Generating documentation form the metadata schema (#6)

* docs from schema

* tables with summary feature

* faq page 404 links fixed

* template update

* disabled template check

---------

Co-authored-by: Karoline Mauer <karoline.mauer@dzne.de>

.deprecated_files

@@ -0,0 +1,16 @@
+# List of all deprecated files and directories that
+# should not exist any more in this repo.
+# This list is similar to the `./mandatory_files`,
+# however, the entries here will be removed if they
+# still exist.
+
+.devcontainer/library-scripts/docker-in-docker-debian.sh
+.devcontainer/library-scripts
+
+.github/workflows/check_mandatory_and_static_files.yaml
+.github/workflows/dev_cd.yaml
+
+scripts/check_mandatory_and_static_files.py
+scripts/update_static_files.py
+
+docs

.deprecated_files_ignore

@@ -0,0 +1,4 @@
+# Optional list of files which are actually deprecated in the template
+# but are still allowed to be used in the current repository
+
+docs

.devcontainer/.dev_config.yaml

@@ -0,0 +1,3 @@
+# Please only mention the non-default settings here:
+
+language: Greek

.devcontainer/Dockerfile

@@ -0,0 +1,19 @@
+FROM mcr.microsoft.com/devcontainers/python:1-3.12-bookworm
+
+ENV PYTHONUNBUFFERED 1
+
+# Update args in docker-compose.yaml to set the UID/GID of the "vscode" user.
+ARG USER_UID=1000
+ARG USER_GID=$USER_UID
+RUN if [ "$USER_GID" != "1000" ] || [ "$USER_UID" != "1000" ]; then groupmod --gid $USER_GID vscode && usermod --uid $USER_UID --gid $USER_GID vscode; fi
+
+# [Option] Install Node.js
+ARG INSTALL_NODE="false"
+ARG NODE_VERSION="lts/*"
+RUN if [ "${INSTALL_NODE}" = "true" ]; then su vscode -c "umask 0002 && . /usr/local/share/nvm/nvm.sh && nvm install ${NODE_VERSION} 2>&1"; fi
+
+# Copy install and launcher script to bin:
+COPY ./dev_install /bin
+COPY ./dev_launcher /bin
+
+CMD ["sleep", "infinity"]

.devcontainer/dev_install

@@ -0,0 +1,11 @@
+#!/bin/bash
+# install service in dev container
+
+cd /workspace
+
+# Install requirements
+pip install --upgrade -r requirements.txt
+
+# install pre-commit hooks to git
+pip install --upgrade pre-commit
+pre-commit install

.devcontainer/dev_launcher

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+# adapt to package name
+cd /workspace
+mkdocs serve

.devcontainer/docker-compose.yml

@@ -0,0 +1,28 @@
+version: '3'
+
+services:
+  app:
+    build:
+      context: .
+      dockerfile: ./Dockerfile
+      args:
+        # [Choice] Python version: 3, 3.8, 3.7, 3.6
+        VARIANT: 3.9
+        # [Choice] Install Node.js
+        INSTALL_NODE: "true"
+        NODE_VERSION: "lts/*"
+        # On Linux, you may need to update USER_UID and USER_GID below if not your local UID is not 1000.
+        USER_UID: 1000
+        USER_GID: 1000
+
+    init: true
+    privileged: true
+
+    volumes:
+      - ..:/workspace:cached
+
+    # Overrides default command so things don't shut down after the process ends.
+    command: sleep infinity
+
+    # Uncomment the next line to use a non-root user for all processes.
+    user: vscode

.devcontainer/license_header.txt

@@ -0,0 +1,14 @@
+Copyright 2021 - 2024 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+for the German Human Genome-Phenome Archive (GHGA)
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+    http://www.apache.org/licenses/LICENSE-2.0
+
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.

.editorconfig

@@ -0,0 +1,14 @@
+# Top-most EditorConfig file.
+root = true
+
+# For all files ...
+[*]
+
+# Unix-style LF newlines.
+end_of_line = lf
+
+# Force a newline at the end of the file.
+insert_final_newline = true
+
+# Use UTF-8.
+charset = utf-8

.flake8

@@ -0,0 +1,21 @@
+; Copyright 2021 - 2023 Universität Tübingen, DKFZ, EMBL, and Universität zu Köln
+; for the German Human Genome-Phenome Archive (GHGA)
+;
+; Licensed under the Apache License, Version 2.0 (the "License");
+; you may not use this file except in compliance with the License.
+; You may obtain a copy of the License at
+;
+;     http://www.apache.org/licenses/LICENSE-2.0
+;
+; Unless required by applicable law or agreed to in writing, software
+; distributed under the License is distributed on an "AS IS" BASIS,
+; WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+; See the License for the specific language governing permissions and
+; limitations under the License.
+
+[flake8]
+ignore = E, W
+    # ignore all style checks from pycodestyle
+    # as they are already checked by black
+exclude = .git,__pycache__,build,dist
+max-complexity = 10

