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c990fce
added refine cell in phonopy
mkphuthi Jan 10, 2025
b24fa2a
parity bug fix
mkphuthi Jan 10, 2025
96aa10c
asimrun shouldn't need env_id
mkphuthi Jan 20, 2025
9c92520
precommand bug fix
mkphuthi Jan 20, 2025
7a24795
Merge branch 'mkphuthi/develop' of https://github.com/BattModels/asim…
mkphuthi Jan 20, 2025
114cb65
vasp,lammps,espresso
Feb 14, 2025
e6fd240
placeholders
Mar 11, 2025
354ae34
placeholder bug fix, time_unit ase_md
mkphuthi Mar 15, 2025
e2dbce2
ase_md update
mkphuthi Mar 18, 2025
52572a3
minor bug fixes
mkphuthi Mar 18, 2025
cac8f46
ase_md enhancements, write_atoms, minor cleanup
mkphuthi Mar 28, 2025
73a8470
write_images
mkphuthi Mar 29, 2025
7c36145
return molecules
mkphuthi Mar 30, 2025
528402e
cleanup
mkphuthi Apr 1, 2025
1f60741
use write_atoms, lammps bug fix
mkphuthi Apr 18, 2025
cc04034
write_atoms test
mkphuthi Apr 25, 2025
14b8d14
FixSymmetry bugs related ASE update
mkphuthi Jun 3, 2025
c32eb35
write_atoms tests
mkphuthi Jun 3, 2025
8e902c2
Cleanup for DFT apps
mkphuthi Jun 3, 2025
ec788f0
Cleanup matgl
mkphuthi Jun 3, 2025
44bba9f
write_atoms modifications
mkphuthi Jun 3, 2025
d15d3f4
get_atoms constraints, asim-check job_ids
mkphuthi Jun 18, 2025
2ff2827
vasp ibrion,fairchem calc
mkphuthi Jul 21, 2025
97470a1
hostname
mkphuthi Jul 21, 2025
1994537
Merge branch 'mkphuthi/develop' of https://github.com/BattModels/asim…
mkphuthi Jul 21, 2025
a16ae2e
template_sim_input for image_array
mkphuthi Aug 11, 2025
c4df253
lammps restart, image_array args
mkphuthi Nov 6, 2025
c198886
aqcat, vasp optional run
mkphuthi Nov 6, 2025
3afdbb1
minor
mkphuthi Nov 26, 2025
5346f27
Merge branch 'mkphuthi/develop' of https://github.com/BattModels/asim…
mkphuthi Nov 26, 2025
be3f15f
properties in collect
mkphuthi Dec 15, 2025
c6bed38
aqcat calculator
mkphuthi Jan 13, 2026
a7d648e
fairchem calc fix
mkphuthi Feb 3, 2026
fdc231b
minor aesthetic things, as_integers
mkphuthi Apr 3, 2026
7b1cc19
distance arg in phonopy
mkphuthi Apr 4, 2026
aa9b22c
pylintrc
mkphuthi Apr 4, 2026
a05f574
utils.py linting
mkphuthi Apr 4, 2026
8989277
calculators.py linting
mkphuthi Apr 4, 2026
0db9fbb
lammps utils.py linting
mkphuthi Apr 4, 2026
3ff35c4
utils.py linting
mkphuthi Apr 4, 2026
7b11aac
job.py linting
mkphuthi Apr 4, 2026
6037d39
src refactor
mkphuthi Apr 4, 2026
37bcf3d
precommit config
mkphuthi Apr 4, 2026
f9bd211
general linting
mkphuthi Apr 4, 2026
a30aab7
add more utils tests
mkphuthi Apr 4, 2026
a4effe7
job.py tests
mkphuthi Apr 4, 2026
7ef9206
docs update
mkphuthi Apr 4, 2026
6b8bb79
optimizations and version bump
mkphuthi Apr 6, 2026
b33ff5a
Add calculator dict interface to load_calc and UnitJob
mkphuthi May 7, 2026
2f86a7b
Update tests to use new calculator dict interface
mkphuthi May 7, 2026
9e07646
Update singlepoint to use calculator dict interface
mkphuthi May 7, 2026
903f01b
Remove dead calc_id assignment from create_unitjob helper
mkphuthi May 7, 2026
7c3fa9a
Update atom_relax to use calculator dict interface
mkphuthi May 7, 2026
497a23c
Update cell_relax to use calculator dict interface
mkphuthi May 7, 2026
61a22c5
Update symmetric_cell_relax to use calculator dict interface
mkphuthi May 7, 2026
2b6aadd
Update ase_cubic_eos_optimization to use calculator dict interface
mkphuthi May 7, 2026
5654a6a
refactor(optimize): replace calc_id with calculator dict
mkphuthi May 7, 2026
557ee9f
refactor(ase_phonons): replace calc_id with calculator dict
mkphuthi May 7, 2026
a79cd34
refactor(phonopy/forces): replace calc_id with calculator dict
mkphuthi May 7, 2026
a3f00c5
refactor(phonopy/phonon_bands_and_dos): replace calc_id with calculat…
mkphuthi May 7, 2026
8837947
refactor(phonopy/full_qha): replace calc_id with calculator dict
mkphuthi May 7, 2026
912249a
refactor(vacancy_formation_energy): replace calc_id with calculator dict
mkphuthi May 7, 2026
03955ad
refactor(benchmarking/parity): replace calc_id with calculator dict
mkphuthi May 7, 2026
b167d7e
refactor(elastic_constants/cubic_energy_expansion): replace calc_id w…
mkphuthi May 7, 2026
c59a54f
refactor(surface_energies): replace calc_id with calculator dict
mkphuthi May 7, 2026
1ef633f
refactor(active_learning/compute_deviation): replace calc_ids with ca…
mkphuthi May 7, 2026
6bd0cea
refactor(workflows/calc_array): add calculator/template_calculator wi…
mkphuthi May 7, 2026
094a35c
refactor(examples): update all sim_input.yaml files to use calculator…
mkphuthi May 7, 2026
dbdae3a
refactor(ase_md): replace calc_spec with calculator dict
mkphuthi May 7, 2026
05121f8
refactor(examples/active_learning): replace calc_spec with calculator…
mkphuthi May 7, 2026
f9b1fd3
ase_eos bug fixing
mkphuthi May 7, 2026
0faaac8
refactor(job): modernize type annotations, fix wrong return types
mkphuthi May 7, 2026
268cde7
Add dry_run option to UnitJob: writes inputs but skips submission
mkphuthi May 8, 2026
5942d5a
Bump version to 0.3.0; update docs and changelog for calculator inter…
mkphuthi May 8, 2026
0bba70a
Single-source version from pyproject.toml via importlib.metadata; add…
mkphuthi May 8, 2026
1bdc4b9
Improve CI workflows: restrict release to tags, fix docs deps, remove…
mkphuthi May 8, 2026
601df18
Update deprecated action versions: upload-artifact v3→v4, setup-pytho…
mkphuthi May 8, 2026
1a1fb19
Remove draft-pdf.yaml workflow
mkphuthi May 8, 2026
99505af
Remove pip cache from tests workflow to fix cache service 400 error
mkphuthi May 8, 2026
f7c3541
Fix job_array.sh failing on Ubuntu: use bash instead of sh
mkphuthi May 8, 2026
593091c
Rewrite job_array.sh generation to use POSIX sh instead of bash arrays
mkphuthi May 8, 2026
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22 changes: 11 additions & 11 deletions .github/workflows/docs.yaml
Original file line number Diff line number Diff line change
@@ -1,26 +1,26 @@
name: documentation

