ComDAS 0.1.0__tar.gz

comdas-0.1.0/.github/workflows/docs.yml

@@ -0,0 +1,57 @@
+name: Documentation
+
+on:
+  push:
+    branches: [main]
+    paths:
+      - "docs/**"
+      - "comdas/**"
+      - ".github/workflows/docs.yml"
+  workflow_dispatch:
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Set up Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+          cache: pip
+
+      - name: Install package and documentation dependencies
+        run: python -m pip install --upgrade pip && python -m pip install -e ".[dev]"
+
+      - name: Configure GitHub Pages
+        uses: actions/configure-pages@v5
+
+      - name: Build documentation
+        run: sphinx-build --fail-on-warning docs docs/_build/html
+
+      - name: Upload GitHub Pages artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: docs/_build/html
+
+  deploy:
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    runs-on: ubuntu-latest
+    needs: build
+    steps:
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4

comdas-0.1.0/.github/workflows/publish.yml

@@ -0,0 +1,53 @@
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+
+permissions:
+  contents: read
+
+jobs:
+  release-build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: actions/setup-python@v5
+        with:
+          python-version: "3.x"
+
+      - name: Build release distributions
+        run: |
+          python -m pip install build
+          python -m build
+
+      - name: Upload distributions
+        uses: actions/upload-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+  pypi-publish:
+    runs-on: ubuntu-latest
+    needs:
+      - release-build
+    permissions:
+      id-token: write
+
+    environment:
+      name: pypi
+      url: https://pypi.org/project/ComDAS
+
+    steps:
+      - name: Retrieve release distributions
+        uses: actions/download-artifact@v4
+        with:
+          name: release-dists
+          path: dist/
+
+      - name: Publish release distributions to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1
+        with:
+          packages-dir: dist/

comdas-0.1.0/.github/workflows/testing.yml

@@ -0,0 +1,41 @@
+name: Run Tests
+
+on:
+    push:
+        branches: [main]
+        paths:
+            - "comdas/**"
+            - "tests/**"
+            - ".github/workflows/testing.yml"
+    pull_request:
+        branches: [main]
+
+permissions:
+    contents: read
+
+jobs:
+    build:
+        runs-on: ubuntu-latest
+        strategy:
+            matrix:
+                python-version: ["3.10", "3.11", "3.12", "3.13", "3.14"]
+        
+        steps:
+            - uses: actions/checkout@v4
+
+            - name: Set up Python
+              uses: actions/setup-python@v4
+              with:
+                  python-version: ${{ matrix.python-version }}
+
+            - name: Install dependencies
+              run: |
+                  python -m pip install --upgrade pip
+                  pip install .[dev]
+
+            - name: Lint with ruff
+              run: ruff check .
+
+            - name: Test with pytest
+              run: |
+                  pytest

comdas-0.1.0/.gitignore

@@ -0,0 +1,105 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# 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/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# logs:
+*.log
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# pyenv python configuration file
+.python-version
+.pdm-python
+
+# pycharm
+.idea
+
+# Ipython stuff
+.ipynb_checkpoints
+
+# linux/osx garbage
+*~
+*.swp
+.DS_store*
+
+# docs
+docs/api/generated/
+_autosummary
+.quarto/
+docs/site_libs
+docs/_quarto.yml
+.cross_ref.json
+
+# profile stuff from asv
+.asv
+.codspeed
+
+# misc
+scratch/**
+.ruff_cache
+uv.lock
+
+docs/index_files
+docs/index.quarto_ipynb
+
+# Agent stuff
+.claude
+CLAUDE.md
+.agents/worktrees/
+
+# profile stuff
+prof/
+
+# VSCode stuff
+.vscode/

