snakemake-report-plugin-nanopub 0.1.0__tar.gz

snakemake_report_plugin_nanopub-0.1.0/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "monthly"

snakemake_report_plugin_nanopub-0.1.0/.github/workflows/announce-release.yml

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+name: Announce Release on Mastodon
+
+on:
+  push:
+    branches:
+      - main
+    paths:
+      - 'CHANGELOG.md'
+
+permissions:
+  pull-requests: read
+
+jobs:
+  post_to_mastodon:
+    if: "${{ contains(github.event.head_commit.message, 'chore(main): release') }}"
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v6
+      
+      - name: Verify logo file exists
+        run: |
+          ls -la ${{ github.workspace }}/pr_logo/
+          if [ ! -f "${{ github.workspace }}/pr_logo/logo_dark.png" ]; then
+            echo "ERROR: Logo file not found!"
+            exit 1
+          fi
+          echo "Logo file found at: ${{ github.workspace }}/pr_logo/logo_dark.png"
+      
+      - name: Post to Mastodon
+        uses: snakemake/mastodon-release-post-action@main # == latest
+        with:
+          access-token: ${{ secrets.MASTODONBOT }}
+          pr-title: ${{ github.event.head_commit.message }}
+          image: "logo_dark.png"
+          image-description: "Snakemake Logo"
+          repotitle: "Snakemake Reporter PLugin for Nanopubs"
+          message: |
+            Beep, Beep - I am your friendly #Snakemake release announcement bot.
+            
+            There is a new release of the {{ repotitle }} systems. Its version now is {{ version }}!
+            
+            Give us some time, and you will automatically find the plugin on #Bioconda and #Pypi.
+            
+            This plugin is relevant for Snakemake users willing to publish 
+            Software Metadata easyly.
+            The maintainer is here on Mastodon @rupdecat.
+            
+            If you discover any issues, please report them on {{ issue_url }}.
+
+            See {{ changelog }} for details. Here is the header of the changelog:
+            
+            ${{ steps.extract-release-notes.outputs.release_notes }}
+            

snakemake_report_plugin_nanopub-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+
+env:
+  TEST_ENV_DIR: /tmp/test-env
+
+jobs:
+  formatting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v6
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
+
+      - name: Check formatting
+        run: pixi run format --check .
+
+  linting:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out the code
+        uses: actions/checkout@v6
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
+
+      - name: Check code
+        run: pixi run lint
+
+  testing:
+    runs-on: ubuntu-latest
+    # only run if commit message does not start with "chore(main): release"
+    if: >-
+      !startsWith(github.event.head_commit.message, 'chore(main): release')
+    steps:
+      - uses: actions/checkout@v6
+
+      - name: Setup pixi
+        uses: prefix-dev/setup-pixi@v0
+
+      - uses: conda-incubator/setup-miniconda@v3
+        with:
+          channels: conda-forge,nodefaults
+
+      - name: Deploy external test env
+        shell: bash -el {0}
+        run: |
+          conda create -n test-env stress-ng
+          conda create -p $TEST_ENV_DIR stress-ng
+
+      - name: Run pytest
+        env:
+          TEST_NAMED_ENV: "1"
+          TEST_DIRECTORY_ENV: "1"
+        run: pixi run test -v
+
+      - name: Run Coverage
+        run: pixi run coverage-report

snakemake_report_plugin_nanopub-0.1.0/.github/workflows/codespell.yml

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+# Codespell configuration is within pyproject.toml
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    if: github.event.pull_request.merged != true || github.ref != 'refs/heads/main'
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2
+        with:
+          ignore_words_list: Crate,crate

snakemake_report_plugin_nanopub-0.1.0/.github/workflows/conventional-prs.yml

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+name: PR
+on:
+  pull_request_target:
+    types:
+      - opened
+      - reopened
+      - edited
+      - synchronize
+
+jobs:
+  title-format:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: amannn/action-semantic-pull-request@v6
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

snakemake_report_plugin_nanopub-0.1.0/.github/workflows/release-please.yml

@@ -0,0 +1,50 @@
+on:
+  push:
+    branches:
+      - main
+
+name: release-please
+
+jobs:
+  release-please:
+    runs-on: ubuntu-latest
+    outputs:
+      release_created: ${{ steps.release.outputs.release_created }}
+    steps:
+      - uses: googleapis/release-please-action@v4
+        id: release
+        with:
+          release-type: python
+          token: ${{ secrets.RELEASE_PLEASE_PR_CI_TOKEN }}
+
+  publish:
+    runs-on: ubuntu-latest
+    needs: release-please
+    if: ${{ needs.release-please.outputs.release_created }}
+    steps:
+      - uses: actions/checkout@v6
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+
+      - name: Install poetry
+        run: pip install poetry
+
+      - name: Determine dependencies
+        run: poetry lock
+
+      - uses: actions/setup-python@v6
+        with:
+          python-version: "3.12"
+          cache: poetry
+
+      - name: Install dependencies
+        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_nanopub-0.1.0/.github/workflows/stale.yml

