From 83f3faccb432df7cd1c0031e76b2cdfa9ba4ad50 Mon Sep 17 00:00:00 2001
From: fbartusch <felix.bartusch@uni-tuebingen.de>
Date: Fri, 7 Jun 2024 18:22:12 +0200
Subject: [PATCH] Add snakemake reporter plugin skeleton

Created a new reporter from the Snakemake plugin template
Added some documentation to README
---
 README.md                                     |  82 +++++++++++++++
 .../.github/workflows/ci.yml                  |  94 ++++++++++++++++++
 .../.github/workflows/conventional-prs.yml    |  16 +++
 .../.github/workflows/release-please.yml      |  53 ++++++++++
 snakemake-report-plugin-wrroc/README.md       |   0
 ...report_plugin_wrroc-0.1.0-py3-none-any.whl | Bin 0 -> 2555 bytes
 ...snakemake_report_plugin_wrroc-0.1.0.tar.gz | Bin 0 -> 2043 bytes
 snakemake-report-plugin-wrroc/poetry.lock     |  61 ++++++++++++
 snakemake-report-plugin-wrroc/pyproject.toml  |  17 ++++
 snakemake-report-plugin-wrroc/setup.cfg       |   7 ++
 .../snakemake_report_plugin_wrroc/__init__.py |  63 ++++++++++++
 snakemake-report-plugin-wrroc/tests/tests.py  |  16 +++
 12 files changed, 409 insertions(+)
 create mode 100644 snakemake-report-plugin-wrroc/.github/workflows/ci.yml
 create mode 100644 snakemake-report-plugin-wrroc/.github/workflows/conventional-prs.yml
 create mode 100644 snakemake-report-plugin-wrroc/.github/workflows/release-please.yml
 create mode 100644 snakemake-report-plugin-wrroc/README.md
 create mode 100644 snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0-py3-none-any.whl
 create mode 100644 snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0.tar.gz
 create mode 100644 snakemake-report-plugin-wrroc/poetry.lock
 create mode 100644 snakemake-report-plugin-wrroc/pyproject.toml
 create mode 100644 snakemake-report-plugin-wrroc/setup.cfg
 create mode 100644 snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py
 create mode 100644 snakemake-report-plugin-wrroc/tests/tests.py

diff --git a/README.md b/README.md
index cdbe509..97d43dd 100644
--- a/README.md
+++ b/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
+```
\ No newline at end of file
diff --git a/snakemake-report-plugin-wrroc/.github/workflows/ci.yml b/snakemake-report-plugin-wrroc/.github/workflows/ci.yml
new file mode 100644
index 0000000..e9a18aa
--- /dev/null
+++ b/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
diff --git a/snakemake-report-plugin-wrroc/.github/workflows/conventional-prs.yml b/snakemake-report-plugin-wrroc/.github/workflows/conventional-prs.yml
new file mode 100644
index 0000000..c777f4b
--- /dev/null
+++ b/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/action-semantic-pull-request@v3.4.0
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
diff --git a/snakemake-report-plugin-wrroc/.github/workflows/release-please.yml b/snakemake-report-plugin-wrroc/.github/workflows/release-please.yml
new file mode 100644
index 0000000..faba04e
--- /dev/null
+++ b/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
diff --git a/snakemake-report-plugin-wrroc/README.md b/snakemake-report-plugin-wrroc/README.md
new file mode 100644
index 0000000..e69de29
diff --git a/snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0-py3-none-any.whl b/snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0-py3-none-any.whl
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diff --git a/snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0.tar.gz b/snakemake-report-plugin-wrroc/dist/snakemake_report_plugin_wrroc-0.1.0.tar.gz
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diff --git a/snakemake-report-plugin-wrroc/poetry.lock b/snakemake-report-plugin-wrroc/poetry.lock
new file mode 100644
index 0000000..b149307
--- /dev/null
+++ b/snakemake-report-plugin-wrroc/poetry.lock
@@ -0,0 +1,61 @@
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
+
+[[package]]
+name = "argparse-dataclass"
+version = "2.0.0"
+description = "Declarative CLIs with argparse and dataclasses"
+optional = false
+python-versions = ">=3.8"
+files = [
+    {file = "argparse_dataclass-2.0.0-py3-none-any.whl", hash = "sha256:3ffc8852a88d9d98d1364b4441a712491320afb91fb56049afd8a51d74bb52d2"},
+    {file = "argparse_dataclass-2.0.0.tar.gz", hash = "sha256:09ab641c914a2f12882337b9c3e5086196dbf2ee6bf0ef67895c74002cc9297f"},
+]
+
+[[package]]
+name = "configargparse"
+version = "1.7"
+description = "A drop-in replacement for argparse that allows options to also be set via config files and/or environment variables."
+optional = false
+python-versions = ">=3.5"
+files = [
+    {file = "ConfigArgParse-1.7-py3-none-any.whl", hash = "sha256:d249da6591465c6c26df64a9f73d2536e743be2f244eb3ebe61114af2f94f86b"},
+    {file = "ConfigArgParse-1.7.tar.gz", hash = "sha256:e7067471884de5478c58a511e529f0f9bd1c66bfef1dea90935438d6c23306d1"},
+]
+
+[package.extras]
+test = ["PyYAML", "mock", "pytest"]
+yaml = ["PyYAML"]
+
+[[package]]
+name = "snakemake-interface-common"
+version = "1.17.2"
+description = "Common functions and classes for Snakemake and its plugins"
+optional = false
+python-versions = "<4.0,>=3.8"
+files = [
+    {file = "snakemake_interface_common-1.17.2-py3-none-any.whl", hash = "sha256:ca5043ee707c071d9fed7e659df4803e8eeeaf1fe0d0bdb6716deb0141208748"},
+    {file = "snakemake_interface_common-1.17.2.tar.gz", hash = "sha256:7a2bba88df98c1a0a5cec89b835c62dd2e6e72c1fb8fd104fe73405c800b87c0"},
+]
+
+[package.dependencies]
+argparse-dataclass = ">=2.0.0,<3.0.0"
+ConfigArgParse = ">=1.7,<2.0"
+
+[[package]]
+name = "snakemake-interface-report-plugins"
+version = "1.0.0"
+description = "The interface for Snakemake report plugins."
