Update dependencies (#18)

* Update dependencies

* Run autopep8 on everything; flake8 fixes everywhere; create "make test" command; add docker-compose.yaml

* Add note about running arango with docker-compose

Makefile

@@ -0,0 +1,4 @@
+.PHONY: test
+
+test:
+	pipenv run sh scripts/run_tests.sh

Pipfile

@@ -6,12 +6,12 @@ verify_ssl = true
 [dev-packages]
 
 [packages]
-requests = "==2.19.1"
-biopython = "==1.72"
+requests = "==2.22.0"
+biopython = "==1.74"
 parsec = "==3.3"
-networkx = "==2.3"
-pytest = "*"
-python-arango = "==4.4.0"
+networkx = "==2.4"
+pytest = "==5.2.2"
+python-arango = "==5.2.1"
 
 [requires]
 python_version = "3.7"

README.md

@@ -13,25 +13,22 @@ Build status (master):
 
 ## Setup
 
-For Ubuntu (and possibly other distributions) ensure that the appropriate `python-dev` package
-is installed, e.g. `sudo apt install python3.7-dev`. 
+Install Python 3.7, preferably using pyenv: https://github.com/pyenv/pyenv
 
-With [pipenv](https://github.com/pypa/pipenv) installed, run:
+Then install [pipenv](https://github.com/pypa/pipenv) and run:
 
 ```sh
 pipenv install
 ```
 
-Alternatively, you can use [pyenv](https://github.com/pyenv/pyenv) to manage your python
-installations.
-
 ## Running tests
 
-To run tests, arangodb must be running locally on the default port with default root credentials.
+To run tests, arangodb must be running locally on the default port with default root credentials. You can run arangodb using docker-compose with `docker-compse up`.
+
 Then from the repository root:
-```
-$ pipenv shell
-$ export PYTHONPATH=$(pwd):$(pwd)/src/; pytest
+
+```sh
+make test
 ```
 
 ## Standard loader usage
@@ -211,4 +208,4 @@ one-off scripts there.
   * Merge edges are never expired.
   * Currently only handles merge edges where
     * The merged node was present in the prior load and
-    * The target node is present in the current load.
+    * The target node is present in the current load.

docker-compose.yaml

@@ -0,0 +1,12 @@
+version: '3'
+
+# This docker-compose is for developer convenience, not for running in production.
+
+services:
+
+  # Arangodb server in cluster mode
+  arangodb:
+    image: arangodb:3.5
+    ports:
+      - "127.0.0.1:8529:8529"
+    command: sh -c "arangodb --starter.local"