diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index f9eacb5..20b0e5c 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -9,39 +9,35 @@ jobs: strategy: matrix: python-version: - - 3.6 - - 3.7 - - 3.8 - 3.9 steps: - - name: Install Python via conda. - uses: s-weigand/setup-conda@v1 - with: - python-version: ${{ matrix.python-version }} - conda-channels: defaults,bioconda,conda-forge - name: Checkout repository - uses: actions/checkout@v2 + uses: actions/checkout@v4 with: lfs: true - - name: Install test dependencies via pip - run: pip install -r requirements/test_black.txt - - name: Run tests - run: pytest - - name: Create text report - run: coverage report - - name: Create XML report for codacy - run: coverage xml - - name: Coveralls - uses: AndreMiras/coveralls-python-action@develop - - name: Run codacy-coverage-reporter - uses: codacy/codacy-coverage-reporter-action@master + - name: Setup conda conda. + uses: conda-incubator/setup-miniconda@v3 + with: + conda-channels: conda-forge,bioconda + - name: Install uv + uses: astral-sh/setup-uv@v3 with: - project-token: ${{ secrets.CODACY_PROJECT_TOKEN }} - coverage-reports: coverage.xml - if: ${{ matrix.python-version == '3.7' && (github.ref == 'refs/heads/main') }} - - name: Check style with black - run: black --check --line-length 100 . - if: ${{ matrix.python-version < '3.9' }} - - name: Check style with flake8 - run: flake8 . + # Install a specific version of uv and enable caching. + version: "0.5.16" + enable-cache: true + + - name: Set up Python + run: uv python install ${{ matrix.python-version }} + + - name: Install the project + run: uv sync --all-extras --dev + + - name: Run tests + run: uv run pytest + + - name: Check formatting + run: uv run ruff format --check + + - name: Lint + run: uv run ruff check diff --git a/MANIFEST.in b/MANIFEST.in index 14b36bd..d6c85c2 100644 --- a/MANIFEST.in +++ b/MANIFEST.in @@ -2,7 +2,9 @@ include AUTHORS.rst include CONTRIBUTING.rst include HISTORY.rst include LICENSE -include README.rst +include README.md + +graft src recursive-include tests requirements * recursive-exclude * __pycache__ @@ -10,7 +12,4 @@ recursive-exclude * *.py[co] recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif -include versioneer.py -recursive-include sodar_cli *.py - include requirements.txt requirements/*.txt diff --git a/Makefile b/Makefile index 739bbc4..29b6d4e 100644 --- a/Makefile +++ b/Makefile @@ -1,37 +1,15 @@ .PHONY: all -all: black +all: format lint pytest -.PHONY: black -black: - black -l 100 . +.PHONY: format +format: + uv run ruff format . -.PHONY: test -test: - black -l 100 --check . +.PHONY: lint +lint: + uv run ruff check . .PHONY: pytest pytest: - pytest . + uv run pytest -.PHONY: lint-all -lint-all: bandit pyflakes pep257 prospector - -.PHONY: bandit -bandit: - bandit -c bandit.yml -r sodar_cli - -.PHONY: pyflakes -pyflakes: - pyflakes sodar_cli tests - -.PHONY: pep257 -pep257: - pep257 - -.PHONY: flake8 -flake8: - flake8 - -.PHONY: prospector -prospector: - prospector diff --git a/README.md b/README.md new file mode 100644 index 0000000..555edd9 --- /dev/null +++ b/README.md @@ -0,0 +1,57 @@ +[![Continuous Integration Status](https://github.com/bihealth/sodar-cli/workflows/CI/badge.svg)](https://github.com/bihealth/sodar-cli/actions) + +[![image](https://app.codacy.com/project/badge/Grade/0bf5c6d8a91e4a7380676672e466525d)](https://www.codacy.com/gh/bihealth/sodar-cli/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/sodar-cli&utm_campaign=Badge_Grade) + +[![image](https://app.codacy.com/project/badge/Coverage/0bf5c6d8a91e4a7380676672e466525d)](https://www.codacy.com/gh/bihealth/sodar-cli/dashboard?utm_source=github.com&utm_medium=referral&utm_content=bihealth/sodar-cli&utm_campaign=Badge_Coverage) + +[![image](https://coveralls.io/repos/github/bihealth/sodar-cli/badge.svg?branch=main)](https://coveralls.io/github/bihealth/sodar-cli?branch=main) + +[![MIT License](https://img.shields.io/badge/License-MIT-green.svg)](https://opensource.org/licenses/MIT) + +# SODAR CLI + +Command line interface for [SODAR +Server](https://github.com/bihealth/sodar-server). + +## Getting Started + +- [SODAR Homepage](https://www.cubi.bihealth.org/software/sodar/) +- [Manual](https://sodar-server.readthedocs.io/en/latest/) + +## SODAR Repositories + +[sodar-server](https://github.com/bihealth/sodar-server) + +: SODAR web server for meta and mass data management. + +[sodar-taskflow](https://github.com/bihealth/sodar-taskflow) + +: Helper component for running tasks with rollback functionality. + +## Installation + +``` bash +$ git clone git@github.com:bihealth/sodar-cli.git +$ cd sodar-cli +$ conda create -n sodar-cli python=3.7 +$ conda activate sodar-cli +$ pip install -e . +$ cat >~/.sodarrc.toml <`__. - ---------------- -Getting Started ---------------- - -- `SODAR Homepage `__ -- `Manual `__ - --------------------- -SODAR Repositories --------------------- - -`sodar-server `__ - SODAR web server for meta and mass data management. -`sodar-taskflow `__ - Helper component for running tasks with rollback functionality. - ------------- -Installation ------------- - -.. code-block:: bash - - $ git clone git@github.com:bihealth/sodar-cli.git - $ cd sodar-cli - $ conda create -n sodar-cli python=3.7 - $ conda activate sodar-cli - $ pip install -e . - $ cat >~/.sodarrc.toml <=24.3.0", + "cattrs>=24.1.2", + "logzero>=1.7.0", + "python-dateutil>=2.9.0.post0", + "python-levenshtein>=0.26.1", + "requests>=2.32.3", + "simplejson>=3.19.3", + "tabulate>=0.9.0", + "toml>=0.10.2", + "tqdm>=4.67.1", +] + +[project.license] +file = "LICENSE" + +[project.scripts] +sodar-cli = "sodar_cli.__main__:main" + +[tool.setuptools.dynamic] +version = {attr = "sodar_cli.version.__version__"} + + +[tool.coverage.run] +omit = [] +relative_files = true + +[tool.coverage.report] +exclude_lines = ["pragma: no cover", "def __repr__", "if __name__ == '__main__':"] + +[tool.ruff] +# Exclude a variety of commonly ignored directories. +exclude = [ + ".bzr", + ".direnv", + ".eggs", + ".git", + ".git-rewrite", + ".hg", + ".ipynb_checkpoints", + ".mypy_cache", + ".nox", + ".pants.d", + ".pyenv", + ".pytest_cache", + ".pytype", + ".ruff_cache", + ".svn", + ".tox", + ".venv", + ".vscode", + "__pypackages__", + "_build", + "buck-out", + "build", + "dist", + "node_modules", + "site-packages", + "venv", +] +line-length = 120 +indent-width = 4 + +[tool.ruff.lint] +ignore = ["E203", "E266", "E501"] +select = ["B", "C", "E", "F", "W"] + +[tool.ruff.lint.mccabe] +# Flag errors (`C901`) whenever the complexity level exceeds 18. +max-complexity = 18 + +[tool.pytest.ini_options] +addopts = [ + "--import-mode=importlib", +] + +[dependency-groups] +dev = [ + "factory-boy==2.12.0", + "pytest>=8.3.4", + "requests-mock>=1.7.0", + "ruff>=0.9.0", +] diff --git a/requirements.txt b/requirements.txt deleted file mode 120000 index 2d8105f..0000000 --- a/requirements.txt +++ /dev/null @@ -1 +0,0 @@ -requirements/base.txt \ No newline at end of file diff --git a/requirements/base.txt b/requirements/base.txt deleted file mode 100644 index 621987f..0000000 --- a/requirements/base.txt +++ /dev/null @@ -1,28 +0,0 @@ -# Base requirements - -# Attrs, helpful for removing boilerplate, cattr is for serialization/deserializaton. -attrs -cattrs -# Easy date parsing (e.g., from API). -python-dateutil - -# Easy logging. -logzero - -# Compact, round-tripable configuration format. -toml - -# simplejson has better encoders/decoders -simplejson - -# HTTP requests for humans. -requests - -# Useful progress display. -tqdm - -# Tabular display. -tabulate - -# Levenshtein distance. -python-Levenshtein diff --git a/requirements/develop.txt b/requirements/develop.txt deleted file mode 100644 index 273314f..0000000 --- a/requirements/develop.txt +++ /dev/null @@ -1,7 +0,0 @@ --r test_black.txt - -pip==9.0.1 -wheel==0.30.0 -watchdog==0.8.3 - -twine diff --git a/requirements/test.txt b/requirements/test.txt deleted file mode 100644 index f0adb72..0000000 --- a/requirements/test.txt +++ /dev/null @@ -1,36 +0,0 @@ --r base.txt - -# Multi-environment testing -tox ==2.9.1 - -# Wonderful py.test for testing -pytest >=3.6.0 -pytest-runner >=2.11.1 -pytest-cache >=1.0 -pytest-cov >=2.4.0 -pytest-mock >=2.0.0 - -# Faking of file systems -pyfakefs >=3.7.1 - -# Helper for model creation -factory-boy ==2.12.0 - -# Easier testing of requests -requests-mock >=1.7.0 - -# Coverage report -coverage==5.3.1 -codacy-coverage >=1.3.6 - -# Flake8 for linting -flake8 >=3.5.0 - -# Building documentation is part of the tests -sphinx >=1.7.0 -sphinx-rtd-theme >=0.4.3 -sphinx-argparse >=0.2.5 -m2r - -# Type checking. -mypy diff --git a/requirements/test_black.txt b/requirements/test_black.txt deleted file mode 100644 index f0a377f..0000000 --- a/requirements/test_black.txt +++ /dev/null @@ -1,7 +0,0 @@ -# Requirements including black for code formatting/checking. - -# Include base requirements --r test.txt - -# Black for formatting -black ==18.9b0 diff --git a/setup.cfg b/setup.cfg deleted file mode 100644 index a1cc265..0000000 --- a/setup.cfg +++ /dev/null @@ -1,41 +0,0 @@ -[bdist_wheel] -universal = 1 - -[aliases] -test = pytest - -[flake8] -exclude = - .github - .tox - docs/ - sodar_cli/__init__.py - versioneer.py - -ignore = E203, E266, E501, W503 -max-line-length = 80 -max-complexity = 18 -select = B,C,E,F,W,T4,B9 - -[tool:pytest] -addopts = --cov=sodar_cli --cov-report=xml -testpaths = tests - -[coverage:run] -omit = - sodar_cli/_version.py - -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -VCS = git -style = pep440 -versionfile_source = sodar_cli/_version.py -versionfile_build = sodar_cli/_version.py -tag_prefix = v -parentdir_prefix = sodar_cli - -[mypy] -ignore_missing_imports = true diff --git a/setup.py b/setup.py deleted file mode 100644 index a5ac954..0000000 --- a/setup.py +++ /dev/null @@ -1,64 +0,0 @@ -#!/usr/bin/env python -# -*- coding: utf-8 -*- - -import os.path - -from setuptools import setup, find_packages - -import versioneer - - -def parse_requirements(path): - """Parse ``requirements.txt`` at ``path``.""" - requirements = [] - with open(path, "rt") as reqs_f: - for line in reqs_f: - line = line.strip() - if line.startswith("-r"): - fname = line.split()[1] - inner_path = os.path.join(os.path.dirname(path), fname) - requirements += parse_requirements(inner_path) - elif line != "" and not line.startswith("#"): - requirements.append(line) - return requirements - - -with open("README.rst") as readme_file: - readme = readme_file.read() - -with open("HISTORY.rst") as history_file: - history = history_file.read() - -test_requirements = parse_requirements("requirements/test.txt") -install_requirements = parse_requirements("requirements/base.txt") - -setup( - author="Manuel Holtgrewe", - author_email=("manuel.holtgrewe@bihealth.de"), - classifiers=[ - "Development Status :: 4 - Beta", - "Intended Audience :: Developers", - "License :: OSI Approved :: MIT License", - "Natural Language :: English", - "Topic :: Scientific/Engineering :: Bio-Informatics", - "Programming Language :: Python :: 3", - "Programming Language :: Python :: 3.6", - "Programming Language :: Python :: 3.7", - "Programming Language :: Python :: 3.8", - ], - entry_points={"console_scripts": ("sodar-cli = sodar_cli.