Include empty resources in summary stats (#61)

* template update

* include empty resource classes in statistics

* remove auto readme because of custom content

* version bump

* adapt template changes

* more template-related updates

* fix

* roll requirements back to main

* fix typo

* adapt Dockerfile

.devcontainer/dev_install

@@ -7,7 +7,7 @@ cd /workspace
 python -m pip install --upgrade pip
 
 # install or upgrade dependencies for development and testing
-pip install --no-deps -r requirements-dev.txt
+pip install --no-deps -r ./lock/requirements-dev.txt
 
 # install the package itself in edit mode:
 pip install --no-deps -e .

.github/workflows/check_config_docs.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check config docs
         run: |

.github/workflows/check_pyproject.yaml

@@ -0,0 +1,16 @@
+name: Check if the config schema and the example are up to date.
+
+on: push
+
+jobs:
+  static-code-analysis:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - id: common
+        uses: ghga-de/gh-action-common@v4
+
+      - name: Check pyproject.toml
+        run: |
+          ./scripts/update_pyproject.py --check

.github/workflows/check_readme.yaml

@@ -9,7 +9,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - name: Check readme
         run: |

.github/workflows/static_code_analysis.yaml

@@ -10,7 +10,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - uses: pre-commit/action@v3.0.0
         env:

.github/workflows/tests.yaml

@@ -11,7 +11,7 @@ jobs:
       - uses: actions/checkout@v3
 
       - id: common
-        uses: ghga-de/gh-action-common@v3
+        uses: ghga-de/gh-action-common@v4
 
       - id: pytest
         run: |

.pre-commit-config.yaml

@@ -47,18 +47,12 @@ repos:
         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/astral-sh/ruff-pre-commit
     rev: v0.1.7
     hooks:
       - id: ruff
         args: [--fix, --exit-non-zero-on-fix]
-  - repo: https://github.com/psf/black
-    rev: 23.9.1
-    hooks:
-      - id: black
+      - id: ruff-format
   - repo: https://github.com/pre-commit/mirrors-mypy
     rev: v1.7.1
     hooks:

.pyproject_generation/README.md

@@ -0,0 +1,29 @@
+<!--
+ 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.
+
+-->
+
+# Generating the pyproject.toml
+
+The pyproject.toml of the service is generated by combining static configuration
+captured in [`./pyproject_template.toml`](./pyproject_template.toml) and custom
+package metadata specified in [`./pyproject_custom.toml`](./pyproject_custom.toml).
+
+The `./pyproject_template.toml` is managed by the template, please do not edit manually.
+
+You may specify properties in the `./pyproject_custom.toml` which are already specified
+in the `./pyproject_template.toml`. In that case, the `./pyproject_custom.toml` takes
+priority.

.pyproject_generation/pyproject_custom.toml

@@ -0,0 +1,19 @@
+[project]
+name = "metldata"
+version = "1.2.0"
+description = "metldata - A framework for handling metadata based on ETL, CQRS, and event sourcing."
+dependencies = [
+    "hexkit[akafka,mongodb]~=1.0.0",
+    "ghga-service-commons[api,auth]~=1.1.0",
+    "ghga-event-schemas~=1.0.0",
+    "typer~=0.9.0",
+    "linkml==1.6.1",
+    "linkml-runtime==1.6.0",
+    "linkml-validator==0.4.5",
+]
+
+[project.urls]
+Repository = "https://github.com/ghga-de/metldata"
+
+[project.scripts]
+metldata = "metldata.__main__:run"

