diff --git a/.codecov.yml b/.codecov.yml new file mode 100644 index 000000000..a3ed7f477 --- /dev/null +++ b/.codecov.yml @@ -0,0 +1,14 @@ +# Codecov configuration to make it a bit less noisy +coverage: + status: + patch: false + project: + default: + threshold: 50% +comment: + layout: "header" + require_changes: false + branches: null + behavior: default + flags: null + paths: null \ No newline at end of file diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md new file mode 100644 index 000000000..9582c7873 --- /dev/null +++ b/.github/CONTRIBUTING.md @@ -0,0 +1,42 @@ +# How to contribute + +We welcome contributions from external contributors, and this document +describes how to merge code changes into this openmmtools. + +## Getting Started + +* Make sure you have a [GitHub account](https://github.com/signup/free). +* [Fork](https://help.github.com/articles/fork-a-repo/) this repository on GitHub. +* On your local machine, + [clone](https://help.github.com/articles/cloning-a-repository/) your fork of + the repository. + +## Making Changes + +* Add some really awesome code to your local fork. It's usually a [good + idea](http://blog.jasonmeridth.com/posts/do-not-issue-pull-requests-from-your-master-branch/) + to make changes on a + [branch](https://help.github.com/articles/creating-and-deleting-branches-within-your-repository/) + with the branch name relating to the feature you are going to add. +* When you are ready for others to examine and comment on your new feature, + navigate to your fork of openmmtools on GitHub and open a [pull + request](https://help.github.com/articles/using-pull-requests/) (PR). Note that + after you launch a PR from one of your fork's branches, all + subsequent commits to that branch will be added to the open pull request + automatically. Each commit added to the PR will be validated for + mergability, compilation and test suite compliance; the results of these tests + will be visible on the PR page. +* If you're providing a new feature, you must add test cases and documentation. +* When the code is ready to go, make sure you run the test suite using pytest. +* When you're ready to be considered for merging, check the "Ready to go" + box on the PR page to let the openmmtools devs know that the changes are complete. + The code will not be merged until this box is checked, the continuous + integration returns checkmarks, + and multiple core developers give "Approved" reviews. + +# Additional Resources + +* [General GitHub documentation](https://help.github.com/) +* [PR best practices](http://codeinthehole.com/writing/pull-requests-and-other-good-practices-for-teams-using-github/) +* [A guide to contributing to software packages](http://www.contribution-guide.org) +* [Thinkful PR example](http://www.thinkful.com/learn/github-pull-request-tutorial/#Time-to-Submit-Your-First-PR) diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index a7ef2650d..60c2e74c0 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,4 +1,11 @@ - - [ ] Implement feature / fix bug - - [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests) - - [ ] Update [documentation](https://github.com/choderalab/openmmtools/tree/master/docs) as needed - - [ ] Update [changelog](https://github.com/choderalab/openmmtools/blob/master/docs/releasehistory.rst) \ No newline at end of file +## Description +Provide a brief description of the PR's purpose here. + +## Todos +- [ ] Implement feature / fix bug +- [ ] Add [tests](https://github.com/choderalab/openmmtools/tree/master/openmmtools/tests) +- [ ] Update [documentation](https://github.com/choderalab/openmmtools/tree/master/docs) as needed +- [ ] Update [changelog](https://github.com/choderalab/openmmtools/blob/master/docs/releasehistory.rst)Notable points that this PR has either accomplished or will accomplish. + +## Status +- [ ] Ready to go diff --git a/.gitignore b/.gitignore index 6f8cee03a..e08538a58 100644 --- a/.gitignore +++ b/.gitignore @@ -1,12 +1,102 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ *.py[cod] +*$py.class -openmmtools/version.py +# C extensions +*.so -# Packages -*.egg-info -dist -build -__pycache__ +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +.eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +wheels/ +*.egg-info/ +.installed.cfg +*.egg -# PyCharm -.idea +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.coverage.