Merge remote-tracking branch 'mp/main' into patch_wavede

Author: jmmshn

.github/workflows/deploy.yml

@@ -10,7 +10,6 @@ jobs:
   deploy-docs:
 
     # only run if commit is a push to master and the testing finished
-    # if: github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && ( github.event.workflow_run.head_branch == 'main' || startsWith(github.event.workflow_run.head_branch, 'v') )
     if: github.repository_owner == 'materialsproject' && github.event.workflow_run.conclusion == 'success' && github.event.workflow_run.event == 'push' && startsWith(github.event.workflow_run.head_branch, 'v0.')
     runs-on: ubuntu-latest
 
@@ -80,7 +79,10 @@ 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 } ' 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
+          echo "" >> release_info.txt
+          awk '/CONTRIBUTOR SECTION/{f=1; c=0} f' CHANGELOG.md >> release_info.txt
 
       - name: Release
         uses: actions/create-release@v1

.github/workflows/testing.yml

@@ -18,13 +18,7 @@ jobs:
           cache: pip
           cache-dependency-path: pyproject.toml
 
-      - name: Install dependencies
-        run: |
-          python -m pip install --upgrade pip
-          pip install .[strict,tests,dev]
-
-      - name: Lint
-        run: pre-commit run --all-files --show-diff-on-failure
+      - uses: pre-commit/[email protected]
 
   test:
     services:
@@ -50,7 +44,7 @@ jobs:
       - name: Install dependencies
         run: |
           python -m pip install --upgrade pip
-            pip install .[strict,tests,docs]
+            pip install .[strict,tests]
 
       - name: Test
         env:

.pre-commit-config.yaml

@@ -60,3 +60,4 @@ repos:
   - id: codespell
     stages: [commit, commit-msg]
     args: [--ignore-words-list, 'titel,statics,ba,nd,te']
+    types_or: [python, rst, markdown]

CHANGELOG.md

@@ -1,68 +1,91 @@
 Change log
 ==========
 
+v0.0.9
+------
+
+New features:
+
+- Defect formation energy workflow with VASP implementation ([@jmmshn][jmmshn], [#215](https://github.com/materialsproject/atomate2/pull/215))
+- Job to retrieve a structure from the MP API at run-time ([@mkhorton][mkhorton], [#176](https://github.com/materialsproject/atomate2/pull/176]))
+
+Enhancements:
+
+- Documentation of phonon workflow ([@QuantumChemist][quantumchemist], [#232](https://github.com/materialsproject/atomate2/pull/232))
+- Refactor defect code ([@jmmshn][jmmshn], [#214](https://github.com/materialsproject/atomate2/pull/214))
+- Use `ruff` for linting ([@janosh][janosh], [#250](https://github.com/materialsproject/atomate2/pull/250))
+
+
+Bug fixes:
+
+- Use correct k-point density in phonon workflow ([@JaGeo][jageo], [#177](https://github.com/materialsproject/atomate2/pull/177))
+- Fix use of `expanduser` path ([@nwinner][nwinner], [#180](https://github.com/materialsproject/atomate2/pull/180))
+- Correct `calcs_reversed` to be in the proper order ([@Zhuoying][zhuoying], [#182](https://github.com/materialsproject/atomate2/pull/182))
+- Bugfix for `store_volumetric_data` ([@jmmshn][jmmshn], [#212](https://github.com/materialsproject/atomate2/pull/212))
+
+
 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))
+- VASP Phonopy workflow ([@JaGeo][jageo], [#137](https://github.com/materialsproject/atomate2/pull/137))
+- Molecular dynamics VASP job ([@mjwen][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))
+- Update IO classes to use pymatgen base classes ([@rkingsbury][rkingsbury], [#141](https://github.com/materialsproject/atomate2/pull/141))
+- Read and write VASP structures with higher precision ([@JaGeo][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))
+- Fix code examples in docs ([@JaGeo][jageo], [#169](https://github.com/materialsproject/atomate2/pull/169))
+- Fix f-orbital DOS properties ([@arosen93][arosen], [#138](https://github.com/materialsproject/atomate2/pull/138))
+- Fix `mock_run_vasp` testing to accept args ([@mjwen][mjwen], [#151](https://github.com/materialsproject/atomate2/pull/151))
+- Regenerate calc_types enum ([@mjwen][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))
+  VASP schema ([@arosen93][arosen], [#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))
+- Docs improvements ([@janosh][janosh], [@mjwen][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))
+- Make potcar_spec argument usable ([@jmmshn][jmmshn], [#83](https://github.com/materialsproject/atomate2/pull/83))
+- Replace monty which with shutil which ([@arosen93][arosen], [#92](https://github.com/materialsproject/atomate2/pull/92))
+- Fix `calculate_deformation_potentials()` ([@janosh][janosh], [#94](https://github.com/materialsproject/atomate2/pull/94))
+- Fix gzipping of files with numerical suffixes ([@jmmshn][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))
+  ([@arosen93][arosen], [#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))
+- Add mag_density to VASP output doc ([@arosen93][arosen], [#65](https://github.com/materialsproject/atomate2/pull/66))
+- Double relax maker now supports two different Makers ([@arosen93][arosen], [#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))
+- Store band structure efermi in CalculationOutput ([@arosen93][arosen], [#66](https://github.com/materialsproject/atomate2/pull/66))
+- Support for VASP6 and latest pymatgen ([@arosen93][arosen], [#75](https://github.com/materialsproject/atomate2/pull/75))
 - Fixed atomate2 version string.
 - Disabled orbital projections in the electron-phonon workflow.
 
