From 44f8909054d743d37da02b7d83e1e169f34c9643 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Fri, 9 Sep 2022 16:19:03 -0700
Subject: [PATCH 1/3] customization

---
 cookiecutter.json                             |   7 +-
 {{cookiecutter.project_name}}/mkdocs.yml      |  20 +--
 .../{{cookiecutter.__project_slug}}.yaml      | 148 ++++--------------
 3 files changed, 37 insertions(+), 138 deletions(-)

diff --git a/cookiecutter.json b/cookiecutter.json
index 428e8be..5339080 100644
--- a/cookiecutter.json
+++ b/cookiecutter.json
@@ -1,7 +1,10 @@
 {
-    "project_name": "Project_X",
+    "project_name": "my-awesome-schema",
     "__project_slug": "{{ cookiecutter.project_name|lower()|replace(' ', '_')|replace('-', '_') }}",
+    "github_org": "my-org",
     "project_description": "This is the project description.",
     "author": "Harshad Hegde <hhegde@lbl.gov>",
-    "github_token_for_pypi_deployment": "PYPI_PASSWORD"
+    "main_schema_class": "Person",
+    "create_python_classes": "Yes/No",
+    "github_token_for_pypi_deployment": "PYPI_PASSWORD (leave blank if not a python project)"
 }
diff --git a/{{cookiecutter.project_name}}/mkdocs.yml b/{{cookiecutter.project_name}}/mkdocs.yml
index c4a293f..8c64603 100644
--- a/{{cookiecutter.project_name}}/mkdocs.yml
+++ b/{{cookiecutter.project_name}}/mkdocs.yml
@@ -1,4 +1,4 @@
-site_name: "My Datamodel"
+site_name: "{{cookiecutter.project_name}}"
 theme:
   name: material
   analytics:
@@ -10,22 +10,10 @@ theme:
     - content.tabs.link
 plugins:
   - search
-markdown_extensions:
-  - pymdownx.highlight:
-      anchor_linenums: true
-  - pymdownx.inlinehilite
-  - pymdownx.snippets
-  - pymdownx.superfences
-  - pymdownx.tabbed:
-      alternate_style: true
-  - pymdownx.critic
-  - pymdownx.caret
-  - pymdownx.keys
-  - pymdownx.mark
-  - pymdownx.tilde
+  - mermaid2
 nav:
 #  - Home: home.md
   - Index: index.md
   - About: about.md
-site_url: https://my-org.github.io/my-datamodel/
-repo_url: https://github.com/my-org/my-datamodel/
+site_url: https://{{cookiecutter.my_org}}.github.io/{{cookiecutter.project_name}}
+repo_url: https://github.com/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}
diff --git a/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml b/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
index 67d8725..5bd32e7 100644
--- a/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
+++ b/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
@@ -1,43 +1,22 @@
-id: https://w3id.org/my_org/my_datamodel
-name: my_datamodel
-title: My Datamodel
+id: https://w3id.org/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}
+name: {{cookiecutter.project_name}}
+title: {{cookiecutter.project_name}}
 description: |-
-  Enter a detailed description of your project here
-default_curi_maps:
-  - semweb_context
+  {{cookiecutter.project_description}}
 imports:
   - linkml:types
+  
 prefixes:
-  my_datamodel: https://w3id.org/my_org/my_datamodel
+  {{cookiecutter.__project_slug}}: https://w3id.org/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}/
   linkml: https://w3id.org/linkml/
   biolink: https://w3id.org/biolink/
   schema: http://schema.org/
   PATO: http://purl.obolibrary.org/obo/PATO_
-  famrel: http://example.org/famrel/
-default_prefix: my_datamodel
+default_prefix: {{cookiecutter.__project_slug}}
 default_range: string
-see_also:
-  - https://example.org/
-
 
 classes:
 
