[MAINT] add tests and refactor (#11)

* start adding cli parser

* rename variables

* add smoke end to end test

* add tests

* add pyaml

* use path

* refactor

* refactor

* extract function

* refactor

* fix workflow

* refactor

Author: Remi-Gau

.dockerignore

@@ -1,7 +1,6 @@
 # ignoring this might speed up build
 # by preventing passing extra content to the docker daemon
 
-
 # General
 .DS_Store
 

.flake8

@@ -9,10 +9,11 @@ exclude =
 	doc/_build
 docstring-convention = numpy
 max-line-length = 90
-max_complexity = 15
+max_complexity = 17
 max_function_length = 100
 per-file-ignores =
 	**/__init__.py: D104
+	./tests/*: D100, D103
 # for compatibility with black
 # https://black.readthedocs.io/en/stable/guides/using_black_with_other_tools.html#flake8
 extend-ignore = E203

.github/workflows/docker.yml

@@ -17,7 +17,5 @@ jobs:
         steps:
         -   name: Clone
             uses: actions/checkout@v3
-            with:
-                fetch-depth: 0
         -   name: Build docker image
             run: docker build -t eye2bids:latest .

.github/workflows/tests.yml

@@ -0,0 +1,51 @@
+---
+name: test
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: ['*']
+
+jobs:
+    test:
+
+        strategy:
+            fail-fast: false
+            matrix:
+                python-version: ['3.8', '3.9', '3.10', '3.11']
+
+        runs-on: ubuntu-latest
+
+        steps:
+
+        -   name: Clone
+            uses: actions/checkout@v3
+
+        -   uses: actions/setup-python@v4
+            with:
+                python-version: ${{ matrix.python-version }}
+
+        -   name: Install dependencies
+            run: |
+                sudo add-apt-repository universe
+                sudo apt-get update
+                sudo apt-get install ca-certificates
+                sudo apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key
+                sudo add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'
+                sudo apt update
+                sudo apt install eyelink-display-software
+                python -m pip install --upgrade pip
+
+        -   name: Install package
+            run: pip install .[test]
+
+        -   name: Install data
+            run: make test_data
+
+        -   name: unit tests
+            run: python -m pytest tests --cov-report=xml

.gitignore

@@ -1,4 +1,5 @@
 tests/data/test_data.zip
+tests/data/**/*.json
 **/*.asc
 **/*.edf
 **/*.EDF

Dockerfile

@@ -6,6 +6,7 @@ RUN apt-get update -qq \
                   ca-certificates \
                   curl \
                   gcc \
+                  git \
                   gnupg2 \
                   pip \
                   python3 \
@@ -45,15 +46,16 @@ RUN printf '{ \
           "ca-certificates", \
           "software-properties-common", \
           "python3", \
-          "pip" \
+          "pip", \
+          "git" \
         ], \
         "opts": null \
       } \
     }, \
     { \
       "name": "run", \
       "kwds": { \
-        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           ca-certificates \\\\\\n           curl \\\\\\n           gcc \\\\\\n           gnupg2 \\\\\\n           pip \\\\\\n           python3 \\\\\\n           software-properties-common \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
+        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           ca-certificates \\\\\\n           curl \\\\\\n           gcc \\\\\\n           git \\\\\\n           gnupg2 \\\\\\n           pip \\\\\\n           python3 \\\\\\n           software-properties-common \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
       } \
     }, \
     { \

Makefile

@@ -4,7 +4,7 @@ Dockerfile:
 	docker run --rm repronim/neurodocker:0.9.5 generate docker \
 		--pkg-manager apt \
 		--base-image ubuntu:22.04 \
-		--install gnupg2 curl gcc ca-certificates software-properties-common python3 pip \
+		--install gnupg2 curl gcc ca-certificates software-properties-common python3 pip git \
 		--run "apt-key adv --fetch-keys https://apt.sr-research.com/SRResearch_key && add-apt-repository 'deb [arch=amd64] https://apt.sr-research.com SRResearch main'" \
 		--install eyelink-display-software \
 		--run "mkdir /eye2bids" \

README.md

@@ -45,12 +45,6 @@ pip install .
 
     - edf file by EyeLink Eye Tracker
 
-To try it, you can install our test data from OSF by running the following command:
-
-```bash
-python tools/download_test_data.py
-```
-
 - manual_metadata.yml file (find template and an example in conversion_json folder)
 
 ### Run code
@@ -77,4 +71,11 @@ Make sure you install eye2bids in editable mode (see above) and install the deve
 pip install --editable .[dev]
 ```
 
+To run the tests, you need to install the [test data from OSF](https://osf.io/jdv7n/)
+by running the following command:
+
+```bash
+python tools/download_test_data.py
+```
+
 ## Related projects

eye2bids/_parser.py

@@ -0,0 +1,16 @@
+import argparse
+
+
+def global_parser():
+    """Parse command line arguments.
+
+    Returns
+    -------
+        parser: An ArgumentParser object.
+
+    """
+    parser = argparse.ArgumentParser()
+    parser.add_argument("--input_file", type=str)
+    parser.add_argument("--metadata_file", type=str)
+    parser.add_argument("--output_dir", type=str)
+    return parser