Successful E2E intersection (#2)

.bandit

@@ -0,0 +1,2 @@
+assert_used:
+  skips: ['tests/**.py']

.github/workflows/python-package.yaml

@@ -19,7 +19,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        python-version: ["3.11", "3.12"]
+        python-version: ["3.10", "3.11", "3.12"]
     steps:
       #----------------------------------------------
       # check-out repo and set-up python
@@ -75,3 +75,10 @@ jobs:
         run: |
           source .venv/bin/activate
           pytest
+
+  build_success:
+    name: Build Success
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - run: echo Done!

.github/workflows/trunk-check.yaml

@@ -15,7 +15,6 @@ permissions: read-all
 
 jobs:
   trunk_check:
-    name: Trunk Check Runner
     runs-on: ubuntu-latest
     permissions:
       checks: write # For trunk to post annotations

.gitignore

@@ -0,0 +1,165 @@
+# 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/
+
+# ----- vcf_isec -----
+
+logs/
+output/

.trunk/configs/.isort.cfg

@@ -0,0 +1,2 @@
+[settings]
+profile=black

.trunk/configs/.markdownlint.yaml

@@ -8,3 +8,6 @@ line_length: false
 spaces: false
 url: false
 whitespace: false
+no-trailing-punctuation: false
+no-duplicate-heading:
+  siblings_only: true

.trunk/configs/bandit.yaml

@@ -0,0 +1,2 @@
+assert_used:
+  skips: [./tests/*.py]

.trunk/trunk.yaml

@@ -3,6 +3,8 @@
 version: 0.1
 cli:
   version: 1.20.1
+  shell_hooks:
+    enforce: true
 # Trunk provides extensibility via plugins. (https://docs.trunk.io/plugins)
 plugins:
   sources:
@@ -12,22 +14,36 @@ plugins:
 # Many linters and tools depend on runtimes - configure them here. (https://docs.trunk.io/runtimes)
 runtimes:
   enabled:
+    - [email protected]
     - [email protected]
     - [email protected]
 # This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
 lint:
+  disabled:
+    - sourcery
+    - isort
+    - black
+  definitions:
+    - name: bandit
+      direct_configs: [bandit.yaml]
+      commands:
+        - name: lint
+          run: bandit --exit-zero -c bandit.yaml --format json --output ${tmpfile} ${target}
   enabled:
+    - [email protected]
+    - [email protected]
+    - [email protected]
     - [email protected]
-    - [email protected].31
+    - [email protected].32
     - [email protected]
     - [email protected]
-    - [email protected].0
+    - [email protected].1
     - git-diff-check
     - [email protected]
     - [email protected]
     - [email protected]
     - [email protected]
-    - [email protected].4
+    - [email protected].5
 actions:
   disabled:
     - trunk-announce

.vscode/launch.json

@@ -0,0 +1,20 @@
+{
+  // Use IntelliSense to learn about possible attributes.
+  // Hover to view descriptions of existing attributes.
+  // For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
+  "version": "0.2.0",
+  "configurations": [
+    {
+      "name": "Python Debugger: CLI",
+      "type": "debugpy",
+      "request": "launch",
+      "module": "vcf_isec.cli",
+      "args": [
+        "tests/resources/cmp-test-a.vcf",
+        "tests/resources/cmp-test-b.vcf",
+        "-p",
+        "tmp"
+      ]
+    }
+  ]
+}