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+name: Close inactive issues
+on:
+  schedule:
+    - cron: "1 1 * * 1"
+
+jobs:
+  close-issues:
+    runs-on: ubuntu-latest
+    permissions:
+      issues: write
+      pull-requests: write
+    steps:
+      - uses: actions/stale@v10
+        with:
+          days-before-issue-stale: 180
+          days-before-issue-close: 365
+          stale-issue-label: "stale"
+          stale-issue-message: >-
+            This issue was marked as stale because it has been open for 6 months
+            with no activity. First, we apologize for not (yet) being active as 
+            human beings on this issue. If there is still interest in this issue, please
+            comment and remove the 'stale' label. Also note that this does not
+            mean that we do not value your contribution. We do, but development
+            on Snakemake is a community effort, and that means that we can always
+            miss something due to the sheer amount of activity.
+            Also consider contacting us via Discord (see the docs).
+          close-issue-message: >-
+            This issue was closed because it has been inactive for 1 year since
+            being marked as stale. Feel free to re-open it if you have any further
+            comments."
+          days-before-pr-stale: 180
+          days-before-pr-close: -1
+          stale-pr-message: >-
+            This issue was marked as stale because it has been open for 6 months
+            with no activity. First, we apologize for not (yet) being active as 
+            human beings on this issue. If there is still interest in this issue, please
+            comment and remove the 'stale' label. Also note that this does not
+            mean that we do not value your contribution. We do, but development
+            on Snakemake is a community effort, and that means that we can always
+            miss something due to the sheer amount of activity.
+            Also consider contacting us via Discord (see the docs).
+          repo-token: ${{ secrets.GITHUB_TOKEN }}

snakemake_report_plugin_nanopub-0.1.0/.gitignore

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+# 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/
+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/
+cover/
+
+# 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
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .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
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__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/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+.aider*