__main__:main",)}, - description="Command line interface client for SODAR REST API.", - install_requires=install_requirements, - license="MIT license", - long_description=readme + "\n\n" + history, - include_package_data=True, - keywords="sodar_cli", - name="sodar-cli", - packages=find_packages(include=["sodar_cli"]), - test_suite="tests", - tests_require=test_requirements, - url="https://github.com/bihealth/sodar-cli", - version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), - zip_safe=False, -) diff --git a/sodar_cli/__init__.py b/sodar_cli/__init__.py deleted file mode 100644 index 1387520..0000000 --- a/sodar_cli/__init__.py +++ /dev/null @@ -1,4 +0,0 @@ -from ._version import get_versions # type: ignore - -__version__ = get_versions()["version"] -del get_versions diff --git a/sodar_cli/_version.py b/sodar_cli/_version.py deleted file mode 100644 index 0ef7c28..0000000 --- a/sodar_cli/_version.py +++ /dev/null @@ -1,545 +0,0 @@ -# type: ignore - -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "$Format:%d$" - git_full = "$Format:%H$" - git_date = "$Format:%ci$" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "pep440" - cfg.tag_prefix = "v" - cfg.parentdir_prefix = "vcfpy" - cfg.versionfile_source = "vcfpy/_version.py" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - ) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( - GITS, - ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%s*" % tag_prefix], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split("/"): - root = os.path.dirname(root) - except NameError: - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None, - } - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } diff --git a/src/sodar_cli/__init__.py b/src/sodar_cli/__init__.py new file mode 100644 index 0000000..614d684 --- /dev/null +++ b/src/sodar_cli/__init__.py @@ -0,0 +1 @@ +from .version import __version__ as __version__ diff --git a/sodar_cli/__main__.py b/src/sodar_cli/__main__.py similarity index 84% rename from sodar_cli/__main__.py rename to src/sodar_cli/__main__.py index 4be1366..0b126c4 100644 --- a/sodar_cli/__main__.py +++ b/src/sodar_cli/__main__.py @@ -34,7 +34,12 @@ def setup_argparse(): """Create argument parser.""" # Construct argument parser and set global options. parser = argparse.ArgumentParser(prog="sodar-cli") - parser.add_argument("--verbose", action="store_true", default=False, help="Increase verbosity.") + parser.add_argument( + "--verbose", + action="store_true", + default=False, + help="Increase verbosity.", + ) parser.add_argument("--version", action="version", version="%%(prog)s %s" % __version__) group = parser.add_argument_group("Basic Configuration") @@ -65,12 +70,8 @@ def setup_argparse(): subparsers = parser.add_subparsers(dest="cmd") setup_argparse_project(subparsers.add_parser("project", help="Work with projects.")) - setup_argparse_samplesheet( - subparsers.add_parser("samplesheet", help="Work with sample sheets.") - ) - setup_argparse_landingzone( - subparsers.add_parser("landingzone", help="Work with landing zones.") - ) + setup_argparse_samplesheet(subparsers.add_parser("samplesheet", help="Work with sample sheets.")) + setup_argparse_landingzone(subparsers.add_parser("landingzone", help="Work with landing zones.")) return parser, subparsers @@ -88,9 +89,7 @@ def main(argv=None): level = logging.DEBUG else: # Remove module name and line number if not running in debug mode.s - formatter = logzero.LogFormatter( - fmt="%(color)s[%(levelname)1.1s %(asctime)s]%(end_color)s %(message)s" - ) + formatter = logzero.LogFormatter(fmt="%(color)s[%(levelname)1.1s %(asctime)s]%(end_color)s %(message)s") logzero.formatter(formatter) level = logging.INFO logzero.loglevel(level=level) @@ -108,7 +107,10 @@ def main(argv=None): break else: toml_config = None - logger.info("Could not find any of the global configuration files %s.", config_paths) + logger.info( + "Could not find any of the global configuration files %s.", + config_paths, + ) # Merge configuration from command line/environment args and configuration file. config = CommonConfig.create(args, toml_config) @@ -122,7 +124,11 @@ def main(argv=None): } res = cmds[args.cmd]( - config, toml_config, args, parser, subparsers.choices[args.cmd] if args.cmd else None + config, + toml_config, + args, + parser, + subparsers.choices[args.cmd] if args.cmd else None, ) if not res: logger.info("All done. Have a nice day!") diff --git a/sodar_cli/api/__init__.py b/src/sodar_cli/api/__init__.py similarity index 100% rename from sodar_cli/api/__init__.py rename to src/sodar_cli/api/__init__.py diff --git a/sodar_cli/api/landingzone.py b/src/sodar_cli/api/landingzone.py similarity index 90% rename from sodar_cli/api/landingzone.py rename to src/sodar_cli/api/landingzone.py index 01dc5fb..1afebcd 100644 --- a/sodar_cli/api/landingzone.py +++ b/src/sodar_cli/api/landingzone.py @@ -14,7 +14,10 @@ def retrieve(*, sodar_url, sodar_api_token, landingzone_uuid): while sodar_url.endswith("/"): sodar_url = sodar_url[:-1] url_tpl = "%(sodar_url)s/landingzones/api/retrieve/%(landingzone_uuid)s" - url = url_tpl % {"sodar_url": sodar_url, "landingzone_uuid": landingzone_uuid} + url = url_tpl % { + "sodar_url": sodar_url, + "landingzone_uuid": landingzone_uuid, + } logger.debug("HTTP GET request to %s", url) headers = {"Authorization": "Token %s" % sodar_api_token} @@ -45,7 +48,9 @@ def create(*, sodar_url, sodar_api_token, project_uuid, assay_uuid=None): # Retrieve sample sheet for assay if not given. if not assay_uuid: investigation = samplesheet.retrieve( - sodar_url=sodar_url, sodar_api_token=sodar_api_token, project_uuid=project_uuid + sodar_url=sodar_url, + sodar_api_token=sodar_api_token, + project_uuid=project_uuid, ) if len(investigation.studies) != 1: # pragma: no cover logger.error("Expected one study, found %d", len(investigation.studies)) @@ -76,7 +81,10 @@ def submit_move(*, sodar_url, sodar_api_token, landingzone_uuid): # Move landing zone through API. url_tpl = "%(sodar_url)s/landingzones/api/submit/move/%(landingzone_uuid)s" - url = url_tpl % {"sodar_url": sodar_url, "landingzone_uuid": landingzone_uuid} + url = url_tpl % { + "sodar_url": sodar_url, + "landingzone_uuid": landingzone_uuid, + } logger.debug("HTTP POST request to %s", url) headers = {"Authorization": "Token %s" % sodar_api_token} r = requests.post(url, headers=headers) @@ -95,7 +103,10 @@ def submit_validate(*, sodar_url, sodar_api_token, landingzone_uuid): # Move landing zone through API. url_tpl = "%(sodar_url)s/landingzones/api/submit/validate/%(landingzone_uuid)s" - url = url_tpl % {"sodar_url": sodar_url, "landingzone_uuid": landingzone_uuid} + url = url_tpl % { + "sodar_url": sodar_url, + "landingzone_uuid": landingzone_uuid, + } logger.debug("HTTP POST request to %s", url) headers = {"Authorization": "Token %s" % sodar_api_token} r = requests.post(url, headers=headers) diff --git a/sodar_cli/api/models.py b/src/sodar_cli/api/models.py similarity index 95% rename from sodar_cli/api/models.py rename to src/sodar_cli/api/models.py index 3145325..155e279 100644 --- a/sodar_cli/api/models.py +++ b/src/sodar_cli/api/models.py @@ -16,10 +16,7 @@ def _setup_converter() -> cattr.Converter: result.register_structure_hook(datetime.datetime, lambda d, _: dateutil.parser.parse(d)) result.register_unstructure_hook( datetime.datetime, - lambda obj: obj.replace(tzinfo=datetime.timezone.utc) - .astimezone() - .replace(microsecond=0) - .isoformat(), + lambda obj: obj.replace(tzinfo=datetime.timezone.utc).astimezone().replace(microsecond=0).isoformat(), ) return result diff --git a/sodar_cli/api/project.py b/src/sodar_cli/api/project.py similarity index 100% rename from sodar_cli/api/project.py rename to src/sodar_cli/api/project.py diff --git a/sodar_cli/api/samplesheet.py b/src/sodar_cli/api/samplesheet.py similarity index 93% rename from sodar_cli/api/samplesheet.py rename to src/sodar_cli/api/samplesheet.py index 76751d7..1207517 100644 --- a/sodar_cli/api/samplesheet.py +++ b/src/sodar_cli/api/samplesheet.py @@ -57,7 +57,10 @@ def upload(*, sodar_url, sodar_api_token, project_uuid, file_paths): for no, path in enumerate(file_paths): p = pathlib.Path(path) files.append( - ("file_%d" % no, (p.name, stack.enter_context(p.open("rt")), "text/plain")) + ( + "file_%d" % no, + (p.name, stack.enter_context(p.open("rt")), "text/plain"), + ) ) r = requests.post(url, headers=headers, files=files) r.raise_for_status() diff --git a/sodar_cli/common.py b/src/sodar_cli/common.py similarity index 77% rename from sodar_cli/common.py rename to src/sodar_cli/common.py index 9b6fe1e..768ba06 100644 --- a/sodar_cli/common.py +++ b/src/sodar_cli/common.py @@ -25,12 +25,8 @@ def create(args, toml_config=None): return CommonConfig( verbose=args.verbose, verify_ssl=args.verify_ssl, - sodar_api_token=( - args.sodar_api_token or toml_config.get("global", {}).get("sodar_api_token") - ), - sodar_server_url=( - args.sodar_server_url or toml_config.get("global", {}).get("sodar_server_url") - ), + sodar_api_token=(args.sodar_api_token or toml_config.get("global", {}).get("sodar_api_token")), + sodar_server_url=(args.sodar_server_url or toml_config.get("global", {}).get("sodar_server_url")), ) diff --git a/sodar_cli/exceptions.py b/src/sodar_cli/exceptions.py similarity index 100% rename from sodar_cli/exceptions.py rename to src/sodar_cli/exceptions.py diff --git a/sodar_cli/landingzone/__init__.py b/src/sodar_cli/landingzone/__init__.py similarity index 81% rename from sodar_cli/landingzone/__init__.py rename to src/sodar_cli/landingzone/__init__.py index 0300d94..0fb1709 100644 --- a/sodar_cli/landingzone/__init__.py +++ b/src/sodar_cli/landingzone/__init__.py @@ -5,9 +5,13 @@ from sodar_cli.common import run_nocmd from sodar_cli.landingzone.config import LandingZoneConfig from sodar_cli.landingzone.list import setup_argparse as setup_argparse_list -from sodar_cli.landingzone.retrieve import setup_argparse as setup_argparse_retrieve +from sodar_cli.landingzone.retrieve import ( + setup_argparse as setup_argparse_retrieve, +) from sodar_cli.landingzone.create import setup_argparse as setup_argparse_create -from sodar_cli.landingzone.validate import setup_argparse as setup_argparse_validate +from sodar_cli.landingzone.validate import ( + setup_argparse as setup_argparse_validate, +) from sodar_cli.landingzone.move import setup_argparse as setup_argparse_move @@ -18,9 +22,7 @@ def setup_argparse(parser: argparse.ArgumentParser) -> None: setup_argparse_list(subparsers.add_parser("list", help="List landing zones.")) setup_argparse_retrieve(subparsers.add_parser("retrieve", help="Retrieve