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♻️ Initialization of the refactoring of the LAMMPS plugin #35

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merged 73 commits into from
Apr 5, 2022
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9eb62c9
Fixing the examples so that they correspond to the new potential setup.
Oct 21, 2020
2c35ea2
Fixed formatting error which caused the pre-commit hooks to fail
Oct 21, 2020
2d5cbe7
Merge remote-tracking branch 'upstream/master'
Jun 16, 2021
a320fe7
Merge branch 'master' of git://github.com/aiidaplugins/aiida-lammps
Jun 17, 2021
2c20ded
Adding a new auxiliary file to auto-generate the lammps input file.
Nov 8, 2021
34ef3ee
Added a pre-commit in the style of the one in aiida-core. Change many…
Nov 8, 2021
c54d8ff
(WIP) Adding a new file for the automatic generation of the lammps in…
Nov 8, 2021
96d24dc
(WIP) Improving the input file generation.
Nov 9, 2021
c30875c
(WIP) Improving the input generation.
Nov 10, 2021
5469404
(WIP) Makign the input generation more flexible.
Nov 10, 2021
abb2016
(WIP) make the input file generation more flexible.
Nov 10, 2021
a693920
(WIP) making the input more flexible.
Nov 15, 2021
e948a42
(WIP) Make the input generation more flexible.
Nov 17, 2021
8697b35
(WIP) Improving the potential storage by making it similar to the Pse…
Nov 19, 2021
bce0bd9
(WIP) Improving the potential.
Nov 22, 2021
a3dfff8
(WIP) Improving the potential storage.
Nov 23, 2021
d04660f
(WIP) improving the generation of the input file.
Nov 23, 2021
6391d57
(WIP) Improving the potential.
Nov 23, 2021
e3304a5
(WIP) Improvements on the input generation. Changes to ensure that th…
Nov 25, 2021
92d4173
(WIP) Improvement of the input generation.
Nov 26, 2021
62a8636
(WIP) Improving the input file generation.
Nov 29, 2021
afd09e2
(WIP) Improvement of the dosctrings and format to make it compatible …
Nov 30, 2021
9b22f21
(WIP) Fixing the format and docstrings so that they follow the pylint…
Dec 1, 2021
0aaeed6
(WIP) Updating the pre-commit packages
Dec 1, 2021
2b9a592
(WIP) setting so that the correct pre-commit runs
Dec 1, 2021
e4578d2
(WIP) Trying to fix the format to fit the pre-commit standard.
Dec 3, 2021
f1379d6
Setting the version of pylint to 2.5
Dec 3, 2021
ad59d3f
(WIP) Fixing formatting issues with pylint.
Dec 3, 2021
d75db21
(WIP) Fixing issues with pylint formatting.
Dec 3, 2021
57af613
(WIP) Trying to fix the issues with pylint checking for duplicate code
Dec 3, 2021
4e2ad56
(WIP) Removing pre-commit from the installation of the tests
Dec 3, 2021
1317df5
(WIP) Fixing an issue with github actions.
Dec 3, 2021
f75fef0
(WIP) Fixing an issue with github actions.
Dec 3, 2021
955767d
(WIP) Fixing the tests so that they correctly refer to potential_type…
Dec 3, 2021
1241994
(WIP) Fixing an issue with the kind_symbols not being properly replac…
Dec 3, 2021
f80f15e
(WIP) Fixing issues with the tests.
Dec 3, 2021
36e73ec
(WIP) Making the trajectory generation compatible with aiida-core 1.65
Dec 3, 2021
1426d3a
(WIP) Fixing trajectories to make them compatible to aiida-core 1.65
Dec 3, 2021
9ce3960
(WIP) Fixing an issue in which the trajectories could not be properly…
Dec 6, 2021
a749b59
(WIP) Fixing a small issue with the formatting.
Dec 6, 2021
658c190
