diff --git a/Deliverable5.5/README.md b/Deliverable5.5/README.md index 8234a1f..e7c25e6 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 + + ```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. - 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