#7: update BioCypher version

biocypher · Mar 14, 2024 · 63a6893 · 63a6893
1 parent f018f14
commit 63a6893
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Showing 7 changed files with 498 additions and 241 deletions.
diff --git a/.gitignore b/.gitignore
@@ -8,3 +8,4 @@ speed_test
 .DS_Store
 *.swp
 .venv
+.idea
diff --git a/ckgb/adapter.py b/ckgb/adapter.py
@@ -31,10 +31,10 @@ def __init__(
 
         # read driver
         self.driver = nu.Driver(
-            db_name="neo4j",
+            db_name="graph.db",
             db_uri="bolt://localhost:7687",
             db_user="neo4j",
-            db_passwd="your_password_here",
+            db_passwd="testtest",
             multi_db=False,
             max_connection_lifetime=7200,
         )

diff --git a/poetry.lock b/poetry.lock
diff --git a/pyproject.toml b/pyproject.toml
@@ -1,14 +1,13 @@
 [tool.poetry]
 name = "ckg"
-version = "0.1.0"
+version = "0.2.0"
 description = "CKG migration to BioCypher"
 authors = ["Sebastian Lobentanzer <sebastian.lobentanzer@gmail.com>"]
 
 [tool.poetry.dependencies]
 python = "^3.9"
-pandas = "^1.4.3"
-# biocypher = {path = "../BioCypher", develop = true}
-biocypher = "^0.5.4"
+pandas = "^2.0.1"
+biocypher = "^0.5.38"
 
 [tool.poetry.dev-dependencies]
 

diff --git a/scripts/embedding_ckg_script.py b/scripts/embedding_ckg_script.py
@@ -27,6 +27,4 @@
 
 # convenience and import stats
 bc.write_import_call()
-bc.log_missing_bl_types()
-bc.log_duplicates()
-bc.show_ontology_structure()
+bc.summary()
diff --git a/scripts/full_ckg_script.py b/scripts/full_ckg_script.py
@@ -24,6 +24,4 @@
 
 # convenience and import stats
 bc.write_import_call()
-bc.log_missing_bl_types()
-bc.log_duplicates()
-bc.show_ontology_structure()
+bc.summary()
diff --git a/scripts/subset_ckg_script.py b/scripts/subset_ckg_script.py
@@ -27,6 +27,4 @@
 
 # convenience and import stats
 bc.write_import_call()
-bc.log_missing_bl_types()
-bc.log_duplicates()
-bc.show_ontology_structure()
+bc.summary()
-Original file line number
+Diff line change
@@ Expand Up / @@ -8,3 +8,4 @@ speed_test @@
     .DS_Store
     *.swp
     .venv
+    .idea