(WIP) Fixing an issue in which the trajectory_filename is not being p…
Dec 6, 2021
d78fc54
(WIP) Adding test files for the new potential data format.
Dec 6, 2021
2726162
Adding tests for the new potential type in aiida-lammps.
Dec 7, 2021
af90443
(WIP) Adding tests for the potential block for the new potential style.
Dec 7, 2021
ba5bb86
(WIP) Making the input file more flexible.
Dec 8, 2021
9ea3f6a
Fixing mislablled potential test from eam -> eam/alloy
Dec 8, 2021
9952cfd
Fixing an issue resulting from the re-labelling of the eam/alloy test…
Dec 8, 2021
b46609c
(WIP) Improving the input file generation.
Dec 8, 2021
76630d7
Fix an issue that could lead the tests to fail due to how the block h…
Dec 8, 2021
b943eab
(WIP) Adding tests for the generation input files.
Dec 8, 2021
24e327d
(WIP) Adding tests for the input file generation
Dec 8, 2021
7caadc6
Adding tests for the input file generation.
Dec 9, 2021
bdb30d4
(WIP) Improving the flexibility of the input file.
Dec 9, 2021
0aa1d24
(WIP) Improving input file generation.
Dec 9, 2021
faec2d1
(WIP) Making the lammps calculations more flexible.
Dec 10, 2021
06f00cf
Adding tests for the new parser.
Dec 10, 2021
1e9cce4
(WIP) Making the calculations more flexible. Adding a new base calcul…
Dec 10, 2021
9d651d2
(WIP) Making the calculation more flexible. Adding proper documentati…
Dec 13, 2021
850fb95
(WIP) Improving the flexibility of the calculation. Start of adding a…
Dec 13, 2021
883a8d9
Fixed issues with respect to the parsing of for the new base calculat…
Dec 14, 2021
8276360
Fixing issues with potential tests after reverting behaviour of poten…
Dec 14, 2021
feee651
(WIP) Working in the documentation of the package.
Jan 28, 2022
a49a0ec
Improving the documentation of the package, specifically adding examp…
Feb 9, 2022
45385d4
Fixing pre-commit issues arising from pinning the pylint version to t…
Feb 9, 2022
bd8d667
Merge branch 'develop' into refactoring
chrisjsewell Apr 5, 2022
4eee307
Re-establish upstream formatting
chrisjsewell Apr 5, 2022
92063e3
Simplify pre-commit ci
chrisjsewell Apr 5, 2022
3e1a9e2
Update .pre-commit-config.yaml
chrisjsewell Apr 5, 2022
7456bc0
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Apr 5, 2022
b2350a3
Remove dynaphonopy code
chrisjsewell Apr 5, 2022
5c34a9b
Move tests out of package
chrisjsewell Apr 5, 2022
46408b3
Fix docs
chrisjsewell Apr 5, 2022
48e2c0e
Delete utils.py
chrisjsewell Apr 5, 2022
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23 changes: 3 additions & 20 deletions .github/workflows/cd.yml
Original file line number Diff line number Diff line change
@@ -12,31 +12,14 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v1
with:
python-version: 3.8
id: cache-pip
- uses: actions/cache@v1
with:
path: ~/.cache/pip
key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
restore-keys:
pip-${{ matrix.python-version }}-tests
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python }}
python-version: 3.8
- name: Upgrade pip
run: |
pip install --upgrade pip
pip --version
- name: Install wheel
run: pip install wheel
run: pip install --upgrade pip
- name: Install AiiDA-LAMMPS
run: |
pip install -e .[testing,pre-commit]
pip freeze
run: pip install pre-commit
- name: Run pre-commit
run: pre-commit run --all-files || ( git diff; git status; exit 1; )

