make md concise. Add instructions for test

README.md

@@ -14,18 +14,21 @@ biological models, associated research papers, URLs, and books.
 ## Use this Python3 library to:
 
   1) Run [**Reactome's Neo4j Tutorial**](https://reactome.org/dev/graph-database/extract-participating-molecules)
-     from one of the [**Jupyter notebooks**](src/ipy/tutorial) or a plain [**Python script**](src/bin_neo4j/tutorial)
+     from one of the [**Jupyter notebooks**](https://github.com/dvklopfenstein/ReactomePy/tree/master/src/ipy/tutorial)
+     or a plain [**Python script**](https://github.com/dvklopfenstein/ReactomePy/tree/master/src/bin_neo4j/tutorial)
 
-  2) Find enriched pathways [**from the command line**](doc/md/README_analyses.md),
-     accessing Reactome's online [**Pathway Analysis Service**](https://reactome.org/AnalysisService/) 
+  2) Find enriched pathways
+     [**from the command line**](https://github.com/dvklopfenstein/ReactomePy/blob/master/doc/md/README_analyses.md),
+     accessing Reactome's online
+     [**Pathway Analysis Service**](https://reactome.org/AnalysisService/) 
 
   3) Write your own Python scripts accessing the Reactome database through Neo4j
 
 
 ## Links
   * **User's Download hints**:
-    * [1) Install Neo4j](/doc/md/README_install_neo4j.md)
-    * [2) Download Reactome Knowledgebase](/doc/md/README_download_hints.md)    
+    * [1) Install Neo4j](https://github.com/dvklopfenstein/ReactomePy/blob/master/doc/md/README_install_neo4j.md)    
+    * [2) Download Reactome Knowledgebase](https://github.com/dvklopfenstein/ReactomePy/blob/master/doc/md/README_download_hints.md)   
   * **Reactome Publications**
     * 2018 | [Reactome graph database: Efficient access to complex pathway data](https://journals.plos.org/ploscompbiol/article?rev=2&id=10.1371/journal.pcbi.1005968)
   * **Reactome Documentation**    

doc/md/README_download_hints.md

@@ -1,10 +1,8 @@
 # Reactome Download Hints
-Please see [**Reactome's official documentation**](https://reactome.org/dev/graph-database#GetStarted)
+See [**Reactome's official documentation**](https://reactome.org/dev/graph-database#GetStarted)
 regarding downloading the Reactome Knowledgebase.
 
-**Please direct questions** regarding **loading the Reactome Knowledgebase** to **Reactome**,
-rather than open an issue in this repo.
-
+See below for user hints ...
 
 ## Hints for downloading the Reactome Knowledgebase
 1. [**Download the Reactome database**](#1-download-the-reactome-database)

doc/md/README_install_neo4j.md

@@ -2,11 +2,7 @@
 Please see [**Reactome's official documentation**](https://reactome.org/dev/graph-database#GetStarted)
 regarding installing Neo4j.
 
-
-**Please direct questions** regarding **downloading and installing Neo4j** to **Reactome**,
-rather than open an issue in this repo.
-
-Please contribute to this page if you would like to share a helpful install hint.
+See below for user hints ...
 
 
 ## Hints for installing Neo4j

makefile

@@ -66,9 +66,9 @@ prep_conda:
 	conda remove --name myenv --all
 	conda create --name myenv
 # conda activate myenv
-# conda install -c dvklopfenstein enrichmentanalysis_dvklopfenstein
+# conda install -c dvklopfenstein reactomepy
 # pwy_enrichment_reactome.py
-# pwy_enrichment_reactome.py data/exgo/study data/exgo/population data/exgo/association
+# pwy_enrichment_reactome.py data/enrich/studyids/Gene_NCBI_Entrez.txt
 
 # --------------------------------------------------------------------------------
 upload_pypi_test:

requirements.txt

@@ -1,4 +1,3 @@
-docopt
-timeit
-datetime
+neobolt
 neo4j
+

setup.py

@@ -24,7 +24,11 @@ def get_install_requires():
     base = ['enrichmentanalysis_dvklopfenstein', 'requests']
     # conda: Anaconda installs all needed to run scripts
     if sys.argv[1:2] == ['bdist_conda']:
-        base.append('neo4j-python-driver')
+        pkgs = [
+            'neobolt',
+            'neo4j-python-driver',
+        ]
+        base.extend(pkgs)
     return base
 
 PACKAGES = [