
-        hello_two_world(
-            config["example"]["input"]["name"],
-            config["example"]["input"]["alternative_name"],
-        )
-    )
+    print(f"Hello World! {config['example']['input']['name']}")
diff --git a/bifrost_bridge/config/config.default.env b/bifrost_bridge/config/config.default.env
@@ -22,3 +22,4 @@ BIFROST_BRIDGE_OUTPUT_DIR=./output
 BIFROST_BRIDGE_OUTPUT_FILE=${BIFROST_BRIDGE_OUTPUT_DIR}/output.txt
 BIFROST_BRIDGE_USER_INPUT_NAME=Kim
 
+
diff --git a/bifrost_bridge/config/config.default.yaml b/bifrost_bridge/config/config.default.yaml
@@ -7,3 +7,4 @@ example:
     input:
         name: ${BIFROST_BRIDGE_USER_INPUT_NAME}
         alternative_name: Lee
+