Merge branch 'main' into stable

.github/workflows/test.yml

@@ -14,7 +14,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.8, 3.9]
+        python-version: ['3.8', '3.9', '3.10', '3.11']
     defaults:
       run:
         shell: bash -l {0}
@@ -41,36 +41,3 @@ jobs:
         run: |
           pip install --no-deps .
           python -m pytest tests
-
-  Coverage:
-    needs: [Build]
-    runs-on: ubuntu-latest
-    defaults:
-      run:
-        shell: bash -l {0}
-    steps:
-      - name: 'Checkout'
-        uses: actions/checkout@v3
-        with:
-          ref: ${{ github.ref }}
-      - name: 'Setup Neo4j with APOC'
-        uses: mdanics/[email protected]
-      - name: 'Deploying miniconda'
-        uses: conda-incubator/setup-miniconda@v2
-        with:
-          miniconda-version: "latest"
-          environment-file: recipes/workflow.yaml
-          python-version: '3.9'
-          mamba-version: "*"
-          channel-priority: true
-          use-mamba: true
-      - name: 'Run tests'
-        run: |
-          pip install --no-deps .
-          coverage run -m pytest
-          coverage lcov
-      - name: 'Coveralls'
-        uses: coverallsapp/github-action@master
-        with:
-          github-token: ${{ secrets.GITHUB_TOKEN }}
-          path-to-lcov: ./coverage.lcov

README.md

@@ -1,18 +1,13 @@
 # Neo4jSbml
 
-[![Github Version](https://img.shields.io/github/v/release/brsynth/neo4jsbml?display_name=tag&sort=semver)](version)  
-[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)  
-[![GitHub Super-Linter](https://github.com/brsynth/brsynth/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter) [![Coverage](https://img.shields.io/coveralls/github/brsynth/neo4jsbml)](coveralls)  
+[![Github Version](https://img.shields.io/github/v/release/brsynth/neo4jsbml?display_name=tag&sort=semver)](version) [![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)  
+[![Documentation Status](https://readthedocs.org/projects/neo4jsbml/badge/?version=latest)](https://neo4jsbml.readthedocs.io/en/latest/?badge=latest) [![GitHub Super-Linter](https://github.com/brsynth/neo4jsbml/workflows/Tests/badge.svg)](https://github.com/marketplace/actions/super-linter)  
 [![DOI](https://zenodo.org/badge/585859244.svg)](https://zenodo.org/badge/latestdoi/585859244)  
 
 ## Install
 
 ```sh
-git clone [email protected]:brsynth/neo4jsbml.git
-cd neo4jsbml
-conda env create -n neo4jsbml -f recipes/workflow.yml
-conda activate neo4jsbml
-pip install --no-deps .
+conda install -c conda-forge neo4jsbml
 ```
 
 ## Usage
@@ -40,7 +35,7 @@ Import your data with `neo4jsbml` into Neo4j.
 ```sh
 neo4jsbml \
     # Database parameters
-    --input-protocol-str ["neo4j", "bolt"] \
+    --input-protocol-str ["neo4j", "neo4j+s", "neo4j+ssc", "bolt", "bolt+s", "bolt+ssc"] \
     --input-url-str "localhost" \
     --input-port-int 7687 \
     --input-user-str "neo4j" \

docs/example.rst

@@ -4,7 +4,7 @@ Example
 View shared metabolite
 ----------------------
 
-View shared metabolite, fumarat, between two models: *iAF1260* and *iML1515* available from `BiGG <http://bigg.ucsd.edu>`_
+View shared metabolite, fumarate, between two models: *iAF1260* and *iML1515* available from `BiGG <http://bigg.ucsd.edu>`_
 
 .. code-block:: console
 

docs/usage.rst

@@ -4,18 +4,18 @@ Usage
 Installation
 ------------
 
-To use neo4jsbml, first install it using conda:
+With conda:
 
 .. code-block:: console
 
-   $ conda install -c conda-forge -n neo4jsbml
+   $ conda install -c conda-forge neo4jsbml
 
 Principles
 ----------
 
 Import data from SBML into the Neo4j database is conducted in several steps:
 
-1. Define your schema with `Arrows <https://arrows.app>`_ and download the schema at the JSON format
+1. Define your schema with `Arrows <https://arrows.app>`_ and download the schema at the ``JSON`` format
 2. Import your data into Neo4j
 
 
@@ -41,7 +41,7 @@ Configure access to Neo4j
 
 The connection to the Neo4j database needs to have several parameters defined:
 
-* protocol: ``neo4j`` or ``bolt`` (default: ``neo4j``)
+* protocol: ``neo4j``, ``neo4j+s``, ``neo4j+ssc``, ``bolt``, ``bolt+s``, ``bolt+ssc`` (default: ``neo4j``)
 * url (default: ``localhost``)
 * port (default: ``7687``)
 * user name (default: ``neo4j``)
@@ -98,7 +98,7 @@ Command line
 ~~~~~~~~~~~~
 To import your data with ``neo4jsbml`` into Neo4j, you will need:
 1. the database parameters
-2. the ``SBML`` file, the model
+2. the ``SBML`` file, e.g. the model
 3. the ``JSON`` file downloaded from `arrows <https://arrows.app>`_
 
 .. code-block:: console

recipes/meta.yaml

@@ -22,6 +22,8 @@ requirements:
   run:
     - python-libsbml
     - neo4j-python-driver
+    - sphinx
+    - sphinx_rtd_theme
 
 test:
   imports:

src/neo4jsbml/connect.py

@@ -51,7 +51,7 @@ def from_config(cls, path: str) -> "Connect"
         create a Connect from an .ini file
     """
 
-    PROTOCOLS = ["neo4j", "bolt"]
+    PROTOCOLS = ["neo4j", "neo4j+s", "neo4j+ssc", "bolt", "bolt+s", "bolt+ssc"]
 
     def __init__(
         self,