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Update standards based on Nov 2019 PyHC meeting discussion #16

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Update standards based on Nov 2019 PyHC meeting discussion #16

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ae5c121
Update standards based on Nov 2019 PyHC meeting
namurphy Nov 7, 2019
046132a
Update date of amendments
namurphy Jan 6, 2020
69c7488
Recommend that private functions, etc have docstrings too
namurphy Jan 10, 2020
a5ac9be
Make Python 3 compatibility a must
namurphy Jan 10, 2020
15a470c
Update names and affiliations
namurphy Sep 14, 2020
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28 changes: 17 additions & 11 deletions standards.md
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Expand Up @@ -4,13 +4,19 @@

---

Drafted during the Heliopython Meeting of November 2018.
Drafted during the Python in Heliophysics Community Meeting of November 2018.

Amended during the Python in Heliophysics Community Meeting of November 2019.

---

Agreed on 10-Dec-2018 by (in alpahbetical order)
Agreed on 10-Dec-2018 by (in alphabetical order)

**A. Annex** (JHU), **B. L. Alterman** (Univ. of Michigan), **A. Azari** (Univ. of Michigan), **W. Barnes** (NRC Postdoc residing at NRL), **M. Bobra** (Stanford), **B. Cecconi** (Observartoire de Paris), **S. Christe** (NASA GSFC), **J. Coxon** (Univ. of Southampton), **A. DeWolfe** (LASP), **A. Halford** (NASA GSFC), **B. Harter** (LASP), **J. Ireland** (NASA GSFC), **J. Jahn** (SwRI), **J. Klenzing** (NASA GSFC), **M. Liu** (SunPy), **J. Mason** (NASA GSFC), **R. McGranaghan** (NASA JPL), **N. Murphy** (CfA), **S. Murray** (Trinity College Dublin), **J. Niehof** (Univ. of New Hampshire), **M.D. Nguyen** (Lomonosov Moscow State Univ.), **R. Panneton** (CU/LASP), **A. Pembroke** (NASA GSFC), **D. Pérez-Suárez** (University College London), **C. Piker** (Univ. of Iowa), **A. Roberts** (NASA GSFC), **D. Ryan** (NASA GSFC), **S. Savage** (NASA GSFC), **J. Smith** (NASA GSFC, Catholic Univ.), **D. Stansby** (Imperial College London), **J. Vandegriff** (JHU/APL), **R. S. Weigel** (George Mason University)

**A. Annex** (JHU), **B. L. Alterman** (Univ. of Michigan), **A. Azari** (Univ. of Michigan), **W. Barnes** (Rice Univ.), **M. Bobra** (Stanford), **B. Cecconi** (Observartoire de Paris), **S. Christe** (NASA GSFC), **J. Coxon** (Univ. of Southampton), **A. DeWolfe** (LASP), **A. Halford** (Aerospace Corporation), **B. Harter** (LASP), **J. Ireland** (NASA GSFC), **J. Jahn** (SwRI), **J. Klenzing** (NASA GSFC), **M. Liu** (SunPy), **J. Mason** (NASA GSFC), **R. McGranaghan** (NASA JPL), **N. Murphy** (CfA), **S. Murray** (Trinity College Dublin), **J. Niehof** (Univ. of New Hampshire), **M.D. Nguyen** (Lomonosov Moscow State Univ.), **R. Panneton** (CU/LASP), **A. Pembroke** (NASA GSFC), **D. Pérez-Suárez** (University College London), **C. Piker** (Univ. of Iowa), **A. Roberts** (NASA GSFC), **D. Ryan** (NASA GSFC), **S. Savage** (NASA GSFC), **J. Smith** (NASA GSFC, Catholic Univ.), **D. Stansby** (Imperial College London), **J. Vandegriff** (JHU/APL), **R. S. Weigel** (George Mason University)
Amended on 06-Jan-2020 by (in alphabetical order)

**N. Murphy** (CfA),

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A. G. Burrell (NRL). Also, A. Halford is now at NASA GSFC.