comdas-0.1.0/ComDAS.egg-info/PKG-INFO

@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: ComDAS
+Version: 0.1.0
+Summary: DASCORE companion package that adds support for compressed DAS data
+Author-email: Byron-Selvage <bselvage@mines.edu>
+License: LGPL-3.0-or-later
+Keywords: dascore,compression,das,dasdae
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: dascore>=0.1.0
+Requires-Dist: h5py
+Requires-Dist: PyWavelets
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
+Requires-Dist: myst-nb; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Dynamic: license-file
+
+# ComDAS
+
+![Python versions tested](https://img.shields.io/badge/Python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue)
+
+ComDAS (Compressed DAS) lets you store and work with compressed distributed acoustic sensing (DAS) data using ordinary [DASCore](https://dascore.org/) tools.
+
+With ComDAS you can:
+
+- **Shrink DAS data in memory.** Compress a DASCore patch and keep using it like any other.
+- **Save compressed files.** Write patches, spools, or whole directories of raw data to a compressed HDF5 file or files.
+- **Read compressed files with plain DASCore.** Once ComDAS is installed, `dascore.spool()` opens compressed files directly without needing to know how the data was compressed.
+- **Choose your compression level.** Pick a codec and set how much detail to keep, from near-lossless to aggressive compression.
+- **Implement your own algorithm.** Add a new compression method by writing a codec class.
+
+> [!NOTE]
+> ComDAS is in active development. The file format and public API may change between releases.
+
+## Supported codecs
+
+| Codec | Main setting | Reference |
+| --- | --- | --- |
+| [SVD](https://byron-selvage.github.io/ComDAS/codecs/svd.html) | `rank` or retained `energy` | [NumPy SVD](https://numpy.org/doc/1.22/reference/generated/numpy.linalg.svd.html) |
+| [Wavelet](https://byron-selvage.github.io/ComDAS/codecs/wavelet.html) | `keep_fraction` or `threshold` | [PyWavelets](https://doi.org/10.21105/joss.01237); [DeVore et al. (1992)](https://doi.org/10.1109/18.119733) |
+
+## Installation
+
+ComDAS requires Python 3.10 or newer.
+
+```bash
+pip install comdas
+```
+
+## Documentation
+
+Full documentation is available at [byron-selvage.github.io/ComDAS](https://byron-selvage.github.io/ComDAS/), including:
+
+- [Quick start](https://byron-selvage.github.io/ComDAS/quickstart.html): compress a patch, save a compressed file, and read it back
+- [Codecs](https://byron-selvage.github.io/ComDAS/codecs/svd.html): configuration options and examples for each codec
+- [Examples](https://byron-selvage.github.io/ComDAS/examples/compression_comparison.html)
+- [API reference](https://byron-selvage.github.io/ComDAS/api/index.html)
+
+## License
+
+ComDAS is licensed under the [GNU Lesser General Public License](LICENSE).

comdas-0.1.0/ComDAS.egg-info/SOURCES.txt

@@ -0,0 +1,40 @@
+.gitignore
+LICENSE
+README.md
+pyproject.toml
+.github/workflows/docs.yml
+.github/workflows/publish.yml
+.github/workflows/testing.yml
+ComDAS.egg-info/PKG-INFO
+ComDAS.egg-info/SOURCES.txt
+ComDAS.egg-info/dependency_links.txt
+ComDAS.egg-info/entry_points.txt
+ComDAS.egg-info/requires.txt
+ComDAS.egg-info/top_level.txt
+comdas/__init__.py
+comdas/utils.py
+comdas/arrays/__init__.py
+comdas/arrays/duck_array.py
+comdas/codecs/__init__.py
+comdas/codecs/base.py
+comdas/codecs/svd.py
+comdas/codecs/wavelet.py
+comdas/io/__init__.py
+comdas/io/h5_container.py
+docs/Makefile
+docs/conf.py
+docs/index.rst
+docs/installation.rst
+docs/make.bat
+docs/quickstart.rst
+docs/api/index.rst
+docs/codecs/add_a_codec.rst
+docs/codecs/svd.rst
+docs/codecs/wavelet.rst
+docs/examples/compression_comparison.ipynb
+tests/__init__.py
+tests/_dummy_codec.py
+tests/test_codec_base.py
+tests/test_codecs.py
+tests/test_duck_array.py
+tests/test_h5_container.py

comdas-0.1.0/ComDAS.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

comdas-0.1.0/ComDAS.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[dascore.fiber_io]
+COMDAS__V1 = comdas.io.h5_container:ComdasV1

comdas-0.1.0/ComDAS.egg-info/requires.txt

@@ -0,0 +1,14 @@
+numpy>=1.24
+dascore>=0.1.0
+h5py
+PyWavelets
+
+[dev]
+pytest
+ruff
+sphinx
+furo
+sphinx-autodoc-typehints
+myst-nb
+matplotlib
+ipykernel

