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release v8.0.4
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jzhang-github committed Dec 19, 2023
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34 changes: 34 additions & 0 deletions .github/workflows/pypi-package.yml
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# This workflow uses actions that are not certified by GitHub.
# They are provided by a third-party and are governed by
# separate terms of service, privacy policy, and support
# documentation.

# GitHub recommends pinning actions to a commit SHA.
# To get a newer version, you will need to update the SHA.
# You can also reference a tag or branch, but the action may change without warning.

name: Upload Python Package

on:
release:
types: [published]

jobs:
deploy:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python
uses: actions/setup-python@v4
with:
python-version: '3.x'
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install build
- name: Build package
run: python -m build
- name: Publish package
uses: pypa/gh-action-pypi-publish@release/v1
with:
password: ${{ secrets.PYPI_API_TOKEN }}
40 changes: 40 additions & 0 deletions .github/workflows/python-package.yml
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# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python

name: Python package

on:
push:
branches: [ "main" ]
pull_request:
branches: [ "main" ]

jobs:
build:

runs-on: ubuntu-latest
strategy:
fail-fast: false
matrix:
python-version: ["3.9", "3.10", "3.11"]

steps:
- uses: actions/checkout@v3
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v3
with:
python-version: ${{ matrix.python-version }}
- name: Install dependencies
run: |
python -m pip install --upgrade pip
python -m pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
# - name: Test with pytest
# run: |
# pytest
18 changes: 10 additions & 8 deletions Change_log.md
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@@ -1,10 +1,13 @@
# [main](https://github.com/jzhang-github/AGAT/tree/main)
- Modify [agat/lib/model_lib.py#L40-L45](https://github.com/jzhang-github/AGAT/blob/main/agat/lib/model_lib.py#L40-L45)

# [v8.0.3](https://github.com/jzhang-github/AGAT/tree/v8.0.4)
- Modify [agat/lib/model_lib.py#L40-L45](https://github.com/jzhang-github/AGAT/blob/v8.0.4/agat/lib/model_lib.py#L40-L45)
- Modify [agat/app/cata/high_throughput_predict.py#L208](https://github.com/jzhang-github/AGAT/blob/v8.0.4/agat/app/cata/high_throughput_predict.py#L208)

# [v8.0.3](https://github.com/jzhang-github/AGAT/tree/v8.0.3)
- Modify [agat/lib/model_lib.py#L178-L193](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/lib/model_lib.py#L178-L193)
- Add default parameter: `vasp_bash_path`[high_throughput_dft_calculation.py#L71](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/app/cata/high_throughput_dft_calculation.py#L71); [default_parameters.py#L242](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/default_parameters.py#L242).
- Modify `run_vasp()` function: [high_throughput_lib.py#L124-L149](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/lib/high_throughput_lib.py#L124-L149).
- Modify `run_vasp()` function: [high_throughput_lib.py#L124-L149](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/lib/high_throughput_lib.py#L124-L149).
- Add transfer learning: [default_parameters.py#L97](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/default_parameters.py#L97). [agat/model/fit.py#L169-L174](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/model/fit.py#L169-L174)
- Add split graphs: [agat/data/build_dataset.py#L795-L824](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/data/build_dataset.py#L795-L824)

Expand All @@ -14,7 +17,7 @@

# [v7.14.0](https://github.com/jzhang-github/AGAT/tree/v7.14.0)
- Add API for controling HP DFT calculation. [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L246-L251)
- Add `mask_reversed_magnetic_moments` in [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L58) and [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py)
- Add `mask_reversed_magnetic_moments` in [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L58) and [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py)
- Modify [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py):
- Include stress in the graph: [agat/data/data.py#L273-L275](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L273-L275), [agat/data/data.py#L350-L352](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L350-L352).
- Update method of parsing the vasp data: [agat/data/data.py#L610](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L610), [agat/data/data.py#L625-L656](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L625-L656), [agat/data/data.py#L661-L675](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L661-L675).
Expand All @@ -29,7 +32,7 @@
- Upgrade docs.