-  Registry:
-    description: Top level data container
-    tree_root: true
-    attributes:
-      persons:
-        range: Person
-        inlined: true
-        inlined_as_list: true
-        multivalued: true
-      organizations:
-        range: Organization
-        inlined_as_list: true
-        inlined: true
-        multivalued: true
-    
-
   NamedThing:
     description: >-
       A generic grouping for any identifiable entity
@@ -45,120 +24,57 @@ classes:
       - id
       - name
       - description
-      - image
     close_mappings:
      - schema:Thing
 
-  Person:
+  {{cookiecutter.main_schema_class}}:
     is_a: NamedThing
     description: >-
-      A person (alive, dead, undead, or fictional).
-    class_uri: schema:Person
-    mixins:
-      - HasAliases
+      ADD YOUR DESCRIPTION HERE
     slots:
       - primary_email
       - birth_date
       - age_in_years
-      - current_address
-      - has_familial_relationships
+      - vital_status
     slot_usage:
       primary_email:
         pattern: "^\\S+@[\\S+\\.]+\\S+"
-  
-  HasAliases:
+        
+  {{cookiecutter.main_schema_class}}Collection:
+    tree_root: true
     description: >-
-      A mixin applied to any class that can have aliases/alternateNames
-    mixin: true
+      A holder for {{cookiecutter.main_schema_class}} objects
     attributes:
-      aliases:
+      entries:
+        range: {{cookiecutter.main_schema_class}}
         multivalued: true
-        exact_mappings:
-          - schema:alternateName
-
-
-  Organization:
-    description: >-
-      An organization such as a company or university
-    is_a: NamedThing
-    class_uri: schema:Organization
-    mixins:
-      - HasAliases
-    slots:
-      - mission_statement
-      - founding_date
-
-  Address:
-    class_uri: schema:PostalAddress
-    slots:
-      - street
-      - city
-      - postal_code
-
-
-  Relationship:
-    slots:
-      - started_at_time
-      - ended_at_time
-      - related_to
-      - type
-
-  FamilialRelationship:
-    is_a: Relationship
-    slot_usage:
-      type:
-        range: FamilialRelationshipType
-        required: true
-      related to:
-        range: Person
-        required: true
-
+        inlined: true
 
 slots:
   id:
     identifier: true
     slot_uri: schema:identifier
+    range: uriorcurie
+    description: A unique identifier for a thing
   name:
     slot_uri: schema:name
+    description: A human-readable name for a thing
   description:
     slot_uri: schema:description
-  image:
-    slot_uri: schema:image
+    description: A human-readable description for a thing
   primary_email:
     slot_uri: schema:email
+    description: The main email address of a person
   birth_date:
     slot_uri: schema:birthDate
-  employed_at:
-    range: Organization
-  is_current:
-    range: boolean
-  has_familial_relationships:
-    range: FamilialRelationship
-    multivalued: true
-    inlined_as_list: true
-  current_address:
-    description: >-
-      The address at which a person currently lives
-    range: Address
+    range: date
+    description: Date on which a person is born
   age_in_years:
     range: integer
-    minimum_value: 0
-    maximum_value: 999
-  related_to:
-  type:
-  street:
-  city:
-  mission_statement:
-  founding_date:
-  postal_code:
-    range: string
-  started_at_time:
-    slot_uri: prov:startedAtTime
-    range: date
-  ended_at_time:
-    slot_uri: prov:endedAtTime
-    range: date
-
+    description: Number of years since birth
+  vital_status:
+    range: PersonStatus
+    description: living or dead status
     
 enums:
   PersonStatus:
@@ -173,11 +89,3 @@ enums:
         description: the vital status is not known
         todos:
           - map this to an ontology
-  FamilialRelationshipType:
-    permissible_values:
-      SIBLING_OF:
-        meaning: famrel:01
-      PARENT_OF:
-        meaning: famrel:02
-      CHILD_OF:
-        meaning: famrel:01

From e37f6cd494f55ec4e9012cf5e5d82032f9b0c437 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Fri, 9 Sep 2022 16:26:21 -0700
Subject: [PATCH 2/3] fixes

