Change name

MANIFEST.in

@@ -1 +1 @@
-include pyscal_rdf/data/*.??l
+include atomrdf/data/*.??l

atomrdf/__init__.py

@@ -0,0 +1,3 @@
+from atomrdf.graph import KnowledgeGraph
+from atomrdf.structure import System
+from atomrdf.workflow.workflow import Workflow

pyscal_rdf/graph.py → atomrdf/graph.py

@@ -1,5 +1,5 @@
 """
-Graph module contains the basic RDFGraph object in pyscal_rdf. This object gets a structure
+Graph module contains the basic RDFGraph object in atomrdf. This object gets a structure
 as an input and annotates it with the CMSO ontology (PLDO and PODO too as needed). The annotated
 object is stored in triplets.
 """
@@ -17,18 +17,19 @@
 import json
 import shutil
 import tarfile
-import pyscal_rdf.json_io as json_io
-
-from pyscal_rdf.visualize import visualize_graph
-from pyscal_rdf.network.network import OntologyNetwork
-from pyscal_rdf.network.ontology import read_ontology
-from pyscal_rdf.structure import System
-import pyscal_rdf.properties as prp
-from pyscal_rdf.stores import create_store
 
 #from pyscal3.core import System
 from pyscal3.atoms import Atoms
 
+from atomrdf.visualize import visualize_graph
+from atomrdf.network.network import OntologyNetwork
+from atomrdf.network.ontology import read_ontology
+from atomrdf.structure import System
+import atomrdf.properties as prp
+from atomrdf.stores import create_store
+import atomrdf.json_io as json_io
+
+
 
 CMSO = Namespace("http://purls.helmholtz-metadaten.de/cmso/")
 PLDO = Namespace("http://purls.helmholtz-metadaten.de/pldo/")

pyscal_rdf/json_io.py → atomrdf/json_io.py

@@ -1,6 +1,6 @@
 import json
 import yaml
-from pyscal_rdf.encoder import NumpyArrayEncoder
+from atomrdf.encoder import NumpyArrayEncoder
 
 def write_file(outfile, data):
     """

pyscal_rdf/network/network.py → atomrdf/network/network.py

@@ -4,10 +4,11 @@
 import numpy as np
 import os
 import warnings
-from pyscal_rdf.network.parser import OntoParser
-from pyscal_rdf.network.term import OntoTerm, strip_name
 from pyscal3.atoms import AttrSetter
 
+from atomrdf.network.parser import OntoParser
+from atomrdf.network.term import OntoTerm, strip_name
+
 owlfile = os.path.join(os.path.dirname(__file__), "../data/cmso.owl")
 
 def _replace_name(name):

pyscal_rdf/network/ontology.py → atomrdf/network/ontology.py

@@ -1,7 +1,6 @@
-from pyscal_rdf.network.network import OntologyNetwork
 import os
+from atomrdf.network.network import OntologyNetwork
 
-#prov = OntologyNetwork('pyscal_rdf/data/prov.rdf', delimiter='#')
 def read_ontology():
 	#read in ontologies
 	file_location = os.path.dirname(__file__).split('/')

pyscal_rdf/network/parser.py → atomrdf/network/parser.py

@@ -1,5 +1,3 @@
-from pyscal_rdf.network.term import OntoTerm, strip_name 
-from pyscal_rdf.network.patch import patch_terms
 
 from owlready2 import get_ontology
 import owlready2
@@ -9,6 +7,9 @@
 import numpy as np
 import itertools
 
+from atomrdf.network.term import OntoTerm, strip_name 
+from atomrdf.network.patch import patch_terms
+
 
 class OntoParser:
     def __init__(self, infile, delimiter='/'):

pyscal_rdf/network/patch.py → atomrdf/network/patch.py

@@ -1,5 +1,5 @@
 """
-These are patches specifically designed for pyscal-rdf.
+These are patches specifically designed for atomrdf.
 
 These may or may not be implemented in the ontology. As it is implemented; it can be removed
 from the patches

pyscal_rdf/stores.py → atomrdf/stores.py

@@ -4,7 +4,7 @@
 
 import os
 #special methods; for supporting workflow envs
-from pyscal_rdf.workflow import inform_graph
+from atomrdf.workflow import inform_graph
 
 
 def create_store(kg, store, identifier, 

pyscal_rdf/structure.py → atomrdf/structure.py

@@ -1,6 +1,6 @@
 """
-StructureGraph is the central object in pyscal_rdf which combines all the functionality
-of :py:class:`pyscal_rdf.graph.RDFGraph` along with easy structural creation routines.
+StructureGraph is the central object in atomrdf which combines all the functionality
+of :py:class:`atomrdf.graph.RDFGraph` along with easy structural creation routines.
 """
 import numpy as np
 import copy
@@ -12,15 +12,15 @@
 import shutil
 import tarfile
 
