Neo4j

.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.0.25
+current_version = 1.0.37
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(?:-(?P<release>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?(?:\+(?P<build>[0-9A-Za-z-]+(?:\.[0-9A-Za-z-]+)*))?
@@ -14,14 +14,14 @@ serialize =
 [bumpverion:part:build]
 values = [0-9A-Za-z-]+
 
-[bumpversion:file:setup.cfg]
-search = version = {current_version}
-replace = version = {new_version}
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
 
 [bumpversion:file:mkdocs.yml]
 search = version: {current_version}
 replace = version: {new_version}
 
 [bumpversion:file:ebel/__init__.py]
-search = __version__ = '{current_version}'
-replace = __version__ = '{new_version}'
+search = __version__ = "{current_version}"
+replace = __version__ = "{new_version}"

.readthedocs.yml

@@ -1,14 +1,21 @@
 # See: https://docs.readthedocs.io/en/latest/yaml-config.html
 version: 2
 
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.10"
+  jobs:
+    pre_create_environment:
+      - echo "Creating environment"
+    post_build:
+      - echo "Build finished successfully"
+      - echo `date`
+
 python:
-  version: "3.7"
   install:
     - requirements: docs/requirements.txt
-    - method: pip
-      path: .
-      extra_requirements:
-        - requirements.txt
+    - requirements: requirements.txt
 
 mkdocs:
   configuration: mkdocs.yml

README.rst

@@ -5,7 +5,7 @@ e(BE:L) is a Python package built for both validating and modeling information e
 This software package serves a comprehensive tool for all of your BEL needs and serves to create enriched knowledge graphs
 for developing and testing new theories and hypotheses.
 
-**e(BE:L)** have implemented several other knowledge bases to extend the BEL knowledge graph or map identifiers.
+**e(BE:L)** has implemented several other knowledge bases to extend the BEL knowledge graph or map identifiers:
 
 * `BioGrid <https://thebiogrid.org/>`_
 * `ChEBI <https://www.ebi.ac.uk/chebi/>`_
@@ -44,6 +44,53 @@ But we want to encourage you to use the latest development version which can be
 
     $ pip install git+https://github.com/e-bel/ebel
 
+
+Docker Installation
+-------------------
+
+Make sure `docker <https://docs.docker.com/get-docker/>`_ and `docker-compose <https://docs.docker.com/compose/install/>`_ are installed.
+
+.. code-block::
+
+    docker-compose up --build -d
+    docker exec -it ebel_ebel ebel settings
+
+Several question will follow. You can accept the default values (just press RETURN) except the following questions:
+
+.. code-block::
+
+    OrientDB server [localhost] ?
+    ebel_orientdb
+    OrientDB root password (to create database and users)
+    ebel
+    MySQL/MariaDB sever name [localhost]
+    ebel_mysql
+    MySQL root password (will be not stored) to create database and user
+    ebel
+
+It's strongly recommended, if you are using ebel in the production environment, to change the
+standard root MySQL and OrientDB passwords in the docker-compose.yml file.
+
+To load example files in container and import.
+
+.. code-block::
+
+    docker exec -it ebel_ebel git clone https://github.com/e-bel/example_json_bel_files.git
+    docker exec -it ebel_ebel ebel import-json example_json_bel_files/phago.bel.json -e
+
+
+To enrich the network:
+
+.. code-block::
+
+    docker exec -it ebel_ebel ebel enrich
+
+Following services are now available:
+
+1. `OrientDB Studio <http://localhost:2480/studio/index.html#/>`_
+2. `e(BE:L) REST server <http://localhost:5000/ui/>`_
+3. `phpMyAdmin <http://localhost:8089>`_
+
 Package Requirements
 ====================
 
@@ -235,51 +282,6 @@ To specify a different graph database to connect to than the one in your config
     # To overwrite your default values in the config file
     bel = Bel(graph_config=config_params, overwrite_config=True)
 
-Docker installation
-===================
-
-Make sure `docker <https://docs.docker.com/get-docker/>`_ and `docker-compose <https://docs.docker.com/compose/install/>`_ are installed.
-
-.. code-block::
-
-    docker-compose up --build -d
-    docker exec -it ebel_ebel ebel settings
-
-Several question will follow. You can accept the default values (just press RETURN) except the following questions:
-
-.. code-block::
-
-    OrientDB server [localhost] ?
-    ebel_orientdb
-    OrientDB root password (to create database and users)
-    ebel
-    MySQL/MariaDB sever name [localhost]
-    ebel_mysql
-    MySQL root password (will be not stored) to create database and user
-    ebel
-
-It's strongly recommended, if you are using ebel in the production environment, to change the
-standard root MySQL and OrientDB passwords in the docker-compose.yml file.
-
-To load example files in container and import.
-
-.. code-block::
-
-    docker exec -it ebel_ebel git clone https://github.com/e-bel/example_json_bel_files.git
-    docker exec -it ebel_ebel ebel ebel import-json example_json_bel_files/phago.json -e
-
-
-To enrich the network:
-
-.. code-block::
-
-    docker exec -it ebel_ebel ebel enrich
-
-Following services are now available:
-
-1. `OrientDB Studio <http://localhost:2480/studio/index.html#/>`_
-2. `e(BE:L) REST server <http://localhost:5000/ui/>`_
-3. `phpMyAdmin <http://localhost:8089>`_
 
 API
 ===

docker-compose.yml

@@ -5,8 +5,6 @@ services:
         container_name: ebel_ebel
         ports: 
             - 5000:5000
-        networks:
-            - ebel_network
         depends_on:
             - mysql
             - orientdb
@@ -23,8 +21,6 @@ services:
             MYSQL_USER: ebel
             MYSQL_PASSWORD: ebel
             MYSQL_DATABASE: ebel
-        networks:
-            - ebel_network
         volumes:
             - ebel_mysql:/var/lib/mysql
     orientdb:
@@ -36,8 +32,6 @@ services:
         ports:           
             - 2424:2424
             - 2480:2480
-        networks:
-            - ebel_network    
         volumes: 
             - ebel_orientdb_db:/orientdb/databases
             - ebel_orientdb_backup:/orientdb/backup
@@ -48,13 +42,10 @@ services:
         container_name: ebel_phpmyadmin
         ports:
             - 8089:80
-        networks:
-            - ebel_network
         environment:
             - PMA_ARBITRARY=1
-networks:
-    ebel_network:
-        driver: bridge
+            - PMA_HOST=mysql
+
 volumes:
     ebel_orientdb_db:
     ebel_orientdb_backup: