yoki5 0.1.0__tar.gz

yoki5-0.1.0/.github/ISSUE_TEMPLATE.md

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+* yoki5 version:
+* Python version:
+* Operating System:
+
+### Description
+
+Describe what you were trying to get done.
+Tell us what happened, what went wrong, and what you expected to happen.
+
+### What I Did
+
+```
+Paste the command(s) you ran and the output.
+If there was a crash, please include the traceback here.
+```

yoki5-0.1.0/.github/TEST_FAIL_TEMPLATE.md

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+---
+title: "{{ env.TITLE }}"
+labels: [bug]
+---
+The {{ workflow }} workflow failed on {{ date | date("YYYY-MM-DD HH:mm") }} UTC
+
+The most recent failing test was on {{ env.PLATFORM }} py{{ env.PYTHON }}
+with commit: {{ sha }}
+
+Full run: https://github.com/{{ repo }}/actions/runs/{{ env.RUN_ID }}
+
+(This post will be updated if another test fails, as long as this issue remains open.)

yoki5-0.1.0/.github/dependabot.yml

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+# https://docs.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "weekly"
+    commit-message:
+      prefix: "ci(dependabot):"

yoki5-0.1.0/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches:
+      - main
+    tags:
+      - "v*"
+  pull_request:
+  workflow_dispatch:
+  schedule:
+    - cron: "0 0 * * 0" # every week (for --pre release tests)
+
+jobs:
+  check-manifest:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - run: pipx run check-manifest
+
+  test:
+
+    name: ${{ matrix.platform }} (${{ matrix.python-version }})
+    runs-on: ${{ matrix.platform }}
+    timeout-minutes: 10
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ['3.8', '3.9', '3.10', '3.11']
+        platform: [ubuntu-latest, macos-latest, windows-latest]
+
+    steps:
+      - name: Cancel Previous Runs
+        uses: styfle/cancel-workflow-action@0.12.1
+        with:
+          access_token: ${{ github.token }}
+
+      - uses: actions/checkout@v4
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v5
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache-dependency-path: "pyproject.toml"
+          cache: "pip"
+
+      # if running a cron job, we add the --pre flag to test against pre-releases
+      - name: Install dependencies
+        run: |
+          python -m pip install -U pip
+          python -m pip install .[test] ${{ github.event_name == 'schedule' && '--pre' || ''  }}
+
+      - name: Test
+        run: pytest --color=yes --cov --cov-report=xml --cov-report=term-missing
+
+      # If something goes wrong, we can open an issue in the repo
+      - name: Report --pre Failures
+        if: failure() && github.event_name == 'schedule'
+        uses: JasonEtco/create-an-issue@v2
+        env:
+          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+          PLATFORM: ${{ matrix.platform }}
+          PYTHON: ${{ matrix.python-version }}
+          RUN_ID: ${{ github.run_id }}
+          TITLE: '[test-bot] pip install --pre is failing'
+        with:
+          filename: .github/TEST_FAIL_TEMPLATE.md
+          update_existing: true
+
+      - name: Coverage
+        uses: codecov/codecov-action@v3
+
+  deploy_test:
+    name: Deploy to PyPI (test)
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          git tag
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+
+      - name: Build and publish
+        run: twine upload --repository testpypi dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.TEST_PYPI_TOKEN }}
+
+  deploy:
+    name: Deploy
+    needs: test
+    if: success() && startsWith(github.ref, 'refs/tags/') && github.event_name != 'schedule'
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: install
+        run: |
+          git tag
+          pip install -U pip build twine
+          python -m build
+          twine check dist/*
+          ls -lh dist
+
+      - name: Build and publish
+        run: twine upload dist/*
+        env:
+          TWINE_USERNAME: __token__
+          TWINE_PASSWORD: ${{ secrets.PYPI_TOKEN }}
+
+      - uses: softprops/action-gh-release@v1
+        with:
+          generate_release_notes: true

yoki5-0.1.0/.idea/inspectionProfiles/Project_Default.xml

@@ -0,0 +1,61 @@
+<component name="InspectionProjectProfileManager">
+  <profile version="1.0">
+    <option name="myName" value="Project Default" />
+    <inspection_tool class="DuplicatedCode" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
+    <inspection_tool class="PyCompatibilityInspection" enabled="true" level="WARNING" enabled_by_default="true">
+      <option name="ourVersions">
+        <value>
+          <list size="4">
+            <item index="0" class="java.lang.String" itemvalue="3.8" />
+            <item index="1" class="java.lang.String" itemvalue="3.9" />
+            <item index="2" class="java.lang.String" itemvalue="3.10" />
+            <item index="3" class="java.lang.String" itemvalue="3.11" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyMissingOrEmptyDocstringInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true" />
+    <inspection_tool class="PyPackageRequirementsInspection" enabled="false" level="WARNING" enabled_by_default="false">
+      <option name="ignoredPackages">
+        <value>
+          <list size="19">
+            <item index="0" class="java.lang.String" itemvalue="coverage" />
+            <item index="1" class="java.lang.String" itemvalue="autopep8" />
+            <item index="2" class="java.lang.String" itemvalue="peakutils" />
+            <item index="3" class="java.lang.String" itemvalue="tabulate" />
+            <item index="4" class="java.lang.String" itemvalue="pytest" />
+            <item index="5" class="java.lang.String" itemvalue="matplotlib" />
+            <item index="6" class="java.lang.String" itemvalue="bokeh" />
+            <item index="7" class="java.lang.String" itemvalue="numpy" />
+            <item index="8" class="java.lang.String" itemvalue="Pillow" />
+            <item index="9" class="java.lang.String" itemvalue="astropy" />
+            <item index="10" class="java.lang.String" itemvalue="Cython" />
+            <item index="11" class="java.lang.String" itemvalue="gdecomp" />
+            <item index="12" class="java.lang.String" itemvalue="pyimzml" />
+            <item index="13" class="java.lang.String" itemvalue="scikit-learn" />
+            <item index="14" class="java.lang.String" itemvalue="pylint" />
+            <item index="15" class="java.lang.String" itemvalue="black" />
+            <item index="16" class="java.lang.String" itemvalue="pep8" />
+            <item index="17" class="java.lang.String" itemvalue="flake8" />
+            <item index="18" class="java.lang.String" itemvalue="seaborn" />
+          </list>
+        </value>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8Inspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="E203" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyPep8NamingInspection" enabled="true" level="WEAK WARNING" enabled_by_default="true">
+      <option name="ignoredErrors">
+        <list>
+          <option value="N802" />
+        </list>
+      </option>
+    </inspection_tool>
+    <inspection_tool class="PyProtectedMemberInspection" enabled="false" level="WEAK WARNING" enabled_by_default="false" />
+  </profile>
+</component>

yoki5-0.1.0/.idea/inspectionProfiles/profiles_settings.xml

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+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

yoki5-0.1.0/.idea/modules.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectModuleManager">
+    <modules>
+      <module fileurl="file://$PROJECT_DIR$/.idea/yoki5.iml" filepath="$PROJECT_DIR$/.idea/yoki5.iml" />
+    </modules>
+  </component>
+</project>

yoki5-0.1.0/.idea/workspace.xml

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+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="ProjectViewState">
+    <option name="autoscrollToSource" value="true" />
+    <option name="compactDirectories" value="true" />
+    <option name="hideEmptyMiddlePackages" value="true" />
+    <option name="showLibraryContents" value="true" />
+    <option name="showMembers" value="true" />
+  </component>
+  <component name="PropertiesComponent">{
+  &quot;keyToString&quot;: {
+    &quot;settings.editor.selected.configurable&quot;: &quot;MTConfigurable&quot;
+  }
+}</component>
+</project>

yoki5-0.1.0/.pre-commit-config.yaml

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+ci:
+  autoupdate_schedule: monthly
+  autofix_commit_msg: "style(pre-commit.ci): auto fixes [...]"
+  autoupdate_commit_msg: "ci(pre-commit.ci): autoupdate"
+
+default_install_hook_types: [pre-commit, commit-msg]
+
+repos:
+#  -   repo: https://github.com/pre-commit/pre-commit-hooks
+#      rev: v4.4.0
+#      hooks:
+#      - id: no-commit-to-branch
+#        args: ['--branch', 'master', "--branch", "main"]
+
+  -   repo: https://github.com/MarcoGorelli/absolufy-imports
+      rev: v0.3.1
+      hooks:
+      -   id: absolufy-imports
+          exclude: _vendor|vendored
+
+  -   repo: https://github.com/hadialqattan/pycln
+      rev: v2.1.3
+      hooks:
+      - id: pycln
+
+  - repo: https://github.com/abravalheri/validate-pyproject
+    rev: v0.12.1
+    hooks:
+      - id: validate-pyproject
+
+  -   repo: https://github.com/psf/black
+      rev: 23.1.0
+      hooks:
+      - id: black
+        pass_filenames: true
+
+  -   repo: https://github.com/charliermarsh/ruff-pre-commit
+      rev: v0.0.252
+      hooks:
+        - id: ruff
+          args: [--fix]
+
+#  - repo: https://github.com/pre-commit/mirrors-mypy
+#    rev: v1.0.1
+#    hooks:
+#      - id: mypy
+#        files: "^src/"
+#        # # you have to add the things you want to type check against here
+#        # additional_dependencies:
+#        #   - numpy

