Merge pull request #174 from materialsproject/docs

Tidy docs and update changelog

Author: utf

.github/workflows/deploy.yml

@@ -80,7 +80,7 @@ jobs:
           ref: ${{ github.event.workflow_run.head_branch }}
 
       - name: Write release info
-        run: awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' docs/about/changelog.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
+        run: awk 'BEGIN {p = 0} {a = 0 }; /^v\d*.\d*.\d*./ { p += 1; a = 1}; p + a == 1 { print } ' CHANGELOG.md | sed -e '1,1d' | sed  -e '/./,$!d' -e :a -e '/^\n*$/{$d;N;ba' -e '}' > release_info.txt
 
       - name: Release
         uses: actions/create-release@v1

ADMIN.md

@@ -0,0 +1,7 @@
+# Releasing a new atomate2 version
+
+Version releases on Pypi and GitHub are handled automatically through GitHub
+actions. The steps to push a new release are:
+1. Update `CHANGELOG.md` with a new version and release notes.
+2. Create a tagged Git commit with the above changes: `git tag v0.0.1`
+3. Push the commit and tags to GitHub using: `git push origin --tags`

CHANGELOG.md

@@ -0,0 +1,137 @@
+Change log
+==========
+
+v0.0.8
+------
+
+New features:
+
+- VASP Phonopy workflow ([@JaGeo](https://github.com/JaGeo), [#137](https://github.com/materialsproject/atomate2/pull/137))
+- Molecular dynamics VASP job ([@mjwen](https://github.com/mjwen), [#134](https://github.com/materialsproject/atomate2/pull/134))
+
+Enhancements:
+
+- Update IO classes to use pymatgen base classes ([@rkingsbury](https://github.com/rkingsbury), [#141](https://github.com/materialsproject/atomate2/pull/141))
+- Read and write VASP structures with higher precision ([@JaGeo](https://github.com/JaGeo), [#167](https://github.com/materialsproject/atomate2/pull/167))
+
+Bug fixes:
+
+- Fix code examples in docs ([@JaGeo](https://github.com/JaGeo), [#169](https://github.com/materialsproject/atomate2/pull/169))
+- Fix f-orbital DOS properties ([@arosen93](https://github.com/arosen93), [#138](https://github.com/materialsproject/atomate2/pull/138))
+- Fix `mock_run_vasp` testing to accept args ([@mjwen](https://github.com/mjwen), [#151](https://github.com/materialsproject/atomate2/pull/151))
+- Regenerate calc_types enum ([@mjwen](https://github.com/mjwen), [#153](https://github.com/materialsproject/atomate2/pull/153))
+
+v0.0.7
+------
+
+New features:
+
+- Include band-related features (e.g. band center, bandwidth, skewness, kurtosis) in
+  VASP schema ([@arosen93](https://github.com/arosen93), [#92](https://github.com/materialsproject/atomate2/pull/92))
+- Add `use_auto_ispin` and `update_user_potcar_functional` powerups
+
+Enhancements:
+
+- Add `is_hubbard` and `hubbards` to VASP task doc.
+- Migrate build system to pyproject.toml.
+- Migrate docs to jupyter-book.
+- Docs improvements ([@janosh](https://github.com/janosh), [@mjwen](https://github.com/mjwen))
+
+Bug fixes:
+
+- Fix HSE tags.
+- Fix running bader.
+- Make potcar_spec argument usable ([@jmmshn](https://github.com/jmmshn), [#83](https://github.com/materialsproject/atomate2/pull/83))
+- Replace monty which with shutil which ([@arosen93](https://github.com/arosen93), [#92](https://github.com/materialsproject/atomate2/pull/92))
+- Fix `calculate_deformation_potentials()` ([@janosh](https://github.com/janosh), [#94](https://github.com/materialsproject/atomate2/pull/94))
+- Fix gzipping of files with numerical suffixes ([@jmmshn](https://github.com/jmmshn), [#116](https://github.com/materialsproject/atomate2/pull/116))
+
+v0.0.6
+------
+
+New features:
+
+- cclib task document supporting virtually all popular molecular DFT codes out-of-the-box
+  ([@arosen93](https://github.com/arosen93), [#64](https://github.com/materialsproject/atomate2/pull/64))
+
+Enhancements:
+
+- Add mag_density to VASP output doc ([@arosen93](https://github.com/arosen93), [#65](https://github.com/materialsproject/atomate2/pull/66))
+- Double relax maker now supports two different Makers ([@arosen93](https://github.com/arosen93), [#32](https://github.com/materialsproject/atomate2/pull/32))
+
+Bug fixes:
+
+- Store band structure efermi in CalculationOutput ([@arosen93](https://github.com/arosen93), [#66](https://github.com/materialsproject/atomate2/pull/66))
+- Support for VASP6 and latest pymatgen ([@arosen93](https://github.com/arosen93), [#75](https://github.com/materialsproject/atomate2/pull/75))
+- Fixed atomate2 version string.
+- Disabled orbital projections in the electron-phonon workflow.
+
+v0.0.5
+------
+
+This version removed Python 3.7 support following numpy and pymatgen.
+
+New features:
+
+- Base schema for molecule task documents ([@arosen93](https://github.com/arosen93), [#54](https://github.com/materialsproject/atomate2/pull/54))
+
+Bug fixes:
+
+- Fix VASP relaxation using custodian "FULL_OPT" ([@arosen93](https://github.com/arosen93), [#42](https://github.com/materialsproject/atomate2/pull/42))
+- Fix supercell generation and input sets in electron-phonon workflow.
+- Fix `HSEBSSetGenerator` INCAR settings.
+- Fix issue with magnetism in SOC structures.
+- Fix bug with Fermi level and IBRION=1
+- Better handling of URI generation.
+- Tweak k-spacing formula to stop large band gaps giving negative values
+
+v0.0.4
+------
+
+Lots of improvements and bug fixes this release.
+
+New features:
+
+- AMSET workflow.
+- Electron phonon band gap renormalisation workflow.
+- Specific uniform and line mode band structure makers.
+- Optics maker.
+- Transmuter maker.
+
+Enhancements:
+
+- Support for automatic handling of ISPIN.
+- Add MP base sets ([@arosen93](https://github.com/arosen93), [#27](https://github.com/materialsproject/atomate2/pull/27))
+- Docs updates ([@arosen93](https://github.com/arosen93), [#13](https://github.com/materialsproject/atomate2/pull/13) [#17](https://github.com/materialsproject/atomate2/pull/17))
+- Options to strip band structure and DOS projects to reduce object sizes.
+- Input sets now use generators to avoid serialization issues.
+- Use smart efermi finding to remove errors with tetrahedron integration in VASP 6.
+- Powerups can now work on `Maker` objects directly.
+
+Bug fixes:
+
+- Use PBEsol by default.
+- Increase number of significant figures when writing POSCAR files.
+- Remove unused INCAR settings ([@arosen93](https://github.com/arosen93))
+- Add missing LASPH flags on vdW functionals ([@arosen93](https://github.com/arosen93), [#31](https://github.com/materialsproject/atomate2/pull/31))
+- Use `NSW=0` in static calculations ([@arosen93](https://github.com/arosen93), [#10](https://github.com/materialsproject/atomate2/pull/10))
+- `LREAL = False` in static jobs by default ([@arosen93](https://github.com/arosen93), [#23](https://github.com/materialsproject/atomate2/pull/23))
+- Add missing functionals in output schema ([@arosen93](https://github.com/arosen93), [#12](https://github.com/materialsproject/atomate2/pull/12))
+- Many output schema fixes.
+- Better support for FireWorks.
+- Support writing additional files in VASP jobs.
+
+v0.0.3
+------
+
+Many updates to use the latest jobflow store features.
+
+v0.0.2
+------
+
+Automated releases.
+
+v0.0.1
+------
+
+Initial release.