---
 {{cookiecutter.project_name}}/mkdocs.yml      |   4 +-
 {{cookiecutter.project_name}}/poetry.lock     | 245 +++++++++++++++---
 {{cookiecutter.project_name}}/pyproject.toml  |   3 +-
 .../{{cookiecutter.__project_slug}}.yaml      |   4 +-
 4 files changed, 217 insertions(+), 39 deletions(-)

diff --git a/{{cookiecutter.project_name}}/mkdocs.yml b/{{cookiecutter.project_name}}/mkdocs.yml
index 8c64603..9c18f2c 100644
--- a/{{cookiecutter.project_name}}/mkdocs.yml
+++ b/{{cookiecutter.project_name}}/mkdocs.yml
@@ -15,5 +15,5 @@ nav:
 #  - Home: home.md
   - Index: index.md
   - About: about.md
-site_url: https://{{cookiecutter.my_org}}.github.io/{{cookiecutter.project_name}}
-repo_url: https://github.com/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}
+site_url: https://{{cookiecutter.github_org}}.github.io/{{cookiecutter.project_name}}
+repo_url: https://github.com/{{cookiecutter.github_org}}/{{cookiecutter.project_name}}
diff --git a/{{cookiecutter.project_name}}/poetry.lock b/{{cookiecutter.project_name}}/poetry.lock
index 21bd69c..32a3260 100644
--- a/{{cookiecutter.project_name}}/poetry.lock
+++ b/{{cookiecutter.project_name}}/poetry.lock
@@ -14,14 +14,6 @@ category = "dev"
 optional = false
 python-versions = "*"
 
-[[package]]
-name = "argparse"
-version = "1.4.0"
-description = "Python command-line parsing library"
-category = "dev"
-optional = false
-python-versions = "*"
-
 [[package]]
 name = "attrs"
 version = "22.1.0"
@@ -47,6 +39,21 @@ python-versions = ">=3.6"
 [package.dependencies]
 pytz = ">=2015.7"
 
+[[package]]
+name = "beautifulsoup4"
+version = "4.11.1"
+description = "Screen-scraping library"
+category = "dev"
+optional = false
+python-versions = ">=3.6.0"
+
+[package.dependencies]
+soupsieve = ">1.2"
+
+[package.extras]
+html5lib = ["html5lib"]
+lxml = ["lxml"]
+
 [[package]]
 name = "certifi"
 version = "2022.6.15"
@@ -126,6 +133,14 @@ wrapt = ">=1.10,<2"
 [package.extras]
 dev = ["tox", "bump2version (<1)", "sphinx (<2)", "importlib-metadata (<3)", "importlib-resources (<4)", "configparser (<5)", "sphinxcontrib-websupport (<2)", "zipp (<2)", "PyTest (<5)", "PyTest-Cov (<2.6)", "pytest", "pytest-cov"]
 
+[[package]]
+name = "distlib"
+version = "0.3.6"
+description = "Distribution utilities"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "docutils"
 version = "0.18.1"
@@ -134,6 +149,14 @@ category = "dev"
 optional = false
 python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
 
+[[package]]
+name = "editorconfig"
+version = "0.12.3"
+description = "EditorConfig File Locator and Interpreter for Python"
+category = "dev"
+optional = false
+python-versions = "*"
+
 [[package]]
 name = "et-xmlfile"
 version = "1.1.0"
@@ -142,6 +165,18 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "filelock"
+version = "3.8.0"
+description = "A platform independent file lock."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2022.6.21)", "sphinx (>=5.1.1)", "sphinx-autodoc-typehints (>=1.19.1)"]
+testing = ["covdefaults (>=2.2)", "coverage (>=6.4.2)", "pytest (>=7.1.2)", "pytest-cov (>=3)", "pytest-timeout (>=2.1)"]
+
 [[package]]
 name = "ghp-import"
 version = "2.1.0"
@@ -154,7 +189,7 @@ python-versions = "*"
 python-dateutil = ">=2.8.1"
 
 [package.extras]
-dev = ["wheel", "flake8", "markdown", "twine"]
+dev = ["twine", "markdown", "flake8", "wheel"]
 
