From 2192bac293fde5be6d21e62f1b1add2d65bb491d Mon Sep 17 00:00:00 2001 From: Vitor Hideyoshi Nakazone Batista Date: Wed, 24 Jul 2024 00:47:58 -0300 Subject: [PATCH 1/2] Adds Extra Parameter to Logs and Updates Version Variable --- .pre-commit-config.yaml | 4 +- config.example.yml | 5 +- crystalpol/__init__.py | 3 + crystalpol/__main__.py | 41 ++- crystalpol/polarization.py | 38 ++- crystalpol/shared/utils/log.py | 52 ++- poetry.lock | 584 ++++++++++++++++----------------- pyproject.toml | 18 +- tests/shared/utils/test_log.py | 115 ++++--- 9 files changed, 427 insertions(+), 433 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4e05511..cb334fb 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,12 +1,12 @@ repos: - repo: https://github.com/psf/black - rev: 23.3.0 + rev: 24.4.2 hooks: - id: black args: [--config=pyproject.toml] - repo: https://github.com/pycqa/isort - rev: 5.12.0 + rev: 5.13.2 hooks: - id: isort files: "\\.(py)$" diff --git a/config.example.yml b/config.example.yml index c768993..98c4f06 100644 --- a/config.example.yml +++ b/config.example.yml @@ -1,8 +1,9 @@ crystal_pol: mem: 24 - n_procs: 20 + n_procs: 24 level: "b3lyp/aug-cc-pVDZ" pop: "chelpg" mult: [0, 1] n_atoms: 18 - comment: "Crystal" \ No newline at end of file + comment: "Crystal" + charge_tolerance: 0.0001 \ No newline at end of file diff --git a/crystalpol/__init__.py b/crystalpol/__init__.py index e69de29..36d7bc1 100644 --- a/crystalpol/__init__.py +++ b/crystalpol/__init__.py @@ -0,0 +1,3 @@ +from importlib import metadata + +VERSION = metadata.version("crystalpol") diff --git a/crystalpol/__main__.py b/crystalpol/__main__.py index 410dfdc..1d99e42 100644 --- a/crystalpol/__main__.py +++ b/crystalpol/__main__.py @@ -1,19 +1,19 @@ +from crystalpol import VERSION from crystalpol.polarization import Polarization from crystalpol.shared.config import Config from crystalpol.shared.utils.log import Log -from yaml.loader import SafeLoader -from pathlib import Path import setproctitle +import yaml +from yaml.loader import SafeLoader + import argparse import logging -import yaml import os +from pathlib import Path - -__VERSION = "v0.0.1" os.nice(+19) -setproctitle.setproctitle("crystalpol-{}".format(__VERSION)) +setproctitle.setproctitle("crystalpol-{}".format(VERSION)) def main(): @@ -24,28 +24,31 @@ def main(): parser = argparse.ArgumentParser(prog="CrystalPol") parser.add_argument( - "-v", "--version", action="version", version=f"crystalpol-{__VERSION}" + "-v", "--version", action="version", version=f"crystalpol-{VERSION}" ) parser.add_argument( - "-c", "--config", + "-c", + "--config", dest="config", default="config.yml", metavar="INFILE", - help="Config file of crystalpol [default = config.yml]" + help="Config file of crystalpol [default = config.yml]", ) parser.add_argument( - "-i", "--input", + "-i", + "--input", dest="infile", default="crystal.xyz", metavar="INFILE", - help="Input file of crystalpol [default = crystal.xyz]" + help="Input file of crystalpol [default = crystal.xyz]", ) parser.add_argument( - "-o", "--output", + "-o", + "--output", dest="outfile", default="run.log", metavar="OUTFILE", - help="Output file of crystalpol [default = run.log]" + help="Output file of crystalpol [default = run.log]", ) args = parser.parse_args() @@ -53,20 +56,16 @@ def main(): if log_file.exists(): log_file.rename(log_file.with_suffix(".log.backup")) - logging.basicConfig( - filename=args.outfile, - format='%(message)s', - level=logging.INFO - ) + logging.basicConfig(filename=args.outfile, format="%(message)s", level=logging.INFO) try: with open(args.config) as file: data = yaml.load(file, Loader=SafeLoader) - config = Config(**data.get('crystal_pol')) + config = Config(**data.get("crystal_pol")) except IOError: - raise RuntimeError('Invalid or Missing Config File.') + raise RuntimeError("Invalid or Missing Config File.") - Log.make_header(__VERSION, config.to_dict()) + Log.make_header(VERSION, config.to_dict()) pol = Polarization(args.infile, args.outfile, config) pol.run() diff --git a/crystalpol/polarization.py b/crystalpol/polarization.py index 3f36138..e3d0218 100644 --- a/crystalpol/polarization.py +++ b/crystalpol/polarization.py @@ -1,18 +1,16 @@ -from crystalpol.shared.system.molecule import Molecule -from crystalpol.shared.system.crystal import Crystal -from crystalpol.shared.system.atom import Atom -from crystalpol.shared.config import Config from crystalpol.gaussian import Gaussian - -from typing import List, Tuple +from crystalpol.shared.config import Config +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.system.molecule import Molecule +from crystalpol.shared.utils.log import Log import sys - -from crystalpol.shared.utils.log import Log +from typing import List, Tuple class Polarization: - __slots__ = ('geom_file', 'outfile', 'config', 'gaussian', 'crystal') + __slots__ = ("geom_file", "outfile", "config", "gaussian", "crystal") def __init__(self, geom_file: str, outfile: str, config: Config) -> None: self.crystal = None @@ -33,21 +31,22 @@ class Polarization: max_charge_diff = sys.float_info.max while max_charge_diff >= self.config.charge_tolerance: - max_charge_diff, charge_diff = self.update_crystal_charges( + max_charge_diff, min_charge_diff, charge_diff = self.update_crystal_charges( self.gaussian.run(cycle, self.crystal), ) Log.make_run( cycle, max_charge_diff if cycle != 1 else 0, + min_charge_diff if cycle != 1 else 0, charge_diff, - self.crystal + self.crystal, ) cycle += 1 def read_crystal(self) -> None: - with open(self.geom_file, 'r') as geom_file: + with open(self.geom_file, "r") as geom_file: lines = geom_file.readlines() molecules = self._get_molecules_from_lines(lines) @@ -57,7 +56,7 @@ class Polarization: for molecule in molecules: self.crystal.add_cell([molecule]) - def update_crystal_charges(self, charges: List[float]) -> Tuple[float, list]: + def update_crystal_charges(self, charges: List[float]) -> Tuple[float, float, list]: charge_diff = [] @@ -68,9 +67,12 @@ class Polarization: charge_diff.append(abs(atom.chg - charges[index])) atom.chg = charges[index] - max_charge_diff = abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max + max_charge_diff = ( + abs(max(charge_diff, key=abs)) if charge_diff else sys.float_info.max + ) + min_charge_diff = abs(min(charge_diff, key=abs)) if charge_diff else 0 - return max_charge_diff, charge_diff + return max_charge_diff, min_charge_diff, charge_diff def _get_molecules_from_lines(self, lines: List[str]) -> List[Molecule]: if (len(lines) % self.config.n_atoms) == 0: @@ -82,7 +84,9 @@ class Polarization: symbol, rx, ry, rz = tuple(atom_line.split()) mol.add_atom( Atom( - rx, ry, rz, + rx, + ry, + rz, symbol=symbol.ljust(2), ) ) @@ -105,4 +109,4 @@ class Polarization: @staticmethod def split(array: List, partitions: int): for i in range(0, len(array), partitions): - yield array[i: i + partitions] + yield array[i : i + partitions] diff --git a/crystalpol/shared/utils/log.py b/crystalpol/shared/utils/log.py index 8b018b8..c24d23d 100644 --- a/crystalpol/shared/utils/log.py +++ b/crystalpol/shared/utils/log.py @@ -19,31 +19,55 @@ class Log: logger.info(f"Your python version is {sys.version}\n") logger.info(f"Program started on {weekday_date_time()}\n") - logger.info("------------------------------------------------------------------------------------------") - logger.info(" CRYSTALPOL variables being used in this run: ") - logger.info("------------------------------------------------------------------------------------------\n") + logger.info( + "------------------------------------------------------------------------------------------" + ) + logger.info( + " CRYSTALPOL variables being used in this run: " + ) + logger.info( + "------------------------------------------------------------------------------------------\n" + ) for key, value in config_dict.items(): logger.info(f"\t{key} = {(value if value else 'Not set')}") - logger.info("------------------------------------------------------------------------------------------") - logger.info(f" RUN Results: ") - logger.info("------------------------------------------------------------------------------------------\n") + logger.info( + "------------------------------------------------------------------------------------------" + ) + logger.info( + f" RUN Results: " + ) + logger.info( + "------------------------------------------------------------------------------------------\n" + ) @staticmethod - def make_run(cycle, max_charge_diff, charge_diff, crystal, logger=None): + def make_run( + cycle, max_charge_diff, min_charge_diff, charge_diff, crystal, logger=None + ): if logger is None: logger = logging.getLogger() - logger.info(f"cycle: {cycle}") - logger.info(f"\nMax charge diff: {max_charge_diff:.5f}") + logger.info(f"cycle: {cycle}\n") + logger.info(f"Max charge diff: {max_charge_diff:.5f}") + logger.info(f"Min charge diff: {min_charge_diff:.5f}") logger.info(f"Charge Diff: {charge_diff}\n") - logger.info(f"------------------------------------------------------------------------------------------") - logger.info(f" S rx ry rz chg ") - logger.info(f"------------------------------------------------------------------------------------------") + logger.info( + f"------------------------------------------------------------------------------------------" + ) + logger.info( + f" S rx ry rz chg " + ) + logger.info( + f"------------------------------------------------------------------------------------------" + ) for atom in crystal[0][0]: logger.info( - f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} ") + f" {atom.symbol.rjust(2)} {float(atom.rx):.6f} {float(atom.ry):.6f} {float(atom.rz):.6f} {float(atom.chg):.6f} " + ) - logger.info("\n------------------------------------------------------------------------------------------\n") + logger.info( + "\n------------------------------------------------------------------------------------------\n" + ) diff --git a/poetry.lock b/poetry.lock index 6bb7ecf..a33c1b1 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,38 +1,34 @@ -# This file is automatically @generated by Poetry 1.4.2 and should not be changed by hand. +# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand. 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-[tool.coverage.lcov] -output = "coverage/lcov.info" +hooks = "pre-commit install --config .pre-commit-config.yaml" [tool.isort] profile = "black" diff --git a/tests/shared/utils/test_log.py b/tests/shared/utils/test_log.py index 2225aee..bae2f05 100644 --- a/tests/shared/utils/test_log.py +++ b/tests/shared/utils/test_log.py @@ -1,12 +1,11 @@ -from crystalpol.shared.system.molecule import Molecule -from crystalpol.shared.system.crystal import Crystal -from crystalpol.shared.system.atom import Atom from crystalpol.shared.config import Config +from crystalpol.shared.system.atom import Atom +from crystalpol.shared.system.crystal import Crystal +from crystalpol.shared.system.molecule import Molecule from crystalpol.shared.utils.log import Log -from io import StringIO import logging - +from io import StringIO from unittest import TestCase, mock @@ -16,53 +15,50 @@ class TestLog(TestCase): self.log_stream = StringIO() logging.basicConfig( - stream=self.log_stream, - format='%(message)s', - level=logging.INFO + stream=self.log_stream, format="%(message)s", level=logging.INFO ) self.logger = logging.getLogger() def tearDown(self): - logging.getLogger().removeHandler( - logging.getLogger().handlers[0] - ) + logging.getLogger().removeHandler(logging.getLogger().handlers[0]) del self.logger del self.log_stream - @mock.patch('crystalpol.shared.utils.log.sys') - @mock.patch('crystalpol.shared.utils.log.weekday_date_time') + @mock.patch("crystalpol.shared.utils.log.sys") + @mock.patch("crystalpol.shared.utils.log.weekday_date_time") def test_make_header(self, weekday_date_time_mock, sys_mock): - weekday_date_time_mock.return_value = 'Test Day' - sys_mock.version = 'Test Version' + weekday_date_time_mock.return_value = "Test Day" + sys_mock.version = "Test Version" - config = Config( - mem=1, - level="b3lyp/aug-cc-pVDZ", - n_atoms=10 - ) - Log.make_header('test', config.to_dict(), logger=self.logger) + config = Config(mem=1, level="b3lyp/aug-cc-pVDZ", n_atoms=10) + Log.make_header("test", config.to_dict(), logger=self.logger) expected_log_stream = [ - '##########################################################################################\n', - '############## Welcome to CRYSTALPOL version test ##############\n', - '##########################################################################################\n', '\n', - 'Your python version is Test Version\n', '\n', - 'Program started on Test Day\n', '\n', - '------------------------------------------------------------------------------------------\n', - ' CRYSTALPOL