# [v7.13.3](https://github.com/jzhang-github/AGAT/tree/v7.13.3)
- Using self-defined tf-based functions to calculate Pearson r: [agat/lib/GatLib.py#L248-L259](https://github.com/jzhang-github/AGAT/tree/v7.13.3/agat/lib/GatLib.py#L248-L259)
- Using self-defined tf-based functions to calculate Pearson r: [agat/lib/GatLib.py#L248-L259](https://github.com/jzhang-github/AGAT/tree/v7.13.3/agat/lib/GatLib.py#L248-L259)

This self-defined function can handle `ValueError: array must not contain infs or NaNs`.

Expand All @@ -45,7 +48,7 @@
- [agat/app/GatApp.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2ain/agat/app/GatApp.py#L69-L70)
- [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/default_parameters.py#L133)

- Deprecate redundant training configurations:
- Deprecate redundant training configurations:
- `train_energy_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L96) and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L198)
- `train_force_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L274) and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L398)
- `new_energy_train`
Expand Down Expand Up @@ -80,10 +83,9 @@

# [v7.12](https://github.com/jzhang-github/AGAT/tree/v7.12)

- Release pip wheel.
- Release pip wheel.
- Simplify packages. See [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) for more details of the first release.

# [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) [![DOI](https://zenodo.org/badge/545430295.svg)](https://zenodo.org/badge/latestdoi/545430295)
# [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) [![DOI](https://zenodo.org/badge/545430295.svg)](https://zenodo.org/badge/latestdoi/545430295)

First release to reproduce results and support conclusions of [***Design High-Entropy Electrocatalyst via Interpretable Deep Graph Attention Learning***](https://doi.org/10.1016/j.joule.2023.06.003).

2 changes: 1 addition & 1 deletion agat/__init__.py
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Expand Up @@ -5,7 +5,7 @@
@author: ZHANG Jun
"""

__version__ = '8.0.3'
__version__ = '8.0.4'

import os
# os.environ['DGLBACKEND']="pytorch"
Expand Down
27 changes: 16 additions & 11 deletions docs/sphinx/source/Change_log/Change_log.md
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@@ -1,17 +1,23 @@
# [main](https://github.com/jzhang-github/AGAT/tree/main)
- Modify [agat/lib/model_lib.py#L178-L193](https://github.com/jzhang-github/AGAT/blob/dcb777cdede4947f7c033de35604b554bec39d66/agat/lib/model_lib.py#L178-L193)
- Add default parameter: `vasp_bash_path`[high_throughput_dft_calculation.py#L71](https://github.com/jzhang-github/AGAT/blob/main/agat/app/cata/high_throughput_dft_calculation.py#L71); [default_parameters.py#L242](https://github.com/jzhang-github/AGAT/blob/main/agat/default_parameters.py#L242).
- Modify `run_vasp()` function: [high_throughput_lib.py#L124-L149](https://github.com/jzhang-github/AGAT/blob/main/agat/lib/high_throughput_lib.py#L124-L149).
- Add transfer learning: [default_parameters.py#L97](https://github.com/jzhang-github/AGAT/blob/main/agat/default_parameters.py#L97). [agat/model/fit.py#L169-L174](https://github.com/jzhang-github/AGAT/blob/main/agat/model/fit.py#L169-L174)
- Add split graphs: [agat/data/build_dataset.py#L795-L824](https://github.com/jzhang-github/AGAT/blob/main/agat/data/build_dataset.py#L795-L824)

# [v8.0.3](https://github.com/jzhang-github/AGAT/tree/v8.0.4)
- Modify [agat/lib/model_lib.py#L40-L45](https://github.com/jzhang-github/AGAT/blob/v8.0.4/agat/lib/model_lib.py#L40-L45)
- Modify [agat/app/cata/high_throughput_predict.py#L208](https://github.com/jzhang-github/AGAT/blob/v8.0.4/agat/app/cata/high_throughput_predict.py#L208)

