initial-commit

.gitignore

@@ -0,0 +1,135 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+.idea
+.openai_cache.db
+
+# specific
+tests/output/eval-*

Makefile

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+RUN = poetry run
+PACKAGE = ontogpt
+TEMPLATE_DIR = src/$(PACKAGE)/templates
+EVAL_DIR = src/$(PACKAGE)/evaluation
+TEMPLATES = core gocam mendelian_disease biological_process treatment environmental_sample metagenome_study reaction recipe ontology_class metabolic_process drug ctd halo
+ENTRY_CLASSES = recipe.Recipe gocam.GoCamAnnotations reaction.ReactionDocument ctd.ChemicalToDiseaseDocument
+
+all: all_pydantic all_projects
+
+all_pydantic: $(patsubst %, $(TEMPLATE_DIR)/%.py, $(TEMPLATES))
+all_projects: $(patsubst %, projects/%, $(TEMPLATES))
+all_docs: $(patsubst %, docs/%/index.md, $(TEMPLATES))
+
+test:
+	$(RUN) pytest
+
+$(TEMPLATE_DIR)/%.py: src/$(PACKAGE)/templates/%.yaml
+	$(RUN) gen-pydantic $< > $@.tmp && mv $@.tmp $@
+
+%.py: %.yaml
+	$(RUN) gen-pydantic $< > $@
+
+all_images: $(patsubst %, docs/images/%.png, $(ENTRY_CLASSES))
+docs/images/%.png:
+	$(RUN) erdantic ontogpt.templates.$* -o $@
+
+projects/%: src/$(PACKAGE)/templates/%.yaml
+	$(RUN) gen-project $< -d $@ && cp -pr $@/docs docs/$*
+
+docs/index.md: README.md
+	cp $< $@
+
+docs/%/index.md: src/$(PACKAGE)/templates/%.yaml
+	$(RUN) gen-doc $< -d docs/$*
+
+
+serve:
+	$(RUN) mkdocs serve