---

Expand All @@ -29,12 +35,12 @@ Definitions:
5. **License**: Projects must provide a license. Projects should use permissive licenses for open source scientific software (e.g., the BSD 2-clause, BSD 3-clause, or BSD+Patent licenses). Copyleft licenses such as GPL are not recommended and OSI-approved permissive licenses are recommended.
6. **Version control**: All code must use version control. It is strongly recommended that projects make use of a distributed version control system (e.g., git).
7. **Coding Style**: Projects must adopt the basic style recommendations of [PEP 8](https://www.python.org/dev/peps/pep-0008/) and static analysis tools should be used to identify deviations from the basic style recommendations (e.g. pylint, flake8, pycodestyle).
8. **Documentation**: All functions, classes, and modules must have documentation strings (docstrings) provided in a standard [conventions](https://www.python.org/dev/peps/pep-0257/) (e.g. [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html)). Docstrings must describe the code’s purpose, describe all inputs and outputs, and provide examples. High level documentation must also be provided as guides, tutorials, and developer docs. Documentation must be provided in version control with the code and be made available online in a readable form.
9. **Testing**: Stable packages must provide unit tests of individual components (e.g. functions, classes) as well as integration tests that test the interaction between components that covers most of the code. Testing coverage should be measured. Automated testing is recommended, in which tests are run before any code is merged. System[link] and acceptance[link] testing are also recommended.
8. **Documentation**: All functions, classes, and modules in the public-facing application programming interface (API) must have documentation strings (docstrings) provided in a standard [convention](https://www.python.org/dev/peps/pep-0257/) (e.g. [numpydoc](https://numpydoc.readthedocs.io/en/latest/format.html)). Functions, classes, and modules that are not public-facing should generally have docstring to enable developers to maintain them. Docstrings must describe the code’s purpose, describe all inputs and outputs, and provide examples. High level documentation must also be provided as guides, tutorials, and developer docs. Documentation must be provided in version control with the code and be made available online in a readable form.
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"should generally have docstring" --should be plural.

9. **Testing**: Stable packages must provide unit tests of individual components (e.g. functions, classes) as well as integration tests that test the interaction between components that covers most of the code. Testing coverage should be measured. Automated testing is recommended, in which tests are run before any code is merged. System and acceptance testing are also recommended.
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I believe we should add links to all the four types of tests that are mentioned here. I've just found the software testing fundamentals website which describe them quite well. Otherwise, people that haven't obtained any software development training wouldn't really understand the differences.

10. **Dependencies**: Projects should import the minimum number of packages necessary. Adding new dependencies should be a __considered__ decision.
11. **Python 3**: All packages must be compatible or work towards being compatible with Python 3. Providing ongoing support for Python 2 is not recommended as the end of life for Python 2 is January 1, 2020 (see [PEP 373](https://www.python.org/dev/peps/pep-0373/)).
12. **Duplication**: Duplication of code and functionality is discouraged. Forking projects into new projects is strongly discouraged.
13. **Collaboration**: Contributions to packages must be encouraged. Packages must provide contribution guidelines and clearly explain when a contribution is not accepted.
14. **Binaries**: Binary files should be added to the package repository only when necessary in order to keep packages as light as possible. Jupyter notebooks can be binary files and should not be committed to the package repository but can be provided in other repositories.
15. **Code of conduct**: Each project must adopt a code of conduct that is compatible with the [Contributor Covenant](https://www.contributor-covenant.org) and make it publicly available.

11. **Python 3**: All packages must be compatible with Python 3. Providing ongoing support for Python 2 is not recommended as the end of life for Python 2 was January 1, 2020 (see [PEP 373](https://www.python.org/dev/peps/pep-0373/)).
12. **Deprecation Policy** (in accordance with [NEP 29](https://numpy.org/neps/nep-0029-deprecation_policy.html)): Each project should support (1) all minor versions of Python released 42 months prior to the project, and at minimum the two latest minor versions; and (2) all minor versions of NumPy released in the 24 months prior to the project, and at minimum the last three minor versions. In ``setup.py``, the ``python_requires`` variable should be set to the minimum supported version of Python. All supported minor versions of Python should be in the test matrix and have binary artifacts built for the release. Minimum Python and NumPy version support should be adjusted upward only on major and minor releases, and never on a patch release.
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...In setup.py or setup.cfg, the python_requires ...

Although perhaps too technical for the standards document, in my opinion setup.cfg should be used as much as possible to allow better tool introspection without needing to install. For security, best practices, etc.

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Agree with @scivision. We should encourage to keep that metadata on setup.cfg or pyproject.toml.

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Can't this just be "projects should comply with NEP 29"?

13. **Duplication**: Duplication of code and functionality is discouraged. Forking projects into new projects is strongly discouraged.
14. **Collaboration**: Contributions to packages must be encouraged. Packages must provide contribution guidelines, and clearly and constructively explain when a contribution is not accepted.
15. **Binaries**: Binary files should be added to the package repository only when necessary in order to keep packages as light as possible. Jupyter notebooks can be binary files and should not be committed to the package repository but can be provided in other repositories.
16. **Code of conduct**: Each project must adopt a code of conduct that is compatible with the [Contributor Covenant](https://www.contributor-covenant.org) and make it publicly available. Each project should have a reporting procedure for reporting violations of the code of conduct and make it publicly available (for a highly detailed example, refer to the [Code of Conduct Response and Enforcement Manual for NumFOCUS](https://numfocus.org/code-of-conduct/response-and-enforcement-events-meetups)).