CODE_OF_CONDUCT.md

@@ -0,0 +1,48 @@
+# Contributor Code of Conduct
+
+As contributors and maintainers of this project, and in the interest of
+fostering an open and welcoming community, we pledge to respect all people who
+contribute through reporting issues, posting feature requests, updating
+documentation, submitting pull requests or patches, and other activities.
+
+We are committed to making participation in this project a harassment-free
+experience for everyone, regardless of level of experience, gender, gender
+identity and expression, sexual orientation, disability, personal appearance,
+body size, race, ethnicity, age, religion, or nationality.
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery
+* Personal attacks
+* Trolling or insulting/derogatory comments
+* Public or private harassment
+* Publishing other's private information, such as physical or electronic
+  addresses, without explicit permission
+* Other unethical or unprofessional conduct
+
+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.
+
+By adopting this Code of Conduct, project maintainers commit themselves to
+fairly and consistently applying these principles to every aspect of managing
+this project. Project maintainers who do not follow or enforce the Code of
+Conduct may be permanently removed from the project team.
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community.
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting a project maintainer at [INSERT EMAIL ADDRESS]. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. Maintainers are
+obligated to maintain confidentiality with regard to the reporter of an
+incident.
+
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage],
+version 1.3.0, available at https://www.contributor-covenant.org/version/1/3/0/code-of-conduct.html
+
+[homepage]: https://www.contributor-covenant.org

