From 8d341d3ccb53b0741d41af05e48b170d9e1ebd2b Mon Sep 17 00:00:00 2001 From: Liam Huber Date: Wed, 21 Dec 2022 13:33:20 -0800 Subject: [PATCH] Initial commit --- .binder/environment.yml | 4 + .binder/postBuild | 31 + .ci_support/environment.yml | 5 + .ci_support/exclude | 0 .coveragerc | 5 + .gitattributes | 1 + .github/ISSUE_TEMPLATE/bug_report.md | 32 + .github/ISSUE_TEMPLATE/feature_request.md | 20 + .github/PULL_REQUEST_TEMPLATE/bug_fix.md | 24 + .github/PULL_REQUEST_TEMPLATE/new_feature.md | 24 + .github/delete-merged-branch-config.yml | 3 + .github/dependabot.yml | 8 + .github/stale.yml | 58 + .github/workflows/daily.yml | 12 + .github/workflows/dependabot-pr.yml | 10 + .github/workflows/pr-labeled.yml | 12 + .github/workflows/pr-target-opened.yml | 12 + .github/workflows/push-pull-main.yml | 14 + .github/workflows/release.yml | 11 + .github/workflows/weekly.yml | 12 + .gitignore | 11 + .gitpod | 3 + .readthedocs.yml | 26 + CODE_OF_CONDUCT.md | 76 + CONTRIBUTING.rst | 477 +++++ LICENSE | 29 + MANIFEST.in | 3 + README.md | 88 + docs/__init__.py | 0 docs/_static/pyiron-logo.png | Bin 0 -> 66292 bytes docs/_static/pyiron_logo.ico | Bin 0 -> 21238 bytes docs/conf.py | 311 +++ docs/environment.yml | 6 + docs/index.rst | 13 + docs/source/indices.rst | 12 + notebooks/version.ipynb | 36 + pyiron_module_template/__init__.py | 4 + pyiron_module_template/_version.py | 556 ++++++ setup.cfg | 13 + setup.py | 34 + tests/__init__.py | 0 tests/benchmark/__init__.py | 3 + tests/benchmark/test_benchmark.py | 6 + tests/integration/__init__.py | 3 + tests/integration/test_integration.py | 6 + tests/unit/__init__.py | 3 + tests/unit/test_tests.py | 9 + update_module_name.sh | 29 + versioneer.py | 1822 ++++++++++++++++++ 49 files changed, 3877 insertions(+) create mode 100644 .binder/environment.yml create mode 100644 .binder/postBuild create mode 100644 .ci_support/environment.yml create mode 100644 .ci_support/exclude create mode 100644 .coveragerc create mode 100644 .gitattributes create mode 100644 .github/ISSUE_TEMPLATE/bug_report.md create mode 100644 .github/ISSUE_TEMPLATE/feature_request.md create mode 100644 .github/PULL_REQUEST_TEMPLATE/bug_fix.md create mode 100644 .github/PULL_REQUEST_TEMPLATE/new_feature.md create mode 100644 .github/delete-merged-branch-config.yml create mode 100644 .github/dependabot.yml create mode 100644 .github/stale.yml create mode 100644 .github/workflows/daily.yml create mode 100644 .github/workflows/dependabot-pr.yml create mode 100644 .github/workflows/pr-labeled.yml create mode 100644 .github/workflows/pr-target-opened.yml create mode 100644 .github/workflows/push-pull-main.yml create mode 100644 .github/workflows/release.yml create mode 100644 .github/workflows/weekly.yml create mode 100644 .gitignore create mode 100644 .gitpod create mode 100644 .readthedocs.yml create mode 100644 CODE_OF_CONDUCT.md create mode 100644 CONTRIBUTING.rst create mode 100644 LICENSE create mode 100644 MANIFEST.in create mode 100644 README.md create mode 100644 docs/__init__.py create mode 100644 docs/_static/pyiron-logo.png create mode 100644 docs/_static/pyiron_logo.ico create mode 100644 docs/conf.py create mode 100644 docs/environment.yml create mode 100644 docs/index.rst create mode 100644 docs/source/indices.rst create mode 100644 notebooks/version.ipynb create mode 100644 pyiron_module_template/__init__.py create mode 100644 pyiron_module_template/_version.py create mode 100644 setup.cfg create mode 100644 setup.py create mode 100644 tests/__init__.py create mode 100644 tests/benchmark/__init__.py create mode 100644 tests/benchmark/test_benchmark.py create mode 100644 tests/integration/__init__.py create mode 100644 tests/integration/test_integration.py create mode 100644 tests/unit/__init__.py create mode 100644 tests/unit/test_tests.py create mode 100644 update_module_name.sh create mode 100644 versioneer.py diff --git a/.binder/environment.yml b/.binder/environment.yml new file mode 100644 index 0000000..748806a --- /dev/null +++ b/.binder/environment.yml @@ -0,0 +1,4 @@ +channels: +- conda-forge +dependencies: +- pyiron_base diff --git a/.binder/postBuild b/.binder/postBuild new file mode 100644 index 0000000..aa97083 --- /dev/null +++ b/.binder/postBuild @@ -0,0 +1,31 @@ +# pip install master +pip install --no-deps . +# Note: This produces build and pyiron_module_template.egg-info directories + +# clean up +if [ -d "notebooks" ]; then + mv notebooks/* . +fi +if [ -d "${HOME}/pyiron_module_template" ]; then + rm -r ${HOME}/.binder \ + ${HOME}/.ci_support \ + ${HOME}/.github \ + ${HOME}/build \ + ${HOME}/docs \ + ${HOME}/notebooks \ + ${HOME}/pyiron_module_template \ + ${HOME}/pyiron_module_template.egg-info \ + ${HOME}/tests \ + ${HOME}/.gitattributes \ + ${HOME}/.gitignore \ + ${HOME}/.gitpod \ + ${HOME}/.readthedocs.yml \ + ${HOME}/CODE_OF_CONDUCT.md \ + ${HOME}/CONTRIBUTING.rst \ + ${HOME}/LICENSE \ + ${HOME}/MANIFEST.in \ + ${HOME}/README.md \ + ${HOME}/setup.cfg \ + ${HOME}/setup.py \ + ${HOME}/versioneer.py +fi diff --git a/.ci_support/environment.yml b/.ci_support/environment.yml new file mode 100644 index 0000000..cf17d45 --- /dev/null +++ b/.ci_support/environment.yml @@ -0,0 +1,5 @@ +channels: + - conda-forge +dependencies: + - pyiron_base + diff --git a/.ci_support/exclude b/.ci_support/exclude new file mode 100644 index 0000000..e69de29 diff --git a/.coveragerc b/.coveragerc new file mode 100644 index 0000000..0176c43 --- /dev/null +++ b/.coveragerc @@ -0,0 +1,5 @@ +# .coveragerc to control coverage.py +[run] +source = pyiron_module_template +omit = pyiron_module_template/_version.py +concurrency = multiprocessing \ No newline at end of file diff --git a/.gitattributes b/.gitattributes new file mode 100644 index 0000000..84b63df --- /dev/null +++ b/.gitattributes @@ -0,0 +1 @@ +pyiron_module_template/_version.py export-subst diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md new file mode 100644 index 0000000..3a29cab --- /dev/null +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -0,0 +1,32 @@ +--- +name: Bug report +about: Create a bug report to help us eliminate issues and improve pyiron_module_template +title: '' +labels: bug +assignees: '' + +--- + +**Summary** + + + +**pyiron Version and Platform** + + + +**Expected Behavior** + + + +**Actual Behavior** + + + +**Steps to Reproduce** + + + +**Further Information, Files, and Links** + + diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md new file mode 100644 index 0000000..f96aa7b --- /dev/null +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -0,0 +1,20 @@ +--- +name: Feature request +about: Make a suggestion for a new feature or a change to pyiron_module_template +title: '' +labels: enhancement +assignees: '' + +--- + +**Summary** + + + +**Detailed Description** + + + +**Further Information, Files, and Links** + + diff --git a/.github/PULL_REQUEST_TEMPLATE/bug_fix.md b/.github/PULL_REQUEST_TEMPLATE/bug_fix.md new file mode 100644 index 0000000..6d27b2f --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/bug_fix.md @@ -0,0 +1,24 @@ +--- +name: Bug fix +about: Submit a pull request that fixes one or more bugs +title: '' +labels: bug +assignees: '' + +--- + +**Summary** + + + +**Related Issue(s)** + + + +**Backward Compatibility** + + + +**Detailed Description** + + diff --git a/.github/PULL_REQUEST_TEMPLATE/new_feature.md b/.github/PULL_REQUEST_TEMPLATE/new_feature.md new file mode 100644 index 0000000..7c5db00 --- /dev/null +++ b/.github/PULL_REQUEST_TEMPLATE/new_feature.md @@ -0,0 +1,24 @@ +--- +name: New Feature +about: Submit a pull request that adds new Features (complete files) to pyiron +title: '' +labels: enhancement +assignees: '' + +--- + +**Summary** + + + +**Related Issue(s)** + + + +**Backward Compatibility** + + + +**Implementation Notes** + + diff --git a/.github/delete-merged-branch-config.yml b/.github/delete-merged-branch-config.yml new file mode 100644 index 0000000..8a1c49b --- /dev/null +++ b/.github/delete-merged-branch-config.yml @@ -0,0 +1,3 @@ +exclude: + - master +delete_closed_pr: false diff --git a/.github/dependabot.yml b/.github/dependabot.yml new file mode 100644 index 0000000..01b023f --- /dev/null +++ b/.github/dependabot.yml @@ -0,0 +1,8 @@ +version: 2 +updates: +- package-ecosystem: pip + directory: "/" + schedule: + interval: weekly + day: monday + open-pull-requests-limit: 10 diff --git a/.github/stale.yml b/.github/stale.yml new file mode 100644 index 0000000..1c8b019 --- /dev/null +++ b/.github/stale.yml @@ -0,0 +1,58 @@ +# Configuration for probot-stale - https://github.com/probot/stale + +# Number of days of inactivity before an Issue or Pull Request becomes stale +daysUntilStale: 14 + +# Number of days of inactivity before an Issue or Pull Request with the stale label is closed. +# Set to false to disable. If disabled, issues still need to be closed manually, but will remain marked as stale. +daysUntilClose: 14 + +# Only issues or pull requests with all of these labels are check if