Add snakemake reporter plugin skeleton

Created a new reporter from the Snakemake plugin template
Added some documentation to README

README.md

@@ -1,2 +1,84 @@
 # ro-crate_snakemake_tooling
 Collection of python tools for processing snakemake metadata for RO-Crate creation
+
+
+## Snakemake reporter plugin
+
+Documentation how the wrroc reporter plugin is built.
+
+### Setup poetry
+
+Poetry is used for setting up a new plugin from a template.  
+In my experience, the Python version used here has to match the Python version used with Snakemake environment, otherwise the plugin does not work.  
+But this should be a solvable problem.
+
+```
+conda create --name poetry python=3.12
+conda activate poetry
+pip install poetry
+```
+
+### Create new plugin from the template
+
+Note: The poetry project was added to this repository.  
+You only have to install the poetry plugin and can use the project in this repository.
+
+```
+# Install poetry plugin via
+poetry self add poetry-snakemake-plugin
+
+# Create a new poetry project via
+poetry new snakemake-report-plugin-wrroc
+
+cd snakemake-report-plugin-wrroc
+
+# Scaffold the project as a snakemake report plugin
+poetry scaffold-snakemake-report-plugin
+
+# Next, edit the scaffolded code according to your needs, and publish
+# the resulting plugin into a github repository. The scaffold command also 
+# creates github actions workflows that will immediately start to check and test
+# the plugin.
+```
+
+### Implement plugin
+
+Implement the report `render` method here:
+
+```
+snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py
+```
+
+For plugin development one can take a look what information the base class [ReporterBase](https://github.com/snakemake/snakemake-interface-report-plugins/blob/main/snakemake_interface_report_plugins/reporter.py) provides.
+
+### Build and install plugin
+
+Build wheel and tar.gz:
+
+```
+poetry build
+```
+
+Install the plugin.
+
+```
+pip install --force-reinstall dist/snakemake_report_plugin_wrroc-0.1.0-py3-none-any.whl
+```
+
+Snakemake should find the plugin! Note that there are many copy&paste errors for the reporter plugin, even in the poetry template repository. Most of the time the term `executor plugin` is used instead of `reporter plugin`.
+
+```
+snakemake -h
+[...]
+wrroc executor settings:
+  --report-wrroc-myparam VALUE
+                        Some help text (default: <dataclasses._MISSING_TYPE object at 0x7f0091b3f140>)
+```
+
+### Create a report
+
+Test the reporter plugin in the skim2mt directory, where the `.snakemake/metadata` resides:
+
+```
+snakemake --reporter wrroc
+```

snakemake-report-plugin-wrroc/.github/workflows/ci.yml

@@ -0,0 +1,94 @@
+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+env:
+  PYTHON_VERSION: 3.11
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: poetry
+
+      - name: Install Dependencies using Poetry
+        run: poetry install
+
+      - name: Check formatting
+        run: poetry run black --check .
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: poetry
+
+      - name: Install Dependencies using Poetry
+        run: poetry install
+
+      - name: Check code
+        run: poetry run flake8
+
+  testing:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: poetry
+
+      - name: Install dependencies
+        run: poetry install
+
+      - name: Run pytest
+        run: poetry run coverage run -m pytest tests/tests.py
+
+      - name: Run Coverage
+        run: poetry run coverage report -m

snakemake-report-plugin-wrroc/.github/workflows/conventional-prs.yml

@@ -0,0 +1,16 @@
+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/[email protected]
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

snakemake-report-plugin-wrroc/.github/workflows/release-please.yml

@@ -0,0 +1,53 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+env:
+  PYTHON_VERSION: 3.11
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+    steps:
+      - uses: GoogleCloudPlatform/release-please-action@v3
+        id: release
+        with:
+          release-type: python
+          package-name: snakemake-report-plugin-wrroc
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created }}
+    steps:
+      - uses: actions/checkout@v3
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v4
+        with:
+          python-version: ${{ env.PYTHON_VERSION }}
+          cache: poetry
+
+      - name: Install Dependencies using Poetry
+        run: |
+          poetry install
+
+      - name: Publish to PyPi
+        env:
+          PYPI_USERNAME: __token__
+          PYPI_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+        run: poetry publish --build --username $PYPI_USERNAME --password $PYPI_PASSWORD

snakemake-report-plugin-wrroc/pyproject.toml

@@ -0,0 +1,17 @@
+[build-system]
+requires = [ "poetry-core",]
+build-backend = "poetry.core.masonry.api"
+
+[tool.poetry]
+name = "snakemake-report-plugin-wrroc"
+version = "0.1.0"
+description = ""
+authors = [ "fbartusch <[email protected]>",]
+readme = "README.md"
+repository = "https://github.com/your/plugin"
+documentation = "https://snakemake.github.io/snakemake-plugin-catalog/plugins/report/wrroc.html"
+
+[tool.poetry.dependencies]
+python = "^3.12"
+snakemake-interface-common = "^1.17.2"
+snakemake-interface-report-plugins = "^1.0.0"

snakemake-report-plugin-wrroc/setup.cfg

@@ -0,0 +1,7 @@
+[flake8]
+# Recommend matching the black line length (default 88),
+# rather than using the flake8 default of 79:
+max-line-length = 88
+extend-ignore =
+    # See https://github.com/PyCQA/pycodestyle/issues/373
+    E203,