Merge pull request #48 from vivarium-collective/remove-mongo

remove mongo emitter

.github/workflows/pytest.yml

@@ -9,13 +9,7 @@ on:
 jobs:
   run-tests:
     runs-on: ubuntu-latest
-
-    services:
-      mongodb:
-        image: mongo
-        ports:
-          - 27017:27017
-
+
     steps:
     - name: Check out repository
       uses: actions/checkout@main

README.md

@@ -34,77 +34,6 @@ You can install `process-bigraph` using pip:
 pip install process-bigraph
 ```
 
-MongoDB
--------
-
-We use a MongoDB database to store the data collected from running
-simulations via the `DatabaseEmitter` class. The use of this class is specified in the
-`'emitter'` section of the instance declaration for a given process as such:
-
-    ...,
-    'emitter': {
-                    '_type': 'step',
-                    'address': 'local:database-emitter',
-                    'config': {
-                        'ports': {
-                            'inputs': {
-                                'table': 'string',
-
-. This can be a remote server, but for this guide we will
-run a MongoDB server locally.
-
-**Note**: MongoDB is only required if you want to store data in MongoDB
-or want to run experiments that do so via the declaration shown above. You don't need MongoDB to work
-through this guide.
-
-*Check Installation*
-
-    $ mongod --version
-    db version v4.2.3
-    ...
-
-Make sure you see a version at least 3.2.
-
-*Install*
-
-If you are on macOS, you can install MongoDB using [Homebrew](https://brew.sh). You will need to add the MongoDB tap following the
-instructions [here](https://github.com/mongodb/homebrew-brew).
-
-If you are on Linux, see the MongoDB documentation's [instructions](https://docs.mongodb.com/manual/administration/install-on-linux/).
-
-*Setup*
-
-You can get a MongoDB server up and running locally any number of ways.
-Here is one:
-
-1. Create a folder ``process_bigraph_work/mongodb``. This is where MongoDB will
-   store the database We store the database here instead of at the
-   default location in ``/usr/local/var/mongodb`` to avoid permissions
-   issues if you are not running as an administrator.
-2. Make a copy of the ``mongod`` configuration file so we can make
-   changes:
-
-       $ cp /usr/local/etc/mongod.conf process_bigraph_work/mongod.conf
-
-   Note that your configuration file may be somewhere slightly
-   different. Check the MongoDB documentation for your system.
-3. In ``process_bigraph_work/mongod.conf`` change the path after ``dbPath:`` to
-   point to ``process_bigraph_work/mongodb``.
-4. Create a shell script ``process_bigraph_work/mongo.sh`` with the following
-   content:
-
-       #!/bin/bash
-
-       mongod --config mongod.conf
-
-5. Make the script executable:
-
-        $ chmod 700 process_bigraph_work/mongo.sh
-
-6. Now you can launch MongoDB by running this script:
-
-        $ process_bigraph_work/mongo.sh
-
 ## Tutorial
 
 To get started with Bigraph-viz, explore our resources: 

process_bigraph/__init__.py

@@ -1,13 +1,11 @@
 import pprint
-
 from process_bigraph.composite import Process, Step, Composite, ProcessTypes
 
 
 __all__ = [
     'Process',
     'Step',
     'Composite',
-    'core',
     'pp',
     'pf',
 ]

process_bigraph/composite.py

@@ -11,8 +11,8 @@
 from typing import Dict
 
 
-from bigraph_schema import Edge, TypeSystem, get_path, validate_merge, establish_path, set_path, deep_merge
-from bigraph_schema.registry import Registry
+from bigraph_schema import Edge, TypeSystem, get_path, establish_path, set_path, deep_merge
+from bigraph_schema.registry import Registry, validate_merge
 
 from process_bigraph.protocols import local_lookup, local_lookup_module