stale. Defaults to `[]` (disabled) +onlyLabels: [] + +# Issues or Pull Requests with these labels will never be considered stale. Set to `[]` to disable +exemptLabels: [] + +# Set to true to ignore issues in a project (defaults to false) +exemptProjects: false + +# Set to true to ignore issues in a milestone (defaults to false) +exemptMilestones: false + +# Set to true to ignore issues with an assignee (defaults to false) +exemptAssignees: false + +# Label to use when marking as stale +staleLabel: stale + +# Comment to post when marking as stale. Set to `false` to disable +markComment: > + This issue has been automatically marked as stale because it has not had + recent activity. It will be closed if no further activity occurs. Thank you + for your contributions. + +# Comment to post when removing the stale label. +# unmarkComment: > +# Your comment here. + +# Comment to post when closing a stale Issue or Pull Request. +# closeComment: > +# Your comment here. + +# Limit the number of actions per hour, from 1-30. Default is 30 +limitPerRun: 30 + +# Limit to only `issues` or `pulls` +only: pulls + +# Optionally, specify configuration settings that are specific to just 'issues' or 'pulls': +# pulls: +# daysUntilStale: 30 +# markComment: > +# This pull request has been automatically marked as stale because it has not had +# recent activity. It will be closed if no further activity occurs. Thank you +# for your contributions. + +# issues: +# exemptLabels: +# - confirmed diff --git a/.github/workflows/daily.yml b/.github/workflows/daily.yml new file mode 100644 index 0000000..6fed36c --- /dev/null +++ b/.github/workflows/daily.yml @@ -0,0 +1,12 @@ +# This runs cron jobs daily + +name: Daily + +on: + schedule: + - cron: '0 23 * * *' + +jobs: + codeql: + uses: pyiron/actions/.github/workflows/tests-and-coverage.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/dependabot-pr.yml b/.github/workflows/dependabot-pr.yml new file mode 100644 index 0000000..1ec6445 --- /dev/null +++ b/.github/workflows/dependabot-pr.yml @@ -0,0 +1,10 @@ +name: UpdateDependabotPR + +on: + pull_request_target: + branches: [ main ] + +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/dependabot-pr.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/pr-labeled.yml b/.github/workflows/pr-labeled.yml new file mode 100644 index 0000000..4d5e8aa --- /dev/null +++ b/.github/workflows/pr-labeled.yml @@ -0,0 +1,12 @@ +# This runs jobs which pyiron modules should run when a PR is labeled + +name: PR labeled + +on: + pull_request: + types: [labeled] + +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/pr-labeled.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/pr-target-opened.yml b/.github/workflows/pr-target-opened.yml new file mode 100644 index 0000000..afdda9d --- /dev/null +++ b/.github/workflows/pr-target-opened.yml @@ -0,0 +1,12 @@ +# This runs jobs which pyiron modules should run when a PR target is opened + +name: PR opened + +on: + pull_request_target: + types: [opened] + +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/pr-target-opened.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/push-pull-main.yml b/.github/workflows/push-pull-main.yml new file mode 100644 index 0000000..0ce15da --- /dev/null +++ b/.github/workflows/push-pull-main.yml @@ -0,0 +1,14 @@ +# This runs jobs which pyiron modules should run on pushes or PRs to main + +name: Push-Pull-main + +on: + push: + branches: [ main ] + pull_request: + branches: [ main ] + +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/push-pull-main.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/release.yml b/.github/workflows/release.yml new file mode 100644 index 0000000..6212781 --- /dev/null +++ b/.github/workflows/release.yml @@ -0,0 +1,11 @@ +# This runs jobs which pyiron modules should run on release +name: Release + +on: + release: + types: [ published ] + +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/release.yml@main + secrets: inherit \ No newline at end of file diff --git a/.github/workflows/weekly.yml b/.github/workflows/weekly.yml new file mode 100644 index 0000000..eb67b87 --- /dev/null +++ b/.github/workflows/weekly.yml @@ -0,0 +1,12 @@ +# This runs cron jobs weekly + +name: Weekly + +on: + schedule: + - cron: '0 23 * * 2' + +jobs: + codeql: + uses: pyiron/actions/.github/workflows/codeql.yml@main + secrets: inherit \ No newline at end of file diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..2fa61d3 --- /dev/null +++ b/.gitignore @@ -0,0 +1,11 @@ +*.pyc +.DS_Store +.coverage +nohup.out +pyiron.log +.idea/ +inspectionProfiles/ +_build/ +apidoc/ +.ipynb_checkpoints/ +test_times.dat diff --git a/.gitpod b/.gitpod new file mode 100644 index 0000000..8f19588 --- /dev/null +++ b/.gitpod @@ -0,0 +1,3 @@ +github: + prebuilds: + pullRequestsFromForks: true diff --git a/.readthedocs.yml b/.readthedocs.yml new file mode 100644 index 0000000..3d8981a --- /dev/null +++ b/.readthedocs.yml @@ -0,0 +1,26 @@ +# .readthedocs.yml +# Read the Docs configuration file +# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details + +# Required +version: 2 + +build: + os: ubuntu-20.04 + tools: + python: 'mambaforge-4.10' + +# Build documentation in the docs/ directory with Sphinx +sphinx: + configuration: docs/conf.py + +# Build documentation with MkDocs +#mkdocs: +# configuration: mkdocs.yml + +# Optionally build your docs in additional formats such as PDF and ePub +formats: all + +# Install pyiron from conda +conda: + environment: docs/environment.yml diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md new file mode 100644 index 0000000..92b4451 --- /dev/null +++ b/CODE_OF_CONDUCT.md @@ -0,0 +1,76 @@ +# 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, sex characteristics, gender identity and expression, +level of experience, education, socio-economic status, 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. + +## 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 pyiron@mpie.de. All +complaints will be reviewed and investigated and will result in a response that +is deemed necessary and 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 https://www.contributor-covenant.org/version/1/4/code-of-conduct.html + +[homepage]: https://www.contributor-covenant.org + +For answers to common questions about this code of conduct, see +https://www.contributor-covenant.org/faq diff --git a/CONTRIBUTING.rst b/CONTRIBUTING.rst new file mode 100644 index 0000000..3a2f736 --- /dev/null +++ b/CONTRIBUTING.rst @@ -0,0 +1,477 @@ +====================== +Contributing to pyiron +====================== + +The following is a set of guidelines for contributing to pyiron, which is +hosted and maintained by the `Max Planck Institut für Eisenforschung`_ +on GitHub. These are mostly guidelines to facilitate an efficient +development workflow, and not necessarily rules. Use your best judgment, +and feel free to propose changes even to this document in a pull request. + +You can find all the pyiron packages at our `github page`_ . +To create pull requests, you will need to become part of the +pyiron organization. Please email us if you would like to join. + +Wait I don't want to read this; I just have a quick question/bugfix! +==================================================================== + +1. Check out our `FAQ page`_; your question might already be answered there. +2. If your question relates to a bug in pyiron, please briefly search the `issues page`_ and open a new labeled issue if you don't see anything related to your question there. +3. Please feel free just to send one of us a brief, descriptive email with your question, and we'll do our best to get back to you as ASAP as possible. + +Table of Contents +================= + +`License`_ + +`What should I know before I get started?`_ + * `pyiron developer meetings`_ + +.. + * `The structure of pyiron`_ +.. + * `The principles of pyiron`_ + + +`How can I contribute?`_ + * `Reporting bugs`_ + * `Suggesting enhancements`_ + * `Your first code contribution`_ + * `Pull requests`_ + +`Styleguides`_ + * `Git commit messages`_ + * `Python styleguide`_ + * `Documentation styleguide`_ + +`Additional Notes`_ + * `Issue and pull request labels`_ + * `Build status`_ + * `pyiron releases`_ + +`Debugging`_ + * `My job does not run on the queue`_ + +License +======= +pyiron is released as an open-source project under the BSD 3-Clause License. +Code contributions should also be considered open-source. + +What should I know before I get started? +======================================== + +.. The structure of pyiron +.. ----------------------- + +.. The principles of pyiron +.. ------------------------ + +pyiron developer meetings +------------------------- +If you are interested in discussing pyiron's development, we encourage you to virtually +participate in the weekly pyiron developer meeting at 14:00 german time (GMT+2). +Check the discussion page for details. + +How can I contribute? +===================== + +Reporting bugs +-------------- + + Note: If you find a closed issue that seems like it is the same + thing that you're experiencing, open a new issue and include a + link to the original issue in the body of your new one. + +**Before Submitting A Bug Report** + +Check if you can reproduce the problem in the latest version of pyiron. +Check the `FAQ page`_ for a list of common questions and problems. +Briefly search the issues page for `bugs`_ to see if the problem has already +been reported. If it has and the issue is still open, add a comment +to the existing issue instead of opening a new one. + +**How Do I Submit A (Good) Bug Report?