From 542328c4e1ef97f6b8cba58d2ed031a1953c31e3 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 21 Aug 2023 14:27:10 +0200
Subject: [PATCH 1/3] Added requirements file

---
 Deliverable5.5/requirements.txt | 10 ++++++++++
 1 file changed, 10 insertions(+)
 create mode 100644 Deliverable5.5/requirements.txt

diff --git a/Deliverable5.5/requirements.txt b/Deliverable5.5/requirements.txt
new file mode 100644
index 0000000..09dae3e
--- /dev/null
+++ b/Deliverable5.5/requirements.txt
@@ -0,0 +1,10 @@
+aiida-core==2.4.0
+aiida-pseudo==0.8.0
+aiida-quantumespresso==4.3.0
+aiida-shell==0.3.0
+execflow==0.1.0
+execflowdemo==0.1.0
+oteapi-core==0.4.1
+oteapi-dlite==0.1.3
+otelib==0.2.0
+tripper==0.2.5

From c50b9143378369d0c56bc1cfa9101221275f52d0 Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 21 Aug 2023 14:46:21 +0200
Subject: [PATCH 2/3] Also updated README file

---
 Deliverable5.5/README.md | 23 +++++++++++++++++------
 1 file changed, 17 insertions(+), 6 deletions(-)

diff --git a/Deliverable5.5/README.md b/Deliverable5.5/README.md
index 8234a1f..14c83fd 100644
--- a/Deliverable5.5/README.md
+++ b/Deliverable5.5/README.md
@@ -19,6 +19,19 @@ The local execution of this demonstration requires the following software compon
   sudo apt install git python3-dev python3-pip postgresql postgresql-server-dev-all postgresql-client rabbitmq-server
   ```
 
+  Set up a virtual environment and install needed Python libraries
+
+  ```bash
+  python -m venv ~/envs/aiida
+  source ~/envs/aiida/bin/activate
+  ```
+
+  and install needed Python packages
+
+  ```bash
+  (aiida) pip install -r requirements.txt
+  ```
+
   To avoid clash with locally installed libraries (e.g. VMD), modify the file `$HOME/envs/aiida/bin/activate` by adding the following line:
 
   ```bash
@@ -28,7 +41,6 @@ The local execution of this demonstration requires the following software compon
   Then (from AiiDA instructions):
 
   ```bash
-  python -m venv ~/envs/aiida
   (aiida) verdi quicksetup
   (aiida) verdi daemon start 2
   ```
@@ -57,13 +69,13 @@ The local execution of this demonstration requires the following software compon
   pip install .
   ```
   To avoid changing the names of local files stored in the repository, absolute paths with root `/tmp/Deliverable5.5` have been used. Independently from where your repository is stored, create the following link from a terminal:
-  
+
   ```bash
   cd /tmp
   ln -s /path/to/Public/Deliverable5.5
   ```
 
-> TODO: 
+> TODO:
 >
 > * Replace the dependencies in `pyproject.toml` once those components will be released publicly.
 
@@ -77,11 +89,11 @@ The semantic representation of materials modelling workflows, data, and computat
 A simple query to the OntoKB is presented in the file [`application.py`](./ontoKB/application.py). Basically, the user asks for any route leading to the computation of the density of a fluid, expressed by the ontological class with IRI `http://emmo.info/emmo#FluidDensity`. From a terminal, execute:
 
 ```bash
-cd Public/Deliverable5.5/ontoKB 
+cd Public/Deliverable5.5/ontoKB
 python application.py
 ```
 
-> TODO: 
+> TODO:
 >
 > * describe the OpenModel ontology and OntoKB, i.e. how the workflow is described and stored in a triplestore. Is there a better way to create a KB other than using Protégé?
 > * Verify that a query can be made locally using a free version of StarDog.
@@ -118,4 +130,3 @@ verdi node attributes 5601
 * [entities/](./entities) Data models for the input datasets.
 * [execflowdemo/](./execflowdemo) Additional software used in this demonstration, e.g. a simple LAMMPS parser extracting the density.
 * [ontoKB/](./ontoKB) OpenModel domain ontology and knowledge base for demo number 1.
-

From 0d21b63cdfb76ed8cfe55e87846071b5d8a4189d Mon Sep 17 00:00:00 2001
From: Jesper Friis <jesper.friis@sintef.no>
Date: Mon, 21 Aug 2023 15:02:28 +0200
Subject: [PATCH 3/3] Fix typo

---
 Deliverable5.5/README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/Deliverable5.5/README.md b/Deliverable5.5/README.md
index 14c83fd..e7c25e6 100644
--- a/Deliverable5.5/README.md
+++ b/Deliverable5.5/README.md
@@ -19,7 +19,7 @@ The local execution of this demonstration requires the following software compon
   sudo apt install git python3-dev python3-pip postgresql postgresql-server-dev-all postgresql-client rabbitmq-server
   ```
 
-  Set up a virtual environment and install needed Python libraries
+  Set up a virtual environment
 
   ```bash
   python -m venv ~/envs/aiida