Merge pull request #34 from linkml/improve-documentation

Improve documentation

.github/CODE_OF_CONDUCT.md

@@ -5,7 +5,7 @@
 We as members, contributors, and leaders pledge to make participation in our
 community a harassment-free experience for everyone, regardless of age, body
 size, visible or invisible disability, ethnicity, sex characteristics, gender
-identity and expression, level of experience, education, socio-economic status,
+identity and expression, level of experience, education, socioeconomic status,
 nationality, personal appearance, race, caste, color, religion, or sexual
 identity and orientation.
 

docs/index.md

@@ -26,7 +26,36 @@ Not all parts of the model are implemented in the reference Python framework.
 
 ## Basic idea
 
-Given an object that conforms to a LinkML schema,e.g.:
+Given the LinkML schema 
+
+```yaml
+id: https://w3id.org/linkml/examples/personinfo
+name: personinfo
+prefixes:
+  linkml: https://w3id.org/linkml/
+  personinfo: https://w3id.org/linkml/examples/personinfo
+imports:
+  - linkml:types
+default_range: string
+default_prefix: personinfo
+
+classes:
+  Person:
+    attributes:
+      id:
+      given_name:
+      family_name:
+      aliases:
+        multivalued: true
+      height_in_cm:
+        range: float
+        unit:
+          ucum_code: cm
+      age_in_years:
+        range: integer
+```
+
+and an object that conforms to it, e.g.:
 
 ```yaml
 given_name: Jane
@@ -66,7 +95,7 @@ which themselves consist of one or more [SlotDerivation](schema/SlotDerivation.m
 Transform the data:
 
 ```bash
-linkml-tr map-data -T tr.yaml -s schema.yaml my-data.yaml
+linkml-map map-data -T tr.yaml -s schema.yaml my-data.yaml
 ```
 
 Giving:
@@ -84,7 +113,7 @@ Installation and command line usage:
 ```bash
 pip[x] install linkml-map
 cd tests/input/examples/personinfo_basic
-linkml-tr map-data \
+linkml-map map-data \
   -T transform/personinfo-to-agent.transform.yaml \
   -s source/personinfo.yaml \
    data/Container-001.yaml \
@@ -146,8 +175,8 @@ See:
 ## Running the code
 
 ```bash
-linkml-tr --help
-Usage: linkml-tr [OPTIONS] COMMAND [ARGS]...
+linkml-map --help
+Usage: linkml-map [OPTIONS] COMMAND [ARGS]...
 
   CLI for linkml-map.
 
@@ -168,13 +197,13 @@ through to a complex mappings.
 
 ```
 cd tests/input/examples/personinfo_basic
-linkml-tr map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml  data/Container-001.yaml
+linkml-map map-data -T transform/personinfo-to-agent.transform.yaml -s source/personinfo.yaml  data/Container-001.yaml
 ```
 
 ### derive-schema
 
 ```
 cd tests/input/examples/personinfo_basic
-linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+linkml-map derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
 ```
 

src/linkml_map/cli/cli.py

@@ -1,4 +1,4 @@
-"""Command line interface for linkml-transformer."""
+"""Command line interface for linkml-map."""
 
 import logging
 import sys
@@ -45,7 +45,7 @@
 @click.option("-q", "--quiet")
 # @click.version_option(__version__)
 def main(verbose: int, quiet: bool):
-    """CLI for linkml-transformer."""
+    """CLI for linkml-map."""
     logger = logging.getLogger()
     if verbose >= 2:
         logger.setLevel(level=logging.DEBUG)
@@ -85,7 +85,7 @@ def map_data(
 
     Example:
 
-        linkml-tr map-data -T X-to-Y-tr.yaml -s X.yaml  X-data.yaml
+        linkml-map map-data -T X-to-Y-tr.yaml -s X.yaml  X-data.yaml
     """
     logging.info(f"Transforming {input} conforming to {schema} using {transformer_specification}")
     tr = ObjectTransformer(**kwargs)
@@ -121,7 +121,7 @@ def compile(
 
     Example:
 
-        linkml-tr compile -T X-to-Y-tr.yaml -s X.yaml
+        linkml-map compile -T X-to-Y-tr.yaml -s X.yaml
     """
     logging.info(f"Compiling {transformer_specification} with {schema}")
     compiler_args = {}
@@ -158,7 +158,7 @@ def derive_schema(schema, transformer_specification, output, output_format, **kw
 
     Example:
 
-        linkml-tr derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+        linkml-map derive-schema -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
     """
     logging.info(f"Transforming {schema} using {transformer_specification}")
     tr = ObjectTransformer()
@@ -184,7 +184,7 @@ def invert(schema, transformer_specification, output, output_format, **kwargs):
 
     Example:
 
-        linkml-tr invert -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
+        linkml-map invert -T transform/personinfo-to-agent.transform.yaml source/personinfo.yaml
     """
     logging.info(f"Inverting {transformer_specification} using {schema} as source")
     tr = ObjectTransformer()