** + +Bugs are tracked as GitHub issues. You can create an issue on +the pyiron repository by including the following information: + +* Use a clear and descriptive title for the issue to identify the problem. +* Describe the exact steps you took so we can reproduce the problem as closely as possible. +* Provide sample code that causes the problem. Include code snippets as markdown code blocks. +* Include information about the environment (OS, python version, how packages were installed) in which you were running pyiron. +* Explain what you expected to happen, and what happened instead. + +Suggesting Enhancements +----------------------- + +**How Do I Submit A (Good) Enhancement Suggestion?** + +Enhancement suggestions are tracked as GitHub issues. You can create an issue on +the pyiron repository by including the following information: + +* Use a clear and descriptive title for the issue to identify the suggestion. +* Describe the exact behavior you would expect the suggested feature to produce. +* Provide sample code that you would use to access the feature. If possible, include code for how you think the feature could be built into pyiron's codebase. Include code snippets as markdown code blocks. + +Your first code contribution +---------------------------- + +Unsure where to begin contributing to pyiron? You can start by looking +through these good-first-issue and help-wanted issues: + +* `Good first issues`_ - issues which should only require a few lines of code, and a test or two. +* `Help wanted issues`_ - issues which should be a bit more involved than beginner issues. + +**Local development** + +pyiron can be developed and tested locally. If you are using pyiron to run an +external software package, e.g. VASP or LAMMPS, you might also need to install +those packages locally to run certain integration tests in pyiron. + +To get the developmental (git) version of pyiron, + +.. code-block:: + + git clone https://github.com/pyiron/pyiron.git + conda env update --name pyiron_dev --file pyiron/.ci_support/environment.yml + conda activate pyiron_dev + conda install conda-build + conda develop pyiron + +**Deploy development version to a managed environment** + +If you want to use a development version of pyiron in a managed environment where a version of pyiron is +already installed outside of your control (e.g. on the cmti/cmfe cluster), you can still preload a local +checkout of the repo, while using the dependencies already installed. Assuming pyiron and dependencies +are already installed and setup, clone the repository to a location of your choice + +.. code-block:: + + mkdir -p ~/software + cd ~/software + git clone https://github.com/pyiron/pyiron.git + +add this folder to your python path by adding this line to your `~/.profile` + +.. code-block:: + + export PYTHONPATH="$HOME/software/pyiron:$PYTHONPATH" + +and finally restart any jupyter or jupyterhub session you might still have running. Within this folder +you can then check out any local branchen, push your own dev branches, etc and python will automatically +use this version over the system-wide installation. Check that it works by running the following cell + +.. code-block:: + + import pyiron + print(pyiron.__file__) + +If it doesn't print the path of your checkout, check that you restarted all the relevant shell sessions +and that the environment variables are correctly updated. + +**Local Testing** + +The full test suite is always run automatically when you open a new pull request. Still it +sometimes nice to run all or only specific tests on your machine. To do that run from the repo root, e.g. + +.. code-block:: + + python -m unittest discover tests + python -m unittest discover tests/sphinx + python -m unittest tests/sphinx/test_base.py + +Where the first line runs all tests, the second all the sphinx tests and the final line only the tests in that file. +Keep in mind that to run the tests your repository needs to be inside your pyiron project folder and you need to have +at least the basic resources installed from ``tests/static``. A neat trick when testing/debugging is to combine the +pdb and unittest modules like this + +.. code-block:: + + python -m pdb -m unittest ... + +This allows you to re-use the sometimes complicated setups for your interactive debugging that might be otherwise +difficult to replicate in a REPL. + +Pull requests +------------- + +The process described here has several goals: + +* Maintain pyiron's quality +* Fix problems that are important to users +* Engage the community in working toward the best possible tools +* Enable a sustainable system for pyiron's maintainers to review contributions + +Please follow these steps to have your contribution considered by the maintainers: + +* Keep the changes in your pull request as focused as possible - only address one issue per pull request wherever possible. +* Follow the `Styleguides`_ +* Assign the appropriate label (see `Issue and pull request labels`_) to your pull request. If you are fixing a specific Github issue, reference the issue directly in the pull request comments. +* If you are aware which maintainer is most closely related to the code you've edited, feel free to request their review. +* After you submit your pull request, verify that all status checks are passing. +* If a status check fails and it seems to be unrelated to your changes, explain why the failure is unrelated as a comment in your pull request. +* If you add a new external dependency, please check it is up to date. Packages which have not been updated for five years are considered outdated. +* If you rename an existing python module, please open a separate pull request to simplify the review process. + +While the prerequisites above must be satisfied prior to having your +pull request reviewed, the reviewer(s) may ask you to complete +additional design work, tests, or other changes before your pull +request can be ultimately accepted. + +Styleguides +=========== + +Git commit messages +------------------- + +* Use the present tense ("Add feature" not "Added feature") +* Use the imperative mood ("Move cursor to..." not "Moves cursor to...") +* Limit the first line to 72 characters or less +* Reference issues and pull requests liberally after the first line +* When only changing documentation, include [ci skip] in the commit title +* Consider starting the commit message with an applicable emoji: + +\:art: (``:art:``) improves the format/structure of the code + +\:zap: (``:zap:``) improves performance + +\:memo: (``:memo:``) adds documentation + +\:bug: (``:bug:``) fixes a bug + +\:fire: (``:fire:``) removes code or files + +\:green_heart: (``:green_heart:``) fixes the CI build + +\:white_check_mark: (``:white_check_mark:``) adds tests + +Managing git commits is much easier using an IDE (we recommend PyCharm). + +Python styleguide +----------------- + +Please follow `PEP8 conventions`_ for all python code added to pyiron. Pull +requests will be checked for PEP8 plus a few other security issues with +`Codacy`_, and will be rejected if they do not meet the specified +formatting criteria. + +Any new features should include coverage with a unit test, such that +your pull request does not decrease pyiron's overall coverage. This +will be automatically tested within the ci test suite and `Coveralls`_. + +Deprecation warning template +---------------------------- +*XXX is deprecated as of vers. A.B.C. It is not guaranteed to be in service in vers. D.E.F. Use YYY instead.