 [[package]]
 name = "graphviz"
@@ -245,6 +280,18 @@ MarkupSafe = ">=2.0"
 [package.extras]
 i18n = ["Babel (>=2.7)"]
 
+[[package]]
+name = "jsbeautifier"
+version = "1.14.6"
+description = "JavaScript unobfuscator and beautifier."
+category = "dev"
+optional = false
+python-versions = "*"
+
+[package.dependencies]
+editorconfig = ">=0.12.2"
+six = ">=1.13.0"
+
 [[package]]
 name = "json-flattener"
 version = "0.1.9"
@@ -329,7 +376,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "linkml"
-version = "1.3.2"
+version = "1.3.3"
 description = "Linked Open Data Modeling Language"
 category = "dev"
 optional = false
@@ -337,7 +384,6 @@ python-versions = ">=3.7.6,<4.0.0"
 
 [package.dependencies]
 antlr4-python3-runtime = ">=4.9.0,<4.10"
-argparse = ">=1.4.0"
 click = ">=7.0"
 graphviz = ">=0.10.1"
 hbreader = "*"
@@ -346,11 +392,12 @@ jinja2 = "*"
 jsonasobj2 = ">=1.0.3,<2.0.0"
 jsonschema = ">=3.0.1"
 linkml-dataops = "*"
-linkml-runtime = ">=1.3.0,<2.0.0"
+linkml-runtime = ">=1.3,<1.4"
 myst-parser = "*"
 openpyxl = "*"
 parse = "*"
 prefixcommons = ">=0.1.7"
+prefixmaps = ">=0.1.3,<0.2.0"
 pydantic = "*"
 pyjsg = ">=0.11.6"
 pyshex = ">=0.7.20"
@@ -361,10 +408,11 @@ rdflib = ">=6.0.0"
 requests = ">=2.22"
 sphinx-click = "*"
 sqlalchemy = ">=1.4.31"
+tox = ">=3.25.1,<4.0.0"
 watchdog = ">=0.9.0"
 
 [package.extras]
-docs = ["sphinx", "sphinx-rtd-theme"]
+docs = ["sphinx-rtd-theme", "sphinx"]
 
 [[package]]
 name = "linkml-dataops"
@@ -427,14 +475,14 @@ python-versions = ">=3.7"
 mdurl = ">=0.1,<1.0"
 
 [package.extras]
-testing = ["pytest-regressions", "pytest-cov", "pytest", "coverage"]
-rtd = ["sphinx-book-theme", "sphinx-design", "sphinx-copybutton", "sphinx", "pyyaml", "myst-parser", "attrs"]
-profiling = ["gprof2dot"]
-plugins = ["mdit-py-plugins"]
-linkify = ["linkify-it-py (>=1.0,<2.0)"]
-compare = ["panflute (>=2.1.3,<2.2.0)", "mistune (>=2.0.2,<2.1.0)", "mistletoe (>=0.8.1,<0.9.0)", "markdown (>=3.3.6,<3.4.0)", "commonmark (>=0.9.1,<0.10.0)"]
+benchmarking = ["psutil", "pytest", "pytest-benchmark (>=3.2,<4.0)"]
 code_style = ["pre-commit (==2.6)"]
-benchmarking = ["pytest-benchmark (>=3.2,<4.0)", "pytest", "psutil"]
+compare = ["commonmark (>=0.9.1,<0.10.0)", "markdown (>=3.3.6,<3.4.0)", "mistletoe (>=0.8.1,<0.9.0)", "mistune (>=2.0.2,<2.1.0)", "panflute (>=2.1.3,<2.2.0)"]
+linkify = ["linkify-it-py (>=1.0,<2.0)"]
+plugins = ["mdit-py-plugins"]
+profiling = ["gprof2dot"]
+rtd = ["attrs", "myst-parser", "pyyaml", "sphinx", "sphinx-copybutton", "sphinx-design", "sphinx-book-theme"]
+testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "markupsafe"
@@ -456,9 +504,9 @@ python-versions = "~=3.6"
 markdown-it-py = ">=1.0.0,<3.0.0"
 