23 changes: 3 additions & 20 deletions .github/workflows/ci.yml
Original file line number Diff line number Diff line change
@@ -12,31 +12,14 @@ jobs:

steps:
- uses: actions/checkout@v2
- name: Set up Python
uses: actions/setup-python@v1
with:
python-version: 3.8
id: cache-pip
- uses: actions/cache@v1
with:
path: ~/.cache/pip
key: pip-${{ matrix.python-version }}-tests-${{ hashFiles('**/setup.json') }}
restore-keys:
pip-${{ matrix.python-version }}-tests
- name: Set up Python
uses: actions/setup-python@v2
with:
python-version: ${{ matrix.python }}
python-version: 3.8
- name: Upgrade pip
run: |
pip install --upgrade pip
pip --version
- name: Install wheel
run: pip install wheel
run: pip install --upgrade pip
- name: Install AiiDA-LAMMPS
run: |
pip install -e .[testing,pre-commit]
pip freeze
run: pip install pre-commit
- name: Run pre-commit
run: pre-commit run --all-files || ( git diff; git status; exit 1; )

58 changes: 42 additions & 16 deletions .gitignore
Original file line number Diff line number Diff line change
@@ -1,21 +1,47 @@
*.pyc
*.swo
*.swp
~*
*~

build/
dist/
.project
*.egg*
.DS_Store
.idea/
.tox/
.pytest_cache/
.idea/vcs.xml
postgres*.log
.aiida_envs.yaml
.vscode/
docs/_build/
pip-wheel-metadata/
example_inputs/
pytest_workdir/


*.pyc
*~
*.swp
*.project
*.pydevproject
.settings
.DS_Store
*/.DS_Store
*/*/.DS_Store
*/*/*/.DS_Store
.metadata
.ipynb_checkpoints
.project
.idea/vcs.xml

/venv*/
/.idea/
*.egg-info
.eggs
.vscode
.tox

# files created by coverage
.cache
.pytest_cache
.coverage
coverage.xml

# Files created by RPN tests
**/polish_workchains/polish*

# Build files
dist/
pip-wheel-metadata

# Docs
docs/_build/
docs/build
docs/source/reference/apidoc
16 changes: 6 additions & 10 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -3,42 +3,38 @@

exclude: >
(?x)^(
aiida_lammps/tests/input_files/.*|
aiida_lammps/tests/.*txt
tests/input_files/.*|
tests/.*txt
)$

repos:

- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v3.2.0
rev: v4.1.0
hooks:
- id: check-json
- id: check-yaml
- id: end-of-file-fixer
- id: trailing-whitespace

- repo: https://github.com/timothycrosley/isort
rev: 5.5.3
rev: 5.10.1
hooks:
- id: isort

- repo: https://github.com/psf/black
rev: 20.8b1
rev: 22.3.0
hooks:
- id: black

- repo: https://gitlab.com/pycqa/flake8
rev: 3.8.3
rev: 3.9.2
hooks:
- id: flake8
# additional_dependencies:
# - flake8-bugbear==20.1.4
# - flake8-builtins==1.5.3
# - flake8-comprehensions==3.2.3
exclude: >
(?x)^(
aiida_lammps/calculations/dynaphopy.py
)$

- repo: local
hooks:
2 changes: 1 addition & 1 deletion .readthedocs.yml
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
version: 2

python:
version: 3
version: "3.8"
install:
- method: pip
path: .
1 change: 1 addition & 0 deletions MANIFEST.in
Original file line number Diff line number Diff line change
@@ -2,3 +2,4 @@ include LICENSE
include setup.json
include aiida_lammps/tests/input_files/*
include aiida_lammps/validation/schemas/*.json
include aiida_lammps/data/*
8 changes: 2 additions & 6 deletions README.md
Original file line number Diff line number Diff line change
@@ -11,10 +11,6 @@ This plugin contains 4 code types:
- `lammps.forces`: Atomic single-point forces calculation
- `lammps.optimize`: Crystal structure optimization
- `lammps.md`: Molecular dynamics calculation
- `lammps.combinate`: DynaPhoPy calculation using LAMMPS MD trajectory (currently untested)

Note: `lammps.combinate` requires `aiida-phonopy` (https://github.com/abelcarreras/aiida-phonopy)
plugin to work, DynaPhoPy can be found in: https://github.com/abelcarreras/aiida-phonopy

- [AiiDA LAMMPS plugin](#aiida-lammps-plugin)
- [Installation](#installation)
@@ -53,9 +49,9 @@ and there are many test examples in **/aiida_lammps/tests/test_calculations**.
### Code Setup

```python
from aiida_lammps.tests.utils import (
from tests.utils import (
get_or_create_local_computer, get_or_create_code)
from aiida_lammps.tests.utils import lammps_version
from tests.utils import lammps_version

computer_local = get_or_create_local_computer('work_directory', 'localhost')
code_lammps_force = get_or_create_code('lammps.force', computer_local, 'lammps')
1 change: 1 addition & 0 deletions aiida_lammps/__init__.py
Original file line number Diff line number Diff line change
@@ -1 +1,2 @@
"""AiiDA plugin for the LAMMPS code"""
__version__ = "0.8.0"
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