* + +Documentation styleguide +------------------------ + +All new/modified functions should include a docstring that follows +the `Google Python Docstring format`_. + +Documentation is built automatically with `Sphinx`_; any manually created +documentation should be added as a restructured text (.rst) file +under pyiron/docs/source. + +Notebooks created to exemplify features in pyiron are very useful, and +can even be used as integration tests. If you have added a major feature, +consider creating a notebook to show its usage under pyiron/notebooks/. +See the other examples that are already there. + +Additional notes +================ + +Issue and pull request labels +----------------------------- + +We use the following tags to organize pyiron Github issues +and pull requests: + +* bug: something isn't working +* duplicate: this issue/pull request already existed +* enhancement: new feature or request +* good first issue: easy fix for beginners +* help wanted: extra attention is needed +* invalid: this doesn't seem right +* question: further information is requested +* wontfix: this will not be worked on +* stale: inactive after 2 weeks + +Build status +------------ + +The build status for pyiron and all sub packages are given below + +.. image:: https://coveralls.io/repos/github/pyiron/pyiron/badge.svg?branch=master + :target: https://coveralls.io/github/pyiron/pyiron?branch=master + :alt: Coverage Status + +.. image:: https://api.codacy.com/project/badge/Grade/c513254f10004df5a1f5c76425c6584b + :target: https://app.codacy.com/app/pyiron-runner/pyiron?utm_source=github.com&utm_medium=referral&utm_content=pyiron/pyiron&utm_campaign=Badge_Grade_Settings + :alt: Codacy Badge + +.. image:: https://anaconda.org/conda-forge/pyiron/badges/latest_release_date.svg + :target: https://anaconda.org/conda-forge/pyiron/ + :alt: Release_Date + +.. image:: https://travis-ci.org/pyiron/pyiron.svg?branch=master + :target: https://travis-ci.org/pyiron/pyiron + :alt: Build Status + +.. image:: https://ci.appveyor.com/api/projects/status/wfdgqkxca1i19xcq/branch/master?svg=true + :target: https://ci.appveyor.com/project/pyiron-runner/pyiron/branch/master + :alt: Build status + +pyiron releases +--------------- + +.. image:: https://anaconda.org/conda-forge/pyiron/badges/downloads.svg + :target: https://anaconda.org/conda-forge/pyiron/ + :alt: Downloads + +For the pyiron release management we use git tags:: + + https://git-scm.com/book/en/v2/Git-Basics-Tagging + +The tag format consists of a tag_prefix (-) and the release version, for example:: + + pyiron-0.2.0 + +For the automated versioning we use:: + + https://github.com/warner/python-versioneer/ + +So the configuration of the release is included in setup.cfg:: + + https://github.com/pyiron/pyiron_base/blob/master/setup.cfg + +As the pyiron packages are pure python packages – we use only the Linux Python 3.7 job to build the packages, as defined in the .travis.yml file:: + + https://github.com/pyiron/pyiron_base/blob/master/.travis.yml + +The python 3.7 linux tests therefore takes more time, compared to the other tests on travis. + +Just like each other commit to the master branch the tagged releases are pushed to pypi.org and anaconda.org:: + + https://pypi.org/project/pyiron-base/#history + https://anaconda.org/pyiron/pyiron_base + +The major difference for pypi (pip) is that tagged releases are the default for pip while installing prerelease versions using pip requires the `--pre` flag. +`pip install --pre pyiron` + +Those pre-release versions are named `.post0.dev` :: + + 0.2.0.post0.dev1 + +For anaconda the prereleases are pushed to the pyiron channel and can be installed using: +conda install -c pyiron pyiron + +On the other hand the tagged releases are available through conda-forge, as soon as the corresponding packages are merged:: + + https://github.com/conda-forge/pyiron-feedstock + conda install -c conda-forge pyiron + +So for both conda and pip both the prereleases as well as the official releases are available. + +.. _Max Planck Institut für Eisenforschung: https://mpie.de +.. _github page: https://github.com/pyiron +.. _issues page: https://github.com/pyiron/pyiron/issues +.. _FAQ page: https://pyiron.readthedocs.io/en/latest/source/faq.html +.. _bugs: https://github.com/pyiron/pyiron/issues?q=is%3Aopen+is%3Aissue+label%3A%22bug%22 +.. _Good first issues: https://github.com/pyiron/pyiron/issues?q=is%3Aopen+is%3Aissue+label%3A%22good+first+issue%22 +.. _Help wanted issues: https://github.com/pyiron/pyiron/issues?q=is%3Aissue+is%3Aopen+label%3A%22help+wanted%22 +.. _PEP8 conventions: https://www.python.org/dev/peps/pep-0008/ +.. _Codacy: https://www.codacy.com/ +.. _Coveralls: https://coveralls.io/ +.. _Google Python Docstring format: http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html +.. _Sphinx: https://www.sphinx-doc.org/en/master/ + +Debugging +================ +My job does not run on the queue +----------------------------- + +In case a job runs properly while executing it locally (or on the head node), but not when you submit it to a queue, + +**1. Check if the job class is available in the project:** + +In this example, we want a custom job class ``ProtoMD`` from the module ``pyiron_contrib``: + +.. code-block:: + + from pyiron import Project + import pyiron_contrib # only if importing a custom job class + + pr = Project("debug") + dir(pr.job_type) + +This should output: + +.. code-block:: + + >>> ['AtomisticExampleJob', + 'Atoms', + 'ConvEncutParallel', + ... + ... + 'ProtoMD'] + +If you see your job class in the list, proceed to step 3. If not, + + +**2. Check if the job class in initialized in ``__init__.py`` of the module** + +Make sure that the ``__init__.py`` of your module (here, ``pyiron_contrib``) initializes the job class in the following format: + +.. code-block:: + + from pyiron import Project + from pyiron.base.job.jobtype import JOB_CLASS_DICT + + # Make classes available for new pyiron version + JOB_CLASS_DICT['ProtoMD'] = 'pyiron_contrib.protocol.compound.md' # the path of your job class + + +**3. Confirm that the job class can be instantiatied** + +Create a new job, but instead of running it, save it: + +.. code-block:: + + job = pr.create_job(job_type = pr.job_type.ProtoMD, job_name = 'job') + ... # input parameters that the job requires + ... + job.save() + + >>> 98 # this is the job id of the saved job + +Note down the job id, then run the following line: + +.. code-block:: + + job["TYPE"] + +This should output an instance of the job class: + +.. code-block:: + + >>> "" + +Now we know that the job class is indeed available in the project and can be instantiated. + +**4. Debug using a second notebook** + +Submitting and running a job on the queue, is essentially the same as saving a job in one notebook, but loading and executing it in another notebook. + +In **a new notebook** , load the job that you just saved, using its job id. You may or may not import the module (here, ``pyiron_conntirb``): + +.. code-block:: + + from pyiron import Project + # we do not import pyiron_contrib here, becasue it should not be necessary + + pr = Project("second_notebook") + reloaded_job = pr.load(98) # 98 is the job id of the previously saved job + reloaded_job.run(run_again=True) + +If the job loads and runs properly, the job should also run properly on the queue. This also means that there may be a bug in your custom job class. Debug the job class, and repeat steps 3 and 4 till you no longer get an error in step 4. diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..7e8b397 --- /dev/null +++ b/LICENSE @@ -0,0 +1,29 @@ +BSD 3-Clause License + +Copyright (c) 2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department +All rights reserved. + +Redistribution and use in source and binary forms, with or without +modification, are permitted provided that the following conditions are met: + +* Redistributions of source code must retain the above copyright notice, this + list of conditions and the following disclaimer. + +* Redistributions in binary form must reproduce the above copyright notice, + this list of conditions and the following disclaimer in the documentation + and/or other materials provided with the distribution. + +* Neither the name of the copyright holder nor the names of its + contributors may be used to endorse or promote products derived from + this software without specific prior written permission. + +THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" +AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE +IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE +DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE +FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL +DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR +SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER +CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, +OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE +OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..71f7e8d --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,3 @@ +include versioneer.py +include pyiron_module_template/_version.py +include LICENSE diff --git a/README.md b/README.md new file mode 100644 index 0000000..c7ee708 --- /dev/null +++ b/README.md @@ -0,0 +1,88 @@ +# pyiron_module_template + +## Overview + +This repository is a template for new pyiron modules similar to the existing modules of the +pyiron framework, e.g. +[pyiron_base](https://github.com/pyiron/pyiron_base), +[pyiron_atomistics](https://github.com/pyiron/pyiron_atomistics), +and +[pyiron_contrib](https://github.com/pyiron/pyiron_contrib). + +Within this repository, the new module is called `pyiron_module_template` which should be renamed to `pyiron_IntendedModuleName`. +This can be easily achieved by modifying and running the update_module_name.sh