.pyproject_generation/pyproject_template.toml

@@ -0,0 +1,107 @@
+[build-system]
+requires = ["setuptools>=67.7.2"]
+build-backend = "setuptools.build_meta"
+
+[project]
+readme = "README.md"
+authors = [
+    { name = "German Human Genome Phenome Archive (GHGA)", email = "contact@ghga.de" },
+]
+requires-python = ">=3.9"
+license = { text = "Apache 2.0" }
+classifiers = [
+    "Development Status :: 1 - Planning",
+    "Operating System :: POSIX :: Linux",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "License :: OSI Approved :: Apache Software License",
+    "Topic :: Internet :: WWW/HTTP :: HTTP Servers",
+    "Topic :: Software Development :: Libraries",
+    "Intended Audience :: Developers",
+]
+
+[tool.setuptools.packages.find]
+where = ["src"]
+
+[tool.ruff]
+exclude = [
+    ".git",
+    ".devcontainer",
+    "__pycache__",
+    "build",
+    "dist",
+]
+ignore = [
+    "E", # pycodestyle errors
+    "W", # pycodestyle warnings - pycodestyle covered by black
+    "PLW", # pylint warnings
+    "RUF001", # ambiguous unicode character strings
+    "RUF010", # explicit conversion to string or repr: !s or !r
+    "RUF012", # mutable class variables need typing.ClassVar annotation
+    "N818", # Errors need to have Error suffix
+    "B008", # function call in arg defaults,
+    "PLR2004", # magic numbers should be constants
+    "D205", # blank-line-after-summary
+    "D400", # first doc line ends in period
+    "D401", # non-imperative-mood
+    "D107", # missing docstring in __init__
+    "D206", # indent-with-spaces (ignored for formatter)
+    "D300", # triple-single-quotes (ignored for formatter)
+]
+line-length = 88
+select = [
+    "C90", # McCabe Complexity
+    "F", # pyflakes codes
+    "I", # isort
+    "S", # flake8-bandit
+    "B", # flake8-bugbear
+    "N", # pep8-naming
+    "UP", # pyupgrade
+    "PL", # pylint
+    "RUF", # ruff
+    "SIM", # flake8-simplify
+    "D", # pydocstyle
+]
+fixable = [
+    "UP", # e.g. List -> list
+    "I", # sort imports
+    "D", # pydocstyle
+]
+src = ["src", "tests", "examples", "scripts"]
+target-version = "py39"
+
+[tool.ruff.mccabe]
+max-complexity = 10
+
+[tool.ruff.per-file-ignores]
+"scripts/*" = ["PL", "S", "SIM", "D"]
+"tests/*" = ["S", "SIM", "PLR", "B011"]
+".devcontainer/*" = ["S", "SIM", "D"]
+"examples/*" = ["S", "D"]
+"__init__.py" = ["D"]
+
+[tool.ruff.pydocstyle]
+convention = "pep257"
+
+[tool.mypy]
+disable_error_code = "import"
+show_error_codes = true
+exclude = [
+    'build/lib/',
+]
+warn_redundant_casts = true
+warn_unused_ignores = true
+check_untyped_defs = true
+no_site_packages = false
+
+[tool.pytest.ini_options]
+minversion = "7.1"
+asyncio_mode = "strict"
+
+[tool.coverage.paths]
+source = [
+  "src",
+  "/workspace/src",
+  "**/lib/python*/site-packages",
+]

readme_generation.md → .readme_generation/README.md

@@ -18,30 +18,30 @@
 
 # Readme Generation
 
-The README file is generated by collecting information from different sources as
+The Repository README is generated by collecting information from different sources as
 outlined in the following.
 
 - name: The full name of the package is derived from the remote origin Git repository.
 - title: A title case representation of the name.
 - shortname: An abbreviation of the full name. This is derived from the name mentioned
-  in the [`./pyproject.toml`](./pyproject.toml).
+  in the [`../pyproject.toml`](../pyproject.toml).
 - summary: A short 1-2 sentence summary derived from the description in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - version: The package version derived from the version specified in the
-  [`./pyproject.toml`](./pyproject.toml).
+  [`../pyproject.toml`](../pyproject.toml).
 - description: A markdown-formatted description of the features and use cases of this
-  service or package. Obtained from the [`./.description.md`](./.description.md).
+  service or package. Obtained from the [`./description.md`](./description.md).
 - design_description: A markdown-formatted description of the overall architecture and
-  design of the package. Obtained from the [`./.design.md`](./.design.md).
+  design of the package. Obtained from the [`./design.md`](./design.md).
 - config_description: A markdown-formatted description of all config parameters.
-  This is autogenerated from the [`./config_schema.json`](./config_schema.json).
+  This is autogenerated from the [`../config_schema.json`](../config_schema.json).
 - openapi_doc: A markdown-formatted description of the HTTP API. This is autogenerated
-  and links to the [`./openapi.yaml`](./openapi.yaml). If the openapi.yaml is not
+  and links to the [`../openapi.yaml`](../openapi.yaml). If the openapi.yaml is not
   this documentation is empty.
 
-The [`./.readme_template.md`](./.readme_template.md) serves as a template where the
+The [`./readme_template.md`](./readme_template.md) serves as a template where the
 above variable can be filled in using Pythons `string.Template` utility from the
 standard library.
 
-The [`./scripts/update_readme.py`] script can be used to collect all information and
-fill it into the template to generate the README file.
+The [`../scripts/update_readme.py`](../scripts/update_readme.py) script can be used to
+collect all information and fill it into the template to generate the README file.

.description.md → .readme_generation/description.md

@@ -1,44 +1,40 @@
-<!-- Please provide a short overview of the features of this service.-->
-
-### Scope and Features:
-
 Metldata is a framework for handling the entire lifetime of metadata by addressing the
 a complex combination of challenges that makes it suitable especially for public
 archives for sensitive data:
 
 ![Schematic reprensentation of challenges.](./images/challenges.png)
 **Figure 1| Overview of the combination of challenges during metadata handling.**
 
-#### Immutability
+### Immutability
 It is guaranteed that data entries do not change over time making reproducibility
 possible without having to rely on local snapshots.
 
-#### Accessibility
+### Accessibility
 A stable accession is assigned to each resource. Together with the immutability
 property, this guarantees that you will always get the same data when querying with the
 same accession.
 
-#### Corrections, Improvements, Extensions
+### Corrections, Improvements, Extensions
 
 Even though data is stored in an immutable way, the metldata still allows for
 corrections, improvements, and extensions of submitted data. This is achieved my not
 just storing the current state of a submission but by persisting a version history.
 Thereby, modifications are realized by issuing a new version of the submission without
 affecting the content of existing versions.
 
-#### Transparency
+### Transparency
 
 The version history not only resolved the conflict between immutability and the need to
 evolve and adapt data, it also make the changes transparent to user relying on the data.
 
-#### Multiple Representations
+### Multiple Representations
 
 Often, the requirements regarding the structure and content of data differs depending
 the use case and the audience. Metldata accounts for this by proving a configurable
 workflow engine for transforming submitted metadata into multiple representation of that
 data.
 
-#### GDPR Compliance
+### GDPR Compliance
 
 The GDPR gives data subjects the right to issue a request to delete data. Metldata
 complies with this demand. Thereby, only entire versions of a submission can be deleted.

.design.md → .readme_generation/design.md

@@ -1,7 +1,3 @@
-<!-- Please provide an overview of the architecture and design of the code base.
-Mention anything that deviates from the standard triple hexagonal architecture and
-the corresponding structure. -->
-
 The framework uses a combination of ETL, CQRS, and event sourcing. Currently it is
 designed to mostly run as a CLI application for managing metadata on the local file
 system. However, later, it will be translated into a microservice based-architecture.

.readme_template.md → .readme_generation/readme_template.md

@@ -1,6 +1,5 @@
-
-[![tests](https://github.com/ghga-de/$name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$name/actions/workflows/tests.yaml)
-[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$name?branch=main)
+[![tests](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml/badge.svg)](https://github.com/ghga-de/$repo_name/actions/workflows/tests.yaml)
+[![Coverage Status](https://coveralls.io/repos/github/ghga-de/$repo_name/badge.svg?branch=main)](https://coveralls.io/github/ghga-de/$repo_name?branch=main)
 
 # $title