yoki5-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2023 Lukasz Migas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

yoki5-0.1.0/MANIFEST.in

@@ -0,0 +1,16 @@
+# Things to always exclude
+global-exclude .git*
+global-exclude .ipynb_checkpoints
+global-exclude *.py[co]
+recursive-exclude * __pycache__
+recursive-exclude * *.py[co]
+
+# Top-level config
+include MANIFEST.in
+include LICENSE
+recursive-include tests *
+recursive-include src *.typed
+
+# Always include
+global-include *.pyx
+global-include *.c

yoki5-0.1.0/Makefile

@@ -0,0 +1,89 @@
+.PHONY: clean clean-test clean-pyc clean-build docs help
+.DEFAULT_GOAL := help
+
+define BROWSER_PYSCRIPT
+import os, webbrowser, sys
+
+from urllib.request import pathname2url
+
+webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))
+endef
+export BROWSER_PYSCRIPT
+
+define PRINT_HELP_PYSCRIPT
+import re, sys
+
+for line in sys.stdin:
+	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)
+	if match:
+		target, help = match.groups()
+		print("%-20s %s" % (target, help))
+endef
+export PRINT_HELP_PYSCRIPT
+
+BROWSER := python -c "$$BROWSER_PYSCRIPT"
+
+help:
+	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)
+
+clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts
+
+clean-build: ## remove build artifacts
+	rm -fr build/
+	rm -fr dist/
+	rm -fr .eggs/
+	find . -name '*.egg-info' -exec rm -fr {} +
+	find . -name '*.egg' -exec rm -f {} +
+
+clean-pyc: ## remove Python file artifacts
+	find . -name '*.pyc' -exec rm -f {} +
+	find . -name '*.pyo' -exec rm -f {} +
+	find . -name '*~' -exec rm -f {} +
+	find . -name '__pycache__' -exec rm -fr {} +
+
+clean-test: ## remove test and coverage artifacts
+	rm -fr .tox/
+	rm -f .coverage
+	rm -fr htmlcov/
+	rm -fr .pytest_cache
+
+test: ## run tests quickly with the default Python
+	pytest
+
+test-all: ## run tests on every Python version with tox
+	tox
+
+coverage: ## check code coverage quickly with the default Python
+	coverage run --source src/yoki5 -m pytest
+	coverage report -m
+	coverage html
+	$(BROWSER) htmlcov/index.html
+
+servedocs: docs ## compile the docs watching for changes
+	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .
+
+release: dist ## package and upload a release
+	twine upload dist/*
+
+dist: clean ## builds source and wheel package
+	python setup.py sdist
+	python setup.py bdist_wheel
+	ls -l dist
+
+install: clean ## install the package to the active Python's site-packages
+	python setup.py install
+
+develop:
+	python setup.py develop
+
+pre:
+	pre-commit run -a
+
+lint:
+	ruff format .
+	ruff . --fix
+
+untrack:
+	git rm -r --cached .
+	git add .
+	git commit -m ".gitignore fix"