.gitattributes

@@ -0,0 +1,22 @@
+# CRLF line endings cause problems in Docker, so we force git
+# to check in and out using only LF line endings.
+
+*.cfg					text eol=lf
+*.ini					text eol=lf
+*.json					text eol=lf
+*.md					text eol=lf
+*.py					text eol=lf
+*.txt					text eol=lf
+*.yaml					text eol=lf
+*.yml					text eol=lf
+
+.editorconfig			text eol=lf
+.flake8					text eol=lf
+.pylintrc				text eol=lf
+
+.git*					text eol=lf
+*_files					text eol=lf
+*_files_ignore			text eol=lf
+
+**/dev_*				text eol=lf
+**/Dockerfile			text eol=lf

.gitignore

@@ -50,6 +50,7 @@ coverage.xml
 *.py,cover
 .hypothesis/
 .pytest_cache/
+.ruff_cache/
 prof/
 
 # Translations
@@ -132,6 +133,12 @@ dmypy.json
 # ignore VS Code settings:
 .vscode/
 
+# key stores
+*.key
+*.rnd
+.keystore
+.ssl/
+
 # desktop settings and thumbnails
 .DS_Store
 desktop.ini

.mandatory_files

@@ -0,0 +1,28 @@
+# List of all mandatory files and directories that
+# have to exist in this repo.
+# This list is similar to the `./static_files`,
+# however, the entries here are just checked for
+# existence, their content is not evaluated and
+# may differ from that of the template repository.
+
+.devcontainer/dev_launcher
+.devcontainer/devcontainer.json
+.devcontainer/docker-compose.yml
+.devcontainer/Dockerfile
+
+tests/__init__.py
+tests/fixtures/__init__.py
+
+scripts/script_utils/fastapi_app_location.py
+
+Dockerfile
+config_schema.json
+example_config.yaml
+LICENSE
+README.md
+setup.py
+setup.cfg
+requirements-dev.txt
+
+.description.md
+.design.md

.mandatory_files_ignore

@@ -0,0 +1,19 @@
+# Optional list of files which are actually mandatory in the template
+# but are allowed to be removed in the current repository
+
+
+docs/README.md
+example_data
+tests/__init__.py
+tests/fixtures/__init__.py
+scripts/script_utils/fastapi_app_location.py
+Dockerfile
+config_schema.json
+example_config.yaml
+README.md
+setup.py
+setup.cfg
+requirements-dev.txt
+
+.description.md
+.design.md

.mypy.ini

@@ -0,0 +1,12 @@
+# Global options:
+
+[mypy]
+disable_error_code = import
+show_error_codes = True
+exclude = (?x)(
+    build/lib/
+  )
+warn_redundant_casts = True
+warn_unused_ignores = True
+check_untyped_defs = True
+no_site_packages = False

.pre-commit-config.yaml

@@ -0,0 +1,67 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+
+default_language_version:
+  python: python3.9
+
+minimum_pre_commit_version: 3.0.0
+
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+        exclude: '.*\.json|example_config.yaml'
+      - id: check-added-large-files
+      - id: check-ast
+      - id: check-json
+        exclude: devcontainer.json
+      - id: pretty-format-json
+        args: [--autofix]
+        exclude: devcontainer.json|config_schema.json
+      - id: check-merge-conflict
+      - id: check-symlinks
+      - id: check-executables-have-shebangs
+      - id: check-shebang-scripts-are-executable
+      - id: check-docstring-first
+      - id: debug-statements
+      - id: destroyed-symlinks
+      - id: detect-private-key
+      - id: mixed-line-ending
+        args: [--fix=lf]
+      - id: no-commit-to-branch
+        args: [--branch, dev, --branch, int, --branch, main]
+      - id: debug-statements
+      - id: debug-statements
+      - id: debug-statements
+  - repo: https://github.com/psf/black
+    rev: 23.1.0
+    hooks:
+      - id: black
+  - repo: https://github.com/pycqa/isort
+    rev: 5.12.0
+    hooks:
+      - id: isort
+        args: [--profile, black]
+  - repo: https://github.com/pre-commit/mirrors-mypy
+    rev: v1.0.0
+    hooks:
+      - id: mypy
+        args: [--no-warn-unused-ignores]
+  - repo: https://github.com/PyCQA/pylint
+    rev: v2.16.4
+    hooks:
+      - id: pylint
+        args: [--disable=E0401]
+        exclude: tests|.devcontainer
+  - repo: https://github.com/PyCQA/flake8
+    rev: 6.0.0
+    hooks:
+      - id: flake8
+        args: [--config, .flake8]
+  - repo: https://github.com/PyCQA/bandit
+    rev: 1.7.4
+    hooks:
+      - id: bandit
+        exclude: tests|.devcontainer|scripts