uvotredux 0.1.0__tar.gz

uvotredux-0.1.0/.github/dependabot.yml

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+# To get started with Dependabot version updates, you'll need to specify which
+# package ecosystems to update and where the package manifests are located.
+# Please see the documentation for all configuration options:
+# https://help.github.com/github/administering-a-repository/configuration-options-for-dependency-updates
+
+version: 2
+updates:
+  - package-ecosystem: "pip" # See documentation for possible values
+    directory: "/" # Location of package manifests
+    schedule:
+      interval: "weekly"

uvotredux-0.1.0/.github/workflows/automerge.yml

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+name: Dependabot auto-merge
+
+on:
+  pull_request:
+  merge_group:
+
+permissions:
+  pull-requests: write
+  contents: write
+
+jobs:
+  automerge:
+    runs-on: ubuntu-latest
+    if: ${{ github.actor == 'dependabot[bot]' }}
+    steps:
+      - name: Dependabot metadata
+        id: metadata
+        uses: dependabot/fetch-metadata@v1.1.1
+        with:
+          github-token: "${{ secrets.GITHUB_TOKEN }}"
+
+      - name: Echo auto-merge
+        run: echo "Update type is ${{steps.metadata.outputs.update-type}}, check is ${{contains(steps.metadata.outputs.update-type,'version-update:semver')}}"
+
+      - name: Enable auto-merge for Dependabot PRs
+        if: ${{contains(steps.metadata.outputs.update-type,'version-update:semver')}}
+        run: gh pr merge --auto --squash "$PR_URL"
+        env:
+          PR_URL: ${{github.event.pull_request.html_url}}
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}

uvotredux-0.1.0/.github/workflows/black.yml

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+name: Black
+
+on: [push, pull_request]
+
+jobs:
+  black:
+
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install --editable ".[dev]"
+      - name: Reformat the code with black
+        run: |
+          black . --check

uvotredux-0.1.0/.github/workflows/continuous_integration.yml

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+# This is a basic workflow to help you get started with Actions
+
+name: CI
+
+# Controls when the action will run.
+on:
+  # Triggers the workflow on push or pull request events
+  push:
+
+  pull_request:
+
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+# A workflow run is made up of one or more jobs that can run sequentially or in parallel
+jobs:
+  # This workflow contains a single job called "build"
+  build:
+    # The type of runner that the job will run on
+    runs-on: ubuntu-latest
+
+    # Specify the python versions to test
+    strategy:
+      matrix:
+        python-version: ["3.12"]
+
+    # Steps represent a sequence of tasks that will be executed as part of the job
+    steps:
+      - uses: actions/checkout@v3
+
+      # Set up the python versions
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+
+      - name: install packages
+        run: |
+          pip install --editable ".[dev]"
+
+      - name: Echo tag name
+        run: echo "Tag is ${{ github.ref }}, Tagged is ${{ startsWith(github.ref, 'refs/tags/')}}, Python Check is ${{matrix.python-version == 3.12}},  Deploy is ${{ startsWith(github.ref, 'refs/tags/') && matrix.python-version == 3.12}}"
+
+      - name: Install pypa/build
+        run: >-
+          python -m
+          pip install
+          build
+          --user
+      - name: Build a binary wheel and a source tarball
+        run: >-
+          python -m
+          build
+          --sdist
+          --wheel
+          --outdir dist/
+          .
+
+      - name: Publish distribution 📦 to PyPI
+        if: ${{ startsWith(github.ref, 'refs/tags/') && success() && matrix.python-version == 3.12 && github.event_name == 'push'}}
+        uses: pypa/gh-action-pypi-publish@master
+        with:
+          password: ${{ secrets.PYPI_API_TOKEN }}

uvotredux-0.1.0/.github/workflows/isort.yml

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+name: Run isort
+
+on: [push, pull_request]
+
+jobs:
+  isort:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v4
+      with:
+        python-version: 3.12
+        cache: 'pip'
+        cache-dependency-path: pyproject.toml
+    - name: Install dependencies
+      run: |
+        pip install --upgrade pip
+        pip install --editable ".[dev]"
+    - name: isort
+      uses: isort/isort-action@v1.0.0

uvotredux-0.1.0/.github/workflows/pylint.yml

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+name: Pylint
+
+on: [push, pull_request]
+
+jobs:
+  pylint:
+
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.12
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.12
+          cache: 'pip'
+          cache-dependency-path: pyproject.toml
+      - name: Install dependencies
+        run: |
+          pip install --upgrade pip
+          pip install --editable ".[dev]"
+      - name: Analysing the code with pylint
+        run: |
+           pylint uvotredux --fail-under=10.00

uvotredux-0.1.0/.gitignore

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+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+*.idea
+
+# 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/
+
+# 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/

