README.md

@@ -3,10 +3,8 @@
 This template uses the code-scaffolding tool [copier](https://copier.readthedocs.io/) to create a [LinkML](https://github.com/linkml/linkml) project.
 Copier supports code lifecycle management, allowing you to seamlessly incorporate updates into your project when the template is enhanced.
 
-* Starting from 0.2.x we give up compatibility to introduce new features and to re-organise and clean-up the code.
-* Early releases (0.1.x) have maintained backwards compatibility with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter/). 
-  This facilitates to experiment with the migration of existing cruft/cookiecutter-based projects.
-  Over time  the migration may become more difficult as the cookiecutter template evolves.
+* Early releases (0.1.x) maintain backwards compatibility with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter/). This facilitates to experiment with the migration of existing cruft/cookiecutter-based projects.
+* Starting from 0.2.x we give up compatibility to introduce new features and to re-organise and clean-up the code. The migration from 0.1.x to 0.2.x is not too difficult but requires some manual work.
 
 The generated project uses [just](https://github.com/casey/just) as preferred command runner, even in the 0.1.x releases.
 
@@ -194,7 +192,7 @@ The commands are written to be run at the root of your project.
     The command for migrating to a specific tag/release is:
 
     ```shell
-    copier copy --trust --vcs-ref v0.1.7 gh:dalito/linkml-project-copier .
+    copier copy --trust --vcs-ref v0.1.6 gh:dalito/linkml-project-copier .
     ```
 
     Look into the `.cruft.json` file to find out which values you chose when you created your original project.

copier.yaml

@@ -155,13 +155,6 @@ _message_after_copy: |
   Next step (if you have not previously initialized your project)
   run "just setup" in the root of your project directory.
 
-_migrations:
-  # Migrations are only run on update (not on copy) and only if the update goes
-  # through or to the specified version.
-  - version: v0.2.0
-    command: just _post-upgrade-0.1-to-0.2
-    when: "{{ _stage == 'after' }}"
-
 # _tasks:
 #    Commands to execute after generating or updating a project from the template.
 #    - "git init"

template/examples/README.md.jinja

@@ -3,7 +3,3 @@
 This folder contains examples using the datamodel.
 
 The source of the data used in the example is [tests/data](../tests/data/).
-
-The command `just test` creates different representations of the data in [tests/data](../tests/data/) and writes them to the subfolder `output`.
-It also generates a markdown documentation of the examples which is not very useful in its current form.
-Hence, the `output` sub-folder is git-ignored.

template/justfile

@@ -1,17 +1,18 @@
-# ============ Hint for for Windows Users ============
-
 # On Windows the "sh" shell that comes with Git for Windows should be used.
-# If it is not on path, provide the path to the executable in the following line.
+# If it is not on path, give the path to the executable in the following line.
 #set windows-shell := ["C:/Program Files/Git/usr/bin/sh", "-cu"]
 
-# ============ Variables used in recipes ============
-
 # Load environment variables from config.public.mk or specified file
 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}'
 
-# Set shebang line for cross-platform Python recipes (assumes presence of launcher on Windows)
+
+# List all commands as default command. The prefix "_" hides the command.
+_default: _status
+    @just --list
+
+# Set cross-platform Python shebang line (assumes presence of launcher on Windows)
 shebang := if os() == 'windows' {
   'py'
 } else {
@@ -21,11 +22,13 @@ shebang := if os() == 'windows' {
 # Environment variables with defaults
 schema_name := env_var_or_default("LINKML_SCHEMA_NAME", "")
 source_schema_path := env_var_or_default("LINKML_SCHEMA_SOURCE_PATH", "")
+
 use_schemasheets := env_var_or_default("LINKML_USE_SCHEMASHEETS", "No")
 sheet_module := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_MODULE", "")
 sheet_ID := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_ID", "")
 sheet_tabs := env_var_or_default("LINKML_SCHEMA_GOOGLE_SHEET_TABS", "")
 sheet_module_path := source_schema_path / sheet_module + ".yaml"
+
 config_yaml := if env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "") != "" {
   "--config-file " + env_var_or_default("LINKML_GENERATORS_CONFIG_YAML", "")
 } else {
@@ -43,80 +46,20 @@ dest := "project"
 pymodel := src / schema_name / "datamodel"
 docdir := "docs/elements"  # Directory for generated documentation
 
-# ============== Project recipes ==============
+# Show current project status
+_status: _check-config
+    @echo "Project: {{schema_name}}"
+    @echo "Source: {{source_schema_path}}"
 
-# Initialize a new project (use this for projects not yet under version control)
+# Run initial setup (run this first)
 [group('project management')]
-setup: _check-config
-  git init
-  install
-  git add .
-  git commit -m "Initialise git with minimal project" -a
-  _gen-project
-  _gendoc
-  git add .
-  git commit -m "Add generated docs and project artefacts" -a
+setup: _check-config _git-init install _gen-project gendoc _git-add _git-commit
 
