From f6db0dba086aa3e52facfafdde105d3bbdd7979e Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Tue, 9 Apr 2024 07:41:25 +0200
Subject: [PATCH 1/4] remove sqlalchemy from depedencies

---
 environment-docs.yml | 2 --
 environment.yml      | 2 --
 requirements.txt     | 3 ---
 3 files changed, 7 deletions(-)

diff --git a/environment-docs.yml b/environment-docs.yml
index 93cdd03..a21ba02 100644
--- a/environment-docs.yml
+++ b/environment-docs.yml
@@ -14,8 +14,6 @@ dependencies:
   - networkx
   - pandas
   - owlready2
-  - sqlalchemy <2.0.0
-  - rdflib-sqlalchemy
   - jupyter-book
   - plotly
   - ipywidgets
diff --git a/environment.yml b/environment.yml
index f88eb2c..32ab4ae 100644
--- a/environment.yml
+++ b/environment.yml
@@ -14,7 +14,5 @@ dependencies:
   - networkx
   - pandas
   - owlready2
-  - sqlalchemy <2.0.0
-  - rdflib-sqlalchemy
   - plotly
   - ipywidgets
diff --git a/requirements.txt b/requirements.txt
index 7781120..d048f6d 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -4,10 +4,7 @@ rdflib
 pyyaml
 graphviz
 networkx
-ipycytoscape
 pyscal3
 spglib
-rdflib-sqlalchemy
-sqlalchemy<2.0.0
 pandas
 owlready2

From 2d65662dd72abe11b0768ed3c4ea76271882dd98 Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Tue, 9 Apr 2024 07:57:34 +0200
Subject: [PATCH 2/4] update graph

---
 pyscal_rdf/graph.py | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
index 315a34c..3b0ae0c 100644
--- a/pyscal_rdf/graph.py
+++ b/pyscal_rdf/graph.py
@@ -6,6 +6,7 @@
 
 from rdflib import Graph, Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef, FOAF, SKOS, DCTERMS
 from rdflib.store import NO_STORE, VALID_STORE
+from rdflib import plugin
 
 import os
 import numpy as np
@@ -93,9 +94,24 @@ def __init__(self, graph_file=None,
 
                 
         elif store=="SQLAlchemy":
+            #check for modules
+            try:
+                import sqlalchemy as sa
+            except ImportError:
+                raise RuntimeError('Please install the sqlalchemy package')
+            try:
+                import rdflib_sqlalchemy as rsa
+            except ImportError:
+                raise RuntimeError('Please install the rdllib-sqlalchemy package')
+
+
             if store_file is None:
                 raise ValueError("store file is needed if store is not memory")
-            self.graph = Graph(store="SQLAlchemy", identifier=identifier)
+            try:
+                self.graph = Graph(store="SQLAlchemy", identifier=identifier)
+            except plugin.PluginException:
+                raise 
+
             uri = Literal(f"sqlite:///{store_file}")
             self.graph.open(uri, create=True)        
         else:

From a8babbb48e115b5b03fa3a70b6d23110aaf16857 Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Tue, 9 Apr 2024 07:59:34 +0200
Subject: [PATCH 3/4] add checks for modules

---
 pyscal_rdf/graph.py | 9 ++-------
 1 file changed, 2 insertions(+), 7 deletions(-)

diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
index 3b0ae0c..5ffd75b 100644
--- a/pyscal_rdf/graph.py
+++ b/pyscal_rdf/graph.py
@@ -102,20 +102,15 @@ def __init__(self, graph_file=None,
             try:
                 import rdflib_sqlalchemy as rsa
             except ImportError:
-                raise RuntimeError('Please install the rdllib-sqlalchemy package')
-
+                raise RuntimeError('Please install the rdllib-sqlalchemy package. The development version is needed, please do pip install git+https://github.com/RDFLib/rdflib-sqlalchemy.git@develop')
 
             if store_file is None:
                 raise ValueError("store file is needed if store is not memory")
-            try:
-                self.graph = Graph(store="SQLAlchemy", identifier=identifier)
-            except plugin.PluginException:
-                raise 
 
             uri = Literal(f"sqlite:///{store_file}")
             self.graph.open(uri, create=True)        
         else:
-            raise ValueError("store should be pyiron_project, SQLAlchemy, or Memory")
+            raise ValueError("Memory or SQLAlchemy")
         
         #start the storage
         self.structure_store = _setup_structure_store(self.structure_store)

From 60bacf4be74aae9d32b2debcc23c6fcb933b738c Mon Sep 17 00:00:00 2001
From: Sarath Menon <sarathmenon@mailbox.org>
Date: Tue, 9 Apr 2024 08:15:27 +0200
Subject: [PATCH 4/4] add missing store creation statement

---
 pyscal_rdf/graph.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pyscal_rdf/graph.py b/pyscal_rdf/graph.py
index 5ffd75b..bf0cbcb 100644
--- a/pyscal_rdf/graph.py
+++ b/pyscal_rdf/graph.py
@@ -107,6 +107,7 @@ def __init__(self, graph_file=None,
             if store_file is None:
                 raise ValueError("store file is needed if store is not memory")
 
+            self.graph = Graph(store="SQLAlchemy", identifier=identifier)            
             uri = Literal(f"sqlite:///{store_file}")
             self.graph.open(uri, create=True)        
         else: