init; add base version of all files

.editorconfig

@@ -0,0 +1,19 @@
+# EditorConfig is awesome: http://EditorConfig.org
+
+# top-most EditorConfig file
+root = true
+
+[*]
+end_of_line = lf
+insert_final_newline = true
+trim_trailing_whitespace = true
+charset = utf-8
+indent_style = space
+indent_size = 4
+
+[*.{tsv,tab}]
+indent_style = tab
+
+[*.{yml,yaml,json,toml,tml}]
+indent_style = space
+indent_size = 2

.gitignore

@@ -0,0 +1,210 @@
+# ====================
+# gitignore entries
+# for R
+# ====================
+
+# History files
+.Rhistory
+.Rapp.history
+
+# Session Data files
+.RData
+.RDataTmp
+
+# User-specific files
+.Ruserdata
+
+# Example code in package build process
+*-Ex.R
+
+# Output files from R CMD build
+/*.tar.gz
+
+# Output files from R CMD check
+/*.Rcheck/
+
+# RStudio files
+.Rproj.user/
+
+# produced vignettes
+vignettes/*.html
+vignettes/*.pdf
+
+# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3
+.httr-oauth
+
+# knitr and R markdown default cache directories
+*_cache/
+/cache/
+
+# Temporary files created by R markdown
+*.utf8.md
+*.knit.md
+
+# R Environment Variables
+.Renviron
+
+# pkgdown site
+docs/
+
+# translation temp files
+po/*~
+
+# RStudio Connect folder
+rsconnect/
+
+# ====================
+# gitignore entries
+# for PYTHON
+# ====================
+
+# 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/
+
+# ====================
+# gitignore entries
+# CUSTOM
+# ====================
+
+# VS code
+.vscode/
+
+# Ignore container images
+*.sif
+
+# Ignore folder with Conda development environment
+dev_env/
+
+# Ignore Snakemake metadata folder
+.snakemake/
+
+# Ignore default working directory in case it was accidentally created
+# in the Snakemake repo folder
+wd/

LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2022 Core Unit Bioinformatics, Medical Faculty, HHU
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -1,2 +1,32 @@
-# template-metadata-files
-Collection of metadata files (gitignore, pyprojects, editorconfig, license etc.) to harmonize init of new repositories
+# Template Metadata files
+
+This repository is a collection of metadata files that should be used to initialize new repositories
+if appropriate (no strong arguments speak against it).
+
+## Repository-related metadata files
+
+- `LICENSE`: using this file is mandatory for all CUBI repositories
+- `.editorconfig`: using this file is mandatory for all CUBI repositories
+- `.gitignore`: strongly recommended, contains ignore rules for Python, R and some custom entries by default.
+    There must be a good reason not to use (an extended version of) this file.
+
+## CUBI metdata files
+
+By convention, and for convenience, all CUBI metadata are organized in form of a `pyproject.toml` file
+containing a minimal amount of descriptive entries. This file must be located at the top-level of the
+respective repository. The "hierarchy" in these files is as follows:
+
+1. include [Python tool settings](tomls/tool/pyproject.toml) for coherent formatting of Python code
+  - if the repository does not contain any Python code, this may be omitted
+2. include [the CUBI metadata information](pyproject.toml), i.e., the top-level `pyproject.toml` in this repository
+3. include specific metadata...
+  - ...for a [project repository](tomls/cubi/project/pyproject.toml)
+  - ...for a [workflow template repository](tomls/cubi/workflow/template/pyproject.toml)
+  - ...for a [workflow repository](tomls/cubi/workflow/pyproject.toml)
+
+As a reminder, read the development guidelines to learn about key characteristics
+of workflows and projects, and naming conventions:
+
+[CUBI dev process in the knowledge base](https://github.com/core-unit-bioinformatics/knowledge-base/wiki/Dev-process#repository-types)
+
+[CUBI naming conventions in the knowledge base](https://github.com/core-unit-bioinformatics/knowledge-base/wiki/Naming-and-style#naming-repositories)

envs/conda/metadata.yaml

@@ -0,0 +1,11 @@
+name: cubi_metadata
+dependencies:
+  - Python=3.9.*
+  - pip
+  - mamba=0.25.0
+  - pyyaml=6.0
+  - toml=0.10.2
+  - semver=2.13.0
+  - pylint=2.14.5
+  - isort=5.10.1
+  - black=22.6.0

pyproject.toml

@@ -0,0 +1,14 @@
+[cubi.metadata]
+pid = "undefined"
+version = "protoype"
+
+[cubi.metadata.naming.workflow.system]
+smk="snakemake"
+nxf="nextflow"
+cwl="common-workflow-language"
+wdl="workflow-definition-language"
+
+[cubi.metadata.naming.project.type]
+dev="development"
+run="production-run"
+bmk="benchmark"

tomls/cubi/project/pyproject.toml

@@ -0,0 +1,21 @@
+[cubi.project]
+pid = "undefined"
+type = "type"
+name = "undefined"
+start_date = 2000-01-01
+end_data = 2099-12-31
+
+[[cubi.project.workflow]]
+pid = "pid_a"
+name = "a"
+version = "version_a"
+
+[[cubi.project.workflow]]
+pid = "pid_b"
+name = "b"
+version = "version_b"
+
+[[cubi.project.workflow]]
+pid = "pid_c"
+name = "c"
+version = "version_c"

tomls/cubi/workflow/pyproject.toml

@@ -0,0 +1,9 @@
+[cubi.workflow]
+pid = "undefined"
+name = "undefined"
+version = "prototype"
+
+[cubi.workflow.template]
+pid = "undefined"
+system = "system"
+version = "prototype"

tomls/cubi/workflow/template/pyproject.toml

@@ -0,0 +1,4 @@
+[cubi.workflow.template]
+pid = "undefined"
+system = "system"
+version = "prototype"

tomls/tool/pyproject.toml

@@ -0,0 +1,15 @@
+[tool.black]
+line-length = 88
+
+[tool.pylint.format]
+max-line-length = "88"
+
+[tool.pylint.messages_control]
+disable=[
+  "logging-fstring-interpolation",
+  "useless-return",
+  "missing-module-docstring"
+]
+
+[tool.isort]
+profile = "black"