 # Install project dependencies
 [group('project management')]
 install:
     poetry install
 
-# (Re-)Generate project and documentation locally
-[group('model development')]
-site: _gen-project _gendoc
-
-# Deploy documentation site to Github Pages
-[group('deployment')]
-deploy: site
-  mkd-gh-deploy
-
-# Run all tests
-[group('model development')]
-test: _test-schema _test-python _test-examples
-
-# Run linting
-[group('model development')]
-lint:
-    poetry run linkml-lint {{source_schema_path}}
-
-# Build docs and run test server
-[group('model development')]
-testdoc: _gendoc _serve
-
-# Updates project template and LinkML package
-[group('project management')]
-update: _update-template _update-linkml
-
-# Clean all generated files
-[group('project management')]
-clean: _clean_project
-    rm -rf tmp
-    rm -rf {{docdir}}/*
-
-# ============== Migrations recipes for Copier ==============
-
-# Hidden command to adjust the directory layout after upgrading a project
-# created with linkml-project-copier v0.1.x to v0.2.0 or newer.
-# Use with care! - It may not work for customized projects.
-_post-upgrade-0.1-to-0.2:
-    -mv docs/*.md docs/elements
-    -git mv src/docs/files docs
-    -git mv src/docs/templates docs/templates-linkml
-    -git mv src/data/examples tests/data/
-    echo "Migration to v0.2.0 completed! Check the changes carefully before committing them."
-
-# ============== Hidden internal recipes ==============
-
-# List all commands as default command. The prefix "_" hides the command.
-_default: _status
-    @just --list
-
-# Show current project status
-_status: _check-config
-    @echo "Project: {{schema_name}}"
-    @echo "Source: {{source_schema_path}}"
-
 # Check project configuration
 _check-config:
     #!{{shebang}}
@@ -127,6 +70,10 @@ _check-config:
         exit(1)
     print('Project-status: Ok')
 
+# Updates project template and LinkML package
+[group('project management')]
+update: _update-template _update-linkml
+
 # Update project template
 _update-template:
     copier update --trust --skip-answered --skip-tasks
@@ -135,6 +82,15 @@ _update-template:
 _update-linkml:
     poetry add -D linkml@latest
 
+# (Re-)Generate project and documentation locally
+[group('model development')]
+site: _gen-project gendoc
+
+# Deploy documentation site to Github Pages
+[group('deployment')]
+deploy: site
+  mkd-gh-deploy
+
 _compile_sheets:
     @if [ "{{use_schemasheets}}" != "No" ]; then \
         poetry run sheets2linkml --gsheet-id {{sheet_ID}} {{sheet_tabs}} > {{sheet_module_path}}.tmp && \
@@ -157,6 +113,10 @@ _gen-project: _compile_sheets
       poetry run gen-typescript {{gen_ts_args}} {{source_schema_path}} > {{dest}}/typescript/{{schema_name}}.ts || true ; \
     fi
 
+# Run all tests
+[group('model development')]
+test: _test-schema _test-python _test-examples
+
 # Test schema generation
 _test-schema:
     poetry run gen-project {{config_yaml}} -d tmp {{source_schema_path}}
@@ -175,14 +135,38 @@ _test-examples: _ensure_examples_output
         --output-directory examples/output \
         --schema {{source_schema_path}} > examples/output/README.md
 
-# Generate documentation for the schema
-_gendoc:
+# Run linting
+[group('model development')]
+lint:
+    poetry run linkml-lint {{source_schema_path}}
+
+# Generate markdown documentation for the schema
+gendoc:
     poetry run gen-doc {{gen_doc_args}} -d {{docdir}} {{source_schema_path}}
 
+# Build docs and run test server
+[group('model development')]
+testdoc: gendoc _serve
+
 # Run documentation server
 _serve:
     poetry run mkdocs serve
 
+# Initialize and add everything to git
+_git-init-add: _git-init _git-add _git-commit _git-status
+
+# Initialize git repository
+_git-init:
+    git init
+
+# Add files to git
+_git-add:
+    git add .
+
+# Commit files to git
+_git-commit:
+    git commit -m 'chore: just setup was run' -a
+
 # Show git status
 _git-status:
     git status
@@ -205,9 +189,16 @@ _clean_project:
         else:
             d.unlink()
 
+# Clean all generated files
+[group('project management')]
+clean: _clean_project
+    rm -rf tmp
+    rm -rf {{docdir}}/*
+
+# Private recipes
+
 _ensure_examples_output:
     -mkdir -p examples/output
 
-# ============== Include project-specific recipes ==============
-
+# Include project-specific recipes
 import "project.justfile"