barecat 0.2.5__tar.gz

barecat-0.2.5/.github/workflows/python-publish.yml

@@ -0,0 +1,35 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  pypi-publish:
+    name: Upload release to PyPI
+    runs-on: ubuntu-latest
+    environment: pypi
+    permissions:
+      id-token: write
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Install build dependencies
+        run: python -m pip install --upgrade build
+
+      - name: Build package distribution
+        run: python -m build --sdist
+
+      - name: Publish package distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

barecat-0.2.5/.gitignore

@@ -0,0 +1,162 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+*_cython.c
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

barecat-0.2.5/.readthedocs.yaml

@@ -0,0 +1,13 @@
+version: 2
+
+build:
+  os: ubuntu-24.04
+  tools:
+    python: "3.10"
+  commands:
+    - python -m pip install .
+    - python -m pip install --no-cache-dir -r docs/requirements.txt
+    - python -m sphinx -E -b html docs $READTHEDOCS_OUTPUT/html
+
+sphinx:
+   configuration: docs/conf.py

barecat-0.2.5/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2023 István Sárándi
+
+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.

barecat-0.2.5/MANIFEST.in

@@ -0,0 +1 @@
+include src/barecat/sql/*.sql

barecat-0.2.5/PKG-INFO

@@ -0,0 +1,181 @@
+Metadata-Version: 2.4
+Name: barecat
+Version: 0.2.5
+Summary: Scalable archive format for storing millions of small files with random access and SQLite indexing.
+Author-email: István Sárándi <istvan.sarandi@gmail.com>
+License: MIT License
+        
+        Copyright (c) 2023 István Sárándi
+        
+        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.
+        
+Project-URL: Homepage, https://github.com/isarandi/barecat
+Project-URL: Documentation, https://istvansarandi.com/docs/barecat/api/barecat/Barecat.html
+Project-URL: Repository, https://github.com/isarandi/barecat
+Project-URL: Issues, https://github.com/isarandi/barecat/issues
+Project-URL: Author, https://istvansarandi.com
+Keywords: sqlite,dataset,storage,archive,random-access,image-dataset,filesystem,key-value-store,deep-learning,data-loader,file-indexing
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering :: Information Analysis
+Classifier: Topic :: Software Development :: Libraries
+Classifier: Topic :: System :: Archiving
+Classifier: Topic :: System :: Filesystems
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Cython
+Classifier: Operating System :: POSIX :: Linux
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: multiprocessing-utils
+Requires-Dist: tqdm
+Requires-Dist: crc32c
+Dynamic: license-file
+
+# Barecat
+
+**[Full API Reference Docs](https://istvansarandi.com/docs/barecat/api/barecat/Barecat.html)**
+
+Barecat (**bare** con**cat**enation) is a highly scalable, simple aggregate storage format for
+storing many (tens of millions and more) small files, with focus on fast random access and 
+minimal overhead.
+
+Barecat can be thought of as a simple filesystem, or as something akin to an indexed tarball, or a
+key-value store. Indeed, it can be [mounted via FUSE](https://github.com/isarandi/barecat-mount), converted to a tarball, or used like a dictionary
+within Python.
+
+Barecat associates strings (file paths) with binary data (file contents). It's like a dictionary,
+but it has some special handling for '/' characters in the keys, supporting a filesystem-like
+experience (`listdir`, `walk`, `glob`, etc).
+
+Internally, all the data is simply concatenated one after another into one or more data shard files.
+Additionally, an index is maintained in an SQLite database, which stores the shard number, the offset
+and the size of each inner file (as well as a checksum, and further filesystem-like metadata 
+like modification time). Barecat also maintains aggregate statistics for each directory, such as the
+total number of files and total file size.
+
+
+![Architecture](./figure.png)
+
+As you can see, the Barecat format is very simple. Readers/writers are easy to write in any language, since
+SQLite is a widely-supported format.
+
+