 [package.extras]
-testing = ["pytest-regressions", "pytest-cov", "pytest (>=3.6,<4)", "coverage"]
-rtd = ["sphinx-book-theme (>=0.1.0,<0.2.0)", "myst-parser (>=0.14.0,<0.15.0)"]
 code_style = ["pre-commit (==2.6)"]
+rtd = ["myst-parser (>=0.14.0,<0.15.0)", "sphinx-book-theme (>=0.1.0,<0.2.0)"]
+testing = ["coverage", "pytest (>=3.6,<4)", "pytest-cov", "pytest-regressions"]
 
 [[package]]
 name = "mdurl"
@@ -523,6 +571,23 @@ category = "dev"
 optional = false
 python-versions = ">=3.6"
 
+[[package]]
+name = "mkdocs-mermaid2-plugin"
+version = "0.6.0"
+description = "A MkDocs plugin for including mermaid graphs in markdown sources"
+category = "dev"
+optional = false
+python-versions = ">=3.5"
+
+[package.dependencies]
+beautifulsoup4 = ">=4.6.3"
+jsbeautifier = "*"
+mkdocs = ">=1.0.4"
+mkdocs-material = "*"
+pymdown-extensions = ">=8.0"
+pyyaml = "*"
+requests = "*"
+
 [[package]]
 name = "myst-parser"
 version = "0.18.0"
@@ -576,6 +641,30 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "platformdirs"
+version = "2.5.2"
+description = "A small Python module for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[package.extras]
+docs = ["furo (>=2021.7.5b38)", "proselint (>=0.10.2)", "sphinx-autodoc-typehints (>=1.12)", "sphinx (>=4)"]
+test = ["appdirs (==1.4.4)", "pytest-cov (>=2.7)", "pytest-mock (>=3.6)", "pytest (>=6)"]
+
+[[package]]
+name = "pluggy"
+version = "1.0.0"
+description = "plugin and hook calling mechanisms for python"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.extras]
+dev = ["pre-commit", "tox"]
+testing = ["pytest", "pytest-benchmark"]
+
 [[package]]
 name = "ply"
 version = "3.11"
@@ -595,6 +684,26 @@ python-versions = ">=3.7,<4.0"
 [package.dependencies]
 requests = ">=2.28.1,<3.0.0"
 
+[[package]]
+name = "prefixmaps"
+version = "0.1.3"
+description = ""
+category = "dev"
+optional = false
+python-versions = ">=3.7.6,<4.0.0"
+
+[package.dependencies]
+importlib-metadata = ">=4.12.0,<5.0.0"
+PyYAML = ">=6.0,<7.0"
+
+[[package]]
+name = "py"
+version = "1.11.0"
+description = "library with cross-python path, ini-parsing, io, code, log facilities"
+category = "dev"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+
 [[package]]
 name = "pydantic"
 version = "1.10.2"
@@ -847,6 +956,14 @@ category = "dev"
 optional = false
 python-versions = "*"
 
+[[package]]
+name = "soupsieve"
+version = "2.3.2.post1"
+description = "A modern CSS selector implementation for Beautiful Soup."
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
 [[package]]
 name = "sparqlslurper"
 version = "0.5.1"
@@ -872,10 +989,10 @@ python-versions = ">=3.7"
 rdflib = ">=6.1.1"
 
 [package.extras]
-pandas = ["pandas (>=1.3.5)"]
+dev = ["setuptools (>=3.7.1)", "mypy (>=0.931)", "pandas (>=1.3.5)", "pandas-stubs (>=1.2.0.48)"]
+docs = ["sphinx (<5)", "sphinx-rtd-theme"]
 keepalive = ["keepalive (>=0.5)"]
-docs = ["sphinx-rtd-theme", "sphinx (<5)"]
-dev = ["pandas-stubs (>=1.2.0.48)", "pandas (>=1.3.5)", "mypy (>=0.931)", "setuptools (>=3.7.1)"]
+pandas = ["pandas (>=1.3.5)"]
 
