Merge pull request #211 from daisybio/development

v.1.3.1

Author: JudithBernett

create_report.py

@@ -19,12 +19,13 @@
     parser = argparse.ArgumentParser(description="Generate reports from evaluation results")
     parser.add_argument("--run_id", required=True, help="Run ID for the current execution")
     parser.add_argument("--dataset", required=True, help="Dataset name for which to render the result file")
-    parser.add_argument("--path_data", required=True, help="Path to the data")
+    parser.add_argument("--path_data", required=False, help="Path to the data, default is ./data")
     parser.add_argument("--result_path", required=False, help="Path to the results, default is ./results")
     args = parser.parse_args()
     run_id = args.run_id
     dataset = args.dataset
-    path_data = pathlib.Path(args.path_data).resolve()
+    path_to_data = args.path_data if args.path_data is not None else "data"
+    path_data = pathlib.Path(path_to_data).resolve()
     result_path = args.result_path if args.result_path is not None else "results"
     result_path = pathlib.Path(result_path).resolve()
     # assert that the run_id folder exists

docs/conf.py

@@ -56,9 +56,9 @@
 # the built documents.
 #
 # The short X.Y version.
-version = "1.3.0"
+version = "1.3.1"
 # The full version, including alpha/beta/rc tags.
-release = "1.3.0"
+release = "1.3.1"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/contributing.rst

@@ -31,84 +31,63 @@ Request features on the `Issue Tracker`_.
 How to set up your development environment
 ------------------------------------------
 
-You need Python 3.10+ and Poetry_ to set up your development environment.
+1. Fork the repository on GitHub.
+2. Make a new conda environment with Python 3.11 or 3.12.
+3. ``pip install poetry`` : we use poetry to manage dependencies
+4. ``poetry install`` : this will install all dependencies
+5. Test whether the installation was successful by running the following command:
 
-.. _Poetry: https://python-poetry.org/
+   .. code:: console
 
+      $ python run_suite.py --run_id my_first_run --models NaiveDrugMeanPredictor ElasticNet --dataset TOYv1 --test_mode LCO
 
-How to test the project
------------------------
+6. Visualize the results by running the following command:
 
-For this, you need to install nox and nox-poetry:
+   .. code:: console
 
-.. code:: console
+      $ python create_report.py --run_id my_first_run --dataset TOYv1
 
-   $ pip install nox nox-poetry
+How to test the project
+-----------------------
 
-Run the full test suite:
+Unit tests are located in the ``tests`` directory,
+and are written using the pytest_ testing framework.
 
-.. code:: console
+.. _pytest: https://pytest.readthedocs.io/
 
-   $ nox
+How to submit changes
+---------------------
 
-List the available Nox sessions:
+Open a `pull request`_ to submit changes to this project against the ``development`` branch.
 
-.. code:: console
+Your pull request needs to meet the following guidelines for acceptance:
 
-   $ nox --list-sessions
+- The code must pass all tests.
+- Include unit tests. This project maintains a high code coverage.
+- If your changes add functionality, update the documentation accordingly.
 
-You can also run a specific Nox session.
-For example, invoke the unit test suite like this:
+To run linting and code formatting checks before committing your change, you can install pre-commit as a
+Git hook by running the following command:
 
 .. code:: console
 
-   $ nox --session=tests
+   $ nox --session=pre-commit -- install
 
-Unit tests are located in the ``tests`` directory,
-and are written using the pytest_ testing framework.
+It is recommended to open an issue before starting work on anything.
 
-.. _pytest: https://pytest.readthedocs.io/
+.. _pull request: https://github.com/daisybio/drevalpy/pulls
 
 How to build and view the documentation
 ---------------------------------------
 
 This project uses Sphinx_ together with several extensions to build the documentation.
-
-To install all required dependencies for the documentation run:
-
-.. code:: console
-
-    $ pip install -r docs/requirements.txt
-
-Please note that drevalpy itself must also be installed. To build the documentation run:
+To build the documentation, change into the docs/ directory and run:
 
 .. code:: console
 
     $ make html
 
-from inside the docs folder. The generated static HTML files can be found in the `_build/html` folder.
+The generated static HTML files can be found in the `_build/html` folder.
 Simply open them with your favorite browser.
 
 .. _sphinx: https://www.sphinx-doc.org/en/master/
-
-How to submit changes
----------------------
-
-Open a `pull request`_ to submit changes to this project against the ``development`` branch.
-
-Your pull request needs to meet the following guidelines for acceptance:
-
-- The Nox test suite must pass without errors and warnings.
-- Include unit tests. This project maintains a high code coverage.
-- If your changes add functionality, update the documentation accordingly.
-
-To run linting and code formatting checks before committing your change, you can install pre-commit as a Git hook by running the following command:
-
-.. code:: console
-
-   $ nox --session=pre-commit -- install
-
-It is recommended to open an issue before starting work on anything.
-This will allow a chance to talk it over with the owners and validate your approach.
-
-.. _pull request: https://github.com/daisybio/drevalpy/pulls