on: [push, pull_request, workflow_dispatch]

permissions:
contents: write
on:
push:
branches: ["main"]
pull_request:
branches: ["main"]
workflow_dispatch:

jobs:
docs:
runs-on: ubuntu-latest
permissions:
contents: write
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.9'
python-version: '3.10'
- name: Install dependencies
run: |
pip install sphinx sphinx_rtd_theme myst_parser autodoc
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
pip install -e .
run: pip install -e ".[docs]"
- name: Sphinx build
run: |
sphinx-build docs _build
run: sphinx-build docs _build
- name: Deploy to GitHub Pages
uses: peaceiris/actions-gh-pages@v3
if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' }}
Expand Down
30 changes: 0 additions & 30 deletions .github/workflows/draft-pdf.yaml

This file was deleted.

146 changes: 70 additions & 76 deletions .github/workflows/release.yaml
Original file line number Diff line number Diff line change
@@ -1,6 +1,9 @@
name: Publish Python 🐍 distribution 📦 to PyPI and TestPyPI

on: push
on:
push:
tags:
- 'v*'

jobs:
build:
Expand All @@ -14,11 +17,7 @@ jobs:
with:
python-version: "3.10"
- name: Install pypa/build
run: >-
python3 -m
pip install
build
--user
run: python3 -m pip install build --user
- name: Build a binary wheel and a source tarball
run: python3 -m build
- name: Store the distribution packages
Expand All @@ -27,16 +26,16 @@ jobs:
name: python-package-distributions
path: dist/

publish-to-pypi:
name: >-
Publish Python 🐍 distribution 📦 to PyPI
if: startsWith(github.ref, 'refs/tags/') # only publish to PyPI on tag pushes
publish-to-testpypi:
name: Publish Python 🐍 distribution 📦 to TestPyPI
needs:
- build
runs-on: ubuntu-latest

environment:
name: pypi
url: https://pypi.org/p/asimtools # Replace <package-name> with your PyPI project name
name: testpypi
url: https://test.pypi.org/p/asimtools

permissions:
id-token: write # IMPORTANT: mandatory for trusted publishing

Expand All @@ -46,73 +45,68 @@ jobs:
with:
name: python-package-distributions
path: dist/
- name: Publish distribution 📦 to PyPI
- name: Publish distribution 📦 to TestPyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
verbose: true
repository-url: https://test.pypi.org/legacy/