+## Background
+
+A typical use case for Barecat is storing image files for training deep learning models, where the
+files are accessed randomly during training. The files are typically stored on a network file
+system, where accessing many small files can be slow, and clusters often put a limit on the number
+of files of a user. So it is necessary to somehow merge the small files into big ones.
+However, typical archive formats such as tar are not suitable, since they don't allow fast random
+lookups. In tar, one has to scan the entire archive as there is no central directory.
+Zip is better, but still requires scanning the central directory, which can be slow for very large
+archives with millions or tens of millions of files.
+
+We need an index into the archive, and the index itself cannot be required to be loaded
+into memory, to support very large datasets.
+
+Therefore, in this format the metadata is indexed separately in an SQLite database for fast lookup
+based on paths. The index also allows fast listing of directory contents and contains aggregate
+statistics (total file size, number of files) for each directory.
+
+## Features
+
+- **Fast random access**: The archive can be accessed randomly, addressed by filepath,
+  without having to scan the entire archive or all the metadata.
+  The index is stored in a separate SQLite database file, which itself does not need to be loaded
+  entirely into memory. Ideal for storing training image data for deep learning jobs.
+- **Sharding**: To make it easier to move the data around or to distribute it across multiple
+  storage devices, the archive can be split into multiple files of equal size (shards, or volumes). 
+  The shards do not have to be concatenated to be used, the library will keep all shard files open
+  and load data from the appropriate one during normal operations.
+- **Fast browsing**: The SQLite database contains an index for the parent directories, allowing
+  fast listing of directory contents and aggregate statistics (total file size, number of files).
+- **Intuitive API**: Familiar filesystem-like API, as well as a dictionary-like one.
+- **Mountable**: The archive can be efficiently mounted in readonly or read-write mode.
+- **Simple storage format**: The files are simply concatenated after each other and the index contains
+  the offsets and sizes of each file. There is no header format to understand. The index can be
+  dumped into any format with simple SQL queries.
+
+## Command line interface
+
+To create a Barecat archive, use the `barecat-create` or `barecat-create-recursive` commands, which 
+are automatically installed executables with the pip package.
+
+```bash
+barecat-create --file=mydata.barecat --shard-size=100G < path_of_paths.txt 
+
+find dirname -name '*.jpg' -print0 | barecat-create --null --file=mydata.barecat --shard-size=100G
+
+barecat-create-recursive dir1 dir2 dir3 --file=mydata.barecat --shard-size=100G
+```
+
+This may yield the following files:
+
+```
+mydata.barecat-shard-00001
+mydata.barecat-shard-00002
+mydata.barecat-sqlite-index
+```
+
+The files can be extracted out again. Unix-like permissions, modification times, owner info are
+preserved.
+
+```bash
+barecat-extract --file=mydata.barecat --target-directory=targetdir/
+```
+
+## Python API
+
+```python
+
+import barecat
+
+with barecat.Barecat('mydata.barecat', readonly=False) as bc:
+  bc['path/to/file/as/stored.jpg'] = binary_file_data
+  bc.add_by_path('path/to/file/on/disk.jpg')
+  
+  with open('path', 'rb') as f:
+    bc.add('path/to/file/on/disk.jpg', fileobj=f)
+    
+with barecat.Barecat('mydata.barecat') as bc:
+  binary_file_data = bc['path/to/file.jpg']
+  entrynames = bc.listdir('path/to')
+  for root, dirs, files in bc.walk('path/to/something'):
+    print(root, dirs, files)
+    
+  paths = bc.glob('path/to/**/*.jpg', recursive=True)
+  
+  with bc.open('path/to/file.jpg', 'rb') as f:
+    data = f.read(123)
+```
+
+## Image viewer
+
+Barecat comes with a simple image viewer that can be used to browse the contents of a Barecat
+archive.
+
+```bash
+barecat-image-viewer mydata.barecat
+```
+
+ 

