#296: move debug instructions to docs

alphadia/cli.py

@@ -354,11 +354,6 @@ def run(*args, **kwargs):
         sys.exit(exit_code)
 
 
-# To debug e2e tests with PyCharm:
-# create a configuration with
-# - module: alphadia.cli
-# - script parameters: "--config /abs/path/to/tests/e2e_tests/basic/config.yaml"
-# - working directory: "/abs/path/to/tests/e2e_tests"
-# - uncomment the following:
+# uncomment for debugging:
 # if __name__ == "__main__":
 #     run()

docs/contributing.md → docs/developer_guide.md

@@ -1,5 +1,5 @@
-# Contributing
-This document gathers information on how to contribute to the alphaDIA project.
+# Developer Guide
+This document gathers information on how to develop and contribute to the alphaDIA project.
 
 ## Release process
 ### Tagging of changes
@@ -23,6 +23,16 @@ specifying the release tag (e.g. `vX.Y.Z`).
 
 
 ## Notes for developers
+### Debugging
+To debug e2e tests with PyCharm:
+1. Create a "Run/Debug configuration" with
+ - "module": `alphadia.cli`
+ - "script parameters": `--config /abs/path/to/tests/e2e_tests/basic/config.yaml`
+ - "working directory": `/abs/path/to/tests/e2e_tests`
+2. Uncomment the lines following the `uncomment for debugging` comment in `alphadia/cli.py`.
+3. Run the configuration.
+
+
 ### pre-commit hooks
 It is highly recommended to use the provided pre-commit hooks, as the CI pipeline enforces all checks therein to
 pass in order to merge a branch.

docs/installation.md

@@ -65,7 +65,7 @@ AlphaDIA can be installed in editable (i.e. developer) mode. This allows to full
 
 Make sure you have a conda environment and Mono installed for reading `.raw` files as described [here](https://github.com/MannLabs/alpharaw#installation).
 
-See also the [developer guide](contributing.md) for more information on how to contribute to alphaDIA.
+See also the [developer guide](developer_guide.md) for more information on how to contribute to alphaDIA.
 
 ### 1. Setting up the repository