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

@@ -0,0 +1,33 @@
+repos:
+-   repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v2.3.0
+    hooks:
+    -   id: check-yaml
+    -   id: end-of-file-fixer
+-   repo: local
+    hooks:
+    -   id: black
+        name: black
+        entry: black
+        language: system
+        types: [ python ]
+-   repo: local
+    hooks:
+      - id: isort
+        name: isort (python)
+        entry: isort
+        language: system
+        types: [ python ]
+-   repo: local
+    hooks:
+      - id: pylint
+        name: pylint
+        entry: pylint
+        language: system
+        types: [python]
+        args:
+          [
+            "-rn", # Only display messages
+            "-sn", # Don't display the score
+          ]
+        verbose: true

uvotredux-0.1.0/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Robert David Stein
+
+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.

uvotredux-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: uvotredux
+Version: 0.1.0
+Summary: CLI to reduce Swift UVOT data
+Author-email: Robert Stein <rdstein@caltech.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/robertdstein/uvotredux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pathlib
+Requires-Dist: pre-commit
+Provides-Extra: dev
+Requires-Dist: black==24.2.0; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
+Requires-Dist: pylint==3.1.0; extra == "dev"
+
+# uvotredux

uvotredux-0.1.0/README.md

@@ -0,0 +1 @@
+# uvotredux

uvotredux-0.1.0/pyproject.toml

@@ -0,0 +1,59 @@
+[build-system]
+requires = ["setuptools>=45", "setuptools-scm"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "uvotredux"
+version = "0.1.0"
+description = "CLI to reduce Swift UVOT data"
+authors = [
+    {name = "Robert Stein", email = "rdstein@caltech.edu"}
+]
+license = {text = "MIT"}
+readme = "README.md"
+requires-python = ">=3.10"
+classifiers = [
+    "Programming Language :: Python :: 3",
+    'Programming Language :: Python :: 3.10',
+    'Programming Language :: Python :: 3.11',
+    'Programming Language :: Python :: 3.12',
+    'Intended Audience :: Science/Research',
+    'Intended Audience :: End Users/Desktop',
+    'Intended Audience :: Developers',
+    'Natural Language :: English',
+    'Topic :: Scientific/Engineering',
+    'Topic :: Scientific/Engineering :: Astronomy',
+    'Topic :: Scientific/Engineering :: Physics',
+    'Operating System :: POSIX',
+    'Operating System :: Unix',
+    'Operating System :: MacOS',
+]
+dependencies = [
+    "pathlib",
+    "pre-commit"
+]
+[project.optional-dependencies]
+dev = [
+    "black == 24.2.0",
+    "isort == 5.13.2",
+    "pylint == 3.1.0",
+]
+
+[project.urls]
+Homepage = "https://github.com/robertdstein/uvotredux"
+
+[project.scripts]
+uvotredux = "uvotredux.run:main"
+
+[tool.setuptools]
+packages = ["uvotredux"]
+
+[tool.isort]
+profile = "black"
+
+[tool.pylint.format]
+max-line-length = "88"
+disable=["logging-fstring-interpolation"]
+good-names=["ax", "ra", "df", "pi", "i"]
+exclude-too-few-public-methods=["pydantic.*"]
+extension-pkg-whitelist=["pydantic"]

uvotredux-0.1.0/setup.cfg

@@ -0,0 +1,4 @@
+[egg_info]
+tag_build = 
+tag_date = 0
+

uvotredux-0.1.0/uvotredux/__init__.py

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+"""
+This module contains the main functions for reducing Swift UVOT data.
+"""
+
+from uvotredux.reduce import unpack_swift_directory, unpack_swift_obs

