From bad86d377c7db4a299c29dbdbf4d178e60e89b44 Mon Sep 17 00:00:00 2001 From: liamhuber Date: Wed, 17 Jan 2024 14:09:59 -0800 Subject: [PATCH 1/5] Update single-sentence summary --- docs/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/README.md b/docs/README.md index 6227329..9ac3963 100644 --- a/docs/README.md +++ b/docs/README.md @@ -13,8 +13,7 @@ ## Overview -`pyiron_ontology` is a new pyiron project built on top of `owlready2` for ontologically-guided workflow design. -This project is currently in alpha-stage and subject to rapid change. +`pyiron_ontology` is a pyiron project built on top of `owlready2` to leverage ontologies for guided workflow design and dynamic (use-based) typing. Philosophically, `pyiron_ontology` breaks the construction of ontologies down into two parts: a set of classes that are "universal" to all `pyiron_ontology` ontologies, which describe the core elements of a workflow, and a set of "domain specific" declarations (most or all of which) define From 7adcf79021d7aa0c15889a127be29f9ab3feab1d Mon Sep 17 00:00:00 2001 From: liamhuber Date: Wed, 17 Jan 2024 14:11:02 -0800 Subject: [PATCH 2/5] Complete philosophy --- docs/README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/README.md b/docs/README.md index 9ac3963..dafd3e1 100644 --- a/docs/README.md +++ b/docs/README.md @@ -15,7 +15,7 @@ `pyiron_ontology` is a pyiron project built on top of `owlready2` to leverage ontologies for guided workflow design and dynamic (use-based) typing. -Philosophically, `pyiron_ontology` breaks the construction of ontologies down into two parts: a set of classes that are "universal" to all `pyiron_ontology` ontologies, which describe the core elements of a workflow, and a set of "domain specific" declarations (most or all of which) define +Philosophically, `pyiron_ontology` breaks the construction of ontologies down into two parts: a set of classes that are "universal" to all `pyiron_ontology` ontologies, which describe the core elements of a workflow, and a set of "domain specific" instance declarations (most or all of which) define relationships between different pieces of code. ## Installation and setup From 51ec284c3352a46dc586b5fb3237c615c993e9e3 Mon Sep 17 00:00:00 2001 From: liamhuber Date: Wed, 17 Jan 2024 14:11:59 -0800 Subject: [PATCH 3/5] Update install recommendation --- docs/README.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/docs/README.md b/docs/README.md index dafd3e1..013376c 100644 --- a/docs/README.md +++ b/docs/README.md @@ -19,8 +19,7 @@ Philosophically, `pyiron_ontology` breaks the construction of ontologies down in ## Installation and setup -For the bleeding-edge, clone this repo. -`pyiron_ontology` is also available from Conda Forge via `conda install -c conda-forge pyiron_ontology`. +`pyiron_ontology` available to clone, pip-install, or on conda (recommended) from Conda Forge via `conda install -c conda-forge pyiron_ontology`. `pyiron_ontology` uses `owlready2`, which requires java. In case you try to run and get an `owlready2` error about not finding java, you may need to set the java path (cf. [owlready2 docs](https://owlready2.readthedocs.io/en/latest/reasoning.html#configuration)): `import owlready2; owlready2.JAVA_EXE = "C:\\path\\to\\java.exe"`. From 7deadfb4d896c826f6b77edf7839e10887285c57 Mon Sep 17 00:00:00 2001 From: liamhuber Date: Wed, 17 Jan 2024 14:13:39 -0800 Subject: [PATCH 4/5] Update atomistics example --- docs/README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/docs/README.md b/docs/README.md index 013376c..60d6a3b 100644 --- a/docs/README.md +++ b/docs/README.md @@ -326,7 +326,9 @@ Defining all the individuals that map to a (hypothetical) code base is quite ver ## Reasoning on existing `pyiron_atomistics` data -`pyiron_ontology` also comes with an ontology defined for (a small sub-set of) `pyiron_atomistics`. +`pyiron_ontology` also comes with an ontology defined for (a small sub-set of) `pyiron_atomistics` (an optional dependency). + +For example, if you have `Murnaghan` jobs in your pyiron project, the snippet below will return a nice little dataframe of results: ```python >>> import pyiron_ontology as po @@ -342,5 +344,3 @@ Defining all the individuals that map to a (hypothetical) code base is quite ver Index(['Chemical Formula', 'atomistics.BulkModulus', 'unit', 'Engine'], dtype='object') ``` - -If you have `Murnaghan` jobs in your project, this will return a nice little dataframe. From 30f97921ed24a06fdcf5e83973cd702944d83da8 Mon Sep 17 00:00:00 2001 From: liamhuber Date: Wed, 17 Jan 2024 14:15:13 -0800 Subject: [PATCH 5/5] Update classifier --- setup.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/setup.py b/setup.py index 193c92c..643ae3b 100644 --- a/setup.py +++ b/setup.py @@ -16,7 +16,7 @@ license='BSD', classifiers=[ - 'Development Status :: 3 - Alpha', + 'Development Status :: 5 - Production/Stable', 'Topic :: Scientific/Engineering :: Physics', 'License :: OSI Approved :: BSD License', 'Intended Audience :: Science/Research',