CONTRIBUTING.md

@@ -0,0 +1,68 @@
+# Contributing to atomate2
+
+We love your input! We want to make contributing to as easy and
+transparent as possible, whether it's:
+
+- Reporting a bug
+- Discussing the current state of the code
+- Submitting a fix
+- Proposing or implementing new features
+- Becoming a maintainer
+
+## Reporting bugs, getting help, and discussion
+
+atomate2 is still in development, so at the moment we
+do not have a dedicated help forum. For the time being, please
+submit questions and bugs to the
+[GitHub issues page](https://github.com/materialsproject/atomate2/issues).
+
+If you are making a bug report, incorporate as many elements of the
+following as possible to ensure a timely response and avoid the
+need for followups:
+
+- A quick summary and/or background.
+- Steps to reproduce - be specific! **Provide sample code.**
+- What you expected would happen, compared to what actually happens.
+- The full stack trace of any errors you encounter.
+- Notes (possibly including why you think this might be happening,
+  or steps you tried that didn't work).
+
+We love thorough bug reports as this means the development team can
+make quick and meaningful fixes. When we confirm your bug report,
+we'll move it to the GitHub issues where its progress can be
+further tracked.
+
+## Contributing code modifications or additions through Github
+
+We use github to host code, to track issues and feature requests,
+as well as accept pull requests. We maintain a list of all
+contributors [here](https://materialsproject.github.io/atomate2/contributors.html).
+
+Pull requests are the best way to propose changes to the codebase.
+Follow the [Github flow](https://www.atlassian.com/git/tutorials/comparing-workflows/forking-workflow)
+for more information on this procedure.
+
+The basic procedure for making a PR is:
+
+- Fork the repo and create your branch from master.
+- Commit your improvements to your branch and push to your Github fork (repo).
+- When you're finished, go to your fork and make a Pull Request. It will
+  automatically update if you need to make further changes.
+
+## How to Make a Great Pull Request
+
+We have a few tips for writing good PRs that are accepted into the main repo:
+
+- Use the Numpy Code style for all of your code. Find an example [here](hhttps://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_numpy.html#example-numpy).
+- Your code should have (4) spaces instead of tabs.
+- If needed, update the documentation.
+- **Write tests** for new features! Good tests are 100%, absolutely necessary
+  for good code. We use the python `pytest` framework -- see some of the
+  other tests in this repo for examples, or review the [Hitchhiker's guide
+  to python](https://docs.python-guide.org/writing/tests) for some good
+  resources on writing good tests.
+- Understand your contributions will fall under the same license as this repo.
+
+When you submit your PR, our CI service will automatically run your tests.
+We welcome good discussion on the best ways to write your code, and the comments
+on your PR are an excellent area for discussion.

docs/_config.yml

@@ -90,7 +90,7 @@ sphinx:
         - "https://materialsproject.github.io/jobflow"
         - null
       monty:
-        - "https://guide.materialsvirtuallab.org/monty"
+        - "https://materialsvirtuallab.github.io/monty"
         - null
     language: en
     html_extra_path:
@@ -103,6 +103,7 @@ sphinx:
     templates_path:
       - "_templates"
       - components
+    suppress_warnings: etoc.toctree
 
     # pygments_style: github
 
@@ -130,13 +131,13 @@ sphinx:
     # control pydantic model docs
     autodoc_pydantic_model_show_json: false
     autodoc_pydantic_model_show_field_summary: false
-    autodoc_pydantic_model_show_config: false
+    autodoc_pydantic_model_show_config_member: false
     autodoc_pydantic_model_show_config_summary: false
     autodoc_pydantic_model_show_validator_members: false
     autodoc_pydantic_model_member_order: bysource
     autodoc_pydantic_settings_show_json: false
     autodoc_pydantic_settings_show_field_summary: false
-    autodoc_pydantic_settings_show_config: false
+    autodoc_pydantic_settings_show_config_member: false
     autodoc_pydantic_settings_show_config_summary: false
     autodoc_pydantic_settings_show_validator_members: false
     autodoc_pydantic_settings_member_order: bysource
@@ -150,5 +151,5 @@ sphinx:
     - sphinx.ext.intersphinx
     - sphinx.ext.viewcode
     - sphinx.ext.autosummary
-    - sphinx_panels
+    - sphinx_design
     - sphinxcontrib.autodoc_pydantic