# github-release:
# name: >-
# Sign the Python 🐍 distribution 📦 with Sigstore
# and upload them to GitHub Release
# needs:
# - publish-to-pypi
# runs-on: ubuntu-latest

# permissions:
# contents: write # IMPORTANT: mandatory for making GitHub Releases
# id-token: write # IMPORTANT: mandatory for sigstore

# steps:
# - name: Download all the dists
# uses: actions/download-artifact@v4
# with:
# name: python-package-distributions
# path: dist/
# - name: Sign the dists with Sigstore
# uses: sigstore/gh-action-sigstore-python@v2.1.1
# with:
# inputs: >-
# ./dist/*.tar.gz
# ./dist/*.whl
# - name: Create GitHub Release
# env:
# GITHUB_TOKEN: ${{ github.token }}
# run: >-
# gh release create
# '${{ github.ref_name }}'
# --repo '${{ github.repository }}'
# --notes ""
# - name: Upload artifact signatures to GitHub Release
# env:
# GITHUB_TOKEN: ${{ github.token }}
# # Upload to GitHub Release using the `gh` CLI.
# # `dist/` contains the built packages, and the
# # sigstore-produced signatures and certificates.
# run: >-
# gh release upload
# '${{ github.ref_name }}' dist/**
# --repo '${{ github.repository }}'
publish-to-pypi:
name: Publish Python 🐍 distribution 📦 to PyPI
needs:
- publish-to-testpypi
runs-on: ubuntu-latest
environment:
name: pypi
url: https://pypi.org/p/asimtools
permissions:
id-token: write # IMPORTANT: mandatory for trusted publishing

# publish-to-testpypi:
# name: Publish Python 🐍 distribution 📦 to TestPyPI
# needs:
# - build
# runs-on: ubuntu-latest
steps:
- name: Download all the dists
uses: actions/download-artifact@v4
with:
name: python-package-distributions
path: dist/
- name: Publish distribution 📦 to PyPI
uses: pypa/gh-action-pypi-publish@release/v1

# environment:
# name: testpypi
# url: https://test.pypi.org/p/asimtools
github-release:
name: >-
Sign the Python 🐍 distribution 📦 with Sigstore
and upload them to GitHub Release
needs:
- publish-to-pypi
runs-on: ubuntu-latest

# permissions:
# id-token: write # IMPORTANT: mandatory for trusted publishing
permissions:
contents: write # IMPORTANT: mandatory for making GitHub Releases
id-token: write # IMPORTANT: mandatory for sigstore

# steps:
# - name: Download all the dists
# uses: actions/download-artifact@v4
# with:
# name: python-package-distributions
# path: dist/
# - name: Publish distribution 📦 to TestPyPI
# uses: pypa/gh-action-pypi-publish@release/v1
# with:
# verbose: true
# repository-url: https://test.pypi.org/legacy/
steps:
- name: Download all the dists
uses: actions/download-artifact@v4
with:
name: python-package-distributions
path: dist/
- name: Sign the dists with Sigstore
uses: sigstore/gh-action-sigstore-python@v2.1.1
with:
inputs: >-
./dist/*.tar.gz
./dist/*.whl
- name: Create GitHub Release
env:
GITHUB_TOKEN: ${{ github.token }}
run: >-
gh release create
'${{ github.ref_name }}'
--repo '${{ github.repository }}'
--notes ""
- name: Upload artifact signatures to GitHub Release
env:
GITHUB_TOKEN: ${{ github.token }}
run: >-
gh release upload
'${{ github.ref_name }}' dist/**
--repo '${{ github.repository }}'
43 changes: 0 additions & 43 deletions .github/workflows/static.yaml

This file was deleted.

3 changes: 1 addition & 2 deletions .github/workflows/tests.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -20,10 +20,9 @@ jobs:
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v3
uses: actions/setup-python@v5
with:
python-version: "3.10"
cache: 'pip'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
Expand Down
18 changes: 18 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,18 @@
repos:
- repo: local
hooks:
- id: pylint
name: pylint
entry: conda run -n asimtools-dev pylint
language: system
types: [python]
files: ^src/asimtools/
exclude: ^src/asimtools/asimmodules/
args: [--rcfile=.pylintrc]

- id: pytest
name: pytest
entry: conda run -n asimtools-dev pytest tests/unit/
language: system
pass_filenames: false
always_run: true
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