* +.cache +.pytest_cache +nosetests.xml +coverage.xml +*.cover +.hypothesis/ + +# Translations +*.mo +*.pot + +# Django stuff: +*.log +local_settings.py + +# Flask stuff: +instance/ +.webassets-cache + +# Scrapy stuff: +.scrapy + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# Jupyter Notebook +.ipynb_checkpoints + +# pyenv +.python-version + +# celery beat schedule file +celerybeat-schedule + +# SageMath parsed files +*.sage.py + +# dotenv +.env + +# virtualenv +.venv +venv/ +ENV/ + +# Spyder project settings +.spyderproject +.spyproject + +# Rope project settings +.ropeproject + +# mkdocs documentation +/site + +# mypy +.mypy_cache/ diff --git a/.lgtm.yml b/.lgtm.yml new file mode 100644 index 000000000..933988bfd --- /dev/null +++ b/.lgtm.yml @@ -0,0 +1,12 @@ +# Configure LGTM for this package + +extraction: + python: # Configure Python + python_setup: # Configure the setup + version: 3 # Specify Version 3 +path_classifiers: + library: + - versioneer.py # Set Versioneer.py to an external "library" (3rd party code) + - devtools/* + generated: + - openmmtools/_version.py diff --git a/.travis.yml b/.travis.yml index 33a92f67d..110cf623e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -1,46 +1,55 @@ -language: c -sudo: false -addons: - apt: - sources: - - ubuntu-toolchain-r-test +language: python -install: - - bash -x devtools/travis-ci/install.sh - - export PYTHONUNBUFFERED=true - - export PATH=$HOME/miniconda/bin:$PATH +# Run jobs on container-based infrastructure, can be overridden per job + +matrix: + include: + # Extra includes for OSX since python language is not available by default on OSX + - os: osx + language: generic + env: PYTHON_VER=3.6 + - os: osx + language: generic + env: PYTHON_VER=3.7 -script: - # Create a test environment - - conda create --quiet --yes -n test python=$python - # Activate the test environment - - source activate test - # Add org channel - - conda config --add channels ${ORGNAME} - # Add omnia dev channels - - if [ $DEVOMNIA ]; then conda config --add channels omnia-dev; fi - # Add conda-forge channel back to top priority - - conda config --add channels conda-forge - # Build the recipe - - conda build devtools/conda-recipe - # Install the package - - conda install --yes --quiet --use-local ${PACKAGENAME}-dev - # Install testing dependencies. Without specifying the numpy version, numpy - # is downgraded to 1.9 and we get a "libgfortran not found" issue. - - conda install --yes --quiet nose nose-timer pymbar "numpy>=1.14" - # Test the package - - cd devtools && nosetests $PACKAGENAME --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow' && cd .. + + - os: linux + language: generic # No need to set Python version since its conda + env: PYTHON_VER=3.6 + - os: linux + language: generic + env: PYTHON_VER=3.7 env: - matrix: - - python=3.6 CONDA_PY=36 - - python=3.7 CONDA_PY=37 - - python=3.7 CONDA_PY=37 DEVOMNIA=true # allowed to fail global: - - ORGNAME="omnia" # the name of the organization - - PACKAGENAME="openmmtools" # the name of your package - OPENMM_CPU_THREADS="1" # only use one CPU thread for determinism -matrix: - allow_failures: - - env: python=3.7 CONDA_PY=37 DEVOMNIA=true +before_install: + # Additional info about the build + - uname -a + - df -h + - ulimit -a + + # Install the Python environment + - source devtools/travis-ci/before_install.sh + - python -V + +install: + + # Create test environment for package + - python devtools/scripts/create_conda_env.py -n=test -p=$PYTHON_VER devtools/conda-envs/test_env.yaml + # Activate the test environment + - conda activate test + # Build and install package + - python setup.py develop --no-deps + + +script: + #- pytest -v --cov=openmmtools openmmtools/tests/ + - nosetests openmmtools/tests --nocapture --verbosity=2 --with-timer --with-doctest -a '!slow' + +notifications: + email: false + +after_success: + - codecov diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 000000000..1f73685a1 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,77 @@ +# Contributor Covenant Code of Conduct + +## Our Pledge + +In the interest of fostering an open and welcoming environment, we as +contributors and maintainers pledge to making participation in our project and +our community a harassment-free experience for everyone, regardless of age, +body size, disability, ethnicity, gender identity and expression, level of +experience, nationality, personal appearance, race, religion, or sexual +identity and orientation. + +## Our Standards + +Examples of behavior that contributes to creating a positive environment include: + +* Using welcoming and inclusive language +* Being respectful of differing viewpoints and experiences +* Gracefully accepting constructive criticism +* Focusing on what is best for the community +* Showing empathy towards other community members + +Examples of unacceptable behavior by participants include: + +* The use of sexualized language or imagery and unwelcome sexual attention or advances +* Trolling, insulting/derogatory comments, and personal or political attacks +* Public or private harassment +* Publishing others' private information, such as a physical or electronic address, without explicit permission +* Other conduct which could reasonably be considered inappropriate in a professional setting + +## Our Responsibilities + +Project maintainers are responsible for clarifying the standards of acceptable +behavior and are expected to take appropriate and fair corrective action in +response to any instances of unacceptable behavior. + +Project maintainers have the right and responsibility to remove, edit, or +reject comments, commits, code, wiki edits, issues, and other contributions +that are not aligned to this Code of Conduct, or to ban temporarily or +permanently any contributor for other behaviors that they deem inappropriate, +threatening, offensive, or harmful. + +Moreover, project maintainers will strive to offer feedback and advice to +ensure quality and consistency of contributions to the code. Contributions +from outside the group of project maintainers are strongly welcomed but the +final decision as to whether commits are merged into the codebase rests with +the team of project maintainers. + +## Scope + +This Code of Conduct applies both within project spaces and in public spaces +when an individual is representing the project or its community. Examples of +representing a project or community include using an official project e-mail +address, posting via an official social media account, or acting as an +appointed representative at an online or offline event. Representation of a +project may be further defined and clarified by project maintainers. + +## Enforcement + +Instances of abusive, harassing, or otherwise unacceptable behavior may be +reported by contacting the project team at 'john.chodera@choderalab.org'. The project team will +review and investigate all complaints, and will respond in a way that it deems +appropriate to the circumstances. The project team is obligated to maintain +confidentiality with regard to the reporter of an incident. Further details of +specific enforcement policies may be posted separately. + +Project maintainers who do not follow or enforce the Code of Conduct in good +faith may face temporary or permanent repercussions as determined by other +members of the project's leadership. + +## Attribution + +This Code of Conduct is adapted from the [Contributor Covenant][homepage], +version 1.4, available at +[http://contributor-covenant.org/version/1/4][version] + +[homepage]: http://contributor-covenant.org +[version]: http://contributor-covenant.org/version/1/4/ diff --git a/LICENSE b/LICENSE index eba7475aa..05498a993 100644 --- a/LICENSE +++ b/LICENSE @@ -1,6 +1,6 @@ MIT License -Copyright (c) 2015-2017 Chodera lab // Memorial Sloan Kettering Cancer Center +Copyright (c) 2015-2019 Chodera lab // Memorial Sloan Kettering Cancer Center Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 000000000..9b7f8e8a3 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,6 @@ +include LICENSE +include MANIFEST.in +include versioneer.py + +graft openmmtools +global-exclude *.py[cod] __pycache__ *.so \ No newline at end of file diff --git a/appveyor.yml b/appveyor.yml index 05898e072..3be7a1e38 100644 --- a/appveyor.yml +++ b/appveyor.yml @@ -1,33 +1,46 @@ environment: - global: - # SDK v7.0 MSVC Express 2008's SetEnv.cmd script will fail if the - # /E:ON and /V:ON options are not enabled in the batch script intepreter - # See: http://stackoverflow.com/a/13751649/163740 - CMD_IN_ENV: "cmd /E:ON /V:ON /C .