Merge pull request #8 from tomo-oga/refactor_with_base

Refactoring Trialsynth with Base Module

.github/workflows/stability_tests.yml

@@ -4,12 +4,12 @@ on:
   push:
     branches: [main]
     paths:
-      - ".github/workflows/stability_tests.yml"
-      - "src/*"
+      - .github/workflows/stability_tests.yml
+      - src/*
   pull_request:
     paths:
-      - ".github/workflows/stability_tests.yml"
-      - "src/*"
+      - .github/workflows/stability_tests.yml
+      - src/*
   workflow_dispatch:
 
 jobs:
@@ -21,7 +21,7 @@ jobs:
       - name: Install Cython dependencies
         run: sudo apt update && sudo apt install -y gcc build-essential python3-dev curl
 
-      - name: Install poetry 
+      - name: Install poetry
         run: curl -sSL https://install.python-poetry.org | python3 -
 
       - name: Install python dependencies

.readthedocs.yml

@@ -28,6 +28,5 @@ sphinx:
 # to build your documentation
 # See https://docs.readthedocs.io/en/stable/guides/reproducible-builds.html
 python:
-    install:
+  install:
     - requirements: doc/requirements.txt
-

.trunk/trunk.yaml

@@ -0,0 +1,41 @@
+# This file controls the behavior of Trunk: https://docs.trunk.io/cli
+# To learn more about the format of this file, see https://docs.trunk.io/reference/trunk-yaml
+version: 0.1
+cli:
+  version: 1.22.2
+# Trunk provides extensibility via plugins. (https://docs.trunk.io/plugins)
+plugins:
+  sources:
+    - id: trunk
+      ref: v1.6.1
+      uri: https://github.com/trunk-io/plugins
+# Many linters and tools depend on runtimes - configure them here. (https://docs.trunk.io/runtimes)
+runtimes:
+  enabled:
+    - [email protected]
+    - [email protected]
+# This is the section where you manage your linters. (https://docs.trunk.io/check/configuration)
+lint:
+  enabled:
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - git-diff-check
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+    - [email protected]
+actions:
+  disabled:
+    - trunk-announce
+  enabled:
+    - trunk-upgrade-available
+    - trunk-fmt-pre-commit
+    - trunk-check-pre-push

README.md

@@ -2,13 +2,13 @@
 
 Interpretation and integration of clinical trials data from multiple registries in a computable form
 
-
 ## Adding registries and processors
 
 Getting data of each registry happens via a corresponding `Processor` object, its components, and relevant methods and functions.
 Users create a `Processor` by composition; some require different work than others.
 
 Some common components include:
+
 - Fetcher: get raw data from a source (e.g. a REST API)
 - Transformer: change the data into a desired format for downstream use
 - Storer: save the data to some location(s)
@@ -19,46 +19,44 @@ Some common components include:
 ![Processor with common components](./composition.svg)
 
 A user can add a registry and `Processor` by test-driven development. A pattern for doing this looks like:
+
 - Get a sample response from the API and save it to a file
 - Write the test for API stability
-    - This can detect unexpected API behavior (e.g. changes or outages)
+  - This can detect unexpected API behavior (e.g. changes or outages)
 - Add the file to the imposter to use as a stubbed response
-    - Add a new port for the stubbed service to the imposter and compose files
+  - Add a new port for the stubbed service to the imposter and compose files
 - Write the test for the processor's end-to-end behaviors
-    - The input is the sample response
+  - The input is the sample response
 - Write the components and functions to make the test pass
-    - Set the `url` environment variable for the `Processor` to the stub's port
-
+  - Set the `url` environment variable for the `Processor` to the stub's port
 
 ## Installation
 
 Run the following to install this repository's package in editable mode:
 
-```
+```bash
 $ git clone https://github.com/gyorilab/trialsynth
 $ cd trialsynth
 $ pip install -e
 ```
 
-
 ## Local run
 
 Users can run all system components on their computers via the compose stack, wrapped by a shell script:
-```
+
+```bash
 ./run_e2e.sh
 ```
 
-
 ## Testing
 
 Users can run all the suite of full system tests on their computers via the compose stack, wrapped by a shell script:
-```
+
+```bash
 ./test_e2e.sh
 ```
 
-
 ## References
 
 [Test-driven development](https://tidyfirst.substack.com/p/canon-tdd)
 [Mountebank](https://www.mbtest.org/)
-

doc/conf.py

@@ -8,24 +8,23 @@
 import os
 import sys
 
-sys.path.insert(0, os.path.join(os.path.abspath('..'), 'src'))
+sys.path.insert(0, os.path.join(os.path.abspath(".."), "src"))
 
-project = 'trialsynth'
-copyright = '2024, Gyori lab'
-author = 'Gyori lab'
+project = "trialsynth"
+copyright = "2024, Gyori lab"
+author = "Gyori lab"
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
 extensions = ["sphinx.ext.autodoc"]
 
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
-
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 
 # -- Options for HTML output -------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#options-for-html-output
 
-html_theme = 'sphinx_rtd_theme'
-html_static_path = ['_static']
+html_theme = "sphinx_rtd_theme"
+html_static_path = ["_static"]