 [[package]]
 name = "sphinx"
@@ -931,8 +1048,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-devhelp"
@@ -943,8 +1060,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-htmlhelp"
@@ -955,8 +1072,8 @@ optional = false
 python-versions = ">=3.6"
 
 [package.extras]
-test = ["html5lib", "pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
+lint = ["flake8", "mypy", "docutils-stubs"]
+test = ["pytest", "html5lib"]
 
 [[package]]
 name = "sphinxcontrib-jsmath"
@@ -967,7 +1084,7 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
-test = ["mypy", "flake8", "pytest"]
+test = ["pytest", "flake8", "mypy"]
 
 [[package]]
 name = "sphinxcontrib-qthelp"
@@ -978,8 +1095,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sphinxcontrib-serializinghtml"
@@ -990,8 +1107,8 @@ optional = false
 python-versions = ">=3.5"
 
 [package.extras]
+lint = ["flake8", "mypy", "docutils-stubs"]
 test = ["pytest"]
-lint = ["docutils-stubs", "mypy", "flake8"]
 
 [[package]]
 name = "sqlalchemy"
@@ -1025,6 +1142,36 @@ postgresql_psycopg2cffi = ["psycopg2cffi"]
 pymysql = ["pymysql (<1)", "pymysql"]
 sqlcipher = ["sqlcipher3-binary"]
 
+[[package]]
+name = "tomli"
+version = "2.0.1"
+description = "A lil' TOML parser"
+category = "dev"
+optional = false
+python-versions = ">=3.7"
+
+[[package]]
+name = "tox"
+version = "3.26.0"
+description = "tox is a generic virtualenv management and test command line tool"
+category = "dev"
+optional = false
+python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7"
+
+[package.dependencies]
+colorama = {version = ">=0.4.1", markers = "platform_system == \"Windows\""}
+filelock = ">=3.0.0"
+packaging = ">=14"
+pluggy = ">=0.12.0"
+py = ">=1.4.17"
+six = ">=1.14.0"
+tomli = {version = ">=2.0.1", markers = "python_version >= \"3.7\" and python_version < \"3.11\""}
+virtualenv = ">=16.0.0,<20.0.0 || >20.0.0,<20.0.1 || >20.0.1,<20.0.2 || >20.0.2,<20.0.3 || >20.0.3,<20.0.4 || >20.0.4,<20.0.5 || >20.0.5,<20.0.6 || >20.0.6,<20.0.7 || >20.0.7"
+
+[package.extras]
+docs = ["pygments-github-lexers (>=0.0.5)", "sphinx (>=2.0.0)", "sphinxcontrib-autoprogram (>=0.1.5)", "towncrier (>=18.5.0)"]
+testing = ["flaky (>=3.4.0)", "freezegun (>=0.3.11)", "pytest (>=4.0.0)", "pytest-cov (>=2.5.1)", "pytest-mock (>=1.10.0)", "pytest-randomly (>=1.0.0)", "psutil (>=5.6.1)", "pathlib2 (>=2.3.3)"]
+
 [[package]]
 name = "typing-extensions"
 version = "4.3.0"
@@ -1046,6 +1193,23 @@ brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"]
 secure = ["pyOpenSSL (>=0.14)", "cryptography (>=1.3.4)", "idna (>=2.0.0)", "certifi", "urllib3-secure-extra", "ipaddress"]
 socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"]
 