\\devtools\\appveyor\\run_with_env.cmd" matrix: - - PYTHON: "C:\\Python35_64" - PYTHON_VERSION: "3.5" + - PYTHON: "C:\\Miniconda36-x64" + PYTHON_VERSION: "3.6" PYTHON_ARCH: "64" - CONDA_PY: "35" - CONDA_NPY: "112" - - PYTHON: "C:\\Python36_64" - PYTHON_VERSION: "3.6" + - PYTHON: "C:\\Miniconda37-x64" + PYTHON_VERSION: "3.7" PYTHON_ARCH: "64" - CONDA_PY: "36" - CONDA_NPY: "112" + install: - # this installs the appropriate Miniconda (Py2/Py3, 32/64 bit), - # as well as pip, conda-build, and the binstar CLI - - ps: . ".\\devtools\\appveyor\\install.ps1" + # Make sure pip is around + - python -m ensurepip - "SET PATH=%PYTHON%;%PYTHON%\\Scripts;%PATH%" - - conda config --add channels omnia + + # Add conda-forge channel - conda config --add channels conda-forge - - conda config --add channels omnia/label/rc + + # Add omnia channel + - conda config --add channels omnia + + # Always run commands without asking + - conda config --set always_yes yes + + # Try to update conda first to avoid odd dependency clashes + - conda update --all + + # Create test environment for package + - python devtools\\scripts\\create_conda_env.py -n=test -p=%PYTHON_VERSION% devtools\\conda-envs\\test_env.yaml + + # Activate the test environment + - activate test + + # Build and install package + - python setup.py develop --no-deps + build: false test_script: - - "%CMD_IN_ENV% conda build --quiet devtools\\conda-recipe" + - pytest -v --cov=openmmtools openmmtools\\tests + +on_success: + - codecov diff --git a/devtools/README.md b/devtools/README.md index 998d59756..009e161ae 100644 --- a/devtools/README.md +++ b/devtools/README.md @@ -1,18 +1,60 @@ -Developer Notes / Tools -======================= +# Development, testing, and deployment tools -Assorted notes for developers. +This directory contains a collection of tools for running Continuous Integration (CI) tests, +conda installation, and other development tools not directly related to the coding process. -How to do a release -------------------- -- Update the whatsnew.rst document. Use the github view that shows all the commits to master since the last release to write it. -- Update the version number in `setup.py`, change `ISRELEASED` to `True` -- Commit to master, and [tag](https://github.com/choderalab/openmmtools/releases) the release on github -- To push the source to PyPI, use `python setup.py sdist --formats=gztar,zip upload` -- Conda binaries need to built separately on each platform (`conda build openmmtools; binstar upload `) -- Make an annoucement on github / email -- After tagging the release, make a NEW commit that changes `ISRELEASED` back to `False` in `setup.py` +## Manifest -It's important that the version which is tagged on github for the release be -the one with the ISRELEASED flag in setup.py set to true. +### Continuous Integration + +You should test your code, but do not feel compelled to use these specific programs. You also may not need Unix and +Windows testing if you only plan to deploy on specific platforms. These are just to help you get started + +* `travis-ci`: Linux and OSX based testing through [Travis-CI](https://about.travis-ci.com/) + * `before_install.sh`: Pip/Miniconda pre-package installation script for Travis +* `appveyor`: Windows based testing through [AppVeyor](https://www.appveyor.com/) (there are no files directly related to this) + +### Conda Environment: + +This directory contains the files to setup the Conda environment for testing purposes + +* `conda-envs`: directory containing the YAML