# [v8.0.3](https://github.com/jzhang-github/AGAT/tree/v8.0.3)
- Modify [agat/lib/model_lib.py#L178-L193](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/lib/model_lib.py#L178-L193)
- Add default parameter: `vasp_bash_path`[high_throughput_dft_calculation.py#L71](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/app/cata/high_throughput_dft_calculation.py#L71); [default_parameters.py#L242](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/default_parameters.py#L242).
- Modify `run_vasp()` function: [high_throughput_lib.py#L124-L149](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/lib/high_throughput_lib.py#L124-L149).
- Add transfer learning: [default_parameters.py#L97](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/default_parameters.py#L97). [agat/model/fit.py#L169-L174](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/model/fit.py#L169-L174)
- Add split graphs: [agat/data/build_dataset.py#L795-L824](https://github.com/jzhang-github/AGAT/blob/v8.0.3/agat/data/build_dataset.py#L795-L824)

# [v8.0.0](https://github.com/jzhang-github/AGAT/tree/v8.0.0)
- Convert TensorFlow to PyTorch backend.
- Updata docs.

# [v7.14.0](https://github.com/jzhang-github/AGAT/tree/v7.14.0)
- Add API for controling HP DFT calculation. [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L246-L251)
- Add `mask_reversed_magnetic_moments` in [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L58) and [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py)
- Add `mask_reversed_magnetic_moments` in [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/default_parameters.py#L58) and [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py)
- Modify [agat/data/data.py](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py):
- Include stress in the graph: [agat/data/data.py#L273-L275](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L273-L275), [agat/data/data.py#L350-L352](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L350-L352).
- Update method of parsing the vasp data: [agat/data/data.py#L610](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L610), [agat/data/data.py#L625-L656](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L625-L656), [agat/data/data.py#L661-L675](https://github.com/jzhang-github/AGAT/tree/v7.14.0/agat/data/data.py#L661-L675).
Expand All @@ -26,7 +32,7 @@
- Upgrade docs.

# [v7.13.3](https://github.com/jzhang-github/AGAT/tree/v7.13.3)
- Using self-defined tf-based functions to calculate Pearson r: [agat/lib/GatLib.py#L248-L259](https://github.com/jzhang-github/AGAT/tree/v7.13.3/agat/lib/GatLib.py#L248-L259)
- Using self-defined tf-based functions to calculate Pearson r: [agat/lib/GatLib.py#L248-L259](https://github.com/jzhang-github/AGAT/tree/v7.13.3/agat/lib/GatLib.py#L248-L259)

This self-defined function can handle `ValueError: array must not contain infs or NaNs`.

Expand All @@ -42,7 +48,7 @@
- [agat/app/GatApp.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2ain/agat/app/GatApp.py#L69-L70)
- [agat/default_parameters.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/default_parameters.py#L133)

- Deprecate redundant training configurations:
- Deprecate redundant training configurations:
- `train_energy_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L96) and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L198)
- `train_force_model`: [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L274) and [agat/model/ModelFit.py](https://github.com/jzhang-github/AGAT/tree/v7.13.2/agat/model/ModelFit.py#L398)
- `new_energy_train`
Expand Down Expand Up @@ -77,10 +83,9 @@

# [v7.12](https://github.com/jzhang-github/AGAT/tree/v7.12)

- Release pip wheel.
- Release pip wheel.
- Simplify packages. See [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) for more details of the first release.

# [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) [![DOI](https://zenodo.org/badge/545430295.svg)](https://zenodo.org/badge/latestdoi/545430295)
# [v1.0.0](https://github.com/jzhang-github/AGAT/tree/v1.0.0) [![DOI](https://zenodo.org/badge/545430295.svg)](https://zenodo.org/badge/latestdoi/545430295)

First release to reproduce results and support conclusions of [***Design High-Entropy Electrocatalyst via Interpretable Deep Graph Attention Learning***](https://doi.org/10.1016/j.joule.2023.06.003).

4 changes: 2 additions & 2 deletions setup.py
Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
from distutils.core import setup
from setuptools import find_packages

with open("D:\GitHubRepo\AGAT\README.md", "r") as f:
with open("README.md", "r") as f:
long_description = f.read()

# print(long_description)
Expand All @@ -19,7 +19,7 @@
# long_description = (this_directory / "README.md").read_text()

setup(name='agat',
version='8.0.3',
version='8.0.4',
python_requires='>=3.10',
description='Atomic Graph ATtention networks for predicting atomic energies and forces.',
long_description=long_description,
Expand Down

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