snakemake_report_plugin_nanopub-0.1.0/CHANGELOG.md

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+# Changelog
+
+## 0.1.0 (2026-04-21)
+
+
+### Features
+
+* added announcement CI plus logo image ([8124fc7](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/8124fc72793ee390222cff9a0df80c1a9706ced2))
+* added basic code (automatic scaffold by poetry) ([a81a92f](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a81a92f6fc699f0054bd992d27579513d01cce33))
+* added basic test code (auto generated by poetry ([5858e76](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/5858e7632e4efbddf8834f759b5a3278648e2aa2))
+* added cli script for plotting dependency graphs ([d887696](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/d88769659066e4c442ce85f7c0af6d8f8f6f7aa6))
+* added coverage tests for pixi ([21488dc](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/21488dcd807d5d0a127d6f85fcdbe7a274c55e21))
+* added dependencies ([179d86f](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/179d86f0724c87b3fdf58a8f0329fc5a80a3860e))
+* added example knowledge graph image ([792f6db](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/792f6dba43ff52159e3a48d39acacaed0682bb7e))
+* cli now considering workflow metadata ([2ad0f1b](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/2ad0f1b8e6b6d42cc0d7a9c4f139b615344ddac5))
+* coded skeleton - untested ([aa4f0ec](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/aa4f0ec4364f8507c39969b4d8a9ee79e46c9ed7))
+* consider testing the graph file, too ([cfc2496](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/cfc2496bebfec14671537fbf9baa65773ebd524c))
+* documenting --workflow-configuration-id ([5e60c84](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/5e60c846e08be9b5cf4b533ce66495a19e382416))
+* first working version ([75d6821](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/75d68212077e06939fcf8582e0e6bc8812e8c861))
+* improved balance between published quads and limits ([db8d18b](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/db8d18bb3fba523f640813fa4ba2eec4884665f2))
+* included nanopub py as a dependency ([37ae247](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/37ae247e628274875c488d09a65b236d81a432cb))
+* shrinking content size by stripping comments ([a4089cf](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a4089cf1f74df31f8a0420b677c2dd35d6dc6878))
+* signedby attribute was added ([1a7511c](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/1a7511cb40a2d141a411a5441b1c9cc4da866309))
+* stabilized plotting ([7bab5c1](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/7bab5c158e8e42a5a5c6aac259c6fecb66f9b17e))
+* version 1 ([9bb126e](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/9bb126e617dc3b51c1066cf4805f3c52bf050d66))
+* working version ([c85ecd7](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/c85ecd78498a42d90b7e0e2498fc4f5957ba83ce))
+* working version - needs polishing ([0ba4c51](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/0ba4c51dfe4dd152e9f45897b966236472224651))
+* working version - not yet structured ([7ef3899](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/7ef38992ee2f86bf6e40845a27594ba0e0f10d1f))
+
+
+### Bug Fixes
+
+* added pixi information to toml files ([22b70e6](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/22b70e6c2d1b7c6eaf9401bf0267d27711f3eed5))
+* attempt 2 - should fail in tests, as no nanopub-py is installed, waiting for the new version ([0b85a68](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/0b85a68cff6c7960f26febe40cc0d1edd0aaa4e6))
+* bumped python dep in CI to 3.12 for compatibility checks ([a6c4f0e](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a6c4f0e7e4c99dc29acca7545db6a8687239f2a5))
+* bumped snakemake version to something recent ([136e003](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/136e00367efe87ee325df971bd81a389506fbd87))
+* corrected description handling ([c747028](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/c7470285f9e671d94b5b5ed9404e3151c45bfdec))
+* docstring typo ([ca1f853](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/ca1f853f9aa84667a36f5360e1de8c21bce31003))
+* fixes the pixi CI issue - hopefully ([a426c98](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a426c9820b9c33213320d2f441ed8cbf55cbcba5))
+* formatting ([b65d1a0](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/b65d1a0bcc9c213d508e3d27c802c215dbf359ef))
+* formatting ([dbdd216](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/dbdd216bd492ff33e7971f52ba07726a5f4ff370))
+* formatting ([2f62d66](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/2f62d6699f786115600cc1925c3b217927ec9a35))
+* formatting ([e12b70c](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/e12b70c0238271c51e97fc4f30fa2ee334d4816a))
+* formatting ([4dd16a4](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/4dd16a4a5479b86b2e5787b9462e05a40944fe2c))
+* formatting ([e4004ba](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/e4004ba70b8beadd92c0aa3b741e2bf10cd67933))
+* formatting ([e99f991](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/e99f991ea544391b37c9758802f820d494c59557))
+* formatting ([be4dbf2](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/be4dbf2e82e129537eb80b27c6fbdc0326314e6c))
+* linint - removed unused import ([30f4dd2](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/30f4dd2f84d906b1dd53051c58041a10cf5e7635))
+* linting ([54148e8](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/54148e8740e7e183f6ca7d0f70202810d0200bba))
+* merge conflict ([d793fd4](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/d793fd46fa4ebe54d53ab83d49f70ac53e211c2c))
+* name ([696215c](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/696215c31ee1f1bf2aee2055fe7a25648607537b))
+* nanopub-py is a pypi not a conda dep ([a291029](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a291029da2207360018cd6272de8500a0a4542e6))
+* relaxing system requirements to work on cluster envs ([04c4276](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/04c4276e353c9f7e6488487f615d2efe5169c6ac))
+* removed unused import ([405caf0](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/405caf088f92f6e6c47a936d217f8c63b45fd48a))
+* reverting to snakemake's global logger, added comments ([a245dc3](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/a245dc3d26a4a1efb615df7ace092d5806b24b98))
+* somewhat improved string handling to comply with all tests ([716deb1](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/716deb10d14f7fc8e00dfd26825744b2466de5d2))
+* spelling ([55f4a49](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/55f4a499f59dddfd4e8b3b92f4e886106453b46d))
+* stripping html tags from workflow description ([8e49dce](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/8e49dcee0641f81a0246198fef9bd967b9db4007))
+* switching to 'Dataset() from 'ConjunctiveGraph()' to avoid deprecation warnings ([1604bfb](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/1604bfb5096c2a82b515ac538692ac7dea9c50fd))
+* test dependencies ([e32da0f](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/e32da0fe7a15566f05ccf49f98d86eddde3f2c2e))
+* testing ([c07a189](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/c07a18900dd71fd612f97f3f25d033335d62bc4d))
+* typo ([66b19a2](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/66b19a2eba0754e48074b0a231130515a91baf4c))
+
+
+### Documentation
+
+* added actual documentation ([0a6a619](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/0a6a619245e06a4be8d4393d813c633c8066d413))
+* added intro section about nanopublications ([21fe950](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/21fe950d50a706aa2dd70bfc0fb65890ece30ad5))
+* first rough README ([94853a2](https://github.com/snakemake/snakemake-report-plugin-nanopub/commit/94853a28ebae76d29c0261b2f6f3fa85f898a60f))

snakemake_report_plugin_nanopub-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 Snakemake
+
+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.