uvotredux-0.1.0/uvotredux/reduce.py

@@ -0,0 +1,128 @@
+"""
+Created by Brad Cenko
+
+Updated by Robert Stein on 2024-03-08 to use python3, pathlib, f-strings and gzip
+"""
+
+import gzip
+import logging
+import subprocess
+from pathlib import Path
+
+logger = logging.getLogger(__name__)
+
+filter_dict = {
+    "vv": "V",
+    "bb": "B",
+    "uu": "U",
+    "w1": "UW1",
+    "m2": "UM2",
+    "w2": "UW2",
+    "wh": "W",
+}
+
+
+def unpack_swift_obs(
+    swift_obs_dir: Path,
+    src_region_path: Path,
+    bkg_region_path: Path,
+):
+    """
+    Function to unpack the swift observation and create the uvot images
+
+    :param swift_obs_dir: Single swift observation directory
+    :param src_region_path: Path to the source region file
+    :param bkg_region_path: Path to the background region file
+    :return: None
+    """
+    uvot_dir = swift_obs_dir / "uvot/image"
+
+    swift_images = [x for x in uvot_dir.glob("*_sk.img") if x.is_file()]
+    swift_compressed_images = [x for x in uvot_dir.glob("*_sk.img.gz") if x.is_file()]
+
+    for image in swift_compressed_images:
+        uncompressed_image = image.with_suffix("")
+        if not uncompressed_image.is_file():
+            logger.info(f"Uncompressing image: {image}")
+            with gzip.open(image, "rb") as f_in:
+                with open(uncompressed_image, "wb") as f_out:
+                    f_out.write(f_in.read())
+            swift_images.append(uncompressed_image)
+
+    for image in swift_images:
+        uvot_filter = filter_dict[image.name[14:16]]
+        uvot_save_path = uvot_dir / f"{uvot_filter}.fits"
+        cmd = f"uvotimsum {image} {uvot_save_path}"
+        if uvot_save_path.is_file():
+            logger.info(f"UVOT image already exists: {uvot_save_path}")
+        else:
+            subprocess.run(cmd, shell=True, check=True)
+            logger.info(f"UVOT image created at: {uvot_save_path}")
+
+        if not uvot_save_path.is_file():
+            logger.error(f"UVOT image not created: {uvot_save_path}")
+            logger.error(f"Command: {cmd}")
+            raise FileNotFoundError(f"UVOT image not created: {uvot_save_path}")
+
+        output_path = uvot_dir / f"{uvot_filter}.out"
+
+        cmd = (
+            f"uvotsource image={uvot_save_path} srcreg={src_region_path} "
+            f"bkgreg={bkg_region_path} sigma=3.0 outfile={output_path} "
+            f"syserr=yes output=ALL apercorr=CURVEOFGROWTH "
+            f"> {output_path.with_suffix('.log')}"
+        )
+
+        if output_path.is_file():
+            logger.info(f"UVOT source data already exists: {output_path}")
+        else:
+            subprocess.run(cmd, shell=True, check=True)
+            logger.info(f"UVOT source data created at: {output_path}")
+
+        if not output_path.is_file():
+            logger.error(f"UVOT source data not created: {output_path}")
+            logger.error(f"Command: {cmd}")
+            raise FileNotFoundError(f"UVOT source data not created: {output_path}")
+
+
+def unpack_swift_directory(
+    directory: Path | None = None,
+    src_region_path: Path | None = None,
+    bkg_region_path: Path | None = None,
+):
+    """
+    Function to unpack all the swift observations in a directory
+
+    :param directory: Directory containing the swift observations
+    :param src_region_path: Path to the source region file
+    :param bkg_region_path: Path to the background region file
+    :return: None
+    """
+
+    if directory is None:
+        directory = Path.cwd()
+
+    all_swift_obs = [
+        x for x in directory.glob("*") if (x.is_dir()) & (len(x.name) == 11)
+    ]
+
+    if src_region_path is None:
+        src_region_path = directory / "src.reg"
+        logger.info(f"Source region path not provided, using {src_region_path}")
+
+    if not src_region_path.is_file():
+        raise FileNotFoundError(f"Region file {src_region_path} not found")
+
+    if bkg_region_path is None:
+        bkg_region_path = directory / "bkg.reg"
+        logger.info(f"Background region path not provided, using {bkg_region_path}")
+
+    if not bkg_region_path.is_file():
+        raise FileNotFoundError(f"Region file {bkg_region_path} not found")
+
+    for swift_obs in sorted(all_swift_obs):
+        unpack_swift_obs(
+            swift_obs,
+            src_region_path=src_region_path,
+            bkg_region_path=bkg_region_path,
+        )