-import pyscal_rdf.json_io as json_io
-
 import pyscal3.structure_creator as pcs
 from pyscal3.grain_boundary import GrainBoundary
 from pyscal3.atoms import AttrSetter
-import pyscal_rdf.properties as prp
 import pyscal3.core as pc
 from pyscal3.core import structure_dict, element_dict
 
+import atomrdf.json_io as json_io
+import atomrdf.properties as prp
+
 from rdflib import Graph, Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef, FOAF, SKOS, DCTERMS
 
 CMSO = Namespace("http://purls.helmholtz-metadaten.de/cmso/")

atomrdf/workflow/__init__.py

@@ -0,0 +1,2 @@
+from atomrdf.workflow.pyiron import inform_graph
+

pyscal_rdf/workflow/pyiron.py → atomrdf/workflow/pyiron.py

@@ -4,11 +4,12 @@
 import os
 import numpy as np
 from functools import partial, update_wrapper
-import pyscal_rdf.workflow.workflow as wf
-from pyscal_rdf.structure import _make_crystal
-from pyscal_rdf.structure import System
-from pyscal3.core import structure_dict, element_dict
 import ast
+from pyscal3.core import structure_dict, element_dict
+
+import atomrdf.workflow.workflow as wf
+from atomrdf.structure import _make_crystal
+from atomrdf.structure import System
 
 def _check_if_job_is_valid(job):
     valid_jobs = ['Lammps', ]

pyscal_rdf/workflow/workflow.py → atomrdf/workflow/workflow.py

@@ -11,10 +11,9 @@
 extract_calculated_properties
 inform_graph
 
-See pyscal_rdf.workflow.pyiron for more details
+See atomrdf.workflow.pyiron for more details
 """
 
-from pyscal_rdf.structure import System
 from rdflib import Graph, Literal, Namespace, XSD, RDF, RDFS, BNode, URIRef, FOAF, SKOS, DCTERMS
 
 import warnings
@@ -24,14 +23,16 @@
 import ast
 import uuid
 
+from atomrdf.structure import System
+
 #Move imports to another file
 PROV = Namespace("http://www.w3.org/ns/prov#")
 CMSO = Namespace("http://purls.helmholtz-metadaten.de/cmso/")
 PODO = Namespace("http://purls.helmholtz-metadaten.de/podo/")
 ASO = Namespace("http://purls.helmholtz-metadaten.de/aso/")
 
 #custom imports as needed
-import pyscal_rdf.workflow.pyiron as pi
+import atomrdf.workflow.pyiron as pi
 
 
 class Workflow:

docs/acknowledgements.md

@@ -8,7 +8,7 @@
 
 ## Contributers
 
-Please see the complete list of contributers [here](https://github.com/pyscal/pyscal_rdf/graphs/contributors).
+Please see the complete list of contributers [here](https://github.com/pyscal/atomrdf/graphs/contributors).
 
 
 ## Acknowledgements

docs/examples.md

@@ -1,6 +1,6 @@
 # Examples
 
-The gallery of examples below cover different ways in which pyscal-rdf can be used.
+The gallery of examples below cover different ways in which atomrdf can be used.
 
 ::::{grid} 1 1 2 3
 :class-container: text-center
@@ -10,7 +10,7 @@ The gallery of examples below cover different ways in which pyscal-rdf can be us
 :link: ../examples/01_getting_started
 :link-type: doc
 :class-header: bg-light
-Getting started with pyscal-rdf
+Getting started with atomrdf
 ^^^
 Learn the very basis, including the concepts of creating structures, and querying them.
 :::

docs/extending.md

@@ -2,37 +2,37 @@
 # Support
 
 In case of bugs and feature improvements, you are welcome to create a
-new issue on the [github repo](https://github.com/pyscal/pyscal_rdf). You
+new issue on the [github repo](https://github.com/pyscal/atomrdf). You
 are also welcome to fix a bug or implement a feature. 
 
 Any other questions or suggestions are welcome, please contact
 [us](mailto:[email protected]).
 
-`pyscal-rdf` welcomes and appreciates contribution and extension to the
+`atomrdf` welcomes and appreciates contribution and extension to the
 module. Rather than local modifications, we request that the
 modifications be submitted through a pull request, so that the module
 can be continuously improved.
 
 ## Reporting and fixing bugs
 
 In case a bug is found in the module, it can be reported on the [issues
-page of the repository](https://github.com/pyscal/pyscal_rdf/issues). Once a bug is reported, the status can once again monitored on
+page of the repository](https://github.com/pyscal/atomrdf/issues). Once a bug is reported, the status can once again monitored on
 the issues page. Additionally, you are of course very welcome to fix any
 existing bugs.
 
 ## New features
 
 If you have an idea for new feature, you can submit a feature idea
 through the [issues page of the
-repository](https://github.com/pyscal/pyscal_rdf/issues). As much as
+repository](https://github.com/pyscal/atomrdf/issues). As much as
 information as you can provide about the new feauture would be greatly
 helpful. Additionally, you could also work on feature requests already
 on the issues page. The following instructions will help you get started
 with local feature development.
 