@@ -73,11 +96,11 @@ 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))
+- Base schema for molecule task documents ([@arosen93][arosen], [#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 VASP relaxation using custodian "FULL_OPT" ([@arosen93][arosen], [#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.
@@ -101,8 +124,8 @@ New features:
 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))
+- Add MP base sets ([@arosen93][arosen], [#27](https://github.com/materialsproject/atomate2/pull/27))
+- Docs updates ([@arosen93][arosen], [#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.
@@ -112,11 +135,11 @@ 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))
+- Remove unused INCAR settings ([@arosen93][arosen])
+- Add missing LASPH flags on vdW functionals ([@arosen93][arosen], [#31](https://github.com/materialsproject/atomate2/pull/31))
+- Use `NSW=0` in static calculations ([@arosen93][arosen], [#10](https://github.com/materialsproject/atomate2/pull/10))
+- `LREAL = False` in static jobs by default ([@arosen93][arosen], [#23](https://github.com/materialsproject/atomate2/pull/23))
+- Add missing functionals in output schema ([@arosen93][arosen], [#12](https://github.com/materialsproject/atomate2/pull/12))
 - Many output schema fixes.
 - Better support for FireWorks.
 - Support writing additional files in VASP jobs.
@@ -135,3 +158,15 @@ v0.0.1
 ------
 
 Initial release.
+
+[contributors]: <> (CONTRIBUTOR SECTION)
+[nwinner]: https://github.com/nwinner
+[jageo]: https://github.com/JaGeo
+[zhuoying]: https://github.com/Zhuoying
+[jmmshn]: https://github.com/jmmshn
+[mkhorton]: https://github.com/mkhorton
+[QuantumChemist]: https://github.com/QuantumChemist
+[janosh]: https://github.com/janosh
+[mjwen]: https://github.com/mjwen
+[arosen]: https://github.com/arosen93
+[rkingsbury]: https://github.com/rkingsbury

README.md

@@ -5,7 +5,7 @@
 [![pypi version](https://img.shields.io/pypi/v/atomate2?color=blue)](https://pypi.org/project/atomate2)
 ![supported python versions](https://img.shields.io/pypi/pyversions/atomate2)
 
-**👉 [Full Documentation][docs] 👈**
+[Documentation][docs] | [PyPI][pypi] | [GitHub][github]
 
 Atomate2 is a free, open-source software for performing complex materials science
 workflows using simple Python functions. Features of atomate2 include
@@ -139,3 +139,5 @@ A full list of all contributors can be found [here][contributors].
 [vasp_workflows]: https://materialsproject.github.io/atomate2/user/codes/vasp.html
 [RelaxBandStructure]: https://materialsproject.github.io/atomate2/user/codes/vasp.html#relax-and-band-structure
 [docs]: https://materialsproject.github.io/atomate2/
+[github]: https://github.com/materialsproject/atomate2
+[pypi]: https://pypi.org/project/atomate2

docs/about/contributors.md

@@ -25,11 +25,12 @@ Lawrence Livermore National Laboratory
 [jmmshn]: https://github.com/jmmshn
 [0000-0002-2743-7531]: https://orcid.org/0000-0002-2743-7531
 
-**Janosh Riebesell** [![gh]][janosh] \
+**Janosh Riebesell** [![gh]][janosh] [![orc]][0000-0001-5233-3462]\
 PhD Student \
 Cambridge University
 
 [janosh]: https://github.com/janosh
+[0000-0001-5233-3462]: https://orcid.org/0000-0001-5233-3462
 
 **Ryan Kingsbury** [![gh]][rkingsbury] [![orc]][0000-0002-7168-3967] \
 Incoming Assistant Professor \
@@ -52,3 +53,24 @@ University of Houston
 
 [mjwen]: https://github.com/mjwen
 [0000-0003-0013-575X]: https://orcid.org0000-0003-0013-575X/
+
+**Christina Ertural** [![gh]][QuantumChemist] [![orc]][0000-0002-7696-5824] \
+Postdoctoral Researcher \
+Federal Institute for Materials Research and Testing (Berlin)
+
+[QuantumChemist]: https://github.com/QuantumChemist
+[0000-0002-7696-5824]: https://orcid.org/0000-0002-7696-5824
+
+**Matthew Horton** [![gh]][mkhorton] [![orc]][0000-0001-7777-8871] \
+Senior Research Software Engineer \
+Microsoft Research
+
+[mkhorton]: https://github.com/mkhorton
+[0000-0001-7777-8871]: https://orcid.org/0000-0001-7777-8871
+
+**Zhuoying Zhu** [![gh]][zhuoying] [![orc]][0000-0003-1775-7651] \
+Postdoctoral researcher\
+Lawrence Berkeley National Laboratory
+
+[zhuoying]: https://github.com/zhuoying
+[0000-0003-1775-7651]: https://orcid.org/0000-0003-1775-7651

pyproject.toml

@@ -73,9 +73,9 @@ atm = "atomate2.cli:cli"
 
 [project.urls]
 homepage = "https://materialsproject.github.io/atomate2/"
-repository = "https://github.com/hackingmaterials/atomate2"
+repository = "https://github.com/materialsproject/atomate2"
 documentation = "https://materialsproject.github.io/atomate2/"
-changelog = "https://github.com/hackingmaterials/atomate2/blob/main/CHANGELOG.md"
+changelog = "https://github.com/materialsproject/atomate2/blob/main/CHANGELOG.md"
 
 [tool.setuptools.package-data]
 atomate2 = ["py.typed"]