+[[package]]
+name = "virtualenv"
+version = "20.16.5"
+description = "Virtual Python Environment builder"
+category = "dev"
+optional = false
+python-versions = ">=3.6"
+
+[package.dependencies]
+distlib = ">=0.3.5,<1"
+filelock = ">=3.4.1,<4"
+platformdirs = ">=2.4,<3"
+
+[package.extras]
+docs = ["proselint (>=0.13)", "sphinx (>=5.1.1)", "sphinx-argparse (>=0.3.1)", "sphinx-rtd-theme (>=1)", "towncrier (>=21.9)"]
+testing = ["coverage (>=6.2)", "coverage-enable-subprocess (>=1)", "flaky (>=3.7)", "packaging (>=21.3)", "pytest (>=7.0.1)", "pytest-env (>=0.6.2)", "pytest-freezegun (>=0.4.2)", "pytest-mock (>=3.6.1)", "pytest-randomly (>=3.10.3)", "pytest-timeout (>=2.1)"]
+
 [[package]]
 name = "watchdog"
 version = "2.1.9"
@@ -1080,14 +1244,14 @@ testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-
 [metadata]
 lock-version = "1.1"
 python-versions = "^3.9"
-content-hash = "7f584394ee7adf13fdd9776e9aaab9444226a95a82dc881308b0e7826636078b"
+content-hash = "d0cc2575e51653d8bf0f9a64d32c3b34241abc08b0ab2346bbab064e1d682c3c"
 
 [metadata.files]
 alabaster = []
 antlr4-python3-runtime = []
-argparse = []
 attrs = []
 babel = []
+beautifulsoup4 = []
 certifi = []
 cfgraph = []
 chardet = []
@@ -1096,8 +1260,11 @@ click = []
 colorama = []
 decorator = []
 deprecated = []
+distlib = []
 docutils = []
+editorconfig = []
 et-xmlfile = []
+filelock = []
 ghp-import = []
 graphviz = []
 greenlet = []
@@ -1107,6 +1274,7 @@ imagesize = []
 importlib-metadata = []
 isodate = []
 jinja2 = []
+jsbeautifier = []
 json-flattener = []
 jsonasobj = []
 jsonasobj2 = []
@@ -1126,12 +1294,17 @@ mergedeep = []
 mkdocs = []
 mkdocs-material = []
 mkdocs-material-extensions = []
+mkdocs-mermaid2-plugin = []
 myst-parser = []
 openpyxl = []
 packaging = []
 parse = []
+platformdirs = []
+pluggy = []
 ply = []
 prefixcommons = []
+prefixmaps = []
+py = []
 pydantic = []
 pygments = []
 pyjsg = []
@@ -1153,6 +1326,7 @@ requests = []
 shexjsg = []
 six = []
 snowballstemmer = []
+soupsieve = []
 sparqlslurper = []
 sparqlwrapper = []
 sphinx = []
@@ -1164,8 +1338,11 @@ sphinxcontrib-jsmath = []
 sphinxcontrib-qthelp = []
 sphinxcontrib-serializinghtml = []
 sqlalchemy = []
+tomli = []
+tox = []
 typing-extensions = []
 urllib3 = []
+virtualenv = []
 watchdog = []
 wrapt = []
 zipp = []
diff --git a/{{cookiecutter.project_name}}/pyproject.toml b/{{cookiecutter.project_name}}/pyproject.toml
index 8212e41..6f8b68b 100644
--- a/{{cookiecutter.project_name}}/pyproject.toml
+++ b/{{cookiecutter.project_name}}/pyproject.toml
@@ -11,8 +11,9 @@ python = "^3.9"
 linkml-runtime = "^1.1.24"
 
 [tool.poetry.dev-dependencies]
-linkml = "^1.2.6"
+linkml = "^1.3.3"
 mkdocs-material = "^8.2.8"
+mkdocs-mermaid2-plugin = "^0.6.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
diff --git a/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml b/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
index 5bd32e7..c30b56a 100644
--- a/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
+++ b/{{cookiecutter.project_name}}/src/{{cookiecutter.__project_slug}}/schema/{{cookiecutter.__project_slug}}.yaml
@@ -1,4 +1,4 @@
-id: https://w3id.org/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}
+id: https://w3id.org/{{cookiecutter.github_org}}/{{cookiecutter.project_name}}
 name: {{cookiecutter.project_name}}
 title: {{cookiecutter.project_name}}
 description: |-
@@ -7,7 +7,7 @@ imports:
   - linkml:types
   
 prefixes:
-  {{cookiecutter.__project_slug}}: https://w3id.org/{{cookiecutter.my_org}}/{{cookiecutter.project_name}}/
+  {{cookiecutter.__project_slug}}: https://w3id.org/{{cookiecutter.github_org}}/{{cookiecutter.project_name}}/
   linkml: https://w3id.org/linkml/
   biolink: https://w3id.org/biolink/
   schema: http://schema.org/

