Initial commit

Dockerfile

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+# Stage 1: General ubuntu environment
+# FROM ubuntu:latest AS linux-base
+FROM ubuntu:latest AS linux-base
+
+ENV LC_CTYPE=C.utf8
+ENV UV_PYTHON_INSTALL_DIR="/python"
+ENV UV_COMPILE_BYTECODE=1
+ENV UV_PROJECT_ENVIRONMENT="/home/cotainr/venv"
+ENV UV_PYTHON=python3.12
+ENV PATH="$UV_PROJECT_ENVIRONMENT/bin:$PATH"
+
+ENV PYTHONFAULTHANDLER=1
+ENV PYTHONUNBUFFERED=1
+ENV PYTHONBREAKPOINT=ipdb.set_trace
+
+# Update ubuntu
+RUN apt-get update
+RUN apt-get upgrade -y
+RUN apt-get install --no-install-recommends -y tzdata build-essential gettext
+RUN apt-get install adduser
+RUN passwd --delete root
+RUN adduser cotainr --disabled-password --gecos ""  #  gecos ==> non-interactive
+
+# Most Linux systems these days have a UID and GID of 1000 for the primary
+# user, so it's usually fine to live with the defualt here, but if you've got a
+# different value (run `id -u` and `id -g` in your shell respectively) you can
+# set this value to make sure that the project will operate with the same UID,
+# creating files in *your* name rather than root.
+#ARG UID=1000
+#ARG GID=1000
+#RUN adduser --system --uid=${UID} --ingroup=cotainr --shell=/bin/bash --home=/home/cotainr cotainr
+
+# Stage 2: Python environment
+FROM linux-base AS python-base
+
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /usr/local/bin/uv
+COPY pyproject.toml ./
+COPY uv.lock ./
+RUN uv sync --frozen --no-dev --no-install-project
+
+# Stage 3: Building environment
+FROM python-base AS builder-base
+
+WORKDIR /home/cotainr
+COPY . /home/cotainr
+USER cotainr

Makefile

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+build:
+	docker build  -t test .
+
+build-nocache:
+	docker build --no-cache -t test .
+
+shell:
+	docker run --name container-main -i -t test bash
+
+tests:
+	docker run -t test python3 -m pytest cotainr/tests/cli

pyproject.toml

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+[build-system]
+requires = ["setuptools >= 61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "cotainr"
+version = "2023.11.0"
+dependencies = []
+requires-python = ">=3.9"
+authors = [
+    {name = "Christian Schou Oxvig"},
+    {name = "René Løwe Jacobsen"},
+    {name = "Eske Christiansen"},
+]
+maintainers = [
+    {name = "Christian Schou Oxvig", email = "[email protected]"},
+    {name = "Joachim Sødequist", email = "[email protected]"},
+    {name = "Tor Skovsgaard", email = "[email protected]"},
+]
+description = "A user space Apptainer/Singularity container builder"
+readme = "README.md"
+license = {file = "LICENSE"}
+keywords = ["hpc", "container", "singularity", "apptainer"]
+classifiers = [
+    "Development Status :: 5 - Stable",
+    "Intended Audience :: Users",
+    "Topic :: Software Development :: HPC Tools",
+    "License :: EUPL-1.2",
+    "Programming Language :: Python :: 3",
+    "Programming Language :: Python :: 3.9",
+    "Programming Language :: Python :: 3.10",
+    "Programming Language :: Python :: 3.11",
+    "Programming Language :: Python :: 3.12",
+]
+
+[project.optional-dependencies]
+test = [
+    "pytest>=6.0",
+    "pytest-cov>=2.10",
+]
+docs = [
+    "numpydoc>=1.5.0",
+    "pydata-sphinx-theme>=0.13.3",
+    "sphinx>=7.2.5",
+    "sphinx-design>=0.5.0",
+    "myst-parser>=2.0.0",
+]
+dev-env = [
+    "uv",
+    "ruff~=0.6",
+    "coverage~=7.6",
+]
+
+[project.scripts]
+cotainr = "cotainr.cli:main"
+
+[project.urls]
+Documentation = "https://cotainr.readthedocs.io/en/stable/"
+Repository = "https://github.com/DeiC-HPC/cotainr.git"
+"Bug Tracker" = "https://github.com/DeiC-HPC/cotainr/issues"
+Changelog = "https://cotainr.readthedocs.io/en/stable/release_notes/index.html"
+
+[tool.ruff]
+cache-dir = ".cache/ruff"
+line-length = 88
+lint.extend-select = [
+    "B", # flake8-bugbear
+    "E", # pycodestyle errors
+    "F", # Pyflakes
+    "W", # pycodestyle warnings
+]
+lint.ignore = [
+    "E501",  # Automatic conversion of .format() to f-strings
+]
+lint.exclude = [
+    "examples/**/*.ipynb"
+]
+preview = true
+
+[tool.ruff.extend-per-file-ignores]
+"cotainr/tests/**/test_*.py" = [
+    # The non-standard way to import py.test fixtures in
+    # tests means we will need to ignore "imported but not used"
+    # as well as argument shadowing tests in test modules.
+    "F401",
+    "F811",
+]
+"cotainr/tests/**.py" = [
+    "S101", # assertions are OK in tests
+]
+
+[tool.ruff.lint.pydocstyle]
+convention = "numpy"
+
+[tool.ruff.format]
+exclude = [
+    "examples/**/*.ipynb",
+]
+
+[tool.ruff.lint.isort]
+case-sensitive = true
+lines-after-imports = 2
+lines-between-types = 1
+combine-as-imports = true
+split-on-trailing-comma = true
+
+# Not following pep8
+[tool.ruff.lint.pycodestyle]
+max-line-length = 88
+max-doc-length = 88
+
+
+[tool.coverage.run]
+branch = true
+data_file = "/home/usr/.cache/coverage/data"
+
+[tool.coverage.report]
+ignore_errors = true
+fail_under = 100
+show_missing = true
+skip_covered = true
+omit = [
+    "*/tests/*",
+    "demo/settings.py",
+    "manage.py",
+    ".venv/*"
+]
+exclude_lines = [
+    "pragma: no cover",
+    "raise NotImplementedError"
+]
+
+
+# Coverage reports get written to `.cache`, which is ignored by git thanks to
+# .gitignore
+[tool.coverage.html]
+directory = "/home/usr/.cache/coverage/report"