landing zone.")) setup_argparse_create(subparsers.add_parser("create", help="Create landing zone.")) - setup_argparse_validate( - subparsers.add_parser("validate", help="Validate landing zone (async).") - ) + setup_argparse_validate(subparsers.add_parser("validate", help="Validate landing zone (async).")) setup_argparse_move(subparsers.add_parser("move", help="Move landing zone (async).")) diff --git a/sodar_cli/landingzone/config.py b/src/sodar_cli/landingzone/config.py similarity index 89% rename from sodar_cli/landingzone/config.py rename to src/sodar_cli/landingzone/config.py index 5f073c4..6b483d0 100644 --- a/sodar_cli/landingzone/config.py +++ b/src/sodar_cli/landingzone/config.py @@ -38,7 +38,8 @@ def create(args, landingzone_config, toml_config=None): _ = toml_config # toml_config = toml_config or {} return LandingZoneListConfig( - landingzone_config=landingzone_config, project_uuid=args.project_uuid + landingzone_config=landingzone_config, + project_uuid=args.project_uuid, ) @@ -56,7 +57,8 @@ class LandingZoneRetrieveConfig: def create(args, landingzone_config, toml_config=None): # toml_config = toml_config or {} return LandingZoneRetrieveConfig( - landingzone_config=landingzone_config, landingzone_uuid=args.landingzone_uuid + landingzone_config=landingzone_config, + landingzone_uuid=args.landingzone_uuid, ) @@ -113,7 +115,8 @@ class LandingZoneSubmitDeleteConfig: def create(args, landingzone_config, toml_config=None): # toml_config = toml_config or {} return LandingZoneSubmitDeleteConfig( - landingzone_config=landingzone_config, landingzone_uuid=args.landingzone_uuid + landingzone_config=landingzone_config, + landingzone_uuid=args.landingzone_uuid, ) @@ -131,7 +134,8 @@ class LandingZoneSubmitValidateConfig: def create(args, landingzone_config, toml_config=None): # toml_config = toml_config or {} return LandingZoneSubmitValidateConfig( - landingzone_config=landingzone_config, landingzone_uuid=args.landingzone_uuid + landingzone_config=landingzone_config, + landingzone_uuid=args.landingzone_uuid, ) @@ -149,5 +153,6 @@ class LandingZoneSubmitMoveConfig: def create(args, landingzone_config, toml_config=None): # toml_config = toml_config or {} return LandingZoneSubmitMoveConfig( - landingzone_config=landingzone_config, landingzone_uuid=args.landingzone_uuid + landingzone_config=landingzone_config, + landingzone_uuid=args.landingzone_uuid, ) diff --git a/sodar_cli/landingzone/create.py b/src/sodar_cli/landingzone/create.py similarity index 77% rename from sodar_cli/landingzone/create.py rename to src/sodar_cli/landingzone/create.py index c7913b4..c10e915 100644 --- a/sodar_cli/landingzone/create.py +++ b/src/sodar_cli/landingzone/create.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="landingzone_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "project_uuid", help="UUID of the project to create landing zone within.", type=uuid.UUID + "--hidden-cmd", + dest="landingzone_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "project_uuid", + help="UUID of the project to create landing zone within.", + type=uuid.UUID, ) diff --git a/sodar_cli/landingzone/list.py b/src/sodar_cli/landingzone/list.py similarity index 77% rename from sodar_cli/landingzone/list.py rename to src/sodar_cli/landingzone/list.py index 39f0e0d..037318b 100644 --- a/sodar_cli/landingzone/list.py +++ b/src/sodar_cli/landingzone/list.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="landingzone_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "project_uuid", help="UUID of the project to list landing zones for.", type=uuid.UUID + "--hidden-cmd", + dest="landingzone_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "project_uuid", + help="UUID of the project to list landing zones for.", + type=uuid.UUID, ) diff --git a/sodar_cli/landingzone/move.py b/src/sodar_cli/landingzone/move.py similarity index 78% rename from sodar_cli/landingzone/move.py rename to src/sodar_cli/landingzone/move.py index dba15ff..1947e56 100644 --- a/sodar_cli/landingzone/move.py +++ b/src/sodar_cli/landingzone/move.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="landingzone_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "landingzone_uuid", help="UUID of the landing zone to move.", type=uuid.UUID + "--hidden-cmd", + dest="landingzone_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "landingzone_uuid", + help="UUID of the landing zone to move.", + type=uuid.UUID, ) diff --git a/sodar_cli/landingzone/retrieve.py b/src/sodar_cli/landingzone/retrieve.py similarity index 78% rename from sodar_cli/landingzone/retrieve.py rename to src/sodar_cli/landingzone/retrieve.py index a64240e..3c7ecc5 100644 --- a/sodar_cli/landingzone/retrieve.py +++ b/src/sodar_cli/landingzone/retrieve.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="landingzone_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "landingzone_uuid", help="UUID of the landing zone to retrieve.", type=uuid.UUID + "--hidden-cmd", + dest="landingzone_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "landingzone_uuid", + help="UUID of the landing zone to retrieve.", + type=uuid.UUID, ) diff --git a/sodar_cli/landingzone/validate.py b/src/sodar_cli/landingzone/validate.py similarity index 79% rename from sodar_cli/landingzone/validate.py rename to src/sodar_cli/landingzone/validate.py index 7570043..e37dc27 100644 --- a/sodar_cli/landingzone/validate.py +++ b/src/sodar_cli/landingzone/validate.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="landingzone_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "landingzone_uuid", help="UUID of the landing zone to validate.", type=uuid.UUID + "--hidden-cmd", + dest="landingzone_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "landingzone_uuid", + help="UUID of the landing zone to validate.", + type=uuid.UUID, ) diff --git a/sodar_cli/project/__init__.py b/src/sodar_cli/project/__init__.py similarity index 91% rename from sodar_cli/project/__init__.py rename to src/sodar_cli/project/__init__.py index ff2feba..34e574d 100644 --- a/sodar_cli/project/__init__.py +++ b/src/sodar_cli/project/__init__.py @@ -16,9 +16,7 @@ def setup_argparse(parser: argparse.ArgumentParser) -> None: setup_argparse_list(subparsers.add_parser("list", help="List Projects.")) setup_argparse_retrieve(subparsers.add_parser("retrieve", help="Retrieve project.")) - setup_argparse_create( - subparsers.add_parser("create", help="Create project (there is no delete!).") - ) + setup_argparse_create(subparsers.add_parser("create", help="Create project (there is no delete!).")) setup_argparse_update(subparsers.add_parser("update", help="Update project.")) diff --git a/sodar_cli/project/config.py b/src/sodar_cli/project/config.py similarity index 100% rename from sodar_cli/project/config.py rename to src/sodar_cli/project/config.py diff --git a/sodar_cli/project/create.py b/src/sodar_cli/project/create.py similarity index 91% rename from sodar_cli/project/create.py rename to src/sodar_cli/project/create.py index 635fa66..87d0cf3 100644 --- a/sodar_cli/project/create.py +++ b/src/sodar_cli/project/create.py @@ -16,7 +16,11 @@ def setup_argparse(parser): parser.add_argument("--title", required=True, help="Title of the project") parser.add_argument("--parent-uuid", required=True, help="UUID of the parent project") parser.add_argument("--owner-uuid", required=True, help="UUID of the owner") - parser.add_argument("--type", default="PROJECT", help="Type of the project [PROJECT, CATEGORY]") + parser.add_argument( + "--type", + default="PROJECT", + help="Type of the project [PROJECT, CATEGORY]", + ) parser.add_argument("--description", help="Description text, optional") parser.add_argument("--readme", help="README text, markdown allowed, optional") diff --git a/sodar_cli/project/list.py b/src/sodar_cli/project/list.py similarity index 100% rename from sodar_cli/project/list.py rename to src/sodar_cli/project/list.py diff --git a/sodar_cli/project/retrieve.py b/src/sodar_cli/project/retrieve.py similarity index 100% rename from sodar_cli/project/retrieve.py rename to src/sodar_cli/project/retrieve.py diff --git a/sodar_cli/project/update.py b/src/sodar_cli/project/update.py similarity index 93% rename from sodar_cli/project/update.py rename to src/sodar_cli/project/update.py index 2a70618..fdee986 100644 --- a/sodar_cli/project/update.py +++ b/src/sodar_cli/project/update.py @@ -18,7 +18,10 @@ def setup_argparse(parser): parser.add_argument("--title", help="Title of the project") parser.add_argument("--parent-uuid", help="UUID of the parent project") parser.add_argument("--owner-uuid", help="UUID of the owner") - parser.add_argument("--type", help="Type of the project [PROJECT, CATEGORY], default PROJECT") + parser.add_argument( + "--type", + help="Type of the project [PROJECT, CATEGORY], default PROJECT", + ) parser.add_argument("--description", help="Description text, optional") parser.add_argument("--readme", help="README text, markdown allowed, optional") diff --git a/sodar_cli/samplesheet/__init__.py b/src/sodar_cli/samplesheet/__init__.py similarity index 77% rename from sodar_cli/samplesheet/__init__.py rename to src/sodar_cli/samplesheet/__init__.py index e22f109..6b83d9b 100644 --- a/sodar_cli/samplesheet/__init__.py +++ b/src/sodar_cli/samplesheet/__init__.py @@ -4,8 +4,12 @@ from sodar_cli.common import run_nocmd from sodar_cli.samplesheet.config import SampleSheetConfig -from sodar_cli.samplesheet.retrieve import setup_argparse as setup_argparse_retrieve -from sodar_cli.samplesheet.importisa import setup_argparse as setup_argparse_import +from sodar_cli.samplesheet.retrieve import ( + setup_argparse as setup_argparse_retrieve, +) +from sodar_cli.samplesheet.importisa import ( + setup_argparse as setup_argparse_import, +) from sodar_cli.samplesheet.export import setup_argparse as setup_argparse_export @@ -13,9 +17,7 @@ def setup_argparse(parser: argparse.ArgumentParser) -> None: """Main entry point for subcommand.""" subparsers = parser.add_subparsers(dest="samplesheet_cmd") - setup_argparse_retrieve( - subparsers.add_parser("retrieve", help="Retrieve sample sheet for project.") - ) + setup_argparse_retrieve(subparsers.add_parser("retrieve", help="Retrieve sample sheet for project.")) setup_argparse_import(subparsers.add_parser("import", help="Import ISA-tab into project.")) setup_argparse_export(subparsers.add_parser("export", help="Export ISA-tab from project.")) diff --git a/sodar_cli/samplesheet/config.py b/src/sodar_cli/samplesheet/config.py similarity index 89% rename from sodar_cli/samplesheet/config.py rename to src/sodar_cli/samplesheet/config.py index ff7b67d..ae47dd1 100644 --- a/sodar_cli/samplesheet/config.py +++ b/src/sodar_cli/samplesheet/config.py @@ -36,7 +36,8 @@ def create(args, samplesheet_config, toml_config=None): _ = toml_config # toml_config = toml_config or {} return SampleSheetRetrieveConfig( - samplesheet_config=samplesheet_config, project_uuid=args.project_uuid + samplesheet_config=samplesheet_config, + project_uuid=args.project_uuid, ) @@ -77,7 +78,8 @@ class SampleSheetExportConfig: def create(args, samplesheet_config, toml_config=None): # toml_config = toml_config or {} return SampleSheetExportConfig( - samplesheet_config=samplesheet_config, project_uuid=args.project_uuid + samplesheet_config=samplesheet_config, + project_uuid=args.project_uuid, ) @@ -94,6 +96,4 @@ class SampleDataFileExistsConfig: @staticmethod def create(args, samplesheet_config, toml_config=None): # toml_config = toml_config or {} - return SampleDataFileExistsConfig( - samplesheet_config=samplesheet_config, md5_sum=args.md5_sum - ) + return SampleDataFileExistsConfig(samplesheet_config=samplesheet_config, md5_sum=args.md5_sum) diff --git a/sodar_cli/samplesheet/export.py b/src/sodar_cli/samplesheet/export.py similarity index 80% rename from sodar_cli/samplesheet/export.py rename to src/sodar_cli/samplesheet/export.py index a00e4ff..2ca09c5 100644 --- a/sodar_cli/samplesheet/export.py +++ b/src/sodar_cli/samplesheet/export.py @@ -13,16 +13,29 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="samplesheet_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "--print-output", dest="print_output", action="store_true", help="Print output to stdout" + "--hidden-cmd", + dest="samplesheet_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "--print-output", + dest="print_output", + action="store_true", + help="Print output to stdout", ) parser.add_argument("--write-output", default=None, help="Write output to given path") parser.add_argument( - "--overwrite", default=False, action="store_true", help="Overwrite existing files" + "--overwrite", + default=False, + action="store_true", + help="Overwrite existing files", ) parser.add_argument( - "project_uuid", help="UUID of project to retrieve the sample sheet for", type=uuid.UUID + "project_uuid", + help="UUID of project to retrieve the sample sheet for", + type=uuid.UUID, ) @@ -64,6 +77,4 @@ def run(config, toml_config, args, _parser, _subparser, file=None): with open(path_a, "wt") as outputf: print(assay["tsv"], file=outputf) if not args.print_output and not args.write_output: - logger.warn( - "Did nothing with result. You probably want either --write-output or --print-output" - ) + logger.warn("Did nothing with result. You probably want either --write-output or --print-output") diff --git a/sodar_cli/samplesheet/importisa.py b/src/sodar_cli/samplesheet/importisa.py similarity index 71% rename from sodar_cli/samplesheet/importisa.py rename to src/sodar_cli/samplesheet/importisa.py index 81b9c61..167b3ad 100644 --- a/sodar_cli/samplesheet/importisa.py +++ b/src/sodar_cli/samplesheet/importisa.py @@ -13,11 +13,23 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="samplesheet_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "project_uuid", help="UUID of project to import ISA tab for", type=uuid.UUID + "--hidden-cmd", + dest="samplesheet_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "project_uuid", + help="UUID of project to import ISA tab for", + type=uuid.UUID, + ) + parser.add_argument( + "file_paths", + metavar="files", + nargs="+", + help="paths to files to import", ) - parser.add_argument("file_paths", metavar="files", nargs="+", help="paths to files to import") def run(config, toml_config, args, _parser, _subparser, file=None): diff --git a/sodar_cli/samplesheet/retrieve.py b/src/sodar_cli/samplesheet/retrieve.py similarity index 78% rename from sodar_cli/samplesheet/retrieve.py rename to src/sodar_cli/samplesheet/retrieve.py index d6f16f8..30521d3 100644 --- a/sodar_cli/samplesheet/retrieve.py +++ b/src/sodar_cli/samplesheet/retrieve.py @@ -13,9 +13,16 @@ def setup_argparse(parser): - parser.add_argument("--hidden-cmd", dest="samplesheet_cmd", default=run, help=argparse.SUPPRESS) parser.add_argument( - "project_uuid", help="UUID of project to retrieve sample sheet for", type=uuid.UUID + "--hidden-cmd", + dest="samplesheet_cmd", + default=run, + help=argparse.SUPPRESS, + ) + parser.add_argument( + "project_uuid", + help="UUID of project to retrieve sample sheet for", + type=uuid.UUID, ) diff --git a/src/sodar_cli/version.py b/src/sodar_cli/version.py new file mode 100644 index 0000000..3dc1f76 --- /dev/null +++ b/src/sodar_cli/version.py @@ -0,0 +1 @@ +__version__ = "0.1.0" diff --git a/tests/test_api_project.py b/tests/test_api_project.py index 8bfe0a1..8e46aa3 100644 --- a/tests/test_api_project.py +++ b/tests/test_api_project.py @@ -7,7 +7,10 @@ def test_project_list(requests_mock): - args = {"sodar_url": "https://sodar.example.com/", "sodar_api_token": "token"} + args = { + "sodar_url": "https://sodar.example.com/", + "sodar_api_token": "token", + } tpl = "%(sodar_url)sproject/api/list" expected = [factories.ProjectFactory()] requests_mock.register_uri( diff --git a/tests/test_main.py b/tests/test_main.py index 56883b6..3adc22b 100644 --- a/tests/test_main.py +++ b/tests/test_main.py @@ -8,5 +8,5 @@ def test_no_args(): with pytest.raises(SystemExit) as pytest_wrapped_e: main([]) - assert pytest_wrapped_e.type == SystemExit + assert pytest_wrapped_e.type is SystemExit assert pytest_wrapped_e.value.code == 1 diff --git a/tests/test_samplesheet.py b/tests/test_samplesheet.py index 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a/versioneer.py b/versioneer.py deleted file mode 100644 index 545553e..0000000 --- a/versioneer.py +++ /dev/null @@ -1,1857 +0,0 @@ -# Version: 0.18 - -"""The Versioneer - like a rocketeer, but for versions. - -The Versioneer -============== - -* like a rocketeer, but for versions! -* https://github.com/warner/python-versioneer -* Brian Warner -* License: Public Domain -* Compatible With: python2.6, 2.7, 3.2, 3.3, 3.4, 3.5, 3.6, and pypy -* [![Latest Version] -(https://pypip.in/version/versioneer/badge.svg?style=flat) -](https://pypi.python.org/pypi/versioneer/) -* [![Build Status] -(https://travis-ci.org/warner/python-versioneer.png?branch=master) -](https://travis-ci.org/warner/python-versioneer) - -This is a tool for managing a recorded version number in distutils-based -python projects. The goal is to remove the tedious and error-prone "update -the embedded version string" step from your release process. Making a new -release should be as easy as recording a new tag in your version-control -system, and maybe making new tarballs. - - -## Quick Install - -* `pip install versioneer` to somewhere to your $PATH -* add a `[versioneer]` section to your setup.cfg (see below) -* run `versioneer install` in your source tree, commit the results - -## Version Identifiers - -Source trees come from a variety of places: - -* a version-control system checkout (mostly used by developers) -* a nightly tarball, produced by build automation -* a snapshot tarball, produced by a web-based VCS browser, like github's - "tarball from tag" feature -* a release tarball, produced by "setup.py sdist", distributed through PyPI - -Within each source tree, the version identifier (either a string or a number, -this tool is format-agnostic) can come from a variety of places: - -* ask the VCS tool itself, e.g. "git describe" (for checkouts), which knows - about recent "tags" and an absolute revision-id -* the name of the directory into which the tarball was unpacked -* an expanded VCS keyword ($Id$, etc) -* a `_version.py` created by some earlier build step - -For released software, the version identifier is closely related to a VCS -tag. Some projects use tag names that include more than just the version -string (e.g. "myproject-1.2" instead of just "1.2"), in which case the tool -needs to strip the tag prefix to extract the version identifier. For -unreleased software (between tags), the version identifier should provide -enough information to help developers recreate the same tree, while also -giving them an idea of roughly how old the tree is (after version 1.2, before -version 1.3). Many VCS systems can report a description that captures this, -for example `git describe --tags --dirty --always` reports things like -"0.7-1-g574ab98-dirty" to indicate that the checkout is one revision past the -0.7 tag, has a unique revision id of "574ab98", and is "dirty" (it has -uncommitted changes. - -The version identifier is used for multiple purposes: - -* to allow the module to self-identify its version: `myproject.__version__` -* to choose a name and prefix for a 'setup.py sdist' tarball - -## Theory of Operation - -Versioneer works by adding a special `_version.py` file into your source -tree, where your `__init__.py` can import it. This `_version.py` knows how to -dynamically ask the VCS tool for version information at import time. - -`_version.py` also contains `$Revision$` markers, and the installation -process marks `_version.py` to have this marker rewritten with a tag name -during the `git archive` command. As a result, generated tarballs will -contain enough information to get the proper version. - -To allow `setup.py` to compute a version too, a `versioneer.py` is added to -the top level of your source tree, next to `setup.py` and the `setup.cfg` -that configures it. This overrides several distutils/setuptools commands to -compute the version when invoked, and changes `setup.py build` and `setup.py -sdist` to replace `_version.py` with a small static file that contains just -the generated version data. - -## Installation - -See [INSTALL.md](./INSTALL.md) for detailed installation instructions. - -## Version-String Flavors - -Code which uses Versioneer can learn about its version string at runtime by -importing `_version` from your main `__init__.py` file and running the -`get_versions()` function. From the "outside" (e.g. in `setup.py`), you can -import the top-level `versioneer.py` and run `get_versions()`. - -Both functions return a dictionary with different flavors of version -information: - -* `['version']`: A condensed version string, rendered using the selected - style. This is the most commonly used value for the project's version - string. The default "pep440" style yields strings like `0.11`, - `0.11+2.g1076c97`, or `0.11+2.g1076c97.dirty`. See the "Styles" section - below for alternative styles. - -* `['full-revisionid']`: detailed revision identifier. For Git, this is the - full SHA1 commit id, e.g. "1076c978a8d3cfc70f408fe5974aa6c092c949ac". - -* `['date']`: Date and time of the latest `HEAD` commit. For Git, it is the - commit date in ISO 8601 format. This will be None if the date is not - available. - -* `['dirty']`: a boolean, True if the tree has uncommitted changes. Note that - this is only accurate if run in a VCS checkout, otherwise it is likely to - be False or None - -* `['error']`: if the version string could not be computed, this will be set - to a string describing the problem, otherwise it will be None. It may be - useful to throw an exception in setup.py if this is set, to avoid e.g. - creating tarballs with a version string of "unknown". - -Some variants are more useful than others. Including `full-revisionid` in a -bug report should allow developers to reconstruct the exact code being tested -(or indicate the presence of local changes that should be shared with the -developers). `version` is suitable for display in an "about" box or a CLI -`--version` output: it can be easily compared against release notes and lists -of bugs fixed in various releases. - -The installer adds the following text to your `__init__.py` to place a basic -version in `YOURPROJECT.