comdas-0.1.0/ComDAS.egg-info/top_level.txt

@@ -0,0 +1 @@
+comdas

comdas-0.1.0/LICENSE

@@ -0,0 +1,165 @@
+                   GNU LESSER GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+  This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+  0. Additional Definitions.
+
+  As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+  "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+  An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+  A "Combined Work" is a work produced by combining or linking an
+Application with the Library.  The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+  The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+  The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+  1. Exception to Section 3 of the GNU GPL.
+
+  You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+  2. Conveying Modified Versions.
+
+  If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+   a) under this License, provided that you make a good faith effort to
+   ensure that, in the event an Application does not supply the
+   function or data, the facility still operates, and performs
+   whatever part of its purpose remains meaningful, or
+
+   b) under the GNU GPL, with none of the additional permissions of
+   this License applicable to that copy.
+
+  3. Object Code Incorporating Material from Library Header Files.
+
+  The object code form of an Application may incorporate material from
+a header file that is part of the Library.  You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+   a) Give prominent notice with each copy of the object code that the
+   Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the object code with a copy of the GNU GPL and this license
+   document.
+
+  4. Combined Works.
+
+  You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+   a) Give prominent notice with each copy of the Combined Work that
+   the Library is used in it and that the Library and its use are
+   covered by this License.
+
+   b) Accompany the Combined Work with a copy of the GNU GPL and this license
+   document.
+
+   c) For a Combined Work that displays copyright notices during
+   execution, include the copyright notice for the Library among
+   these notices, as well as a reference directing the user to the
+   copies of the GNU GPL and this license document.
+
+   d) Do one of the following:
+
+       0) Convey the Minimal Corresponding Source under the terms of this
+       License, and the Corresponding Application Code in a form
+       suitable for, and under terms that permit, the user to
+       recombine or relink the Application with a modified version of
+       the Linked Version to produce a modified Combined Work, in the
+       manner specified by section 6 of the GNU GPL for conveying
+       Corresponding Source.
+
+       1) Use a suitable shared library mechanism for linking with the
+       Library.  A suitable mechanism is one that (a) uses at run time
+       a copy of the Library already present on the user's computer
+       system, and (b) will operate properly with a modified version
+       of the Library that is interface-compatible with the Linked
+       Version.
+
+   e) Provide Installation Information, but only if you would otherwise
+   be required to provide such information under section 6 of the
+   GNU GPL, and only to the extent that such information is
+   necessary to install and execute a modified version of the
+   Combined Work produced by recombining or relinking the
+   Application with a modified version of the Linked Version. (If
+   you use option 4d0, the Installation Information must accompany
+   the Minimal Corresponding Source and Corresponding Application
+   Code. If you use option 4d1, you must provide the Installation
+   Information in the manner specified by section 6 of the GNU GPL
+   for conveying Corresponding Source.)
+
+  5. Combined Libraries.
+
+  You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+   a) Accompany the combined library with a copy of the same work based
+   on the Library, uncombined with any other library facilities,
+   conveyed under the terms of this License.
+
+   b) Give prominent notice with the combined library that part of it
+   is a work based on the Library, and explaining where to find the
+   accompanying uncombined form of the same work.
+
+  6. Revised Versions of the GNU Lesser General Public License.
+
+  The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+  Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+  If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.