 ### Setting up local environment
 
-1.  The first step is to fork `pyscal-rdf`. A detailed tutorial on forking can
+1.  The first step is to fork `atomrdf`. A detailed tutorial on forking can
     be found [here](https://help.github.com/en/articles/fork-a-repo).
     After forking, clone the repository to your local machine.
 2.  We recommend creating a virtual environment to test new features or
@@ -42,16 +42,16 @@ with local feature development.
 3.  Once the environment is set up, you can create a new branch for your
     feature by `git checkout -b new_feauture`.
 4.  Now implement the necessary feature.
-5.  Once done, you can reinstall `pyscal-rdf` by `pip install .`.
+5.  Once done, you can reinstall `atomrdf` by `pip install .`.
     After that please make sure that the existing tests work by running
     `pytest tests/` from the main module folder.
 6.  If the tests work, you are almost done! If the new feature is not
     covered in existing tests, you can to write a new test in the tests
-    folder. `pyscal-rdf` uses pytest for tests. [This
+    folder. `atomrdf` uses pytest for tests. [This
     link](http://doc.pytest.org/en/latest/getting-started.html) will
     help you get started.
 7.  Add the necessary docstrings for the new functions implemented.
-    `pyscal-rdf` uses the [numpy docstring
+    `atomrdf` uses the [numpy docstring
     format](https://numpydoc.readthedocs.io/en/latest/format.html) for
     documentation.
 8.  Bonus task: Set up few examples that document how the feature works

docs/gettingstarted.md

@@ -1,33 +1,33 @@
  # Installation
 
-`pyscal-rdf` can be installed on Linux and Mac OS based systems. On Windows systems, it is recommended to use  [Windows subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install). The following instructions will help install `pyscal-rdf`:
+`atomrdf` can be installed on Linux and Mac OS based systems. On Windows systems, it is recommended to use  [Windows subsystem for Linux](https://docs.microsoft.com/en-us/windows/wsl/install). The following instructions will help install `atomrdf`:
 
 ````{tab-set}
 ```{tab-item} pip
-`pip install pyscal-rdf`
+`pip install atomrdf`
 ```
 
 ```{tab-item} conda
-`conda install -c conda-forge pyscal-rdf`
+`conda install -c conda-forge atomrdf`
 ```
 
 ```{tab-item} from source
 We strongly recommend creating a conda environment for the installation. To see how you can install conda see [here](https://docs.conda.io/projects/conda/en/latest/user-guide/install/).
 
-Once a conda distribution is available, the following steps will help set up an environment to use `pyscal_rdf`. First step is to clone the repository.
+Once a conda distribution is available, the following steps will help set up an environment to use `atomrdf`. First step is to clone the repository.
 
-`git clone https://github.com/pyscal/pyscal_rdf.git`
+`git clone https://github.com/pyscal/atomrdf.git`
 
 After cloning, an environment can be created from the included file-
 
-`cd pyscal_rdf`  
+`cd atomrdf`  
 `conda env create -f environment.yml`
 
 This will install the necessary packages and create an environment called rdf. It can be activated by,
 
 `conda activate rdf`
 
-then, install `pyscal_rdf` using,
+then, install `atomrdf` using,
 
 `pip install .`
 ```

docs/license.md

@@ -1,6 +1,6 @@
 # License
 
-pyscal-rdf
+atomrdf
 
 Copyright 2022  (c) Sarath Menon $^1$, Abril Azócar Guzmán $^2$  
 $^1$: Max Planck Institut für Eisenforschung, Dusseldorf, Germany   
@@ -10,7 +10,7 @@ pyscal-rdf is published under the MIT license:
 
 MIT License
 
-Copyright (c) 2023 pyscal-rdf
+Copyright (c) 2023 atomrdf
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

environment-docs.yml

@@ -2,20 +2,18 @@ name: rdf
 channels:
   - conda-forge
 dependencies:
-  - python >3.8
-  - pyscal3 >=3.1.5
+  - python >3.8, <3.12
+  - pyscal3 >=3.1.12
   - rdflib
   - pyyaml
   - jupyterlab
   - graphviz
   - python-graphviz
-  - pyyaml
   - ase 
   - networkx
   - pandas
   - owlready2
   - jupyter-book
   - plotly
   - ipywidgets
-  - sphinx
 

environment-workflows.yml

@@ -3,14 +3,13 @@ channels:
   - conda-forge
 dependencies:
   - python >3.8, <3.12
-  - pyscal3 >=3.1.5
+  - pyscal3 >=3.1.12
   - pyscal-rdf
   - rdflib
   - pyyaml
   - jupyterlab
   - graphviz
   - python-graphviz
-  - pyyaml
   - ase 
   - networkx
   - pandas

environment.yml

@@ -9,7 +9,6 @@ dependencies:
   - jupyterlab
   - graphviz
   - python-graphviz
-  - pyyaml
   - ase 
   - networkx
   - pandas