uvotredux-0.1.0/uvotredux/run.py

@@ -0,0 +1,33 @@
+"""
+Wrapper script to run the swift reduction on a directory using command line arguments
+"""
+
+import argparse
+import logging
+
+from uvotredux.reduce import unpack_swift_directory
+
+logging.basicConfig(level=logging.INFO)
+
+
+def main():
+    """
+    Function to run the swift reduction on a directory
+
+    :return: None
+    """
+
+    parser = argparse.ArgumentParser(description="Unpack a Swift UVOT observation")
+    parser.add_argument(
+        "-d", "--swift_obs_dir", help="Path to the base Swift observation directory"
+    )
+    parser.add_argument(
+        "-s", "--src_region_path", help="Path to the source region file"
+    )
+    parser.add_argument(
+        "-b", "--bkg_region_path", help="Path to the background region file"
+    )
+    args = parser.parse_args()
+    unpack_swift_directory(
+        args.swift_obs_dir, args.src_region_path, args.bkg_region_path
+    )

uvotredux-0.1.0/uvotredux.egg-info/PKG-INFO

@@ -0,0 +1,32 @@
+Metadata-Version: 2.1
+Name: uvotredux
+Version: 0.1.0
+Summary: CLI to reduce Swift UVOT data
+Author-email: Robert Stein <rdstein@caltech.edu>
+License: MIT
+Project-URL: Homepage, https://github.com/robertdstein/uvotredux
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: End Users/Desktop
+Classifier: Intended Audience :: Developers
+Classifier: Natural Language :: English
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Scientific/Engineering :: Astronomy
+Classifier: Topic :: Scientific/Engineering :: Physics
+Classifier: Operating System :: POSIX
+Classifier: Operating System :: Unix
+Classifier: Operating System :: MacOS
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: pathlib
+Requires-Dist: pre-commit
+Provides-Extra: dev
+Requires-Dist: black==24.2.0; extra == "dev"
+Requires-Dist: isort==5.13.2; extra == "dev"
+Requires-Dist: pylint==3.1.0; extra == "dev"
+
+# uvotredux

uvotredux-0.1.0/uvotredux.egg-info/SOURCES.txt

@@ -0,0 +1,20 @@
+.gitignore
+.pre-commit-config.yaml
+LICENSE
+README.md
+pyproject.toml
+.github/dependabot.yml
+.github/workflows/automerge.yml
+.github/workflows/black.yml
+.github/workflows/continuous_integration.yml
+.github/workflows/isort.yml
+.github/workflows/pylint.yml
+uvotredux/__init__.py
+uvotredux/reduce.py
+uvotredux/run.py
+uvotredux.egg-info/PKG-INFO
+uvotredux.egg-info/SOURCES.txt
+uvotredux.egg-info/dependency_links.txt
+uvotredux.egg-info/entry_points.txt
+uvotredux.egg-info/requires.txt
+uvotredux.egg-info/top_level.txt

uvotredux-0.1.0/uvotredux.egg-info/dependency_links.txt

@@ -0,0 +1 @@
+

uvotredux-0.1.0/uvotredux.egg-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+uvotredux = uvotredux.run:main

uvotredux-0.1.0/uvotredux.egg-info/requires.txt

@@ -0,0 +1,7 @@
+pathlib
+pre-commit
+
+[dev]
+black==24.2.0
+isort==5.13.2
+pylint==3.1.0

uvotredux-0.1.0/uvotredux.egg-info/top_level.txt

@@ -0,0 +1 @@
+uvotredux