comdas-0.1.0/PKG-INFO

@@ -0,0 +1,69 @@
+Metadata-Version: 2.4
+Name: ComDAS
+Version: 0.1.0
+Summary: DASCORE companion package that adds support for compressed DAS data
+Author-email: Byron-Selvage <bselvage@mines.edu>
+License: LGPL-3.0-or-later
+Keywords: dascore,compression,das,dasdae
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy>=1.24
+Requires-Dist: dascore>=0.1.0
+Requires-Dist: h5py
+Requires-Dist: PyWavelets
+Provides-Extra: dev
+Requires-Dist: pytest; extra == "dev"
+Requires-Dist: ruff; extra == "dev"
+Requires-Dist: sphinx; extra == "dev"
+Requires-Dist: furo; extra == "dev"
+Requires-Dist: sphinx-autodoc-typehints; extra == "dev"
+Requires-Dist: myst-nb; extra == "dev"
+Requires-Dist: matplotlib; extra == "dev"
+Requires-Dist: ipykernel; extra == "dev"
+Dynamic: license-file
+
+# ComDAS
+
+![Python versions tested](https://img.shields.io/badge/Python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue)
+
+ComDAS (Compressed DAS) lets you store and work with compressed distributed acoustic sensing (DAS) data using ordinary [DASCore](https://dascore.org/) tools.
+
+With ComDAS you can:
+
+- **Shrink DAS data in memory.** Compress a DASCore patch and keep using it like any other.
+- **Save compressed files.** Write patches, spools, or whole directories of raw data to a compressed HDF5 file or files.
+- **Read compressed files with plain DASCore.** Once ComDAS is installed, `dascore.spool()` opens compressed files directly without needing to know how the data was compressed.
+- **Choose your compression level.** Pick a codec and set how much detail to keep, from near-lossless to aggressive compression.
+- **Implement your own algorithm.** Add a new compression method by writing a codec class.
+
+> [!NOTE]
+> ComDAS is in active development. The file format and public API may change between releases.
+
+## Supported codecs
+
+| Codec | Main setting | Reference |
+| --- | --- | --- |
+| [SVD](https://byron-selvage.github.io/ComDAS/codecs/svd.html) | `rank` or retained `energy` | [NumPy SVD](https://numpy.org/doc/1.22/reference/generated/numpy.linalg.svd.html) |
+| [Wavelet](https://byron-selvage.github.io/ComDAS/codecs/wavelet.html) | `keep_fraction` or `threshold` | [PyWavelets](https://doi.org/10.21105/joss.01237); [DeVore et al. (1992)](https://doi.org/10.1109/18.119733) |
+
+## Installation
+
+ComDAS requires Python 3.10 or newer.
+
+```bash
+pip install comdas
+```
+
+## Documentation
+
+Full documentation is available at [byron-selvage.github.io/ComDAS](https://byron-selvage.github.io/ComDAS/), including:
+
+- [Quick start](https://byron-selvage.github.io/ComDAS/quickstart.html): compress a patch, save a compressed file, and read it back
+- [Codecs](https://byron-selvage.github.io/ComDAS/codecs/svd.html): configuration options and examples for each codec
+- [Examples](https://byron-selvage.github.io/ComDAS/examples/compression_comparison.html)
+- [API reference](https://byron-selvage.github.io/ComDAS/api/index.html)
+
+## License
+
+ComDAS is licensed under the [GNU Lesser General Public License](LICENSE).

comdas-0.1.0/README.md

@@ -0,0 +1,44 @@
+# ComDAS
+
+![Python versions tested](https://img.shields.io/badge/Python-3.10%20%7C%203.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue)
+
+ComDAS (Compressed DAS) lets you store and work with compressed distributed acoustic sensing (DAS) data using ordinary [DASCore](https://dascore.org/) tools.
+
+With ComDAS you can:
+
+- **Shrink DAS data in memory.** Compress a DASCore patch and keep using it like any other.
+- **Save compressed files.** Write patches, spools, or whole directories of raw data to a compressed HDF5 file or files.
+- **Read compressed files with plain DASCore.** Once ComDAS is installed, `dascore.spool()` opens compressed files directly without needing to know how the data was compressed.
+- **Choose your compression level.** Pick a codec and set how much detail to keep, from near-lossless to aggressive compression.
+- **Implement your own algorithm.** Add a new compression method by writing a codec class.
+
+> [!NOTE]
+> ComDAS is in active development. The file format and public API may change between releases.
+
+## Supported codecs
+
+| Codec | Main setting | Reference |
+| --- | --- | --- |
+| [SVD](https://byron-selvage.github.io/ComDAS/codecs/svd.html) | `rank` or retained `energy` | [NumPy SVD](https://numpy.org/doc/1.22/reference/generated/numpy.linalg.svd.html) |
+| [Wavelet](https://byron-selvage.github.io/ComDAS/codecs/wavelet.html) | `keep_fraction` or `threshold` | [PyWavelets](https://doi.org/10.21105/joss.01237); [DeVore et al. (1992)](https://doi.org/10.1109/18.119733) |
+
+## Installation
+
+ComDAS requires Python 3.10 or newer.
+
+```bash
+pip install comdas
+```
+
+## Documentation
+
+Full documentation is available at [byron-selvage.github.io/ComDAS](https://byron-selvage.github.io/ComDAS/), including:
+
+- [Quick start](https://byron-selvage.github.io/ComDAS/quickstart.html): compress a patch, save a compressed file, and read it back
+- [Codecs](https://byron-selvage.github.io/ComDAS/codecs/svd.html): configuration options and examples for each codec
+- [Examples](https://byron-selvage.github.io/ComDAS/examples/compression_comparison.html)
+- [API reference](https://byron-selvage.github.io/ComDAS/api/index.html)
+
+## License
+
+ComDAS is licensed under the [GNU Lesser General Public License](LICENSE).