+optional = false
+python-versions = ">=3.11,<4.0"
+files = [
+    {file = "snakemake_interface_report_plugins-1.0.0-py3-none-any.whl", hash = "sha256:e39cf2f27a36bda788dd97ede8fd056f887e00dca2d14ffea91dbc696d1f17cd"},
+    {file = "snakemake_interface_report_plugins-1.0.0.tar.gz", hash = "sha256:02311cdc4bebab2a1c28469b5e6d5c6ac6e9c66998ad4e4b3229f1472127490f"},
+]
+
+[package.dependencies]
+snakemake-interface-common = ">=1.16.0,<2.0.0"
+
+[metadata]
+lock-version = "2.0"
+python-versions = "^3.12"
+content-hash = "5ef0075a4c44525781a793918fc6cbe3e0be535a62cb6923056ae1295388f7e1"
diff --git a/snakemake-report-plugin-wrroc/pyproject.toml b/snakemake-report-plugin-wrroc/pyproject.toml
new file mode 100644
index 0000000..227286a
--- /dev/null
+++ b/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 <felix.bartusch@uni-tuebingen.de>",]
+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"
diff --git a/snakemake-report-plugin-wrroc/setup.cfg b/snakemake-report-plugin-wrroc/setup.cfg
new file mode 100644
index 0000000..43a5b43
--- /dev/null
+++ b/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,
\ No newline at end of file
diff --git a/snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py b/snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py
new file mode 100644
index 0000000..b7269e8
--- /dev/null
+++ b/snakemake-report-plugin-wrroc/snakemake_report_plugin_wrroc/__init__.py
@@ -0,0 +1,63 @@
+from dataclasses import dataclass, field
+from typing import Optional
+
+from snakemake_interface_common.exceptions import WorkflowError  # noqa: F401
+from snakemake_interface_report_plugins.reporter import ReporterBase
+from snakemake_interface_report_plugins.settings import ReportSettingsBase
+
+
+# Optional:
+# Define additional settings for your reporter.
+# They will occur in the Snakemake CLI as --report-<reporter-name>-<param-name>
+# Omit this class if you don't need any.
+# Make sure that all defined fields are Optional (or bool) and specify a default value
+# of None (or False) or anything else that makes sense in your case.
+@dataclass
+class ReportSettings(ReportSettingsBase):
+    myparam: Optional[int] = field(
+        default=None,
+        metadata={
+            "help": "Some help text",
+            # Optionally request that setting is also available for specification
+            # via an environment variable. The variable will be named automatically as
+            # SNAKEMAKE_REPORT_<reporter-name>_<param-name>, all upper case.
+            # This mechanism should ONLY be used for passwords and usernames.
+            # For other items, we rather recommend to let people use a profile
+            # for setting defaults
+            # (https://snakemake.readthedocs.io/en/stable/executing/cli.html#profiles).
+            "env_var": False,
+            # Optionally specify a function that parses the value given by the user.
+            # This is useful to create complex types from the user input.
+            #"parse_func": ...,
+            # If a parse_func is specified, you also have to specify an unparse_func
+            # that converts the parsed value back to a string.
+            #"unparse_func": ...,
+            # Optionally specify that setting is required when the reporter is in use.
+            "required": False,
+        },
+    )
+
+
+# Required:
+# Implementation of your reporter
+class Reporter(ReporterBase):
+    def __post_init__(self):
+        # initialize additional attributes
+        # Do not overwrite the __init__ method as this is kept in control of the base
+        # class in order to simplify the update process.
+        # See https://github.com/snakemake/snakemake-interface-report-plugins/snakemake_interface_report_plugins/reporter.py # noqa: E501
+        # for attributes of the base class.
+        # In particular, the settings of above ReportSettings class are accessible via
+        # self.settings.
+        ...
+
+    def render(self):
+        # Render the report, using attributes of the base class.
+        print("test")
+
+        # print basic information (start/end) of each job
+        for rec in self.jobs:
+            print("rule: " + rec.rule)
+            print("starttime: " + str(rec.starttime))
+            print("endtime: " + str(rec.endtime))
+
diff --git a/snakemake-report-plugin-wrroc/tests/tests.py b/snakemake-report-plugin-wrroc/tests/tests.py
new file mode 100644
index 0000000..17e4f7c
--- /dev/null
+++ b/snakemake-report-plugin-wrroc/tests/tests.py
@@ -0,0 +1,16 @@
+from typing import Optional
+import snakemake.common.tests
+from snakemake_interface_report_plugins.settings import ReportSettingsBase
+
+
+# Check out the base classes found here for all possible options and methods:
+# https://github.com/snakemake/snakemake/blob/main/snakemake/common/tests/__init__.py
+class TestWorkflowsBase(snakemake.common.tests.TestReportBase):
+    __test__ = True
+
+    def get_reporter(self) -> str:
+        return "wrroc"
+
+    def get_report_settings(self) -> Optional[ReportSettingsBase]:
+        # instantiate ReportSettings of this plugin as appropriate
+        ...