__version__`: - - from ._version import get_versions - __version__ = get_versions()['version'] - del get_versions - -## Styles - -The setup.cfg `style=` configuration controls how the VCS information is -rendered into a version string. - -The default style, "pep440", produces a PEP440-compliant string, equal to the -un-prefixed tag name for actual releases, and containing an additional "local -version" section with more detail for in-between builds. For Git, this is -TAG[+DISTANCE.gHEX[.dirty]] , using information from `git describe --tags ---dirty --always`. For example "0.11+2.g1076c97.dirty" indicates that the -tree is like the "1076c97" commit but has uncommitted changes (".dirty"), and -that this commit is two revisions ("+2") beyond the "0.11" tag. For released -software (exactly equal to a known tag), the identifier will only contain the -stripped tag, e.g. "0.11". - -Other styles are available. See [details.md](details.md) in the Versioneer -source tree for descriptions. - -## Debugging - -Versioneer tries to avoid fatal errors: if something goes wrong, it will tend -to return a version of "0+unknown". To investigate the problem, run `setup.py -version`, which will run the version-lookup code in a verbose mode, and will -display the full contents of `get_versions()` (including the `error` string, -which may help identify what went wrong). - -## Known Limitations - -Some situations are known to cause problems for Versioneer. This details the -most significant ones. More can be found on Github -[issues page](https://github.com/warner/python-versioneer/issues). - -### Subprojects - -Versioneer has limited support for source trees in which `setup.py` is not in -the root directory (e.g. `setup.py` and `.git/` are *not* siblings). The are -two common reasons why `setup.py` might not be in the root: - -* Source trees which contain multiple subprojects, such as - [Buildbot](https://github.com/buildbot/buildbot), which contains both - "master" and "slave" subprojects, each with their own `setup.py`, - `setup.cfg`, and `tox.ini`. Projects like these produce multiple PyPI - distributions (and upload multiple independently-installable tarballs). -* Source trees whose main purpose is to contain a C library, but which also - provide bindings to Python (and perhaps other langauges) in subdirectories. - -Versioneer will look for `.git` in parent directories, and most operations -should get the right version string. However `pip` and `setuptools` have bugs -and implementation details which frequently cause `pip install .` from a -subproject directory to fail to find a correct version string (so it usually -defaults to `0+unknown`). - -`pip install --editable .` should work correctly. `setup.py install` might -work too. - -Pip-8.1.1 is known to have this problem, but hopefully it will get fixed in -some later version. - -[Bug #38](https://github.com/warner/python-versioneer/issues/38) is tracking -this issue. The discussion in -[PR #61](https://github.com/warner/python-versioneer/pull/61) describes the -issue from the Versioneer side in more detail. -[pip PR#3176](https://github.com/pypa/pip/pull/3176) and -[pip PR#3615](https://github.com/pypa/pip/pull/3615) contain work to improve -pip to let Versioneer work correctly. - -Versioneer-0.16 and earlier only looked for a `.git` directory next to the -`setup.cfg`, so subprojects were completely unsupported with those releases. - -### Editable installs with setuptools <= 18.5 - -`setup.py develop` and `pip install --editable .` allow you to install a -project into a virtualenv once, then continue editing the source code (and -test) without re-installing after every change. - -"Entry-point scripts" (`setup(entry_points={"console_scripts": ..})`) are a -convenient way to specify executable scripts that should be installed along -with the python package. - -These both work as expected when using modern setuptools. When using -setuptools-18.5 or earlier, however, certain operations will cause -`pkg_resources.DistributionNotFound` errors when running the entrypoint -script, which must be resolved by re-installing the package. This happens -when the install happens with one version, then the egg_info data is -regenerated while a different version is checked out. Many setup.py commands -cause egg_info to be rebuilt (including `sdist`, `wheel`, and installing into -a different virtualenv), so this can be surprising. - -[Bug #83](https://github.com/warner/python-versioneer/issues/83) describes -this one, but upgrading to a newer version of setuptools should probably -resolve it. - -### Unicode version strings - -While Versioneer works (and is continually tested) with both Python 2 and -Python 3, it is not entirely consistent with bytes-vs-unicode distinctions. -Newer releases probably generate unicode version strings on py2. It's not -clear that this is wrong, but it may be surprising for applications when then -write these strings to a network connection or include them in bytes-oriented -APIs like cryptographic checksums. - -[Bug #71](https://github.com/warner/python-versioneer/issues/71) investigates -this question. - - -## Updating Versioneer - -To upgrade your project to a new release of Versioneer, do the following: - -* install the new Versioneer (`pip install -U versioneer` or equivalent) -* edit `setup.cfg`, if necessary, to include any new configuration settings - indicated by the release notes. See [UPGRADING](./UPGRADING.md) for details. -* re-run `versioneer install` in your source tree, to replace - `SRC/_version.py` -* commit any changed files - -## Future Directions - -This tool is designed to make it easily extended to other version-control -systems: all VCS-specific components are in separate directories like -src/git/ . The top-level `versioneer.py` script is assembled from these -components by running make-versioneer.py . In the future, make-versioneer.py -will take a VCS name as an argument, and will construct a version of -`versioneer.py` that is specific to the given VCS. It might also take the -configuration arguments that are currently provided manually during -installation by editing setup.py . Alternatively, it might go the other -direction and include code from all supported VCS systems, reducing the -number of intermediate scripts. - - -## License - -To make Versioneer easier to embed, all its code is dedicated to the public -domain. The `_version.py` that it creates is also in the public domain. -Specifically, both are released under the Creative Commons "Public Domain -Dedication" license (CC0-1.0), as described in -https://creativecommons.org/publicdomain/zero/1.0/ . - -""" - -from __future__ import print_function - -try: - import configparser -except ImportError: - import ConfigParser as configparser -import errno -import json -import os -import re -import subprocess -import sys - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_root(): - """Get the project root directory. - - We require that all commands are run from the project root, i.e. the - directory that contains setup.py, setup.cfg, and versioneer.py . - """ - root = os.path.realpath(os.path.abspath(os.getcwd())) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - # allow 'python path/to/setup.py COMMAND' - root = os.path.dirname(os.path.realpath(os.path.abspath(sys.argv[0]))) - setup_py = os.path.join(root, "setup.py") - versioneer_py = os.path.join(root, "versioneer.py") - if not (os.path.exists(setup_py) or os.path.exists(versioneer_py)): - err = ( - "Versioneer was unable to run the project root directory. " - "Versioneer requires setup.py to be executed from " - "its immediate directory (like 'python setup.py COMMAND'), " - "or in a way that lets it use sys.argv[0] to find the root " - "(like 'python path/to/setup.py COMMAND')." - ) - raise VersioneerBadRootError(err) - try: - # Certain runtime workflows (setup.py install/develop in a setuptools - # tree) execute all dependencies in a single python process, so - # "versioneer" may be imported multiple times, and python's shared - # module-import table will cache the first one. So we can't use - # os.path.dirname(__file__), as that will find whichever - # versioneer.py was first imported, even in later projects. - me = os.path.realpath(os.path.abspath(__file__)) - me_dir = os.path.normcase(os.path.splitext(me)[0]) - vsr_dir = os.path.normcase(os.path.splitext(versioneer_py)[0]) - if me_dir != vsr_dir: - print( - "Warning: build in %s is using versioneer.py from %s" - % (os.path.dirname(me), versioneer_py) - ) - except NameError: - pass - return root - - -def get_config_from_root(root): - """Read the project setup.cfg file to determine Versioneer config.""" - # This might raise EnvironmentError (if setup.cfg is missing), or - # configparser.NoSectionError (if it lacks a [versioneer] section), or - # configparser.NoOptionError (if it lacks "VCS="). See the docstring at - # the top of versioneer.py for instructions on writing your setup.cfg . - setup_cfg = os.path.join(root, "setup.cfg") - parser = configparser.SafeConfigParser() - with open(setup_cfg, "r") as f: - parser.readfp(f) - VCS = parser.get("versioneer", "VCS") # mandatory - - def get(parser, name): - if parser.has_option("versioneer", name): - return parser.get("versioneer", name) - return None - - cfg = VersioneerConfig() - cfg.VCS = VCS - cfg.style = get(parser, "style") or "" - cfg.versionfile_source = get(parser, "versionfile_source") - cfg.versionfile_build = get(parser, "versionfile_build") - cfg.tag_prefix = get(parser, "tag_prefix") - if cfg.tag_prefix in ("''", '""'): - cfg.tag_prefix = "" - cfg.parentdir_prefix = get(parser, "parentdir_prefix") - cfg.verbose = get(parser, "verbose") - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -# these dictionaries contain VCS-specific tools -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen( - [c] + args, - cwd=cwd, - env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr else None), - ) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %s" % dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %s" % (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %s (error)" % dispcmd) - print("stdout was %s" % stdout) - return None, p.returncode - return stdout, p.returncode - - -LONG_VERSION_PY[ - "git" -] = ''' -# This file helps to compute a version number in source