Merge pull request #18 from biolink/patch-missing-justfile-make-targets

Patching justfile to include missing make targets

Author: sierra-moxon

README.md

@@ -64,7 +64,7 @@ pip install uv
 
 ### Getting Started
 
-Note that the following commands assume you are in the project root directory, and the equivalent **`just`** commands may be substituted for  **`make`** (namely `just test` instead of `make test`)
+Note that the following commands assume you are in the project root directory, and the equivalent **`just`** commands may be substituted for several **`make`** targets (namely `just test` instead of `make test`)
 
 1. **Install dependencies:**
    ```bash
@@ -73,38 +73,49 @@ Note that the following commands assume you are in the project root directory, a
 
 2. **Run tests:**
    ```bash
-   make test
+   make test  # or just test
    ```
 
 3. **Generate documentation:**
    ```bash
    make gendoc
    ```
 
-4. **Create a new RIG:**
-   ```bash
-   make new-rig INFORES=infores:example NAME="Example Data Source"
-   ```
-
 ### Working with RIGs
 
 #### Creating a New RIG
 
 ```bash
 # Create a new RIG from the template
-make new-rig INFORES=infores:mydatasource NAME="My Data Source RIG"
+make new-rig INFORES=infores:example NAME="Example Data Source"
 
 # This creates src/docs/rigs/mydatasource_rig.yaml
 # Edit the file to fill in your specific information
 ```
 
+or using the equivalent **`just`** command:
+
+```bash
+just INFORES=infores:example NAME="Example Data Source" new-rig 
+```
+
+Note that for the **`just`** command, the script variables must precede the just recipe ("target") name on the command line (reverse of the make command).
+
 #### Validating RIGs
 
 ```bash
 # Validate all RIG files against the schema
-make validate-rigs
+make validate-rigs  
+```
+
+or
+
+```bash
+just validate-rigs
+```
+To validate a specific RIG:
 
-# Validate a specific RIG
+```bash
 uv run linkml-validate --schema src/resource_ingest_guide_schema/schema/resource_ingest_guide_schema.yaml src/docs/rigs/my_rig.yaml
 ```
 
@@ -139,10 +150,11 @@ make lint
 
 Python utilities are in `src/scripts/`:
 - `create_rig.py`: Generate new RIG from template
-- `rig_to_markdown.py`: Convert RIG YAML to markdown
+- `rig_to_markdown.py`: Convert RIG YAML to Markdown
 - `generate_rig_index.py`: Create RIG index table
 
 To test script changes:
+
 ```bash
 # Run scripts directly
 uv run python src/scripts/create_rig.py --help
@@ -163,6 +175,8 @@ make serve  # or make testdoc
 
 ### Available Commands
 
+Note: some **`make`** targets (like **`new-rig`** and **`validate-rigs`**) have **`just`** command equivalents (remember instead to put the just recipe target name _after_ any command line arguments)
+
 | Command | Description |
 |---------|-------------|
 | `make help` | Show all available commands |

justfile

@@ -7,7 +7,6 @@ set dotenv-load := true
 # set dotenv-filename := env_var_or_default("LINKML_ENVIRONMENT_FILENAME", "config.public.mk")
 set dotenv-filename := x'${LINKML_ENVIRONMENT_FILENAME:-config.public.mk}'
 
-
 # List all commands as default command. The prefix "_" hides the command.
 _default: _status
     @just --list
@@ -42,6 +41,9 @@ gen_owl_args := env_var_or_default("LINKML_GENERATORS_OWL_ARGS", "")
 gen_java_args := env_var_or_default("LINKML_GENERATORS_JAVA_ARGS", "")
 gen_ts_args := env_var_or_default("LINKML_GENERATORS_TYPESCRIPT_ARGS", "")
 
+INFORES:= ""
+NAME := ""
+
 # Directory variables
 src := "src"
 dest := "project"
@@ -123,7 +125,7 @@ _gen-project: _ensure_pymodel_dir _compile_sheets
     fi
 
 # Run all tests
-test: _test-schema _test-python _test-examples
+test: _test-schema _test-python  # _test-examples  # the test examples are not properly set up yet
 
 # Test schema generation
 _test-schema:
@@ -133,15 +135,18 @@ _test-schema:
 _test-python:
     {{run}} python -m pytest
 
+#
+# the test examples are not yet properly set up
+#
 # Run example tests
-_test-examples: _ensure_examples_output
-    {{run}} linkml-run-examples \
-        --output-formats json \
-        --output-formats yaml \
-        --counter-example-input-directory src/data/examples/invalid \
-        --input-directory src/data/examples/valid \
-        --output-directory examples/output \
-        --schema {{source_schema_path}} > examples/output/README.md
+#_test-examples: _ensure_examples_output
+#    {{run}} linkml-run-examples \
+#        --output-formats json \
+#        --output-formats yaml \
+#        --counter-example-input-directory src/data/examples/invalid \
+#        --input-directory src/data/examples/valid \
+#        --output-directory examples/output \
+#        --schema {{source_schema_path}} > examples/output/README.md
 
 # Run linting
 lint:
@@ -187,6 +192,17 @@ _git-commit:
 _git-status:
     git status
 
+# Create a new RIG from template
+# Usage: just new-rig INFORES=infores:ctd NAME="CTD Chemical-Disease Associations"
+new-rig:
+    @if [[ -z "{{INFORES}}" ]]; then \
+        echo "INFORES is required. Usage: just new-rig INFORES=infores:example NAME='Example RIG'"; \
+    elif [[ -z "{{NAME}}" ]]; then \
+        echo "NAME is required. Usage: just new-rig INFORES=infores:example NAME='Example RIG'"; \
+    else \
+       {{run}} python {{src}}/scripts/create_rig.py --infores "{{INFORES}}" --name "{{NAME}}"; \
+    fi
+
 # Validate all RIG files against the schema
 validate-rigs:
     @echo "Validating RIG files against schema..."