script. + +The licence is free to choose, but as a default the BSD3 licence packed here. + +## Continuous Integration + +We collect all files relevant for the continuous integration (CI) pipelines in `.ci_support`, +while the actual CI workflows are handled by GitHub and stored in `.github`. +If you are cloning this template *inside* the pyiron GitHub organization, the full CI should work out-of-the-box by calling reusable workflows from [pyiron/actions](github.com/pyiron/actions) and inheriting organization-wide secrets. +Otherwise, you will either need to modify the CI workflow files, or give your repository the following secrets: +- `DEPENDABOT_WORKFLOW_TOKEN` (GitHub token for an account that has permissions to your repository -- needs to differ from the default `github_token` already available though! In pyiron we have a special [@pyiron_runner account](https://github.com/pyiron-runner) for this purpose.) +- `PYPI_PASSWORD` (Token generated on PyPi to give access to your account there) +- `CODACY_PROJECT_TOKEN` (Token generated on Codacy to give access to your account there) + +The default CI setup from [pyiron/actions](github.com/pyiron/actions) makes some assumptions about your directory structure. +The most important one is that your environment should be specified in `.ci_support/environment.yml`. +There is a base environment there already, giving dependence on `pyiron_base`. +The CI will automatically keep environment files read by readthedocs (which will look at `.readthedocs.yml`) and MyBinder (which looks in `.binder`) up-to-date based on this environment file. + +In case you need extra environment files for some setups, you can modify the workflows in `.github/workflows`, which accept input variables for the docs, tests, and notebooks environments. +For example, it's typically good to not make your project depend on the `lammps` package, since this is not available for windows. +However, you might want to give some demo notebooks that run on MyBinder (a linux environment) and use LAMMPS calculations. +In this case, you could add a new file `.ci_support/environment-notebooks.yml`, and then edit `.github/workflows/push-pull-main.yml` so that instead of reading + +```yaml +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/push-pull-main.yml@main + secrets: inherit + # All the environment files variables point to .ci_support/environment.yml by default +``` + +It instead reads + +```yaml +jobs: + pyiron: + uses: pyiron/actions/.github/workflows/push-pull-main.yml@main + secrets: inherit + with: + notebooks-env-files: .ci_support/environment.yml .ci_support/environment-notebooks.yml +``` + +Where `.ci_support/environment-notebooks.yml` looks like: + +```yaml +channels: + - conda-forge +dependencies: + - lammps +``` + +### Label-based CI + +Some CI triggers when labels get applied to a PR. +In a new repository, you will need to define these labels: +- `format_black`: Runs black analyis and creates a bot-generated commit to fix any format violations +- `run_CodeQL`: Runs the external CodeQL analysis (expensive, only do at the end) +- `run_coverage`: Run all the tests in `tests` and use coveralls to generate a coverage report (also expensive, only run near the end of your PR) + +## Documentation + +You should modify this README to reflect the purpose of your new package. +You can look at the other pyiron modules to get a hint for what sort of information to include, and how to link badges at the head of your README file. + +At a minimum, we suggest creating a meaningful example notebook in the `notebooks/` directory and creating a MyBinder badge so that people can quickly and easily explore your work. + +You can also edit the docs for your package by modifying `docs/index.rst`. +By default, only a simple API section is included. + +## Publishing your package + +If you are inside the pyiron organization or have your own `PYPI_PASSWORD` secret configured, your package will be published on PyPI automatically when you make a new "release" on GitHub -- *as long as* that tag matches the pattern specified in `setup.cfg`; by default any tag that `pyiron_module_template-`, where `pyiron_module_template` is replaced with the name of your module. 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If the directory is relative to the +# documentation root, use os.path.abspath to make it absolute, like shown here. + + +# sys.path.insert(1, os.path.abspath('..')) + + +# -- General configuration ------------------------------------------------ + +# If your documentation needs a minimal Sphinx version, state it here. +# needs_sphinx = '1.0' + +# Add any Sphinx extension module names here, as strings. They can be +# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom +# ones. +extensions = ['nbsphinx', 'sphinx.ext.mathjax', 'sphinx.ext.autodoc', 'sphinx.ext.viewcode', + 'sphinx.ext.autosummary', 'sphinx.ext.napoleon'] + +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + +# The suffix of source filenames. +source_suffix = '.rst' + +# The encoding of source files. +# source_encoding = 'utf-8-sig' + +# The master toctree document. +master_doc = 'index' + +# General information about the project. +project = u'pyiron' +copyright = u'2021, Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department ' \ + u'All rights reserved' + +# The version info for the project you're documenting, acts as replacement for +# |version| and |release|, also used in various other places throughout the +# built documents. +# +# The short X.Y version. +version_full = subprocess.check_output( + "python -c 'import versioneer; print(versioneer.get_version())'", + cwd=os.path.join(os.path.curdir, '..'), + universal_newlines=True, + shell=True +) +version_full = version_full.split('\n')[0] +version = '.'.join(version_full.split('.')[0:2]) +# The full version, including alpha/beta/rc tags. +release = version_full + +# The language for content autogenerated by Sphinx. Refer to documentation +# for a list of supported languages. +# language = None + +# There are two options for replacing |today|: either, you set today to some +# non-false value, then it is used: +# today = '' +# Else, today_fmt is used as the format for a strftime call. +# today_fmt = '%B %d, %Y' + +# List of patterns, relative to source directory, that match files and +# directories to ignore when looking for source files. + +exclude_patterns = ['_build', '**.ipynb_checkpoints', '**/tests'] + +# The reST default role (used for this markup: `text`) to use for all +# documents. +# default_role = None + +# If true, '()' will be appended to :func: etc. cross-reference text. +# add_function_parentheses = True + +# If true, the current module name will be prepended to all description +# unit titles (such as .. function::). +# add_module_names = True + +# If true, sectionauthor and moduleauthor directives will be shown in the +# output. They are ignored by default. +# show_authors = False + +# The name of the Pygments (syntax highlighting) style to use. +pygments_style = 'sphinx' + +# A list of ignored prefixes for module index sorting. +modindex_common_prefix = ['vasp.', 'base.', 'lammps.', + 'pyiron.', 'dft.', 'atomistics.', 'testing.'] + +# If true, keep warnings as "system message" paragraphs in the built documents. +# keep_warnings = False + + +# -- Options for HTML output ---------------------------------------------- + +# The theme to use for HTML and HTML Help pages. See the documentation for +# a list of builtin themes. + +# try: +# import sphinx_bootstrap_theme +# html_theme = 'bootstrap' +# html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() +# html_theme_options = {'bootswatch_theme': "spacelab"} +# except ImportError: +# raise ImportError("You need to install bootstrap: pip install sphinx_bootstrap_theme") +# html_theme = 'default' + +try: + import sphinx_rtd_theme + html_theme = 'sphinx_rtd_theme' +except ImportError: + html_theme = 'default' + + +# Theme options are theme-specific and customize the look and feel of a theme +# further. For a list of options available for each theme, see the +# documentation. +# html_theme_options = {} + +# Add any paths that contain custom themes here, relative to this directory. +# html_theme_path = [] + +# The name for this set of Sphinx documents. If None, it defaults to +# " v documentation". +# html_title = None + +# A shorter title for the navigation bar. Default is the same as html_title. +# html_short_title = None + +# The name of an image file (relative to this directory) to place at the top +# of the sidebar. +html_logo = "_static/pyiron-logo.png" + +# The name of an image file (within the static path) to use as favicon of the +# docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 +# pixels large. +html_favicon = "_static/pyiron_logo.ico" + +# Add any paths that contain custom static files (such as style sheets) here, +# relative to this directory. They are copied after the builtin static files, +# so a file named "default.css" will