[WIP][ENH] add Dockerfile for python version og GLM single

.gitignore

@@ -1,8 +1,10 @@
-#
+# vscode files
 .vscode/
 
+# test related
+tests/outputs/
 
-# data folder
+# data folders
 data/
 
 # example output folders
@@ -13,6 +15,9 @@ figures/
 report.html
 ##*.png
 
+# pyenv
+Pipfile
+
 # Byte-compiled / optimized / DLL files
 __pycache__/
 *.py[cod]
@@ -54,6 +59,7 @@ pip-delete-this-directory.txt
 htmlcov/
 .tox/
 .coverage
+coverage_html
 .coverage.*
 .cache
 nosetests.xml
@@ -153,4 +159,3 @@ codegen/
 
 # Octave session info
 octave-workspace
-

.pre-commit-config.yaml

@@ -0,0 +1,7 @@
+# See https://pre-commit.com for more information
+# See https://pre-commit.com/hooks.html for more hooks
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.1.0
+    hooks:
+      - id: check-yaml

CONTRIBUTING.md

@@ -0,0 +1,56 @@
+# CONTRIBUTING
+
+Information for anyone who would like to contribute to this repository.
+
+## Repository map
+
+```bash
+├── .git
+├── .github
+│   └── workflows         # Github continuous integration set up
+├── examples
+│   ├── data
+│   ├── example1outputs
+│   ├── example2outputs
+├── glmsingle             # Python implementation
+│   ├── cod
+│   ├── design
+│   ├── gmm
+│   ├── hrf
+│   ├── ols
+│   ├── ssq
+│   └── utils
+├── matlab                # Matlab implementation
+│   ├── examples
+│   ├── fracridge
+│   └── utilities
+└── tests                 # Python and Matlab tests
+    └── data
+
+```
+
+## Generic
+
+### Makefile
+
+### pre-commit
+
+## Matlab
+
+### Style guide
+
+### Tests
+
+#### Demos
+
+### Continuous integration
+
+## Python
+
+### Style guide
+
+### Tests
+
+#### Demos
+
+### Continuous integration

Dockerfile

@@ -0,0 +1,127 @@
+# Generated by: Neurodocker version 0.7.0+0.gdc97516.dirty
+# Latest release: Neurodocker version 0.8.0
+# Timestamp: 2022/04/11 12:55:39 UTC
+# 
+# Thank you for using Neurodocker. If you discover any issues
+# or ways to improve this software, please submit an issue or
+# pull request on our GitHub repository:
+# 
+#     https://github.com/ReproNim/neurodocker
+
+FROM python:3.9.12-slim-buster
+
+USER root
+
+ARG DEBIAN_FRONTEND="noninteractive"
+
+ENV LANG="en_US.UTF-8" \
+    LC_ALL="en_US.UTF-8" \
+    ND_ENTRYPOINT="/neurodocker/startup.sh"
+RUN export ND_ENTRYPOINT="/neurodocker/startup.sh" \
+    && apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           apt-utils \
+           bzip2 \
+           ca-certificates \
+           curl \
+           locales \
+           unzip \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/* \
+    && sed -i -e 's/# en_US.UTF-8 UTF-8/en_US.UTF-8 UTF-8/' /etc/locale.gen \
+    && dpkg-reconfigure --frontend=noninteractive locales \
+    && update-locale LANG="en_US.UTF-8" \
+    && chmod 777 /opt && chmod a+s /opt \
+    && mkdir -p /neurodocker \
+    && if [ ! -f "$ND_ENTRYPOINT" ]; then \
+         echo '#!/usr/bin/env bash' >> "$ND_ENTRYPOINT" \
+    &&   echo 'set -e' >> "$ND_ENTRYPOINT" \
+    &&   echo 'export USER="${USER:=`whoami`}"' >> "$ND_ENTRYPOINT" \
+    &&   echo 'if [ -n "$1" ]; then "$@"; else /usr/bin/env bash; fi' >> "$ND_ENTRYPOINT"; \
+    fi \
+    && chmod -R 777 /neurodocker && chmod a+s /neurodocker
+
+ENTRYPOINT ["/neurodocker/startup.sh"]
+
+RUN apt-get update -qq \
+    && apt-get install -y -q --no-install-recommends \
+           build-essential \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+COPY ["glmsingle", "setup.py", "MANIFEST.in", "README.md", "requirements.txt", "/glmsingle/"]
+
+WORKDIR /glmsingle
+
+RUN pip install .
+
+RUN pip install jupyterlab
+
+EXPOSE 8888
+
+RUN test "$(getent passwd neuro)" || useradd --no-user-group --create-home --shell /bin/bash neuro
+USER neuro
+
+WORKDIR /home/neuro
+
+COPY ["examples", "/home/neuro/examples"]
+
+RUN echo '{ \
+    \n  "pkg_manager": "apt", \
+    \n  "instructions": [ \
+    \n    [ \
+    \n      "base", \
+    \n      "python:3.9.12-slim-buster" \
+    \n    ], \
+    \n    [ \
+    \n      "install", \
+    \n      [ \
+    \n        "build-essential" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "copy", \
+    \n      [ \
+    \n        "glmsingle", \
+    \n        "setup.py", \
+    \n        "MANIFEST.in", \
+    \n        "README.md", \
+    \n        "requirements.txt", \
+    \n        "/glmsingle/" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/glmsingle" \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "pip install ." \
+    \n    ], \
+    \n    [ \
+    \n      "run", \
+    \n      "pip install jupyterlab" \
+    \n    ], \
+    \n    [ \
+    \n      "expose", \
+    \n      [ \
+    \n        "8888" \
+    \n      ] \
+    \n    ], \
+    \n    [ \
+    \n      "user", \
+    \n      "neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "workdir", \
+    \n      "/home/neuro" \
+    \n    ], \
+    \n    [ \
+    \n      "copy", \
+    \n      [ \
+    \n        "examples", \
+    \n        "/home/neuro/examples" \
+    \n      ] \
+    \n    ] \
+    \n  ] \
+    \n}' > /neurodocker/neurodocker_specs.json