barecat-0.2.5/README.md

@@ -0,0 +1,128 @@
+# Barecat
+
+**[Full API Reference Docs](https://istvansarandi.com/docs/barecat/api/barecat/Barecat.html)**
+
+Barecat (**bare** con**cat**enation) is a highly scalable, simple aggregate storage format for
+storing many (tens of millions and more) small files, with focus on fast random access and 
+minimal overhead.
+
+Barecat can be thought of as a simple filesystem, or as something akin to an indexed tarball, or a
+key-value store. Indeed, it can be [mounted via FUSE](https://github.com/isarandi/barecat-mount), converted to a tarball, or used like a dictionary
+within Python.
+
+Barecat associates strings (file paths) with binary data (file contents). It's like a dictionary,
+but it has some special handling for '/' characters in the keys, supporting a filesystem-like
+experience (`listdir`, `walk`, `glob`, etc).
+
+Internally, all the data is simply concatenated one after another into one or more data shard files.
+Additionally, an index is maintained in an SQLite database, which stores the shard number, the offset
+and the size of each inner file (as well as a checksum, and further filesystem-like metadata 
+like modification time). Barecat also maintains aggregate statistics for each directory, such as the
+total number of files and total file size.
+
+
+![Architecture](./figure.png)
+
+As you can see, the Barecat format is very simple. Readers/writers are easy to write in any language, since
+SQLite is a widely-supported format.
+
+
+## Background
+
+A typical use case for Barecat is storing image files for training deep learning models, where the
+files are accessed randomly during training. The files are typically stored on a network file
+system, where accessing many small files can be slow, and clusters often put a limit on the number
+of files of a user. So it is necessary to somehow merge the small files into big ones.
+However, typical archive formats such as tar are not suitable, since they don't allow fast random
+lookups. In tar, one has to scan the entire archive as there is no central directory.
+Zip is better, but still requires scanning the central directory, which can be slow for very large
+archives with millions or tens of millions of files.
+
+We need an index into the archive, and the index itself cannot be required to be loaded
+into memory, to support very large datasets.
+
+Therefore, in this format the metadata is indexed separately in an SQLite database for fast lookup
+based on paths. The index also allows fast listing of directory contents and contains aggregate
+statistics (total file size, number of files) for each directory.
+
+## Features
+
+- **Fast random access**: The archive can be accessed randomly, addressed by filepath,
+  without having to scan the entire archive or all the metadata.
+  The index is stored in a separate SQLite database file, which itself does not need to be loaded
+  entirely into memory. Ideal for storing training image data for deep learning jobs.
+- **Sharding**: To make it easier to move the data around or to distribute it across multiple
+  storage devices, the archive can be split into multiple files of equal size (shards, or volumes). 
+  The shards do not have to be concatenated to be used, the library will keep all shard files open
+  and load data from the appropriate one during normal operations.
+- **Fast browsing**: The SQLite database contains an index for the parent directories, allowing
+  fast listing of directory contents and aggregate statistics (total file size, number of files).
+- **Intuitive API**: Familiar filesystem-like API, as well as a dictionary-like one.
+- **Mountable**: The archive can be efficiently mounted in readonly or read-write mode.
+- **Simple storage format**: The files are simply concatenated after each other and the index contains
+  the offsets and sizes of each file. There is no header format to understand. The index can be
+  dumped into any format with simple SQL queries.
+
+## Command line interface
+
+To create a Barecat archive, use the `barecat-create` or `barecat-create-recursive` commands, which 
+are automatically installed executables with the pip package.
+
+```bash
+barecat-create --file=mydata.barecat --shard-size=100G < path_of_paths.txt 
+
+find dirname -name '*.jpg' -print0 | barecat-create --null --file=mydata.barecat --shard-size=100G
+
+barecat-create-recursive dir1 dir2 dir3 --file=mydata.barecat --shard-size=100G
+```
+
+This may yield the following files:
+
+```
+mydata.barecat-shard-00001
+mydata.barecat-shard-00002
+mydata.barecat-sqlite-index
+```
+
+The files can be extracted out again. Unix-like permissions, modification times, owner info are
+preserved.
+
+```bash
+barecat-extract --file=mydata.barecat --target-directory=targetdir/
+```
+
+## Python API
+
+```python
+
+import barecat
+
+with barecat.Barecat('mydata.barecat', readonly=False) as bc:
+  bc['path/to/file/as/stored.jpg'] = binary_file_data
+  bc.add_by_path('path/to/file/on/disk.jpg')
+  
+  with open('path', 'rb') as f:
+    bc.add('path/to/file/on/disk.jpg', fileobj=f)
+    
+with barecat.Barecat('mydata.barecat') as bc:
+  binary_file_data = bc['path/to/file.jpg']
+  entrynames = bc.listdir('path/to')
+  for root, dirs, files in bc.walk('path/to/something'):
+    print(root, dirs, files)
+    
+  paths = bc.glob('path/to/**/*.jpg', recursive=True)
+  
+  with bc.open('path/to/file.jpg', 'rb') as f:
+    data = f.read(123)
+```
+
+## Image viewer
+
+Barecat comes with a simple image viewer that can be used to browse the contents of a Barecat
+archive.
+
+```bash
+barecat-image-viewer mydata.barecat
+```
+
+ 