variables being used in this run: \n', - '------------------------------------------------------------------------------------------\n', '\n', - '\tmem = 1\n', - '\tlevel = b3lyp/aug-cc-pVDZ\n', - '\tn_atoms = 10\n', - '\tn_procs = 1\n', - '\tpop = chelpg\n', - '\tcomment = crystalpol\n', - '\tcharge_tolerance = 0.02\n', - '\tsimulation_dir = simfiles\n', - '\tmult = [0, 1]\n', - '------------------------------------------------------------------------------------------\n', - ' RUN Results: \n', - '------------------------------------------------------------------------------------------\n', '\n' + "##########################################################################################\n", + "############## Welcome to CRYSTALPOL version test ##############\n", + "##########################################################################################\n", + "\n", + "Your python version is Test Version\n", + "\n", + "Program started on Test Day\n", + "\n", + "------------------------------------------------------------------------------------------\n", + " CRYSTALPOL variables being used in this run: \n", + "------------------------------------------------------------------------------------------\n", + "\n", + "\tmem = 1\n", + "\tlevel = b3lyp/aug-cc-pVDZ\n", + "\tn_atoms = 10\n", + "\tn_procs = 1\n", + "\tpop = chelpg\n", + "\tcomment = crystalpol\n", + "\tcharge_tolerance = 0.02\n", + "\tsimulation_dir = simfiles\n", + "\tmult = [0, 1]\n", + "------------------------------------------------------------------------------------------\n", + " RUN Results: \n", + "------------------------------------------------------------------------------------------\n", + "\n", ] self.log_stream.seek(0) @@ -71,17 +67,24 @@ class TestLog(TestCase): def test_make_run(self): - Log.make_run(1, 0.000000, [], self.create_crystal(), logger=self.logger) + Log.make_run( + 1, 0.00001, 0.000001, [], self.create_crystal(), logger=self.logger + ) expected_log_stream = [ - 'cycle: 1\n', '\n', - 'Max charge diff: 0.00000\n', - 'Charge Diff: []\n', '\n', - '------------------------------------------------------------------------------------------\n', - ' S rx ry rz chg \n', - '------------------------------------------------------------------------------------------\n', - ' H 0.000000 0.000000 0.000000 0.000000 \n', '\n', - '------------------------------------------------------------------------------------------\n', '\n' + "cycle: 1\n", + "\n", + "Max charge diff: 0.00001\n", + "Min charge diff: 0.00000\n", + "Charge Diff: []\n", + "\n", + "------------------------------------------------------------------------------------------\n", + " S rx ry rz chg \n", + "------------------------------------------------------------------------------------------\n", + " H 0.000000 0.000000 0.000000 0.000000 \n", + "\n", + "------------------------------------------------------------------------------------------\n", + "\n", ] self.log_stream.seek(0) @@ -90,21 +93,13 @@ class TestLog(TestCase): @staticmethod def create_crystal(): - crystal_structure = [ - ['H '] - ] + crystal_structure = [["H "]] crystal = Crystal(crystal_structure) molecule = Molecule("TESTE") molecule.add_atom( - Atom( - na=1, - rx=0.000000, - ry=0.000000, - rz=0.000000, - chg=0.000000 - ) + Atom(na=1, rx=0.000000, ry=0.000000, rz=0.000000, chg=0.000000) ) crystal.add_cell([molecule]) From b2ad5a26d8807225900ff81091a18e238e072a0b Mon Sep 17 00:00:00 2001 From: Vitor Hideyoshi Nakazone Batista Date: Wed, 24 Jul 2024 00:50:11 -0300 Subject: [PATCH 2/2] Updates Versioning Pipeline --- .github/workflows/python-pypi-test-upload.yml | 35 --------- .github/workflows/python-pypi-upload.yml | 74 +++++++++++++------ .github/workflows/python-tests.yml | 30 -------- pyproject.toml | 6 +- 4 files changed, 57 insertions(+), 88 deletions(-) delete mode 100644 .github/workflows/python-pypi-test-upload.yml delete mode 100644 .github/workflows/python-tests.yml diff --git a/.github/workflows/python-pypi-test-upload.yml b/.github/workflows/python-pypi-test-upload.yml deleted file mode 100644 index 5248c99..0000000 --- a/.github/workflows/python-pypi-test-upload.yml +++ /dev/null @@ -1,35 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - -name: Upload CrystalPol to PyPI Test - -on: - push: - branches: [ develop ] - -permissions: - contents: read - -jobs: - - pypi-upload-test: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.8 - uses: actions/setup-python@v3 - with: - python-version: "3.8" - - name: Install dependencies - run: | - python -m pip install --upgrade pip poetry - python -m poetry install - - name: Test with unittest - run: | - python -m poetry run python -m unittest -v - - name: Upload Pip Package - run: | - python -m poetry config repositories.testpypi https://test.pypi.org/legacy/ - python -m poetry publish --build --username __token__ --password ${{secrets.PYPI_TEST_TOKEN}} --repository testpypi \ No newline at end of file diff --git a/.github/workflows/python-pypi-upload.yml b/.github/workflows/python-pypi-upload.yml index d0dfcbe..1cd7c2f 100644 --- a/.github/workflows/python-pypi-upload.yml +++ b/.github/workflows/python-pypi-upload.yml @@ -4,32 +4,62 @@ name: Upload CrystalPol to PyPI on: - push: - branches: [ main ] + push permissions: - contents: read + contents: read jobs: - pypi-upload: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Install poetry + run: pipx install poetry - runs-on: ubuntu-latest + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: "3.10" + - name: Install dependencies + run: | + poetry self add "poetry-dynamic-versioning[plugin]" + if [ -f pyproject.toml ]; then poetry install; fi + - name: Run unittest + run: | + poetry run python -m unittest - steps: - - uses: actions/checkout@v3 - - name: Set up Python 3.8 - uses: actions/setup-python@v3 - with: - python-version: "3.8" - - name: Install dependencies - run: | - python -m pip install --upgrade pip poetry - python -m poetry install - - name: Test with unittest - run: | - python -m poetry run python -m unittest -v - - name: Upload Pip Package - run: | - python -m poetry config repositories.pypi https://upload.pypi.org/legacy/ - python -m poetry publish --build --username __token__ --password ${{secrets.PYPI_TOKEN}} --repository pypi \ No newline at end of file + pypi-upload: + needs: [test] + if: startsWith(github.ref, 'refs/tags/v') + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v3 + with: + fetch-depth: 0 + - name: Install poetry + run: pipx install poetry + + - name: Set up Python 3.10 + uses: actions/setup-python@v3 + with: + python-version: "3.10" + - name: Install dependencies + run: | + poetry self add "poetry-dynamic-versioning[plugin]" + if [ -f pyproject.toml ]; then poetry install; fi + - name: Build Python Package + run: | + poetry build -f sdist + poetry install + echo "Built CrystalPol - $(poetry version)" + - name: Configure PyPI + run: | + poetry config repositories.pypi https://upload.pypi.org/legacy/ + poetry config pypi-token.pypi ${{secrets.PYPI_TOKEN}} + - name: Upload Python Package + run: | + poetry publish --repository pypi \ No newline at end of file diff --git a/.github/workflows/python-tests.yml b/.github/workflows/python-tests.yml deleted file mode 100644 index 897e0fb..0000000 --- a/.github/workflows/python-tests.yml +++ /dev/null @@ -1,30 +0,0 @@ -# This workflow will install Python dependencies, run tests and lint with a single version of Python -# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python - -name: Python application - -on: - push - -permissions: - contents: read - -jobs: - - run-unitest: - - runs-on: ubuntu-latest - - steps: - - uses: actions/checkout@v2 - - name: Set up Python 3.8 - uses: actions/setup-python@v3 - with: - python-version: "3.8" - - name: Install dependencies - run: | - python -m pip install --upgrade pip poetry - python -m poetry install - - name: Test with unittest - run: | - poetry run python -m unittest -v \ No newline at end of file diff --git a/pyproject.toml b/pyproject.toml index 0c6806a..320f76a 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -21,9 +21,13 @@ poethepoet = "^0.20.0" [tool.poetry.scripts] crystalpol = "crystalpol.__main__:main" +[tool.poetry-dynamic-versioning] +enable = true +vcs = "git" + [build-system] requires = ["poetry-core"] -build-backend = "poetry.core.masonry.api" +build-backend = "poetry_dynamic_versioning.backend" [tool.poe.tasks] hooks = "pre-commit install --config .pre-commit-config.yaml"