overwrite the builtin "default.css". +html_static_path = ['_static'] + +# Add any extra paths that contain custom files (such as robots.txt or +# .htaccess) here, relative to this directory. These files are copied +# directly to the root of the documentation. +# html_extra_path = [] + +# If not '', a 'Last updated on:' timestamp is inserted at every page bottom, +# using the given strftime format. +# html_last_updated_fmt = '%b %d, %Y' + +# If true, SmartyPants will be used to convert quotes and dashes to +# typographically correct entities. +# html_use_smartypants = True + +# Custom sidebar templates, maps document names to template names. +# html_sidebars = {} + +# Additional templates that should be rendered to pages, maps page names to +# template names. +# html_additional_pages = {} + +# If false, no module index is generated. +# html_domain_indices = True + +# If false, no index is generated. +# html_use_index = True + +# If true, the index is split into individual pages for each letter. +# html_split_index = False + +# If true, links to the reST sources are added to the pages. +# html_show_sourcelink = True + +# If true, "Created using Sphinx" is shown in the HTML footer. Default is True. +# html_show_sphinx = True + +# If true, "(C) Copyright ..." is shown in the HTML footer. Default is True. +# html_show_copyright = True + +# If true, an OpenSearch description file will be output, and all pages will +# contain a tag referring to it. The value of this option must be the +# base URL from which the finished HTML is served. +# html_use_opensearch = '' + +# This is the file name suffix for HTML files (e.g. ".xhtml"). +# html_file_suffix = None + +# Output file base name for HTML help builder. +htmlhelp_basename = 'pyironDoc' + + +# -- Options for LaTeX output --------------------------------------------- + +latex_elements = { +# The paper size ('letterpaper' or 'a4paper'). +# 'papersize': 'letterpaper', + +# The font size ('10pt', '11pt' or '12pt'). +#'pointsize': '10pt', + +# Additional stuff for the LaTeX preamble. +#'preamble': '', +} + +# Grouping the document tree into LaTeX files. List of tuples +# (source start file, target name, title, +# author, documentclass [howto, manual, or own class]). +latex_documents = [ + ('index', 'pyiron.tex', u'pyiron Documentation', + u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department', 'manual'), +] + +# The name of an image file (relative to this directory) to place at the top of +# the title page. +#latex_logo = None + +# For "manual" documents, if this is true, then toplevel headings are parts, +# not chapters. +#latex_use_parts = False + +# If true, show page references after internal links. +#latex_show_pagerefs = False + +# If true, show URL addresses after external links. +#latex_show_urls = False + +# Documents to append as an appendix to all manuals. +#latex_appendices = [] + +# If false, no module index is generated. +#latex_domain_indices = True + + +# -- Options for manual page output --------------------------------------- + +# One entry per manual page. List of tuples +# (source start file, name, description, authors, manual section). +man_pages = [ + ('index', + 'pyiron', + u'pyiron Documentation', + [u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department'], 1) +] + +# If true, show URL addresses after external links. +#man_show_urls = False + + +# -- Options for Texinfo output ------------------------------------------- + +# Grouping the document tree into Texinfo files. List of tuples +# (source start file, target name, title, author, +# dir menu entry, description, category) +texinfo_documents = [ + ('index', + 'pyiron_module_template', + u'pyiron Documentation', + u'Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department', + 'pyiron_module_template', + 'One line description of project.', + 'Miscellaneous'), +] + +# Documents to append as an appendix to all manuals. +# texinfo_appendices = [] + +# If false, no module index is generated. +# texinfo_domain_indices = True + +# How to display URL addresses: 'footnote', 'no', or 'inline'. +# texinfo_show_urls = 'footnote' + +# If true, do not generate a @detailmenu in the "Top" node's menu. +# texinfo_no_detailmenu = False + +main(['-e', '-o', 'apidoc', '../pyiron_module_template', '--force']) + +curdir = os.path.dirname(os.path.abspath(__file__)) +if os.path.exists(os.path.join(curdir, 'source/notebooks')): + shutil.rmtree(os.path.join(curdir, 'source/notebooks')) + +shutil.copytree(os.path.join(curdir, '..', 'notebooks'), + os.path.join(curdir, 'source/notebooks')) + +if 'readthedocs.org' in curdir: # write config for readthedocs.org + with open(os.path.join(os.path.expanduser('~/.pyiron')), 'w') as f: + f.writelines(['[DEFAULT]', + 'TOP_LEVEL_DIRS = ' + os.path.join(curdir, '..'), + 'RESOURCE_PATHS = ' + os.path.join(curdir, '..') + '/tests/static']) diff --git a/docs/environment.yml b/docs/environment.yml new file mode 100644 index 0000000..5e6bde4 --- /dev/null +++ b/docs/environment.yml @@ -0,0 +1,6 @@ +channels: +- conda-forge +dependencies: +- ipykernel +- nbsphinx +- pyiron_base diff --git a/docs/index.rst b/docs/index.rst new file mode 100644 index 0000000..1170c40 --- /dev/null +++ b/docs/index.rst @@ -0,0 +1,13 @@ +.. pyiron_module_template documentation master file + +.. _index: + + +====================== +pyiron_module_template +====================== + +.. toctree:: + :hidden: + + source/indices.rst \ No newline at end of file diff --git a/docs/source/indices.rst b/docs/source/indices.rst new file mode 100644 index 0000000..2e2007f --- /dev/null +++ b/docs/source/indices.rst @@ -0,0 +1,12 @@ +.. _indices: + + +API Documentation +================= + +* :ref:`genindex` +* :ref:`modindex` + + +.. toctree:: + :maxdepth:2 diff --git a/notebooks/version.ipynb b/notebooks/version.ipynb new file mode 100644 index 0000000..f5956d8 --- /dev/null +++ b/notebooks/version.ipynb @@ -0,0 +1,36 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": null, + "id": "52a8cfcc", + "metadata": {}, + "outputs": [], + "source": [ + "import pyiron_module_template\n", + "print(pyiron_module_template.__version__)" + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.8.5" + } + }, + "nbformat": 4, + "nbformat_minor": 5 +} diff --git a/pyiron_module_template/__init__.py b/pyiron_module_template/__init__.py new file mode 100644 index 0000000..80edaf0 --- /dev/null +++ b/pyiron_module_template/__init__.py @@ -0,0 +1,4 @@ +from ._version import get_versions + +__version__ = get_versions()["version"] +del get_versions diff --git a/pyiron_module_template/_version.py b/pyiron_module_template/_version.py new file mode 100644 index 0000000..85bcfdd --- /dev/null +++ b/pyiron_module_template/_version.py @@ -0,0 +1,556 @@ +# This file helps to compute a version number in source trees obtained from +# git-archive tarball (such as those provided by githubs download-from-tag +# feature). Distribution tarballs (built by setup.py sdist) and build +# directories (produced by setup.py build) will contain a much shorter file +# that just contains the computed version number. + +# This file is released into the public domain. Generated by +# versioneer-0.18 (https://github.com/warner/python-versioneer) + +"""Git implementation of _version.py.""" + +import errno +import os +import re +import subprocess +import sys + + +def get_keywords(): + """Get the keywords needed to look up the version information.""" + # these strings will be replaced by git during git-archive. + # setup.py/versioneer.py will grep for the variable names, so they must + # each be defined on a line of their own. _version.py will just call + # get_keywords(). + git_refnames = "$Format:%d$" + git_full = "$Format:%H$" + git_date = "$Format:%ci$" + keywords = {"refnames": git_refnames, "full": git_full, "date": git_date} + return keywords + + +class VersioneerConfig: + """Container for Versioneer configuration parameters.""" + + +def get_config(): + """Create, populate and return the VersioneerConfig() object.""" + # these strings are filled in when 'setup.py versioneer' creates + # _version.py + cfg = VersioneerConfig() + cfg.VCS = "git" + cfg.style = "pep440-pre" + cfg.tag_prefix = "pyiron_module_template-" + cfg.parentdir_prefix = "pyiron_module_template" + cfg.versionfile_source = "pyiron_module_template/_version.py" + cfg.verbose = False + return cfg + + +class NotThisMethod(Exception): + """Exception raised if a method is not valid for the current scenario.""" + + +LONG_VERSION_PY = {} +HANDLERS = {} + + +def register_vcs_handler(vcs, method): # decorator + """Decorator to mark a method as the handler for a particular VCS.""" + + def decorate(f): + """Store f in HANDLERS[vcs][method].""" + if vcs not in HANDLERS: + HANDLERS[vcs] = {} + HANDLERS[vcs][method] = f + return f + + return decorate + + +def run_command(commands, args, cwd=None, verbose=False, hide_stderr=False, env=None): + """Call the given command(s).""" + assert isinstance(commands, list) + p = None + for c in commands: + try: + dispcmd = str([c] + args) + # remember shell=False, so use git.cmd on windows, not just git + p = subprocess.Popen( + [c] + args, + cwd=cwd, + env=env, + stdout=subprocess.PIPE, + stderr=(subprocess.PIPE if hide_stderr else None), + ) + break + except EnvironmentError: + e = sys.exc_info()[1] + if e.errno == errno.ENOENT: + continue + if verbose: + print("unable to run %s" % dispcmd) + print(e) + return None, None + else: + if verbose: + print("unable to find command, tried %s" % (commands,)) + return None, None + stdout = p.communicate()[0].strip() + if sys.version_info[0] >= 3: + stdout = stdout.decode() + if p.returncode != 0: + if verbose: + print("unable to run %s (error)" % dispcmd) + print("stdout was %s" % stdout) + return None, p.returncode + return stdout, p.returncode + + +def versions_from_parentdir(parentdir_prefix, root, verbose): + """Try to determine the version from the parent directory name. + + Source tarballs conventionally unpack into a directory that includes both + the project name and a version string. We will also support searching up + two directory levels for an appropriately named parent directory + """ + rootdirs = [] + + for i in range(3): + dirname = os.path.basename(root) + if dirname.startswith(parentdir_prefix): + return { + "version": dirname[len(parentdir_prefix) :], + "full-revisionid": None, + "dirty": False, + "error": None, + "date": None, + } + else: + rootdirs.append(root) + root = os.path.dirname(root) # up a level + + if verbose: + print( + "Tried directories %s but none started with prefix %s" + % (str(rootdirs), parentdir_prefix) + ) + raise NotThisMethod("rootdir doesn't start with parentdir_prefix") + + +@register_vcs_handler("git", "get_keywords") +def git_get_keywords(versionfile_abs): + """Extract version information from the given file.""" + # the code embedded in _version.py can just fetch the value of these + # keywords. When used from setup.py, we don't want to import _version.py, + # so we do it with a regexp instead. This function is not used from + # _version.py. + keywords = {} + try: + f = open(versionfile_abs, "r") + for line in f.readlines(): + if line.strip().startswith("git_refnames ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["refnames"] = mo.group(1) + if line.strip().startswith("git_full ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["full"] = mo.group(1) + if line.strip().startswith("git_date ="): + mo = re.search(r'=\s*"(.*)"', line) + if mo: + keywords["date"] = mo.group(1) + f.close() + except EnvironmentError: + pass + return keywords + + +@register_vcs_handler("git", "keywords") +def git_versions_from_keywords(keywords, tag_prefix, verbose): + """Get version information from git keywords.""" + if not keywords: + raise NotThisMethod("no keywords at all, weird") + date = keywords.get("date") + if date is not None: + # git-2.2.0 added "%cI", which expands to an ISO-8601 -compliant + # datestamp. However we prefer "%ci" (which expands to an "ISO-8601 + # -like" string, which we must then edit to make compliant), because + # it's been around since git-1.5.3, and it's too difficult to + # discover which version we're using, or to work around using an + # older one. + date = date.strip().replace(" ", "T", 1).replace(" ", "", 1) + refnames = keywords["refnames"].strip() + if refnames.startswith("$Format"): + if verbose: + print("keywords are unexpanded, not using") + raise NotThisMethod("unexpanded keywords, not a git-archive tarball") + refs = set([r.strip() for r in refnames.strip("()").split(",")]) + # starting in git-1.8.3, tags are listed as "tag: foo-1.0" instead of + # just "foo-1.0". If we see a "tag: " prefix, prefer those. + TAG = "tag: " + tags = set([r[len(TAG) :] for r in refs if r.startswith(TAG)]) + if not tags: + # Either we're using git < 1.8.3, or there really are no tags. We use + # a heuristic: assume all version tags have a digit. The old git %d + # expansion behaves like git log --decorate=short and strips out the + # refs/heads/ and refs/tags/ prefixes that would let us distinguish + # between branches and tags. By ignoring refnames without digits, we + # filter out many common branch names like "release" and + # "stabilization", as well as "HEAD" and "master". + tags = set([r for r in refs if re.search(r"\d", r)]) + if verbose: + print("discarding '%s', no digits" % ",".join(refs - tags)) + if verbose: + print("likely tags: %s" % ",".join(sorted(tags))) + for ref in sorted(tags): + # sorting will prefer e.g. "2.0" over "2.0rc1" + if ref.startswith(tag_prefix): + r = ref[len(tag_prefix) :] + if verbose: + print("picking %s" % r) + return { + "version": r, + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": None, + "date": date, + } + # no suitable tags, so version is "0+unknown", but full hex is still there + if verbose: + print("no suitable tags, using unknown + full revision id") + return { + "version": "0+unknown", + "full-revisionid": keywords["full"].strip(), + "dirty": False, + "error": "no suitable tags", + "date": None, + } + + +@register_vcs_handler("git", "pieces_from_vcs") +def git_pieces_from_vcs(tag_prefix, root, verbose, run_command=run_command): + """Get version from 'git describe' in the root of the source tree. + + This only gets called if the git-archive 'subst' keywords were *not* + expanded, and _version.py hasn't already been rewritten with a short + version string, meaning we're inside a checked out source tree. + """ + GITS = ["git"] + if sys.platform == "win32": + GITS = ["git.cmd", "git.exe"] + + out, rc = run_command(GITS, ["rev-parse", "--git-dir"], cwd=root, hide_stderr=True) + if rc != 0: + if verbose: + print("Directory %s not under git control" % root) + raise NotThisMethod("'git rev-parse --git-dir' returned error") + + # if there is a tag matching tag_prefix, this yields TAG-NUM-gHEX[-dirty] + # if there isn't one, this yields HEX[-dirty] (no NUM) + describe_out, rc = run_command( + GITS, + [ + "describe", + "--tags", + "--dirty", + "--always", + "--long", + "--match", + "%s*" % tag_prefix, + ], + cwd=root, + ) + # --long was added in git-1.5.5 + if describe_out is None: + raise NotThisMethod("'git describe' failed") + describe_out = describe_out.strip() + full_out, rc = run_command(GITS, ["rev-parse", "HEAD"], cwd=root) + if full_out is None: + raise NotThisMethod("'git rev-parse' failed") + full_out = full_out.strip() + + pieces = {} + pieces["long"] = full_out + pieces["short"] = full_out[:7] # maybe improved later + pieces["error"] = None + + # parse describe_out. It will be like TAG-NUM-gHEX[-dirty] or HEX[-dirty] + # TAG might have hyphens. + git_describe = describe_out + + # look for -dirty suffix + dirty = git_describe.endswith("-dirty") + pieces["dirty"] = dirty + if dirty: + git_describe = git_describe[: git_describe.rindex("-dirty")] + + # now we have TAG-NUM-gHEX or HEX + + if "-" in git_describe: + # TAG-NUM-gHEX + mo = re.search(r"^(.+)-(\d+)-g([0-9a-f]+)$", git_describe) + if not mo: + # unparseable. Maybe git-describe is misbehaving? + pieces["error"] = "unable to parse git-describe output: '%s'" % describe_out + return pieces + + # tag + full_tag = mo.group(1) + if not full_tag.startswith(tag_prefix): + if verbose: + fmt = "tag '%s' doesn't start with prefix '%s'" + print(fmt % (full_tag, tag_prefix)) + pieces["error"] = "tag '%s' doesn't start with prefix '%s'" % ( + full_tag, + tag_prefix, + ) + return pieces + pieces["closest-tag"] = full_tag[len(tag_prefix) :] + + # distance: number of commits since tag + pieces["distance"] = int(mo.group(2)) + + # commit: short hex revision ID + pieces["short"] = mo.group(3) + + else: + # HEX: no tags + pieces["closest-tag"] = None + count_out, rc = run_command(GITS, ["rev-list", "HEAD", "--count"], cwd=root) + pieces["distance"] = int(count_out) # total number of commits + + # commit date: see ISO-8601 comment in git_versions_from_keywords() + date = run_command(GITS, ["show", "-s", "--format=%ci", "HEAD"], cwd=root)[ + 0 + ].strip() + pieces["date"] = date.strip().replace(" ", "T", 1).replace(" ", "", 1) + + return pieces + + +def plus_or_dot(pieces): + """Return a + if we don't already have one, else return a .""" + if "+" in pieces.get("closest-tag", ""): + return "." + return "+" + + +def render_pep440(pieces): + """Build up version string, with post-release "local version identifier". + + Our goal: TAG[+DISTANCE.gHEX[.dirty]] . Note that if you + get a tagged build and then dirty it, you'll get TAG+0.gHEX.dirty + + Exceptions: + 1: no tags. git_describe was just HEX. 0+untagged.DISTANCE.gHEX[.dirty] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += plus_or_dot(pieces) + rendered += "%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + else: + # exception #1 + rendered = "0+untagged.