barecat-0.2.5/docs/Makefile

@@ -0,0 +1,20 @@
+# Minimal makefile for Sphinx documentation
+#
+
+# You can set these variables from the command line, and also
+# from the environment for the first two.
+SPHINXOPTS    ?=
+SPHINXBUILD   ?= sphinx-build
+SOURCEDIR     = .
+BUILDDIR      = _build
+
+# Put it first so that "make" without argument is like "make help".
+help:
+	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+
+.PHONY: help Makefile
+
+# Catch-all target: route all unknown targets to Sphinx using the new
+# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
+%: Makefile
+	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)

barecat-0.2.5/docs/_static/styles/my_theme.css

@@ -0,0 +1,76 @@
+@import url("theme.css");
+@import url("https://fonts.googleapis.com/css2?family=Mona+Sans:ital,wght@0,200..900;1,200..900&family=Geist:wght@100..900&&family=JetBrains+Mono:ital,wght@0,100..800;1,100..800&family=Outfit:wght@100..900&display=swap");
+
+/*@media (min-width: 960px) {
+    .bd-page-width {
+        max-width: 120rem;
+    }
+}*/
+
+#rtd-footer-container {
+    margin-top: 0 !important;
+}
+
+html[data-theme="light"] {
+    --pst-color-table-row-hover-bg: #dfc6ff;
+    --pst-color-link-hover: #845818;
+}
+
+html[data-theme="dark"] {
+    --pst-color-table-row-hover-bg: #41296c;
+    --pst-color-inline-code: #dd8cd4;
+}
+
+
+html[data-theme="dark"] dt:target {
+    background-color: #4f4500;
+}
+
+html[data-theme="dark"] .linkcode-link {
+    color: #9090ff;
+}
+
+html[data-theme="dark"] table.indextable tr.cap {
+    background-color: #464646;
+}
+
+html[data-theme="dark"] a:visited {
+    color: #9E67D0;
+}
+
+.navbar-brand .logo__title {
+    font-family: "Mona Sans", sans-serif;
+    font-size: 2.5rem;
+    font-weight: 400;
+    font-style: normal;
+}
+
+:root {
+    --pst-font-family-monospace: "JetBrains Mono", monospace;
+    --pst-font-family-heading: "Mona Sans", sans-serif;
+    --pst-font-family-base: "Mona Sans", sans-serif;
+}
+
+body {
+    font-weight: 450;
+}
+
+.bd-main .bd-content .bd-article-container {
+  max-width: 100%;  /* default is 60em */
+}
+
+/*.bd-sidebar-primary {
+    max-width: 20%;
+}*/
+
+/* Ensure links in code blocks are underlined */
+.highlight a {
+    text-decoration: underline;
+    color: #394198; /* Adjust color as needed */
+}
+
+/* For additional emphasis, change hover effect */
+.highlight a:hover {
+    text-decoration: underline;
+    color: #9090ff;
+}

barecat-0.2.5/docs/_templates/autoapi/index.rst

@@ -0,0 +1,11 @@
+API Reference
+=============
+
+Start at :class:`barecat.Barecat` to explore the API.
+
+.. toctree::
+   :titlesonly:
+
+   {% for page in pages|selectattr("is_top_level_object") %}
+   {{ page.include_path }}
+   {% endfor %}

barecat-0.2.5/docs/_templates/autoapi/python/attribute.rst

@@ -0,0 +1 @@
+{% extends "python/data.rst" %}