Merge pull request #66 from linkml/doc-schem-change

Make README concise and change documentation theme.

README.md

@@ -18,148 +18,4 @@ These can be composed together. For example, run `tsvs2linkml` followed by `anno
 The toolkit is still experimental. It is intended as an aid to schema creation rather than act as a formal conversion
 tool
 
-## Installation
-
-`schema-automator` and its components require Python 3.9 or greater.
-
-```bash
-chmod 755 environment.sh
-. environment.sh
-pip install -r requirements.txt
-pip install -e . 
-```
-
-## Command Line Usage
-
-### Annotating Enums
-
-This toolkit allows automated annotation of LinkML enums, mapping text strings to ontology terms.
-
-The command line tool `annotate-enums` takes a LinkML schema, with enums and fills in the `meaning` slots.
-
-See the [annotators](schema_automator/annotators/) folder for docs
-
-### Converting TSVs
-
-The `tsv2linkml` command infers a single-class schema from a TSV datafile
-
-```bash
-tsv2linkml --help
-Usage: tsv2linkml [OPTIONS] TSVFILE
-
-  Infer a model from a TSV
-
-Options:
-  -o, --output TEXT        Output file
-  -c, --class_name TEXT    Core class name in schema
-  -n, --schema_name TEXT   Schema name
-  -s, --sep TEXT           separator
-  -E, --enum-columns TEXT  column that is forced to be an enum
-  --robot / --no-robot     set if the TSV is a ROBOT template
-  --help                   Show this message and exit.
-```
-
-Example:
-
-```bash
-tsv2linkml tests/resources/biobank-specimens.tsv 
-```
-
-The `tsvs2linkml` command infers a multi-class schema from multiple TSV datafiles
-
-```bash
-tsvs2linkml --help
-Usage: tsvs2linkml [OPTIONS] [TSVFILES]...
-
-  Infer a model from multiple TSVs
-
-Options:
-  -o, --output TEXT         Output file
-  -n, --schema_name TEXT    Schema name
-  -s, --sep TEXT            separator
-  -E, --enum-columns TEXT   column(s) that is forced to be an enum
-  --enum-mask-columns TEXT  column(s) that are excluded from being enums
-  --max-enum-size INTEGER   do not create an enum if more than max distinct
-                            members
-
-  --enum-threshold FLOAT    if the number of distinct values / rows is less
-                            than this, do not make an enum
-
-  --robot / --no-robot      set if the TSV is a ROBOT template
-  --help                    Show this message and exit.
-```
-
-### Converting OWL
-
-```bash
-owl2linkml --help
-Usage: owl2linkml [OPTIONS] OWLFILE
-
-  Infer a model from OWL Ontology
-
-  Note: input must be in functional syntax
-
-Options:
-  -n, --name TEXT  Schema name
-  --help           Show this message and exit.
-```
-
-Example:
-
-```bash
-owl2linkml -n prov tests/resources/prov.ofn > prov.yaml
-```
-
-Note this works best on schema-style ontologies such as Prov
-
-**NOT** recommended for terminological-style ontologies such as OBO
-
-### Converting RDF instance graphs
-
-```bash
-rdf2linkml --help
-Usage: rdf2linkml [OPTIONS] RDFFILE
-
-  Infer a model from RDF instance data
-
-Options:
-  -d, --dir TEXT  [required]
-  --help          Show this message and exit.
-```
-
-### Converting JSON Instance Data
-
-```bash
-jsondata2linkml --help
-Usage: jsondata2linkml [OPTIONS] INPUT
-
-  Infer a model from JSON instance data
-
-
-
-Options:
-  --container-class-name TEXT   name of root class
-  -f, --format TEXT             json or yaml (or json.gz or yaml.gz)
-  --omit-null / --no-omit-null  if true, ignore null values
-  --help                        Show this message and exit.
-```
-
-### Converting JSON-Schema
-
-```bash
-jsonschema2linkml --help
-Usage: jsonschema2linkml [OPTIONS] INPUT
-
-  Infer a model from JSON Schema
-
-Options:
-  -n, --name TEXT    ID of schema  [required]
-  -f, --format TEXT  JSON Schema format - yaml or json
-  -o, --output TEXT  output path
-  --help             Show this message and exit.
-```
-
-### jsonschema2linkml example
-```bash
-poetry run jsonschema2linkml -n test-model -f yaml -o vrs-linkml.yaml cp tests/resources/jsonschema/vrs.schema.json
-```
+[Full Documentation](https://linkml.io/schema-automator/)

docs/conf.py

@@ -12,14 +12,16 @@
 #
 import os
 import sys
+import sphinx_pdj_theme
+
 sys.path.insert(0, os.path.abspath('../..'))
 
 
 # -- Project information -----------------------------------------------------
 
 project = 'Schema Automator'
 copyright = '2022, Chris Mungall'
-author = 'Chris Mungall'
+author = 'Chris Mungall, Harshad Hegde'
 
 # The full version, including alpha/beta/rc tags
 # release = '0.1.4'
@@ -34,7 +36,7 @@
     'sphinx.ext.autodoc',
     'sphinx.ext.githubpages',
     'sphinx.ext.autosectionlabel',
-    'sphinx_rtd_theme',
+    'sphinx_pdj_theme',
     'sphinx_click',
     'sphinx.ext.viewcode',
     'sphinx.ext.todo',
@@ -64,7 +66,8 @@
 # The theme to use for HTML and HTML Help pages.  See the documentation for
 # a list of builtin themes.
 #
-html_theme = 'sphinx_rtd_theme'
+html_theme = 'sphinx_pdj_theme'
+html_theme_path = [sphinx_pdj_theme.get_html_theme_path()]
 
 # Add any paths that contain custom static files (such as style sheets) here,
 # relative to this directory. They are copied after the builtin static files,

pyproject.toml

@@ -38,7 +38,7 @@ twine = "^4.0.0"
 [tool.poetry.dev-dependencies]
 pytest = "^7.1.1"
 Sphinx = "^4.4.0"
-sphinx-rtd-theme = "^1.0.0"
+sphinx-pdj-theme = "^0.2.0"
 sphinx-click = "^3.1.0"
 sphinxcontrib-mermaid = "^0.7.1"
 
@@ -59,4 +59,4 @@ jsondata2linkml = "schema_automator.importers.json_instance_import_engine:json2m
 jsonschema2linkml = "schema_automator.importers.jsonschema_import_engine:jsonschema2model"
 
 [tool.poetry.extras]
-docs = ["Sphinx", "sphinx-rtd-theme", "sphinxcontrib-mermaid"]
+docs = ["Sphinx", "sphinx-pdj-theme", "sphinxcontrib-mermaid"]