snakemake_report_plugin_nanopub-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: snakemake-report-plugin-nanopub
+Version: 0.1.0
+Summary: Reporter plugin for Snakemake using nanopub-py to create workflow metadata nanopubs
+Project-URL: repository, https://github.com/snakemake/snakemake-report-plugin-nanopub
+Project-URL: documentation, https://snakemake.github.io/snakemake-plugin-catalog/plugins/report/nanopub.html
+Author-email: Christian Meesters <meesters@uni-mainz.de>
+License-File: LICENSE
+Requires-Python: <4.0,>=3.12
+Requires-Dist: nanopub>=2.2.0
+Requires-Dist: snakemake-interface-common<2.0.0,>=1.17.4
+Requires-Dist: snakemake-interface-report-plugins<2.0.0,>=1.1.0
+Description-Content-Type: text/markdown
+
+[![Snakemake](https://img.shields.io/badge/snakemake-≥9.1.3-brightgreen.svg)](https://snakemake.github.io)
+[![Conventional Commits](https://img.shields.io/badge/Conventional%20Commits-1.0.0-%23FE5196?logo=conventionalcommits&logoColor=white)](https://conventionalcommits.org)
+
+**Please note**: This plugin is work in progress and NOT ready to use.
+
+**Its intention**:
+
+- users will be enabled to automatically create a [nanopub](https://nanopub.net/) using a workflow's metadata
+- this nanopub can subsequently be referenced in publications and thereby covering __all__ metadata necessary to scrutinize an analysis (all too often crucial data are missing from publications)
+
+## CLI: plot nanopub knowledge graph
+
+After installation, run:
+
+```bash
+plot-nanopub-knowledge-graph \
+	--dataset-nanopub-id <dataset_nanopub_url> \
+	--workflow-nanopub-id <workflow_nanopub_url> \
+	--workflow-configuration-id <workflow_configuration_nanopub_url> \
+	--report-nanopub-id <report_nanopub_url> \
+	-o graph.png
+```
+
+This generates a Graphviz plot with four rounded boxes (`Dataset`, `Workflow`, `Workflow Configuration`, `Workflow Report`) and arrows labeled `used by`, `used this configuration`, `produces`, and `based upon`.
+
+Optional settings:
+
+- `--line-color "dark brick red"` (default) for node border and arrow color
+- `--format svg|png|pdf` to override output format
+- `--verbose` to print debug logs for nanopub description extraction
+- `--text-width 60` to control line wrapping width in box text
+
+Default output format is `png`.

snakemake_report_plugin_nanopub-0.1.0/README.md

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+[![Snakemake](https://img.shields.io/badge/snakemake-≥9.1.3-brightgreen.svg)](https://snakemake.github.io)
+[![Conventional Commits](https://img.shields.io/badge/Conventional%20Commits-1.0.0-%23FE5196?logo=conventionalcommits&logoColor=white)](https://conventionalcommits.org)
+
+**Please note**: This plugin is work in progress and NOT ready to use.
+
+**Its intention**:
+
+- users will be enabled to automatically create a [nanopub](https://nanopub.net/) using a workflow's metadata
+- this nanopub can subsequently be referenced in publications and thereby covering __all__ metadata necessary to scrutinize an analysis (all too often crucial data are missing from publications)
+
+## CLI: plot nanopub knowledge graph
+
+After installation, run:
+
+```bash
+plot-nanopub-knowledge-graph \
+	--dataset-nanopub-id <dataset_nanopub_url> \
+	--workflow-nanopub-id <workflow_nanopub_url> \
+	--workflow-configuration-id <workflow_configuration_nanopub_url> \
+	--report-nanopub-id <report_nanopub_url> \
+	-o graph.png
+```
+
+This generates a Graphviz plot with four rounded boxes (`Dataset`, `Workflow`, `Workflow Configuration`, `Workflow Report`) and arrows labeled `used by`, `used this configuration`, `produces`, and `based upon`.
+
+Optional settings:
+
+- `--line-color "dark brick red"` (default) for node border and arrow color
+- `--format svg|png|pdf` to override output format
+- `--verbose` to print debug logs for nanopub description extraction
+- `--text-width 60` to control line wrapping width in box text
+
+Default output format is `png`.