From 4589d18a3c29d3cde5fd8da6fb87d972606ff068 Mon Sep 17 00:00:00 2001
From: cmungall <cjm@berkeleybop.org>
Date: Fri, 9 Sep 2022 16:36:22 -0700
Subject: [PATCH 3/3] regen

---
 {{cookiecutter.project_name}}/.gitignore       |  2 +-
 {{cookiecutter.project_name}}/Makefile         |  4 ++++
 {{cookiecutter.project_name}}/README.md        | 18 +++++++++++++++++-
 .../src/docs/about.md                          |  5 +++++
 4 files changed, 27 insertions(+), 2 deletions(-)
 create mode 100644 {{cookiecutter.project_name}}/src/docs/about.md

diff --git a/{{cookiecutter.project_name}}/.gitignore b/{{cookiecutter.project_name}}/.gitignore
index 07bcc77..439c571 100644
--- a/{{cookiecutter.project_name}}/.gitignore
+++ b/{{cookiecutter.project_name}}/.gitignore
@@ -1,4 +1,4 @@
-docs/
+./docs/
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/{{cookiecutter.project_name}}/Makefile b/{{cookiecutter.project_name}}/Makefile
index 42f5a74..89f3c4e 100644
--- a/{{cookiecutter.project_name}}/Makefile
+++ b/{{cookiecutter.project_name}}/Makefile
@@ -24,6 +24,7 @@ help: status
 	@echo "make install -- install dependencies"
 	@echo "make setup -- initial setup"
 	@echo "make test -- runs tests"
+	@echo "make lint -- perfom linting"
 	@echo "make testdoc -- builds docs and runs local test server"
 	@echo "make deploy -- deploys site"
 	@echo "make update -- updates linkml version"
@@ -51,6 +52,9 @@ gen-project: $(PYMODEL)
 test:
 	$(RUN) gen-project -d tmp $(SOURCE_SCHEMA_PATH) 
 
+lint:
+	$(RUN) linkml-lint $(SOURCE_SCHEMA_PATH) 
+
 check-config:
 	@(grep my-datamodel about.yaml > /dev/null && printf "\n**Project not configured**:\n\n  - Remember to edit 'about.yaml'\n\n" || exit 0)
 
diff --git a/{{cookiecutter.project_name}}/README.md b/{{cookiecutter.project_name}}/README.md
index 7a3e149..ef0b538 100644
--- a/{{cookiecutter.project_name}}/README.md
+++ b/{{cookiecutter.project_name}}/README.md
@@ -1,5 +1,21 @@
-# {{cookiecutter.__project_slug}}
+# {{cookiecutter.project_name}}
 
 {{cookiecutter.project_description}}
 
+## Website
 
+* [https://{{cookiecutter.github_org}}.github.io/{{cookiecutter.project_name}}](https://{{cookiecutter.github_org}}.github.io/{{cookiecutter.project_name}})
+
+## Developer Documentation
+
+<details>
+Use the `make` command to generate project artefacts:
+
+- `make all`: make everything
+- `make deploy`: deploys site
+
+</details>
+
+## Credits
+
+this project was made with [linkml-project-cookiecutter](https://github.com/linkml/linkml-project-cookiecutter)
diff --git a/{{cookiecutter.project_name}}/src/docs/about.md b/{{cookiecutter.project_name}}/src/docs/about.md
new file mode 100644
index 0000000..3e3e986
--- /dev/null
+++ b/{{cookiecutter.project_name}}/src/docs/about.md
@@ -0,0 +1,5 @@
+# {{cookiecutter.project_name}}
+
+{{cookiecutter.project_description}}
+
+