trees obtained from -# git-archive tarball (such as those provided by githubs download-from-tag -# feature). Distribution tarballs (built by setup.py sdist) and build -# directories (produced by setup.py build) will contain a much shorter file -# that just contains the computed version number. - -# This file is released into the public domain. Generated by -# versioneer-0.18 (https://github.com/warner/python-versioneer) - -"""Git implementation of _version.py.""" - -import errno -import os -import re -import subprocess -import sys - - -def get_keywords(): - """Get the keywords needed to look up the version information.""" - # these strings will be replaced by git during git-archive. - # setup.py/versioneer.py will grep for the variable names, so they must - # each be defined on a line of their own. _version.py will just call - # get_keywords(). - git_refnames = "%(DOLLAR)sFormat:%%d%(DOLLAR)s" - git_full = "%(DOLLAR)sFormat:%%H%(DOLLAR)s" - git_date = "%(DOLLAR)sFormat:%%ci%(DOLLAR)s" - keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} - return keywords - - -class VersioneerConfig: - """Container for Versioneer configuration parameters.""" - - -def get_config(): - """Create, populate and return the VersioneerConfig() object.""" - # these strings are filled in when 'setup.py versioneer' creates - # _version.py - cfg = VersioneerConfig() - cfg.VCS = "git" - cfg.style = "%(STYLE)s" - cfg.tag_prefix = "%(TAG_PREFIX)s" - cfg.parentdir_prefix = "%(PARENTDIR_PREFIX)s" - cfg.versionfile_source = "%(VERSIONFILE_SOURCE)s" - cfg.verbose = False - return cfg - - -class NotThisMethod(Exception): - """Exception raised if a method is not valid for the current scenario.""" - - -LONG_VERSION_PY = {} -HANDLERS = {} - - -def register_vcs_handler(vcs, method): # decorator - """Decorator to mark a method as the handler for a particular VCS.""" - def decorate(f): - """Store f in HANDLERS[vcs][method].""" - if vcs not in HANDLERS: - HANDLERS[vcs] = {} - HANDLERS[vcs][method] = f - return f - return decorate - - -def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, - env=None): - """Call the given command(s).""" - assert isinstance(commands, list) - p = None - for c in commands: - try: - dispcmd = str([c] + args) - # remember shell=False, so use git.cmd on windows, not just git - p = subprocess.Popen([c] + args, cwd=cwd, env=env, - stdout=subprocess.PIPE, - stderr=(subprocess.PIPE if hide_stderr - else None)) - break - except EnvironmentError: - e = sys.exc_info()[1] - if e.errno == errno.ENOENT: - continue - if verbose: - print("unable to run %%s" %% dispcmd) - print(e) - return None, None - else: - if verbose: - print("unable to find command, tried %%s" %% (commands,)) - return None, None - stdout = p.communicate()[0].strip() - if sys.version_info[0] >= 3: - stdout = stdout.decode() - if p.returncode != 0: - if verbose: - print("unable to run %%s (error)" %% dispcmd) - print("stdout was %%s" %% stdout) - return None, p.returncode - return stdout, p.returncode - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return {"version": dirname[len(parentdir_prefix):], - "full-revisionid": None, - "dirty": False, "error": None, "date": None} - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print("Tried directories %%s but none started with prefix %%s" %% - (str(rootdirs), parentdir_prefix)) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG):] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %%d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r'\d', r)]) - if verbose: - print("discarding '%%s', no digits" %% ",".join(refs - tags)) - if verbose: - print("likely tags: %%s" %% ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix):] - if verbose: - print("picking %%s" %% r) - return {"version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": None, - "date": date} - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return {"version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, "error": "no suitable tags", "date": None} - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, - hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %%s not under git control" %% root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command(GITS, ["describe", "--tags", "--dirty", - "--always", "--long", - "--match", "%%s*" %% tag_prefix], - cwd=root) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[:git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r'^(.+)-(\d+)-g([0-9a-f]+)$', git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = ("unable to parse git-describe output: '%%s'" - %% describe_out) - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%%s' doesn't start with prefix '%%s'" - print(fmt %% (full_tag, tag_prefix)) - pieces["error"] = ("tag '%%s' doesn't start with prefix '%%s'" - %% (full_tag, tag_prefix)) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix):] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], - cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%%ci", "HEAD"], - cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%%d.g%%s" %% (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%%d.g%%s" %% (pieces["distance"], - pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%%d" %% pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%%d" %% pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%%s" %% pieces["short"] - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%%s" %% pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%%d" %% pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%%d-g%%s" %% (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return {"version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None} - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%%s'" %% style) - - return {"version": rendered, "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], "error": None, - "date": pieces.get("date")} - - -def get_versions(): - """Get version information or return default if unable to do so.""" - # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have - # __file__, we can work backwards from there to the root. Some - # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which - # case we can only use expanded keywords. - - cfg = get_config() - verbose = cfg.verbose - - try: - return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, - verbose) - except NotThisMethod: - pass - - try: - root = os.path.realpath(__file__) - # versionfile_source is the relative path from the top of the source - # tree (where the .git directory might live) to this file. Invert - # this to find the root from __file__. - for i in cfg.versionfile_source.split('/'): - root = os.path.dirname(root) - except NameError: - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to find root of source tree", - "date": None} - - try: - pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) - return render(pieces, cfg.style) - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - except NotThisMethod: - pass - - return {"version": "0+unknown", "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", "date": None} -''' - - -@register_vcs_handler("git", "get_keywords") -def git_get_keywords(versionfile_abs): - """Extract version information from the given file.""" - # the code embedded in _version.py can just fetch the value of these - # keywords. When used from setup.py, we don't want to import _version.py, - # so we do it with a regexp instead. This function is not used from - # _version.py. - keywords = {} - try: - f = open(versionfile_abs, "r") - for line in f.readlines(): - if line.strip().startswith("git_refnames ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["refnames"] = mo.group(1) - if line.strip().startswith("git_full ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["full"] = mo.group(1) - if line.strip().startswith("git_date ="): - mo = re.search(r'=\s*"(.*)"', line) - if mo: - keywords["date"] = mo.group(1) - f.close() - except EnvironmentError: - pass - return keywords - - -@register_vcs_handler("git", "keywords") -def git_versions_from_keywords(keywords, tag_prefix, verbose): - """Get version information from git keywords.""" - if not keywords: - raise NotThisMethod("no keywords at all, weird") - date = keywords.get("date") - if date is not None: - # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant - # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 - # -like" string, which we must then edit to make compliant), because - # it's been around since git-1.5.3, and it's too difficult to - # discover which version we're using, or to work around using an - # older one. - date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - refnames = keywords["refnames"].strip() - if refnames.startswith("$Format"): - if verbose: - print("keywords are unexpanded, not using") - raise NotThisMethod("unexpanded keywords, not a git-archive tarball") - refs = set([r.strip() for r in refnames.strip("()").split(",")]) - # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of - # just "foo-1.0". If we see a "tag: " prefix, prefer those. - TAG = "tag: " - tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) - if not tags: - # Either we're using git < 1.8.3, or there really are no tags. We use - # a heuristic: assume all version tags have a digit. The old git %d - # expansion behaves like git log --decorate=short and strips out the - # refs/heads/ and refs/tags/ prefixes that would let us distinguish - # between branches and tags. By ignoring refnames without digits, we - # filter out many common branch names like "release" and - # "stabilization", as well as "HEAD" and "master". - tags = set([r for r in refs if re.search(r"\d", r)]) - if verbose: - print("discarding '%s', no digits" % ",".join(refs - tags)) - if verbose: - print("likely tags: %s" % ",".join(sorted(tags))) - for ref in sorted(tags): - # sorting will prefer e.g. "2.0" over "2.0rc1" - if ref.startswith(tag_prefix): - r = ref[len(tag_prefix) :] - if verbose: - print("picking %s" % r) - return { - "version": r, - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": None, - "date": date, - } - # no suitable tags, so version is "0+unknown", but full hex is still there - if verbose: - print("no suitable tags, using unknown + full revision id") - return { - "version": "0+unknown", - "full-revisionid": keywords["full"].strip(), - "dirty": False, - "error": "no suitable tags", - "date": None, - } - - -@register_vcs_handler("git", "pieces_from_vcs") -def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): - """Get version from 'git describe' in the root of the source tree. - - This only gets called if the git-archive 'subst' keywords were *not* - expanded, and _version.py hasn't already been rewritten with a short - version string, meaning we're inside a checked out source tree. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - - out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) - if rc != 0: - if verbose: - print("Directory %s not under git control" % root) - raise NotThisMethod("'git rev-parse --git-dir' returned error") - - # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] - # if there isn't one, this yields HEX[-dirty] (no NUM) - describe_out, rc = run_command( - GITS, - ["describe", "--tags", "--dirty", "--always", "--long", "--match", "%s*" % tag_prefix], - cwd=root, - ) - # --long was added in git-1.5.5 - if describe_out is None: - raise NotThisMethod("'git describe' failed") - describe_out = describe_out.strip() - full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) - if full_out is None: - raise NotThisMethod("'git rev-parse' failed") - full_out = full_out.strip() - - pieces = {} - pieces["long"] = full_out - pieces["short"] = full_out[:7] # maybe improved later - pieces["error"] = None - - # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] - # TAG might have hyphens. - git_describe = describe_out - - # look for -dirty suffix - dirty = git_describe.endswith("-dirty") - pieces["dirty"] = dirty - if dirty: - git_describe = git_describe[: git_describe.rindex("-dirty")] - - # now we have TAG-NUM-gHEX or HEX - - if "-" in git_describe: - # TAG-NUM-gHEX - mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) - if not mo: - # unparseable. Maybe git-describe is misbehaving? - pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out - return pieces - - # tag - full_tag = mo.group(1) - if not full_tag.startswith(tag_prefix): - if verbose: - fmt = "tag '%s' doesn't start with prefix '%s'" - print(fmt % (full_tag, tag_prefix)) - pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % (full_tag, tag_prefix) - return pieces - pieces["closest-tag"] = full_tag[len(tag_prefix) :] - - # distance: number of commits since tag - pieces["distance"] = int(mo.group(2)) - - # commit: short hex revision ID - pieces["short"] = mo.group(3) - - else: - # HEX: no tags - pieces["closest-tag"] = None - count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) - pieces["distance"] = int(count_out) # total number of commits - - # commit date: see ISO-8601 comment in git_versions_from_keywords() - date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[0].strip() - pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) - - return pieces - - -def do_vcs_install(manifest_in, versionfile_source, ipy): - """Git-specific installation logic for Versioneer. - - For Git, this means creating/changing .gitattributes to mark _version.py - for export-subst keyword substitution. - """ - GITS = ["git"] - if sys.platform == "win32": - GITS = ["git.cmd", "git.exe"] - files = [manifest_in, versionfile_source] - if ipy: - files.append(ipy) - try: - me = __file__ - if me.endswith(".pyc") or me.endswith(".pyo"): - me = os.path.splitext(me)[0] + ".py" - versioneer_file = os.path.relpath(me) - except NameError: - versioneer_file = "versioneer.py" - files.append(versioneer_file) - present = False - try: - f = open(".gitattributes", "r") - for line in f.readlines(): - if line.strip().startswith(versionfile_source): - if "export-subst" in line.strip().split()[1:]: - present = True - f.close() - except EnvironmentError: - pass - if not present: - f = open(".gitattributes", "a+") - f.write("%s export-subst\n" % versionfile_source) - f.close() - files.append(".gitattributes") - run_command(GITS, ["add", "--"] + files) - - -def versions_from_parentdir(parentdir_prefix, root, verbose): - """Try to determine the version from the parent directory name. - - Source tarballs conventionally unpack into a directory that includes both - the project name and a version string. We will also support searching up - two directory levels for an appropriately named parent directory - """ - rootdirs = [] - - for i in range(3): - dirname = os.path.basename(root) - if dirname.startswith(parentdir_prefix): - return { - "version": dirname[len(parentdir_prefix) :], - "full-revisionid": None, - "dirty": False, - "error": None, - "date": None, - } - else: - rootdirs.append(root) - root = os.path.dirname(root) # up a level - - if verbose: - print( - "Tried directories %s but none started with prefix %s" - % (str(rootdirs), parentdir_prefix) - ) - raise NotThisMethod("rootdir doesn't start with parentdir_prefix") - - -SHORT_VERSION_PY = """ -# This file was generated by 'versioneer.py' (0.18) from -# revision-control system data, or from the parent directory name of an -# unpacked source archive. Distribution tarballs contain a pre-generated copy -# of this file. - -import json - -version_json = ''' -%s -''' # END VERSION_JSON - - -def get_versions(): - return json.loads(version_json) -""" - - -def versions_from_file(filename): - """Try to determine the version from _version.py if present.""" - try: - with open(filename) as f: - contents = f.read() - except EnvironmentError: - raise NotThisMethod("unable to read _version.py") - mo = re.search(r"version_json = '''\n(.*)''' # END VERSION_JSON", contents, re.M | re.S) - if not mo: - mo = re.search(r"version_json = '''\r\n(.*)''' # END VERSION_JSON", contents, re.M | re.S) - if not mo: - raise NotThisMethod("no version_json in _version.py") - return json.loads(mo.group(1)) - - -def write_to_version_file(filename, versions): - """Write the given version number to the given _version.py file.""" - os.unlink(filename) - contents = json.dumps(versions, sort_keys=True, indent=1, separators=(",", ": ")) - with open(filename, "w") as f: - f.write(SHORT_VERSION_PY % contents) - - print("set %s to '%s'" % (filename, versions["version"])) - - -def plus_or_dot(pieces): - """Return a + if we don't already have one, else return a .""" - if "+" in pieces.get("closest-tag", ""): - return "." - return "+" - - -def render_pep440(pieces): - """Build up version string, with post-release "local version identifier". - - Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you - get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty - - Exceptions: - 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += plus_or_dot(pieces) - rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - else: - # exception #1 - rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) - if pieces["dirty"]: - rendered += ".dirty" - return rendered - - -def render_pep440_pre(pieces): - """TAG[.post.devDISTANCE] -- No -dirty. - - Exceptions: - 1: no tags. 0.post.devDISTANCE - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += ".post.dev%d" % pieces["distance"] - else: - # exception #1 - rendered = "0.post.dev%d" % pieces["distance"] - return rendered - - -def render_pep440_post(pieces): - """TAG[.postDISTANCE[.dev0]+gHEX] . - - The ".dev0" means dirty. Note that .dev0 sorts backwards - (a dirty tree will appear "older" than the corresponding clean one), - but you shouldn't be releasing software with -dirty anyways. - - Exceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += plus_or_dot(pieces) - rendered += "g%s" % pieces["short"] - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - rendered += "+g%s" % pieces["short"] - return rendered - - -def render_pep440_old(pieces): - """TAG[.postDISTANCE[.dev0]] . - - The ".dev0" means dirty. - - Eexceptions: - 1: no tags. 0.postDISTANCE[.dev0] - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"] or pieces["dirty"]: - rendered += ".post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - else: - # exception #1 - rendered = "0.post%d" % pieces["distance"] - if pieces["dirty"]: - rendered += ".dev0" - return rendered - - -def render_git_describe(pieces): - """TAG[-DISTANCE-gHEX][-dirty]. - - Like 'git describe --tags --dirty --always'. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - if pieces["distance"]: - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render_git_describe_long(pieces): - """TAG-DISTANCE-gHEX[-dirty]. - - Like 'git describe --tags --dirty --always -long'. - The distance/hash is unconditional. - - Exceptions: - 1: no tags. HEX[-dirty] (note: no 'g' prefix) - """ - if pieces["closest-tag"]: - rendered = pieces["closest-tag"] - rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) - else: - # exception #1 - rendered = pieces["short"] - if pieces["dirty"]: - rendered += "-dirty" - return rendered - - -def render(pieces, style): - """Render the given version pieces into the requested style.""" - if pieces["error"]: - return { - "version": "unknown", - "full-revisionid": pieces.get("long"), - "dirty": None, - "error": pieces["error"], - "date": None, - } - - if not style or style == "default": - style = "pep440" # the default - - if style == "pep440": - rendered = render_pep440(pieces) - elif style == "pep440-pre": - rendered = render_pep440_pre(pieces) - elif style == "pep440-post": - rendered = render_pep440_post(pieces) - elif style == "pep440-old": - rendered = render_pep440_old(pieces) - elif style == "git-describe": - rendered = render_git_describe(pieces) - elif style == "git-describe-long": - rendered = render_git_describe_long(pieces) - else: - raise ValueError("unknown style '%s'" % style) - - return { - "version": rendered, - "full-revisionid": pieces["long"], - "dirty": pieces["dirty"], - "error": None, - "date": pieces.get("date"), - } - - -class VersioneerBadRootError(Exception): - """The project root directory is unknown or missing key files.""" - - -def get_versions(verbose=False): - """Get the project version from whatever source is available. - - Returns dict with two keys: 'version' and 'full'. - """ - if "versioneer" in sys.modules: - # see the discussion in cmdclass.py:get_cmdclass() - del sys.modules["versioneer"] - - root = get_root() - cfg = get_config_from_root(root) - - assert cfg.VCS is not None, "please set [versioneer]VCS= in setup.cfg" - handlers = HANDLERS.get(cfg.VCS) - assert handlers, "unrecognized VCS '%s'" % cfg.VCS - verbose = verbose or cfg.verbose - assert cfg.versionfile_source is not None, "please set versioneer.versionfile_source" - assert cfg.tag_prefix is not None, "please set versioneer.tag_prefix" - - versionfile_abs = os.path.join(root, cfg.versionfile_source) - - # extract version from first of: _version.py, VCS command (e.g. 