yoki5-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: yoki5
+Version: 0.1.0
+Summary: Wrapper around h5py to give easier interface around complex files.
+Author-email: "Lukasz G. Migas" <lukas.migas@yahoo.com>
+License: BSD 3-Clause License
+Project-URL: homepage, https://github.com/lukasz-migas/yoki5
+Project-URL: repository, https://github.com/lukasz-migas/yoki5
+Classifier: Development Status :: 3 - Alpha
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Natural Language :: English
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.8
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Typing :: Typed
+Requires-Python: >=3.8
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: h5py
+Requires-Dist: hdf5plugin
+Requires-Dist: natsort
+Requires-Dist: loguru
+Requires-Dist: scipy
+Requires-Dist: koyo
+Requires-Dist: pandas<2
+Provides-Extra: test
+Requires-Dist: pytest>=6.0; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+Provides-Extra: dev
+Requires-Dist: black; extra == "dev"
+Requires-Dist: ipython; extra == "dev"
+Requires-Dist: mypy; extra == "dev"
+Requires-Dist: pdbpp; extra == "dev"
+Requires-Dist: pre-commit; extra == "dev"
+Requires-Dist: rich; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: yoki5[test]; extra == "dev"
+
+# yoki5
+
+[![License](https://img.shields.io/pypi/l/yoki5.svg?color=green)](https://github.com/lukasz-migas/yoki5/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/yoki5.svg?color=green)](https://pypi.org/project/yoki5)
+[![Python Version](https://img.shields.io/pypi/pyversions/yoki5.svg?color=green)](https://python.org)
+[![CI](https://github.com/lukasz-migas/yoki5/actions/workflows/ci.yml/badge.svg)](https://github.com/lukasz-migas/yoki5/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/lukasz-migas/yoki5/branch/main/graph/badge.svg)](https://codecov.io/gh/lukasz-migas/yoki5)
+
+## Overview
+
+A simple wrapper around h5py to give easier interface around complex HDF5 files.
+
+This library is designed to simplify the process of reading and writing HDF5 files by providing several methods
+that make it easy to add/remove datasets or groups. 
+
+## Getting started
+
+```python
+import numpy as np
+from yoki5.base import Store
+from scipy.sparse import csr_matrix
+
+# Create a new HDF5 file
+store = Store('path/to/file.h5')
+store.add_data_to_group(
+    "group-1",
+    {"data": np.random.rand(100, 100)},
+    {"attribute": "value"},
+    compression="gzip",
+    chunks=(10, 10),
+)
+# Retrieve the array
+array = store.get_array("group-1", "data")
+
+# Add sparse matrix
+store.add_data_to_group(
+    "group-2",
+    csr_matrix(np.random.randint(0, 255, (100, 100))),
+    {"attribute": "value"},
+)
+# Retrieve the data
+matrix = store.get_sparse_array("group-2")
+
+```
+
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/lukasz-migas/yoki5.git
+
+pip install -e .[dev]
+```

yoki5-0.1.0/README.md

@@ -0,0 +1,55 @@
+# yoki5
+
+[![License](https://img.shields.io/pypi/l/yoki5.svg?color=green)](https://github.com/lukasz-migas/yoki5/raw/main/LICENSE)
+[![PyPI](https://img.shields.io/pypi/v/yoki5.svg?color=green)](https://pypi.org/project/yoki5)
+[![Python Version](https://img.shields.io/pypi/pyversions/yoki5.svg?color=green)](https://python.org)
+[![CI](https://github.com/lukasz-migas/yoki5/actions/workflows/ci.yml/badge.svg)](https://github.com/lukasz-migas/yoki5/actions/workflows/ci.yml)
+[![codecov](https://codecov.io/gh/lukasz-migas/yoki5/branch/main/graph/badge.svg)](https://codecov.io/gh/lukasz-migas/yoki5)
+
+## Overview
+
+A simple wrapper around h5py to give easier interface around complex HDF5 files.
+
+This library is designed to simplify the process of reading and writing HDF5 files by providing several methods
+that make it easy to add/remove datasets or groups. 
+
+## Getting started
+
+```python
+import numpy as np
+from yoki5.base import Store
+from scipy.sparse import csr_matrix
+
+# Create a new HDF5 file
+store = Store('path/to/file.h5')
+store.add_data_to_group(
+    "group-1",
+    {"data": np.random.rand(100, 100)},
+    {"attribute": "value"},
+    compression="gzip",
+    chunks=(10, 10),
+)
+# Retrieve the array
+array = store.get_array("group-1", "data")
+
+# Add sparse matrix
+store.add_data_to_group(
+    "group-2",
+    csr_matrix(np.random.randint(0, 255, (100, 100))),
+    {"attribute": "value"},
+)
+# Retrieve the data
+matrix = store.get_sparse_array("group-2")
+
+```
+
+
+## Contributing
+
+Contributions are always welcome. Please feel free to submit PRs with new features, bug fixes, or documentation improvements.
+
+```bash
+git clone https://github.com/lukasz-migas/yoki5.git
+
+pip install -e .[dev]
+```