requirements-dev.txt

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+# This file was autogenerated by uv via the following command:
+#    uv pip compile pyproject.toml --all-extras -o requirements-dev.txt
+accessible-pygments==0.0.5
+    # via pydata-sphinx-theme
+alabaster==1.0.0
+    # via sphinx
+babel==2.16.0
+    # via
+    #   pydata-sphinx-theme
+    #   sphinx
+beautifulsoup4==4.12.3
+    # via pydata-sphinx-theme
+certifi==2024.8.30
+    # via requests
+charset-normalizer==3.3.2
+    # via requests
+coverage==7.6.1
+    # via pytest-cov
+docutils==0.21.2
+    # via
+    #   myst-parser
+    #   pydata-sphinx-theme
+    #   sphinx
+idna==3.10
+    # via requests
+imagesize==1.4.1
+    # via sphinx
+iniconfig==2.0.0
+    # via pytest
+jinja2==3.1.4
+    # via
+    #   myst-parser
+    #   sphinx
+markdown-it-py==3.0.0
+    # via
+    #   mdit-py-plugins
+    #   myst-parser
+markupsafe==2.1.5
+    # via jinja2
+mdit-py-plugins==0.4.2
+    # via myst-parser
+mdurl==0.1.2
+    # via markdown-it-py
+myst-parser==4.0.0
+    # via cotainr (pyproject.toml)
+numpydoc==1.8.0
+    # via cotainr (pyproject.toml)
+packaging==24.1
+    # via
+    #   pydata-sphinx-theme
+    #   pytest
+    #   sphinx
+pluggy==1.5.0
+    # via pytest
+pydata-sphinx-theme==0.15.4
+    # via cotainr (pyproject.toml)
+pygments==2.18.0
+    # via
+    #   accessible-pygments
+    #   pydata-sphinx-theme
+    #   sphinx
+pytest==8.3.3
+    # via
+    #   cotainr (pyproject.toml)
+    #   pytest-cov
+pytest-cov==5.0.0
+    # via cotainr (pyproject.toml)
+pyyaml==6.0.2
+    # via myst-parser
+requests==2.32.3
+    # via sphinx
+snowballstemmer==2.2.0
+    # via sphinx
+soupsieve==2.6
+    # via beautifulsoup4
+sphinx==8.0.2
+    # via
+    #   cotainr (pyproject.toml)
+    #   myst-parser
+    #   numpydoc
+    #   pydata-sphinx-theme
+    #   sphinx-design
+sphinx-design==0.6.1
+    # via cotainr (pyproject.toml)
+sphinxcontrib-applehelp==2.0.0
+    # via sphinx
+sphinxcontrib-devhelp==2.0.0
+    # via sphinx
+sphinxcontrib-htmlhelp==2.1.0
+    # via sphinx
+sphinxcontrib-jsmath==1.0.1
+    # via sphinx
+sphinxcontrib-qthelp==2.0.0
+    # via sphinx
+sphinxcontrib-serializinghtml==2.0.0
+    # via sphinx
+tabulate==0.9.0
+    # via numpydoc
+typing-extensions==4.12.2
+    # via pydata-sphinx-theme
+urllib3==2.2.3
+    # via requests
+uv==0.4.17
+    # via cotainr (pyproject.toml)