file(s) which fully describe Conda Environments, their dependencies, and those dependency provenance's + * `test_env.yaml`: Simple test environment file with base dependencies. Channels are not specified here and therefore respect global Conda configuration + +### Additional Scripts: + +This directory contains OS agnostic helper scripts which don't fall in any of the previous categories +* `scripts` + * `create_conda_env.py`: Helper program for spinning up new conda environments based on a starter file with Python Version and Env. Name command-line options + + +## How to contribute changes +- Clone the repository if you have write access to the main repo, fork the repository if you are a collaborator. +- Make a new branch with `git checkout -b {your branch name}` +- Make changes and test your code +- Ensure that the test environment dependencies (`conda-envs`) line up with the build and deploy dependencies (`conda-recipe/meta.yaml`) +- Push the branch to the repo (either the main or your fork) with `git push -u origin {your branch name}` + * Note that `origin` is the default name assigned to the remote, yours may be different +- Make a PR on GitHub with your changes +- We'll review the changes and get your code into the repo after lively discussion! + + +## Checklist for updates +- [ ] Make sure there is an/are issue(s) opened for your specific update +- [ ] Create the PR, referencing the issue +- [ ] Debug the PR as needed until tests pass +- [ ] Tag the final, debugged version + * `git tag -a X.Y.Z [latest pushed commit] && git push --follow-tags` +- [ ] Get the PR merged in + +## Versioneer Auto-version +[Versioneer](https://github.com/warner/python-versioneer) will automatically infer what version +is installed by looking at the `git` tags and how many commits ahead this version is. The format follows +[PEP 440](https://www.python.org/dev/peps/pep-0440/) and has the regular expression of: +```regexp +\d+.\d+.\d+(?\+\d+-[a-z0-9]+) +``` +If the version of this commit is the same as a `git` tag, the installed version is the same as the tag, +e.g. `openmmtools-0.1.2`, otherwise it will be appended with `+X` where `X` is the number of commits +ahead from the last tag, and then `-YYYYYY` where the `Y`'s are replaced with the `git` commit hash. diff --git a/devtools/appveyor/install.ps1 b/devtools/appveyor/install.ps1 deleted file mode 100644 index 5e2f719bc..000000000 --- a/devtools/appveyor/install.ps1 +++ /dev/null @@ -1,91 +0,0 @@ -# Sample script to install Miniconda under Windows -# Authors: Olivier Grisel, Jonathan Helmus and Kyle Kastner, Robert McGibbon -# License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/ - -$MINICONDA_URL = "http://repo.continuum.io/miniconda/" - - -function DownloadMiniconda ($python_version, $platform_suffix) { - $webclient = New-Object System.Net.WebClient - $filename = "Miniconda3-4.5.4-Windows-" + $platform_suffix + ".exe" - $url = $MINICONDA_URL + $filename - - $basedir = $pwd.Path + "\" - $filepath = $basedir + $filename - if (Test-Path $filename) { - Write-Host "Reusing" $filepath - return $filepath - } - - # Download and retry up to 3 times in case of network transient errors. - Write-Host "Downloading" $filename "from" $url - $retry_attempts = 2 - for($i=0; $i -lt $retry_attempts; $i++){ - try { - $webclient.DownloadFile($url, $filepath) - break - } - Catch [Exception]{ - Start-Sleep 1 - } - } - if (Test-Path $filepath) { - Write-Host "File saved at" $filepath - } else { - # Retry once to get the error message if any at the last try - $webclient.DownloadFile($url, $filepath) - } - return $filepath -} - - -function InstallMiniconda ($python_version, $architecture, $python_home) { - Write-Host "Installing Python" $python_version "for" $architecture "bit architecture to" $python_home - if (Test-Path $python_home) { - Write-Host $python_home "already exists, skipping." - return $false - } - if ($architecture -match "32") { - $platform_suffix = "x86" - } else { - $platform_suffix = "x86_64" - } - - $filepath = DownloadMiniconda $python_version $platform_suffix - Write-Host "Installing" $filepath "to" $python_home - $install_log = $python_home + ".log" - $args = "/S /D=$python_home" - Write-Host $filepath $args - Start-Process -FilePath $filepath -ArgumentList $args -Wait -Passthru - if (Test-Path $python_home) { - Write-Host "Python $python_version ($architecture) installation complete" - } else { - Write-Host "Failed to install Python in $python_home" - Get-Content -Path $install_log - Exit 1 - } -} - - -function InstallCondaPackages ($python_home, $spec) { - $conda_path = $python_home + "\Scripts\conda.exe" - $args = "install --yes " + $spec - Write-Host ("conda " + $args) - Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru -} - -function UpdateConda ($python_home) { - $conda_path = $python_home + "\Scripts\conda.exe" - Write-Host "Updating conda..." - $args = "update --yes conda" - Write-Host $conda_path $args - Start-Process -FilePath "$conda_path" -ArgumentList $args -Wait -Passthru -} - -function main () { - InstallMiniconda $env:PYTHON_VERSION $env:PYTHON_ARCH $env:PYTHON - UpdateConda $env:PYTHON - InstallCondaPackages $env:PYTHON "conda-build pip jinja2 binstar" -} - -main diff --git a/devtools/appveyor/run_with_env.cmd b/devtools/appveyor/run_with_env.cmd deleted file mode 100644 index 3a472bc83..000000000 --- a/devtools/appveyor/run_with_env.cmd +++ /dev/null @@ -1,47 +0,0 @@ -:: To build extensions for 64 bit Python 3, we need to configure environment -:: variables to use the MSVC 2010 C++ compilers from GRMSDKX_EN_DVD.iso of: -:: MS Windows SDK for Windows 7 and .NET Framework 4 (SDK v7.1) -:: -:: To build extensions for 64 bit Python 2, we need to configure environment -:: variables to use the MSVC 2008 C++ compilers from GRMSDKX_EN_DVD.iso of: -:: MS Windows SDK for Windows 7 and .NET Framework 3.5 (SDK v7.0) -:: -:: 32 bit builds do not require specific environment configurations. -:: -:: Note: this script needs to be run with the /E:ON and /V:ON flags for the -:: cmd interpreter, at least for (SDK v7.0) -:: -:: More details at: -:: https://github.com/cython/cython/wiki/64BitCythonExtensionsOnWindows -:: http://stackoverflow.com/a/13751649/163740 -:: -:: Author: Olivier Grisel -:: License: CC0 1.0 Universal: http://creativecommons.org/publicdomain/zero/1.0/ -@ECHO OFF - -SET COMMAND_TO_RUN=%* -SET WIN_SDK_ROOT=C:\Program Files\Microsoft SDKs\Windows - -SET MAJOR_PYTHON_VERSION="%PYTHON_VERSION:~0,1%" -IF %MAJOR_PYTHON_VERSION% == "2" ( - SET WINDOWS_SDK_VERSION="v7.0" -) ELSE IF %MAJOR_PYTHON_VERSION% == "3" ( - SET WINDOWS_SDK_VERSION="v7.1" -) ELSE ( - ECHO Unsupported Python version: "%MAJOR_PYTHON_VERSION%" - EXIT 1 -) - -IF "%PYTHON_ARCH%"=="64" ( - ECHO Configuring Windows SDK %WINDOWS_SDK_VERSION% for Python %MAJOR_PYTHON_VERSION% on a 64 bit architecture - SET DISTUTILS_USE_SDK=1 - SET MSSdk=1 - "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Setup\WindowsSdkVer.exe" -q -version:%WINDOWS_SDK_VERSION% - "%WIN_SDK_ROOT%\%WINDOWS_SDK_VERSION%\Bin\SetEnv.cmd" /x64 /release - ECHO Executing: %COMMAND_TO_RUN% - call %COMMAND_TO_RUN% || EXIT 1 -) ELSE ( - ECHO Using default MSVC build environment for 32 bit architecture - ECHO Executing: %COMMAND_TO_RUN% - call %COMMAND_TO_RUN% || EXIT 1 -) diff --git a/devtools/conda-envs/test_env.yaml b/devtools/conda-envs/test_env.yaml new file mode 100644 index 000000000..6566224c7 --- /dev/null +++ b/devtools/conda-envs/test_env.yaml @@ -0,0 +1,39 @@ +name: test +channels: + - conda-forge + - omnia + - defaults +dependencies: + # Base depends + - python + - pip + + - setuptools + - openmm >=7.3.1 + - cython + - python + - numpy + - scipy + - six + - openmm >=7.3.1 + - parmed + - mdtraj + - netcdf4 >=1.4.2 # after bugfix: "always return masked array by default, even if there are no masked values" + - libnetcdf >=4.6.2 # workaround for libssl issues + - pyyaml + - cython + - sphinxcontrib-bibtex + - mpiplus + - pymbar + - pyyaml + + # Testing + - nose + - nose-timer + - pytest + - pytest-cov + - codecov + + # Pip-only installs + - pip: + #- codecov diff --git a/devtools/scripts/create_conda_env.py b/devtools/scripts/create_conda_env.py new file mode 100644 index 000000000..b51adc86d --- /dev/null +++ b/devtools/scripts/create_conda_env.py @@ -0,0 +1,95 @@ +import argparse +import os +import re +import glob +import shutil +import subprocess as sp +from tempfile import TemporaryDirectory +from contextlib import contextmanager +# YAML imports +try: + import yaml # PyYAML + loader = yaml.load +except ImportError: + try: + import ruamel_yaml as yaml # Ruamel YAML + except ImportError: + try: + # Load Ruamel YAML from the base conda environment + from importlib import util as import_util + CONDA_BIN = os.path.dirname(os.environ['CONDA_EXE']) + ruamel_yaml_path = glob.glob(os.path.join(CONDA_BIN, '..', + 'lib', 'python*.*', 'site-packages', + 'ruamel_yaml', '__init__.py'))[0] + # Based on importlib example, but only needs to load_module since its the whole package, not just + # a module + spec = import_util.spec_from_file_location('ruamel_yaml', ruamel_yaml_path) + yaml = spec.loader.load_module() + except (KeyError, ImportError, IndexError): + raise ImportError("No YAML parser could be found in this or the conda environment. " + "Could not find PyYAML or Ruamel YAML in the current environment, " + "AND could not find Ruamel YAML in the base conda environment through CONDA_EXE path. " + "Environment not created!") + loader = yaml.YAML(typ="safe").load # typ="safe" avoids odd typing on output + + +@contextmanager +def temp_cd(): + """Temporary CD Helper""" + cwd = os.getcwd() + with TemporaryDirectory() as td: + try: + os.chdir(td) + yield + finally: + os.chdir(cwd) + + +# Args +parser = argparse.ArgumentParser(description='Creates a conda environment from file for a given Python version.') +parser.add_argument('-n', '--name', type=str, + help='The name of the created Python environment') +parser.add_argument('-p', '--python', type=str, + help='The version of the created Python environment') +parser.add_argument('conda_file', + help='The file for the created Python environment') + +args = parser.parse_args() + +# Open the base file +with open(args.conda_file, "r") as handle: + yaml_script = loader(handle.read()) + +python_replacement_string = "python {}*".format(args.python) + +try: + for dep_index, dep_value in enumerate(yaml_script['dependencies']): + if re.match('python([ ><=*]+[0-9.*]*)?$', dep_value): # Match explicitly 'python' and its formats + yaml_script['dependencies'].pop(dep_index) + break # Making the assumption there is only one Python entry, also avoids need to enumerate in reverse +except (KeyError, TypeError): + # Case of no dependencies key, or dependencies: None + yaml_script['dependencies'] = [] +finally: + # Ensure the python version is added in. Even if the code does not need it, we assume the env does + yaml_script['dependencies'].insert(0, python_replacement_string) + +# Figure out conda path +if "CONDA_EXE" in os.environ: + conda_path = os.environ["CONDA_EXE"] +else: + conda_path = shutil.which("conda") +if conda_path is None: + raise RuntimeError("Could not find a conda binary in CONDA_EXE variable or in executable search path") + +print("CONDA ENV NAME {}".format(args.name)) +print("PYTHON VERSION {}".format(args.python)) +print("CONDA FILE NAME {}".format(args.conda_file)) +print("CONDA PATH {}".format(conda_path)) + +# Write to a temp directory which will always be cleaned up +with temp_cd(): + temp_file_name = "temp_script.yaml" + with open(temp_file_name, 'w') as f: + f.write(yaml.dump(yaml_script)) + sp.call("{} env create -n {} -f {}".format(conda_path, args.name, temp_file_name), shell=True) diff --git a/devtools/travis-ci/before_install.sh b/devtools/travis-ci/before_install.sh new file mode 100755 index 000000000..cfaa07398 --- /dev/null +++ b/devtools/travis-ci/before_install.sh @@ -0,0 +1,41 @@ +# Temporarily change directory to $HOME to install software +pushd . +cd $HOME +# Make sure some level of pip is installed +python -m ensurepip + +# Install Miniconda +if [ "$TRAVIS_OS_NAME" == "osx" ]; then + # Make OSX md5 mimic md5sum from linux, alias does not work + md5sum () { + command md5 -r "$@" + } + MINICONDA=Miniconda3-latest-MacOSX-x86_64.sh +else + MINICONDA=Miniconda3-latest-Linux-x86_64.sh +fi +MINICONDA_HOME=$HOME/miniconda +MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') +wget -q https://repo.continuum.io/miniconda/$MINICONDA +if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then + echo "Miniconda MD5 mismatch" + exit 1 +fi +bash $MINICONDA -b -p $MINICONDA_HOME + +# Configure miniconda +export PIP_ARGS="-U" +# New to conda >=4.4 +echo ". $MINICONDA_HOME/etc/profile.d/conda.sh" >> ~/.bashrc # Source the profile.d file +echo "conda activate" >> ~/.bashrc # Activate conda +source ~/.bashrc # source file to get new commands +#export PATH=$MINICONDA_HOME/bin:$PATH # Old way, should not be needed anymore + +conda config --add channels conda-forge + +conda config --set always_yes yes +conda install conda conda-build jinja2 anaconda-client +conda update --quiet --all + +# Restore original directory +popd diff --git a/devtools/travis-ci/install.sh b/devtools/travis-ci/install.sh deleted file mode 100755 index 1bab8e1b1..000000000 --- a/devtools/travis-ci/install.sh +++ /dev/null @@ -1,23 +0,0 @@ -# Temporarily change directory to $HOME to install software -pushd . -cd $HOME - -# Install Miniconda -MINICONDA=Miniconda2-latest-Linux-x86_64.sh -MINICONDA_HOME=$HOME/miniconda -MINICONDA_MD5=$(curl -s https://repo.continuum.io/miniconda/ | grep -A3 $MINICONDA | sed -n '4p' | sed -n 's/ *\(.*\)<\/td> */\1/p') -wget -q https://repo.continuum.io/miniconda/$MINICONDA -if [[ $MINICONDA_MD5 != $(md5sum $MINICONDA | cut -d ' ' -f 1) ]]; then - echo "Miniconda MD5 mismatch" - exit 1 -fi -bash $MINICONDA -b -p $MINICONDA_HOME - -# Configure miniconda -export PIP_ARGS="-U" -export PATH=$MINICONDA_HOME/bin:$PATH -conda config --add channels conda-forge -conda install --yes conda\>=4.3 conda-build jinja2 anaconda-client pip - -# Restore original directory -popd diff --git a/docs/releasehistory.rst b/docs/releasehistory.rst index e6fc2958b..83d10ffe0 100644 --- a/docs/releasehistory.rst +++ b/docs/releasehistory.rst @@ -9,7 +9,8 @@ New features Bugfixes -------- - +- Update build infrastructure to match `MolSSI cookiecutter `_. +- A bug in the multistate samplers where``logsumexp`` was imported from ``scipy.misc`` (now in ``scipy.special``) was fixed 0.18.1 - Bugfix release ======================= @@ -36,7 +37,7 @@ New features - ``MultiStateSampler``: sample independently from multiple thermodynamic states - ``ReplicaExchangeSampler``: replica exchange among thermodynamic states - ``SAMSSampler``: self-adjusted mixture sampling (SAMS) sampling -- All samplers can use MPI via the ``mpiplus `_ package +- All samplers can use MPI via the `mpiplus `_ package 0.17.0 - Removed Py2 support, faster exact PME treatment ======================================================== diff --git a/openmmtools/multistate/multistateanalyzer.py b/openmmtools/multistate/multistateanalyzer.py index 7a3a1e040..4b0e0b1a1 100644 --- a/openmmtools/multistate/multistateanalyzer.py +++ b/openmmtools/multistate/multistateanalyzer.py @@ -31,7 +31,7 @@ import numpy as np from simtk import openmm import simtk.unit as units -from scipy.misc import logsumexp +from scipy.special import logsumexp from pymbar import MBAR, timeseries from openmmtools import multistate, utils, forces diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 000000000..71d5c913e --- /dev/null +++ b/setup.cfg @@ -0,0 +1,30 @@ +# Helper file to handle all configs + +[coverage:run] +# .coveragerc to control coverage.py and pytest-cov +omit = + # Omit the tests + */tests/* + # Omit generated versioneer + openmmtools/_version.py + +[yapf] +# YAPF, in .style.yapf files this shows up as "[style]" header +COLUMN_LIMIT = 119 +INDENT_WIDTH = 4 +USE_TABS = False + +[flake8] +# Flake8, PyFlakes, etc +max-line-length = 119 + +[versioneer] +# Automatic version numbering scheme +VCS = git +style = pep440 +versionfile_source = openmmtools/_version.py +versionfile_build = openmmtools/_version.py +tag_prefix = '' + +[aliases] +test = pytest diff --git a/versioneer.py b/versioneer.py new file mode 100644 index 000000000..64fea1c89 --- /dev/null +++ b/versioneer.py @@ -0,0 +1,1822 @@ + +# 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)