'git - # describe'), parentdir. This is meant to work for developers using a - # source checkout, for users of a tarball created by 'setup.py sdist', - # and for users of a tarball/zipball created by 'git archive' or github's - # download-from-tag feature or the equivalent in other VCSes. - - get_keywords_f = handlers.get("get_keywords") - from_keywords_f = handlers.get("keywords") - if get_keywords_f and from_keywords_f: - try: - keywords = get_keywords_f(versionfile_abs) - ver = from_keywords_f(keywords, cfg.tag_prefix, verbose) - if verbose: - print("got version from expanded keyword %s" % ver) - return ver - except NotThisMethod: - pass - - try: - ver = versions_from_file(versionfile_abs) - if verbose: - print("got version from file %s %s" % (versionfile_abs, ver)) - return ver - except NotThisMethod: - pass - - from_vcs_f = handlers.get("pieces_from_vcs") - if from_vcs_f: - try: - pieces = from_vcs_f(cfg.tag_prefix, root, verbose) - ver = render(pieces, cfg.style) - if verbose: - print("got version from VCS %s" % ver) - return ver - except NotThisMethod: - pass - - try: - if cfg.parentdir_prefix: - ver = versions_from_parentdir(cfg.parentdir_prefix, root, verbose) - if verbose: - print("got version from parentdir %s" % ver) - return ver - except NotThisMethod: - pass - - if verbose: - print("unable to compute version") - - return { - "version": "0+unknown", - "full-revisionid": None, - "dirty": None, - "error": "unable to compute version", - "date": None, - } - - -def get_version(): - """Get the short version string for this project.""" - return get_versions()["version"] - - -def get_cmdclass(): - """Get the custom setuptools/distutils subclasses used by Versioneer.""" - if "versioneer" in sys.modules: - del sys.modules["versioneer"] - # this fixes the "python setup.py develop" case (also 'install' and - # 'easy_install .'), in which subdependencies of the main project are - # built (using setup.py bdist_egg) in the same python process. Assume - # a main project A and a dependency B, which use different versions - # of Versioneer. A's setup.py imports A's Versioneer, leaving it in - # sys.modules by the time B's setup.py is executed, causing B to run - # with the wrong versioneer. Setuptools wraps the sub-dep builds in a - # sandbox that restores sys.modules to it's pre-build state, so the - # parent is protected against the child's "import versioneer". By - # removing ourselves from sys.modules here, before the child build - # happens, we protect the child from the parent's versioneer too. - # Also see https://github.com/warner/python-versioneer/issues/52 - - cmds = {} - - # we add "version" to both distutils and setuptools - from distutils.core import Command - - class cmd_version(Command): - description = "report generated version string" - user_options = [] - boolean_options = [] - - def initialize_options(self): - pass - - def finalize_options(self): - pass - - def run(self): - vers = get_versions(verbose=True) - print("Version: %s" % vers["version"]) - print(" full-revisionid: %s" % vers.get("full-revisionid")) - print(" dirty: %s" % vers.get("dirty")) - print(" date: %s" % vers.get("date")) - if vers["error"]: - print(" error: %s" % vers["error"]) - - cmds["version"] = cmd_version - - # we override "build_py" in both distutils and setuptools - # - # most invocation pathways end up running build_py: - # distutils/build -> build_py - # distutils/install -> distutils/build ->.. - # setuptools/bdist_wheel -> distutils/install ->.. - # setuptools/bdist_egg -> distutils/install_lib -> build_py - # setuptools/install -> bdist_egg ->.. - # setuptools/develop -> ? - # pip install: - # copies source tree to a tempdir before running egg_info/etc - # if .git isn't copied too, 'git describe' will fail - # then does setup.py bdist_wheel, or sometimes setup.py install - # setup.py egg_info -> ? - - # we override different "build_py" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.build_py import build_py as _build_py - else: - from distutils.command.build_py import build_py as _build_py - - class cmd_build_py(_build_py): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - _build_py.run(self) - # now locate _version.py in the new build/ directory and replace - # it with an updated value - if cfg.versionfile_build: - target_versionfile = os.path.join(self.build_lib, cfg.versionfile_build) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - cmds["build_py"] = cmd_build_py - - if "cx_Freeze" in sys.modules: # cx_freeze enabled? - from cx_Freeze.dist import build_exe as _build_exe - - # nczeczulin reports that py2exe won't like the pep440-style string - # as FILEVERSION, but it can be used for PRODUCTVERSION, e.g. - # setup(console=[{ - # "version": versioneer.get_version().split("+", 1)[0], # FILEVERSION - # "product_version": versioneer.get_version(), - # ... - - class cmd_build_exe(_build_exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _build_exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["build_exe"] = cmd_build_exe - del cmds["build_py"] - - if "py2exe" in sys.modules: # py2exe enabled? - try: - from py2exe.distutils_buildexe import py2exe as _py2exe # py3 - except ImportError: - from py2exe.build_exe import py2exe as _py2exe # py2 - - class cmd_py2exe(_py2exe): - def run(self): - root = get_root() - cfg = get_config_from_root(root) - versions = get_versions() - target_versionfile = cfg.versionfile_source - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, versions) - - _py2exe.run(self) - os.unlink(target_versionfile) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - cmds["py2exe"] = cmd_py2exe - - # we override different "sdist" commands for both environments - if "setuptools" in sys.modules: - from setuptools.command.sdist import sdist as _sdist - else: - from distutils.command.sdist import sdist as _sdist - - class cmd_sdist(_sdist): - def run(self): - versions = get_versions() - self._versioneer_generated_versions = versions - # unless we update this, the command will keep using the old - # version - self.distribution.metadata.version = versions["version"] - return _sdist.run(self) - - def make_release_tree(self, base_dir, files): - root = get_root() - cfg = get_config_from_root(root) - _sdist.make_release_tree(self, base_dir, files) - # now locate _version.py in the new base_dir directory - # (remembering that it may be a hardlink) and replace it with an - # updated value - target_versionfile = os.path.join(base_dir, cfg.versionfile_source) - print("UPDATING %s" % target_versionfile) - write_to_version_file(target_versionfile, self._versioneer_generated_versions) - - cmds["sdist"] = cmd_sdist - - return cmds - - -CONFIG_ERROR = """ -setup.cfg is missing the necessary Versioneer configuration. You need -a section like: - - [versioneer] - VCS = git - style = pep440 - versionfile_source = src/myproject/_version.py - versionfile_build = myproject/_version.py - tag_prefix = - parentdir_prefix = myproject- - -You will also need to edit your setup.py to use the results: - - import versioneer - setup(version=versioneer.get_version(), - cmdclass=versioneer.get_cmdclass(), ...) - -Please read the docstring in ./versioneer.py for configuration instructions, -edit setup.cfg, and re-run the installer or 'python versioneer.py setup'. -""" - -SAMPLE_CONFIG = """ -# See the docstring in versioneer.py for instructions. Note that you must -# re-run 'versioneer.py setup' after changing this section, and commit the -# resulting files. - -[versioneer] -#VCS = git -#style = pep440 -#versionfile_source = -#versionfile_build = -#tag_prefix = -#parentdir_prefix = - -""" - -INIT_PY_SNIPPET = """ -from ._version import get_versions -__version__ = get_versions()['version'] -del get_versions -""" - - -def do_setup(): - """Main VCS-independent setup function for installing Versioneer.""" - root = get_root() - try: - cfg = get_config_from_root(root) - except (EnvironmentError, configparser.NoSectionError, configparser.NoOptionError) as e: - if isinstance(e, (EnvironmentError, configparser.NoSectionError)): - print("Adding sample versioneer config to setup.cfg", file=sys.stderr) - with open(os.path.join(root, "setup.cfg"), "a") as f: - f.write(SAMPLE_CONFIG) - print(CONFIG_ERROR, file=sys.stderr) - return 1 - - print(" creating %s" % cfg.versionfile_source) - with open(cfg.versionfile_source, "w") as f: - LONG = LONG_VERSION_PY[cfg.VCS] - f.write( - LONG - % { - "DOLLAR": "$", - "STYLE": cfg.style, - "TAG_PREFIX": cfg.tag_prefix, - "PARENTDIR_PREFIX": cfg.parentdir_prefix, - "VERSIONFILE_SOURCE": cfg.versionfile_source, - } - ) - - ipy = os.path.join(os.path.dirname(cfg.versionfile_source), "__init__.py") - if os.path.exists(ipy): - try: - with open(ipy, "r") as f: - old = f.read() - except EnvironmentError: - old = "" - if INIT_PY_SNIPPET not in old: - print(" appending to %s" % ipy) - with open(ipy, "a") as f: - f.write(INIT_PY_SNIPPET) - else: - print(" %s unmodified" % ipy) - else: - print(" %s doesn't exist, ok" % ipy) - ipy = None - - # Make sure both the top-level "versioneer.py" and versionfile_source - # (PKG/_version.py, used by runtime code) are in MANIFEST.in, so - # they'll be copied into source distributions. Pip won't be able to - # install the package without this. - manifest_in = os.path.join(root, "MANIFEST.in") - simple_includes = set() - try: - with open(manifest_in, "r") as f: - for line in f: - if line.startswith("include "): - for include in line.split()[1:]: - simple_includes.add(include) - except EnvironmentError: - pass - # That doesn't cover everything MANIFEST.in can do - # (http://docs.python.org/2/distutils/sourcedist.html#commands), so - # it might give some false negatives. Appending redundant 'include' - # lines is safe, though. - if "versioneer.py" not in simple_includes: - print(" appending 'versioneer.py' to MANIFEST.in") - with open(manifest_in, "a") as f: - f.write("include versioneer.py\n") - else: - print(" 'versioneer.py' already in MANIFEST.in") - if cfg.versionfile_source not in simple_includes: - print(" appending versionfile_source ('%s') to MANIFEST.in" % cfg.versionfile_source) - with open(manifest_in, "a") as f: - f.write("include %s\n" % cfg.versionfile_source) - else: - print(" versionfile_source already in MANIFEST.in") - - # Make VCS-specific changes. For git, this means creating/changing - # .gitattributes to mark _version.py for export-subst keyword - # substitution. - do_vcs_install(manifest_in, cfg.versionfile_source, ipy) - return 0 - - -def scan_setup_py(): - """Validate the contents of setup.py against Versioneer's expectations.""" - found = set() - setters = False - errors = 0 - with open("setup.py", "r") as f: - for line in f.readlines(): - if "import versioneer" in line: - found.add("import") - if "versioneer.get_cmdclass()" in line: - found.add("cmdclass") - if "versioneer.get_version()" in line: - found.add("get_version") - if "versioneer.VCS" in line: - setters = True - if "versioneer.versionfile_source" in line: - setters = True - if len(found) != 3: - print("") - print("Your setup.py appears to be missing some important items") - print("(but I might be wrong). Please make sure it has something") - print("roughly like the following:") - print("") - print(" import versioneer") - print(" setup( version=versioneer.get_version(),") - print(" cmdclass=versioneer.get_cmdclass(), ...)") - print("") - errors += 1 - if setters: - print("You should remove lines like 'versioneer.VCS = ' and") - print("'versioneer.versionfile_source = ' . This configuration") - print("now lives in setup.cfg, and should be removed from setup.py") - print("") - errors += 1 - return errors - - -if __name__ == "__main__": - cmd = sys.argv[1] - if cmd == "setup": - errors = do_setup() - errors += scan_setup_py() - if errors: - sys.exit(1)