fix docs

.cruft.json

@@ -1,6 +1,6 @@
 {
   "template": "https://github.com/elixir-cloud-aai/cookiecutter-python",
-  "commit": "82a9aebbdff819758c94e7607c052a3fa5ba3b18",
+  "commit": "c9d14eea5af812f12c3e19e1bbdc8affe8759eda",
   "checkout": null,
   "context": {
     "cookiecutter": {

.github/workflows/docs.yaml

@@ -27,15 +27,16 @@ jobs:
 
       - name: Generate API docs
         run: |
-          poetry run sphinx-apidoc -o /tmp/docs tus_storagehandler/
+          poetry run sphinx-apidoc -o /tmp/docs/source/pages tus_storagehandler/
 
       - name: Compare docs with main branch
         id: check_docs_diff
         run: |
-          shasum /tmp/docs/* > /tmp/docs.sha
-          rm -f docs/pages/.gitkeep # Remove placeholder file
-          shasum docs/pages/* > docs/project_doc.sha
-          diff=$(diff /tmp/docs.sha docs/project_doc.sha) || true
+          shasum /tmp/docs/source/pages/* > /tmp/docs.sha
+          shasum docs/source/pages/* > docs/project_doc.sha
+          awk '{print $1}' /tmp/docs.sha > /tmp/docs_hashes.sha
+          awk '{print $1}' docs/project_doc.sha > docs/project_doc_hashes.sha
+          diff=$(diff /tmp/docs_hashes.sha docs/project_doc_hashes.sha) || true
           if [[ -n "$diff" ]]; then
             echo "::error::API documentation is out of date."
             exit 1

Makefile

@@ -14,23 +14,26 @@ help:
 	@echo "\nUsage: make [target] ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
 	@echo "Available targets:\n"
 
-	@echo "Environment Management --------------------------------------------------------"
-	@echo "  \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m"
-	@echo "  \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall dependencies and tus_storagehandler.\033[0m"
-	@echo "  \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n"
-
 	@echo "Code Quality ------------------------------------------------------------------"
 	@echo "  \033[1m\033[35mformat-lint\033[0m \033[37m(fl)\033[0m: \033[36mRun linter, formatter, spellcheck.\033[0m"
 	@echo "  \033[1m\033[35mprecommit-check\033[0m \033[37m(pc)\033[0m: \033[36mRun all pre-commit checks.\033[0m"
 	@echo "  \033[1m\033[35msecurity\033[0m \033[37m(s)\033[0m: \033[36mRun security scans.\033[0m"
 	@echo "  \033[1m\033[35mtype-check\033[0m \033[37m(tc)\033[0m: \033[36mPerform type checking.\033[0m\n"
 
-	@echo "Testing -----------------------------------------------------------------------"
-	@echo "  \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n"
-
 	@echo "Documentation -----------------------------------------------------------------"
 	@echo "  \033[1m\033[35mdocs\033[0m \033[37m(d)\033[0m: \033[36mGenerate project documentation.\033[0m\n"
 
+	@echo "Environment Management --------------------------------------------------------"
+	@echo "  \033[1m\033[35mclean-venv\033[0m \033[37m(cv)\033[0m: \033[36mRemove virtual environment.\033[0m"
+	@echo "  \033[1m\033[35minstall\033[0m \033[37m(i)\033[0m: \033[36mInstall dependencies and tus_storagehandler.\033[0m"
+	@echo "  \033[1m\033[35mvenv\033[0m \033[37m(v)\033[0m: \033[36mCreate virtual environment.\033[0m\n"
+
+	@echo "Miscellaneous -----------------------------------------------------------------"
+	@echo "  \033[1m\033[35mupdate\033[0m \033[37m(u)\033[0m: \033[36mUpdate the template.\033[0m\n"
+
+	@echo "Testing -----------------------------------------------------------------------"
+	@echo "  \033[1m\033[35mtest\033[0m \033[37m(t)\033[0m: \033[36mRun all tests.\033[0m\n"
+
 ## Autogenerated Targets ######################################################
 # NOTE: Keep all the targets in alphabetical order for better readability.
 # NOTE: Do not modify the autogenerated targets, unless necessary, write custom
@@ -47,7 +50,7 @@ cv: clean-venv
 .PHONY: docs
 docs:
 	@echo "\nGenerating project documentation ++++++++++++++++++++++++++++++++++++++++++++++\n"
-	@sphinx-apidoc -f -o docs/source/pages tus_storagehandler
+	@poetry run sphinx-apidoc -f -o docs/source/pages tus_storagehandler
 	@cd docs && make html
 	@echo "\nSummary ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
 	@echo "Documentation generated successfully."
@@ -61,15 +64,15 @@ d: docs
 .PHONY: format-lint
 format-lint:
 	@echo "\nRunning linter and formatter using ruff and typos +++++++++++++++++++++++++++++\n"
-	@ruff format && ruff check --fix
+	@poetry run ruff format && poetry run ruff check --fix
 	@typos .
 
