Merge pull request #10 from Remi-Gau/lint

[ENH] package and container

.dockerignore

@@ -0,0 +1,23 @@
+# ignoring this might speed up build
+# by preventing passing extra content to the docker daemon
+
+
+# General
+.DS_Store
+
+.github
+.vscode
+
+**/data
+**/docs
+**/tests
+**/*.zip
+**/*.asc
+**/*.edf
+**/*.EDF
+
+**/build
+.pytest_cache
+.mypy_cache
+coverage_html
+.coverage

.flake8

@@ -11,6 +11,8 @@ docstring-convention = numpy
 max-line-length = 90
 max_complexity = 15
 max_function_length = 100
+per-file-ignores =
+	**/__init__.py: D104
 # 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

@@ -0,0 +1,23 @@
+---
+name: docker
+
+concurrency:
+    group: ${{ github.workflow }}-${{ github.ref }}
+    cancel-in-progress: true
+
+on:
+    push:
+        branches: [main]
+    pull_request:
+        branches: [main]
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        steps:
+        -   name: Clone
+            uses: actions/checkout@v3
+            with:
+                fetch-depth: 0
+        -   name: Build docker image
+            run: docker build -t eye2bids:latest .

.gitignore

@@ -2,6 +2,10 @@ tests/data/test_data.zip
 **/*.asc
 **/*.edf
 **/*.EDF
+eye2bids/_version.py
+
+# General
+.DS_Store
 
 # Byte-compiled / optimized / DLL files
 __pycache__/

Dockerfile

@@ -0,0 +1,110 @@
+# Generated by Neurodocker and Reproenv.
+
+FROM ubuntu:22.04
+RUN apt-get update -qq \
+           && apt-get install -y -q --no-install-recommends \
+                  ca-certificates \
+                  curl \
+                  gcc \
+                  gnupg2 \
+                  pip \
+                  python3 \
+                  software-properties-common \
+           && rm -rf /var/lib/apt/lists/*
+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'
+RUN apt-get update -qq \
+           && apt-get install -y -q --no-install-recommends \
+                  eyelink-display-software \
+           && rm -rf /var/lib/apt/lists/*
+RUN mkdir /eye2bids
+COPY [".", \
+      "/eye2bids"]
+WORKDIR /eye2bids
+RUN pip install .[dev]
+
+# Save specification to JSON.
+RUN printf '{ \
+  "pkg_manager": "apt", \
+  "existing_users": [ \
+    "root" \
+  ], \
+  "instructions": [ \
+    { \
+      "name": "from_", \
+      "kwds": { \
+        "base_image": "ubuntu:22.04" \
+      } \
+    }, \
+    { \
+      "name": "install", \
+      "kwds": { \
+        "pkgs": [ \
+          "gnupg2", \
+          "curl", \
+          "gcc", \
+          "ca-certificates", \
+          "software-properties-common", \
+          "python3", \
+          "pip" \
+        ], \
+        "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/*" \
+      } \
+    }, \
+    { \
+      "name": "run", \
+      "kwds": { \
+        "command": "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'"'"'" \
+      } \
+    }, \
+    { \
+      "name": "install", \
+      "kwds": { \
+        "pkgs": [ \
+          "eyelink-display-software" \
+        ], \
+        "opts": null \
+      } \
+    }, \
+    { \
+      "name": "run", \
+      "kwds": { \
+        "command": "apt-get update -qq \\\\\\n    && apt-get install -y -q --no-install-recommends \\\\\\n           eyelink-display-software \\\\\\n    && rm -rf /var/lib/apt/lists/*" \
+      } \
+    }, \
+    { \
+      "name": "run", \
+      "kwds": { \
+        "command": "mkdir /eye2bids" \
+      } \
+    }, \
+    { \
+      "name": "copy", \
+      "kwds": { \
+        "source": [ \
+          ".", \
+          "/eye2bids" \
+        ], \
+        "destination": "/eye2bids" \
+      } \
+    }, \
+    { \
+      "name": "workdir", \
+      "kwds": { \
+        "path": "/eye2bids" \
+      } \
+    }, \
+    { \
+      "name": "run", \
+      "kwds": { \
+        "command": "pip install .[dev]" \
+      } \
+    } \
+  ] \
+}' > /.reproenv.json
+# End saving to specification to JSON.

Makefile

@@ -0,0 +1,20 @@
+.PHONY: Dockerfile
+
+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 \
+		--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" \
+		--copy "." "/eye2bids" \
+		--workdir "/eye2bids" \
+		--run "pip install .[dev]" \
+		> Dockerfile
+
+docker_build:
+	docker build -t eye2bids .
+
+test_data:
+	python tools/download_test_data.py

README.md

@@ -1,18 +1,80 @@
 # eye2bids
 
-## Instructions for testing conversion_json
+## Installation
 
 ### Requirements
 
-- edf file by EyeLink Eye Tracker
-- Python3
-- EyeLink Developers Kit. Download from [SR-Research support forum] (forum registration required)
+- Python >= 3.8
+
+If you want to use eye2bids to convert EyeLink data,
+you will need to install the EyeLink Developers Kit.
+It can be downloaded from SR-Research support forum (forum registration required).
+
+The installation on Ubuntu can also be done with the following commands:
+
+Taken from: https://www.sr-research.com/support/docs.php?topic=linuxsoftware
+
+```bash
+sudo add-apt-repository universe
+sudo apt update
+sudo apt 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
+```
+
+### Install eye2bids
+
+- Clone the repository
+
+```bash
+git clone https://github.com/bids-standard/eye2bids.git
+```
+
+- Install the package in editatble mode
+
+```bash
+cd eye2bids
+pip install .
+```
+
+## Using eye2bids
+
+- Supporeted Input data:
+
+    - 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
 
-```
-python3 edf2bids_json.py
+```bash
+python edf2bids_json.py
 ```
 
 [SR-Research support forum]: https://www.sr-research.com/support/forum-9.html
+
+## Docker
+
+You can build the docker image with the following command:
+
+```bash
+docker build -t eye2bids:latest .
+```
+
+## Contributing
+
+Make sure you install eye2bids in editable mode (see above) and install the development dependencies:
+
+```bash
+pip install --editable .[dev]
+```
+
+## Related projects