%d.g%s" % (pieces["distance"], pieces["short"]) + if pieces["dirty"]: + rendered += ".dirty" + return rendered + + +def render_pep440_pre(pieces): + """TAG[.post.devDISTANCE] -- No -dirty. + + Exceptions: + 1: no tags. 0.post.devDISTANCE + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"]: + rendered += ".post.dev%d" % pieces["distance"] + else: + # exception #1 + rendered = "0.post.dev%d" % pieces["distance"] + return rendered + + +def render_pep440_post(pieces): + """TAG[.postDISTANCE[.dev0]+gHEX] . + + The ".dev0" means dirty. Note that .dev0 sorts backwards + (a dirty tree will appear "older" than the corresponding clean one), + but you shouldn't be releasing software with -dirty anyways. + + Exceptions: + 1: no tags. 0.postDISTANCE[.dev0] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["dirty"]: + rendered += ".dev0" + rendered += plus_or_dot(pieces) + rendered += "g%s" % pieces["short"] + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["dirty"]: + rendered += ".dev0" + rendered += "+g%s" % pieces["short"] + return rendered + + +def render_pep440_old(pieces): + """TAG[.postDISTANCE[.dev0]] . + + The ".dev0" means dirty. + + Eexceptions: + 1: no tags. 0.postDISTANCE[.dev0] + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"] or pieces["dirty"]: + rendered += ".post%d" % pieces["distance"] + if pieces["dirty"]: + rendered += ".dev0" + else: + # exception #1 + rendered = "0.post%d" % pieces["distance"] + if pieces["dirty"]: + rendered += ".dev0" + return rendered + + +def render_git_describe(pieces): + """TAG[-DISTANCE-gHEX][-dirty]. + + Like 'git describe --tags --dirty --always'. + + Exceptions: + 1: no tags. HEX[-dirty] (note: no 'g' prefix) + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + if pieces["distance"]: + rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) + else: + # exception #1 + rendered = pieces["short"] + if pieces["dirty"]: + rendered += "-dirty" + return rendered + + +def render_git_describe_long(pieces): + """TAG-DISTANCE-gHEX[-dirty]. + + Like 'git describe --tags --dirty --always -long'. + The distance/hash is unconditional. + + Exceptions: + 1: no tags. HEX[-dirty] (note: no 'g' prefix) + """ + if pieces["closest-tag"]: + rendered = pieces["closest-tag"] + rendered += "-%d-g%s" % (pieces["distance"], pieces["short"]) + else: + # exception #1 + rendered = pieces["short"] + if pieces["dirty"]: + rendered += "-dirty" + return rendered + + +def render(pieces, style): + """Render the given version pieces into the requested style.""" + if pieces["error"]: + return { + "version": "unknown", + "full-revisionid": pieces.get("long"), + "dirty": None, + "error": pieces["error"], + "date": None, + } + + if not style or style == "default": + style = "pep440" # the default + + if style == "pep440": + rendered = render_pep440(pieces) + elif style == "pep440-pre": + rendered = render_pep440_pre(pieces) + elif style == "pep440-post": + rendered = render_pep440_post(pieces) + elif style == "pep440-old": + rendered = render_pep440_old(pieces) + elif style == "git-describe": + rendered = render_git_describe(pieces) + elif style == "git-describe-long": + rendered = render_git_describe_long(pieces) + else: + raise ValueError("unknown style '%s'" % style) + + return { + "version": rendered, + "full-revisionid": pieces["long"], + "dirty": pieces["dirty"], + "error": None, + "date": pieces.get("date"), + } + + +def get_versions(): + """Get version information or return default if unable to do so.""" + # I am in _version.py, which lives at ROOT/VERSIONFILE_SOURCE. If we have + # __file__, we can work backwards from there to the root. Some + # py2exe/bbfreeze/non-CPython implementations don't do __file__, in which + # case we can only use expanded keywords. + + cfg = get_config() + verbose = cfg.verbose + + try: + return git_versions_from_keywords(get_keywords(), cfg.tag_prefix, verbose) + except NotThisMethod: + pass + + try: + root = os.path.realpath(__file__) + # versionfile_source is the relative path from the top of the source + # tree (where the .git directory might live) to this file. Invert + # this to find the root from __file__. + for i in cfg.versionfile_source.split("/"): + root = os.path.dirname(root) + except NameError: + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to find root of source tree", + "date": None, + } + + try: + pieces = git_pieces_from_vcs(cfg.tag_prefix, root, verbose) + return render(pieces, cfg.style) + except NotThisMethod: + pass + + try: + if cfg.parentdir_prefix: + return versions_from_parentdir(cfg.parentdir_prefix, root, verbose) + except NotThisMethod: + pass + + return { + "version": "0+unknown", + "full-revisionid": None, + "dirty": None, + "error": "unable to compute version", + "date": None, + } diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..f64d2cc --- /dev/null +++ b/setup.cfg @@ -0,0 +1,13 @@ + +# 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-pre +versionfile_source = pyiron_module_template/_version.py +#versionfile_build = +tag_prefix = pyiron_module_template- +parentdir_prefix = pyiron_module_template + diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..5d02728 --- /dev/null +++ b/setup.py @@ -0,0 +1,34 @@ +""" +Setuptools based setup module +""" +from setuptools import setup, find_packages +import versioneer + +setup( + name='pyiron_module_template', + version=versioneer.get_version(), + description='pyiron_module_template - module extension to pyiron.', + long_description='http://pyiron.org', + + url='https://github.com/pyiron/pyiron_module_template', + author='Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department', + author_email='@mpie.de', + license='BSD', + + classifiers=['Development Status :: 3 - Alpha', + 'Topic :: Scientific/Engineering :: Physics', + 'License :: OSI Approved :: BSD License', + 'Intended Audience :: Science/Research', + 'Operating System :: OS Independent', + 'Programming Language :: Python :: 3.8', + 'Programming Language :: Python :: 3.9', + 'Programming Language :: Python :: 3.10'], + + keywords='pyiron', + packages=find_packages(exclude=["*tests*", "*docs*", "*binder*", "*conda*", "*notebooks*", "*.ci_support*"]), + install_requires=[ + 'pyiron_base' + ], + cmdclass=versioneer.get_cmdclass(), + + ) diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/benchmark/__init__.py b/tests/benchmark/__init__.py new file mode 100644 index 0000000..102f047 --- /dev/null +++ b/tests/benchmark/__init__.py @@ -0,0 +1,3 @@ +""" +Timed tests to make sure critical components stay sufficiently efficient. +""" \ No newline at end of file diff --git a/tests/benchmark/test_benchmark.py b/tests/benchmark/test_benchmark.py new file mode 100644 index 0000000..9c25ae2 --- /dev/null +++ b/tests/benchmark/test_benchmark.py @@ -0,0 +1,6 @@ +import unittest + + +class TestNothing(unittest.TestCase): + def test_nothing(self): + self.assertTrue(True) diff --git a/tests/integration/__init__.py b/tests/integration/__init__.py new file mode 100644 index 0000000..85f3594 --- /dev/null +++ b/tests/integration/__init__.py @@ -0,0 +1,3 @@ +""" +Large and potentially slower tests to check how the pieces fit together. +""" \ No newline at end of file diff --git a/tests/integration/test_integration.py b/tests/integration/test_integration.py new file mode 100644 index 0000000..9c25ae2 --- /dev/null +++ b/tests/integration/test_integration.py @@ -0,0 +1,6 @@ +import unittest + + +class TestNothing(unittest.TestCase): + def test_nothing(self): + self.assertTrue(True) diff --git a/tests/unit/__init__.py b/tests/unit/__init__.py new file mode 100644 index 0000000..cc7dda6 --- /dev/null +++ b/tests/unit/__init__.py @@ -0,0 +1,3 @@ +""" +Small tests run, relatively fast tests for checking individual bits of the code base. +""" \ No newline at end of file diff --git a/tests/unit/test_tests.py b/tests/unit/test_tests.py new file mode 100644 index 0000000..2d9f5a8 --- /dev/null +++ b/tests/unit/test_tests.py @@ -0,0 +1,9 @@ +import unittest +import pyiron_module_template + + +class TestVersion(unittest.TestCase): + def test_version(self): + version = pyiron_module_template.__version__ + print(version) + self.assertTrue(version.startswith('0')) diff --git a/update_module_name.sh b/update_module_name.sh new file mode 100644 index 0000000..5c3c9e1 --- /dev/null +++ b/update_module_name.sh @@ -0,0 +1,29 @@ +#!/bin/bash + +module_name="pyiron_IntendedModuleName" +rst_delimit="=========================" # This should be as many '=' as the name length. + +for file in .binder/postBuild \ + .github/ISSUE_TEMPLATE/*.md \ + docs/conf.py \ + docs/index.rst \ + notebooks/version.ipynb \ + tests/unit/test_tests.py \ + .coveragerc \ + .gitattributes \ + MANIFEST.in \ + setup.cfg \ + setup.py +do + sed -i "s/pyiron_module_template/${module_name}/g" ${file} +done + +file=docs/index.rst +sed -i "s/pyiron_module_template/${module_name}/g" ${file} +sed -i "s/======================/${rst_delimit}/g" ${file} + +mv pyiron_module_template ${module_name} + +python -m versioneer setup + +rm update_module_name.sh diff --git a/versioneer.py b/versioneer.py new file mode 100644 index 0000000..64fea1c --- /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)