Add package and general structure to this repository (#1)

* Add package

* Add general description on top level.

* Remove .gitignore from top level since there is no code there.

* Fix workflow

* Add gitignore back and fix README

* Small doc improvements

.github/workflows/package-ci.yml

@@ -0,0 +1,52 @@
+name: AquDeM Code Quality Check
+
+on:
+  pull_request:
+    branches: [ main ]
+    paths:
+      - 'package/**'
+  push:
+    branches: [ main ]
+    paths:
+      - 'package/**'
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v2
+    - name: Set up Python
+      uses: actions/setup-python@v2
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        cd package
+        python -m pip install --upgrade pip
+        pip install -r requirements.txt
+        pip install -r requirements_dev.txt
+    - name: Run unit tests with pytest
+      run: |
+        cd package
+        export PYTHONPATH=.
+        pytest
+
+    - name: Make sure coverage is high enough
+      run: |
+        cd package
+        export PYTHONPATH=.
+        coverage run --source=aqudem --branch -m pytest
+        coverage report --fail-under=90
+
+    - name: Lint with pylint
+      run: |
+        cd package
+        pylint aqudem
+        pylint --disable=protected-access,missing-function-docstring tests
+
+    - name: Type checking with mypy
+      run: |
+        cd package
+        mypy aqudem tests --strict

.gitignore

@@ -157,4 +157,4 @@ cython_debug/
 #  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/
+.idea/

README.md

@@ -1 +1,8 @@
-# aqudem
+# AquDeM
+**A**ctivity and Se**qu**ence **De**tection Performance **M**easures: A package to evaluate activity detection results, including the sequence of events given multiple activity types.
+
+The tool has a stand-alone package to use programatically in your Python code, and a web interface to evaluate the results of your activity detection algorithm interactively.
+
+For more info on the package, see `package/`.
+
+For more info on the web interface, see `frontend/`.

package/.editorconfig

@@ -0,0 +1,21 @@
+# http://editorconfig.org
+
+root = true
+
+[*]
+indent_style = space
+indent_size = 4
+trim_trailing_whitespace = true
+insert_final_newline = true
+charset = utf-8
+end_of_line = lf
+
+[*.bat]
+indent_style = tab
+end_of_line = crlf
+
+[LICENSE]
+insert_final_newline = false
+
+[Makefile]
+indent_style = tab

package/.github/ISSUE_TEMPLATE.md

@@ -0,0 +1,15 @@
+* AquDeM version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

package/.gitignore

@@ -0,0 +1,106 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# dotenv
+.env
+
+# virtualenv
+.venv
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+
+# IDE settings
+.vscode/
+.idea/

package/AUTHORS.rst

@@ -0,0 +1,13 @@
+=======
+Credits
+=======
+
+Development Lead
+----------------
+
+* Aaron F. Kurz <[email protected]>
+
+Contributors
+------------
+
+None yet. Why not be the first?

package/CONTRIBUTING.rst

@@ -0,0 +1,120 @@
+.. highlight:: shell
+
+============
+Contributing
+============
+
+Contributions are welcome, and they are greatly appreciated! Every little bit
+helps, and credit will always be given.
+
+You can contribute in many ways:
+
+Types of Contributions
+----------------------
+
+Report Bugs
+~~~~~~~~~~~
+
+Report bugs at https://github.com/ics-unisg/aqudem/issues.
+
+If you are reporting a bug, please include:
+
+* Your operating system name and version.
+* Any details about your local setup that might be helpful in troubleshooting.
+* Detailed steps to reproduce the bug.
+
+Fix Bugs
+~~~~~~~~
+
+Look through the GitHub issues for bugs. Anything tagged with "bug" and "help
+wanted" is open to whoever wants to implement it.
+
+Implement Features
+~~~~~~~~~~~~~~~~~~
+
+Look through the GitHub issues for features. Anything tagged with "enhancement"
+and "help wanted" is open to whoever wants to implement it.
+
+Write Documentation
+~~~~~~~~~~~~~~~~~~~
+
+AquDeM could always use more documentation, whether as part of the
+official AquDeM docs, in docstrings, or even on the web in blog posts,
+articles, and such.
+
+Submit Feedback
+~~~~~~~~~~~~~~~
+
+The best way to send feedback is to file an issue at https://github.com/ics-unisg/aqudem/issues.
+
+If you are proposing a feature:
+
+* Explain in detail how it would work.
+* Keep the scope as narrow as possible, to make it easier to implement.
+* Remember that this is a volunteer-driven project, and that contributions
+  are welcome :)
+
+Get Started!
+------------
+
+Ready to contribute? Here's how to set up `aqudem` for local development.
+
+1. Fork the `aqudem` repo on GitHub.
+2. Clone your fork locally::
+
+    $ git clone [email protected]:your_name_here/aqudem.git
+
+3. Install the requirements using virtualenv (first create a virtualenv)::
+
+    $ pip install -r requirements.txt
+
+4. Create a branch for local development::
+
+    $ git checkout -b name-of-your-bugfix-or-feature
+
+   Now you can make your changes locally.
+
+5. When you're done making changes, check that your changes pass several requirements::
+
+    $ `./code-check.sh
+
+   To get the necessary tools to execute the checks, run::
+
+    $ pip install -r requirements-dev.txt
+
+6. Commit your changes and push your branch to GitHub::
+
+    $ git add .
+    $ git commit -m "Your detailed description of your changes."
+    $ git push origin name-of-your-bugfix-or-feature
+
+7. Submit a pull request through the GitHub website.
+
+Pull Request Guidelines
+-----------------------
+
+Before you submit a pull request, check that it meets these guidelines:
+
+1. The pull request should include tests.
+2. If the pull request adds functionality, the docs should be updated. Put
+   your new functionality into a function with a docstring, and add the
+   feature to the list in README.rst.
+3. The pull request should work for Python 3.12. Make sure that the pipeline passes.
+
+Tips
+----
+
+
+
+Deploying
+---------
+
+A reminder for the maintainers on how to deploy.
+Make sure all your changes are committed (including an entry in HISTORY.rst).
+Then run::
+
+$ bump2version patch # possible: major / minor / patch
+$ git push
+$ git push --tags
+
+Travis will then deploy to PyPI if tests pass.

package/HISTORY.rst

@@ -0,0 +1,8 @@
+=======
+History
+=======
+
+0.1.0 (2024-02-08)
+------------------
+
+* First release on PyPI.