Makefile

@@ -0,0 +1,160 @@
+.DEFAULT_GOAL := help
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+# TODO make more general to use the local matlab version
+MATLAB = /usr/local/MATLAB/R2017a/bin/matlab
+MATLAB_ARG    = -nodisplay -nosplash -nodesktop
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+# determines what "make help" will show
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+################################################################################
+# 	GENERIC
+.PHONY: help clean clean-test lint install_dev
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage artifacts
+
+clean-test: ## remove test and coverage artifacts
+	rm -rf .tox/
+	rm -rf .coverage
+	rm -rf htmlcov/
+	rm -rf .pytest_cache
+	rm -rf tests/data
+	rm -rf test/outputs
+
+install_dev: ## install for both matlab and python developpers
+	pip install -e .
+	pip install -r requirements_dev.txt
+
+lint: lint/black lint/flake8 lint/miss_hit ## check style
+
+test: test-matlab test-python
+
+tests/data/nsdcoreexampledataset.mat: 
+	mkdir tests/data
+	curl -fsSL --retry 5 -o "tests/data/nsdcoreexampledataset.mat" https://osf.io/k89b2/download
+
+################################################################################
+
+################################################################################
+# 	MATLAB
+
+.PHONY: lint/miss_hit
+
+lint/miss_hit: ## lint and checks matlab code
+	mh_style --fix tests && mh_metric --ci tests && mh_lint tests
+
+test-matlab: tests/data/nsdcoreexampledataset.mat
+	$(MATLAB) $(MATLAB_ARG) -r "run_tests; exit()"
+
+coverage-matlab: test-matlab
+	$(BROWSER) coverage_html/index.html
+
+################################################################################
+
+################################################################################
+# 	PYTHON
+
+.PHONY: clean-build clean-pyc coverage-python install lint/flake8 lint/black
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+lint/flake8: ## check style with flake8
+	flake8 tests
+lint/black: ## check style with black
+	black tests
+
+test-python: tests/data/nsdcoreexampledataset.mat ## run tests quickly with the default Python
+	pytest 
+
+test-notebooks:
+	pytest  --nbmake --nbmake-timeout=3000 "./examples"
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage-python: ## check code coverage quickly with the default Python
+	coverage run --source glmsingle -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install
+
+################################################################################
+
+################################################################################
+# 	DOCKER
+
+.PHONY: Dockerfile glmsingle.def
+Dockerfile:
+	docker run --rm repronim/neurodocker:0.7.0 generate docker \
+		--base python:3.9.12-slim-buster \
+		--pkg-manager apt \
+		--install "build-essential" \
+		--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /glmsingle/ \
+		--workdir /glmsingle \
+		--run "pip install ." \
+		--run "pip install jupyterlab" \
+		--expose 8888 \
+		--user neuro \
+		--workdir /home/neuro \
+		--copy examples /home/neuro/examples > Dockerfile
+
+docker_build: Dockerfile
+	docker build . -t glmsingle:latest
+
+docker_run: docker_build
+	mkdir -p $$PWD/tmp
+	docker run -it --rm \
+		--publish 8888:8888 \
+		--volume $$PWD/tmp:/home/neuro/tmp \
+		glmsingle:latest \
+			jupyter-lab --no-browser --ip 0.0.0.0
+
+glmsingle.def:
+	docker run --rm repronim/neurodocker:0.7.0 generate singularity \
+		--base python:3.9.12-slim-buster \
+		--pkg-manager apt \
+		--install "build-essential" \
+		--copy glmsingle setup.py MANIFEST.in README.md requirements.txt /home/glmsingle/ \
+		--workdir /glmsingle \
+		--run "pip install ." \
+		--user neuro \
+		--workdir /home/neuro \
+		--copy examples /home/neuro/examples > glmsingle.def
+
+singularity_build: glmsingle.def
+	sudo singularity build glmsingle.sif glmsingle.def