 .PHONY: fl
 fl: format-lint
 
 .PHONY: install
 install:
-	@echo "\nInstalling all dependencies and with this package +++++++++++++++++++++++++++++++++\n"
+	@echo "\nInstalling dependencies and with this package +++++++++++++++++++++++++++++++++\n"
 	@poetry install --with=code_quality,docs,misc,test,types,vulnerability
 
 .PHONY: i
@@ -78,36 +81,45 @@ i: install
 .PHONY: precommit-check
 precommit-check:
 	@echo "\nRunning pre-commit checks +++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
-	@pre-commit run --all-files
+	@poetry run pre-commit run --all-files
 
 .PHONY: pc
 pc: precommit-check
 
 .PHONY: security
 security:
 	@echo "\nRunning security scans using bandit and safety ++++++++++++++++++++++++++++++++\n"
-	@safety check --full-report
-	@bandit -c pyproject.toml -r tus_storagehandler
+	@poetry run safety check --full-report
+	@poetry run bandit -c pyproject.toml -r tus_storagehandler
 
 .PHONY: s
 s: security
 
 .PHONY: test
 test:
 	@echo "\nRunning tests using pytest ++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
-	@pytest tests/
+	@poetry run pytest tests/
 
 .PHONY: t
 t: test
 
 .PHONY: type-check
 type-check:
 	@echo "\nPerforming type checking with mypy ++++++++++++++++++++++++++++++++++++++++++++\n"
-	@mypy tus_storagehandler
+	@poetry run mypy tus_storagehandler
 
 .PHONY: tc
 tc: type-check
 
+.PHONY: update
+update:
+	@echo "\nUpdating the template +++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n"
+	@echo "Using latest version from remote: https://github.com/elixir-cloud-aai/cookiecutter-python."
+	@poetry run cruff update -y
+
+.PHONY: u
+u: update
+
 .PHONY: venv
 venv:
 	@echo "\nCreating a virtual environment ++++++++++++++++++++++++++++++++++++++++++++++++\n"

README.md

@@ -72,6 +72,9 @@ make i
 >
 > This ensures that the type checker functions correctly.
 
+> **Note**: Since the dependencies are segregated into groups, if you add a new
+> group make sure to add it in `make install` command in [Makefile](Makefile).
+
 - Running tests
 
 ```sh
@@ -90,6 +93,9 @@ make fl
 make d
 ```
 
+> **Note**: If you make changes to the code, make sure to generate and push the
+> documentation using above command, else the documentation check CI will fail.
+
 - Running type checker
 
 ```sh
@@ -102,6 +108,12 @@ make tc
 make pc
 ```
 
+- Update the cookiecutter template
+
+```sh
+make u
+```
+
 > **Note**: This is not the complete list of commands, run `make` to find out if
 > more have been added.
 

docs/pages/modules.rst → docs/source/pages/modules.rst

@@ -1,5 +1,5 @@
 tus_storagehandler
-===================
+==================
 
 .. toctree::
    :maxdepth: 4

docs/source/pages/tus_storagehandler.rst

@@ -0,0 +1,21 @@
+tus\_storagehandler package
+===========================
+
+Submodules
+----------
+
+tus\_storagehandler.main module
+-------------------------------
+
+.. automodule:: tus_storagehandler.main
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Module contents
+---------------
+
+.. automodule:: tus_storagehandler
+   :members:
+   :undoc-members:
+   :show-inheritance:

pyproject.toml

@@ -72,6 +72,9 @@ optional = true
 bandit = ">=1.7.8,<2.0.0"
 safety = ">=3.2.0,<4.0.0"
 
+[tool.poetry.scripts]
+tus_storagehandler = "tus_storagehandler.main:main"
+
 [tool.ruff]
 indent-width = 4