snowblind 0.1.0__tar.gz

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

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+name: ci
+
+on: [push, pull_request]
+
+jobs:
+  test:
+
+    runs-on: ubuntu-latest
+    env:
+      OBSERVATORY: jwst
+      CRDS_PATH: /tmp/crds_cache
+      CRDS_SERVER_URL: https://jwst-crds.stsci.edu
+    strategy:
+      matrix:
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v3
+        with:
+          fetch-depth: 0
+
+      - name: Set up Python ${{ matrix.python-version }}
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: |
+          python -m pip install --upgrade pip
+          pip install ".[test]"
+
+      - name: Lint with flake8
+        run: |
+          # stop the build if there are Python syntax errors or undefined names
+          flake8 . --count --statistics
+          # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
+          flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
+
+      - name: Test with pytest
+        run: |
+          pytest tests

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

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+name: Publish distribution to PyPI
+
+on: push
+
+jobs:
+  build:
+    name: Build distribution
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v4
+    - name: Set up Python
+      uses: actions/setup-python@v4
+      with:
+        python-version: "3.x"
+    - name: Install pypa/build
+      run: >-
+        python3 -m
+        pip install
+        build
+        --user
+    - name: Build a binary wheel and a source tarball
+      run: python3 -m build
+    - name: Store the distribution packages
+      uses: actions/upload-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+
+  publish-to-pypi:
+    name: Publish distribution to PyPI
+    if: startsWith(github.ref, 'refs/tags/')  # only publish to PyPI on tag pushes
+    needs:
+    - build
+    runs-on: ubuntu-latest
+    environment:
+      name: pypi
+      url: https://pypi.org/p/snowblind
+    permissions:
+      id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Publish distribution to PyPI
+      uses: pypa/gh-action-pypi-publish@release/v1
+
+  github-release:
+    name: >-
+      Sign the Python 🐍 distribution 📦 with Sigstore
+      and upload them to GitHub Release
+    needs:
+    - publish-to-pypi
+    runs-on: ubuntu-latest
+
+    permissions:
+      contents: write  # IMPORTANT: mandatory for making GitHub Releases
+      id-token: write  # IMPORTANT: mandatory for sigstore
+
+    steps:
+    - name: Download all the dists
+      uses: actions/download-artifact@v3
+      with:
+        name: python-package-distributions
+        path: dist/
+    - name: Sign the dists with Sigstore
+      uses: sigstore/gh-action-sigstore-python@v1.2.3
+      with:
+        inputs: >-
+          ./dist/*.tar.gz
+          ./dist/*.whl
+    - name: Upload artifact signatures to GitHub Release
+      env:
+        GITHUB_TOKEN: ${{ github.token }}
+      # Upload to GitHub Release using the `gh` CLI.
+      # `dist/` contains the built packages, and the
+      # sigstore-produced signatures and certificates.
+      run: >-
+        gh release upload
+        '${{ github.ref_name }}' dist/**
+        --repo '${{ github.repository }}'
+
+#   publish-to-testpypi:
+#     name: Publish Python 🐍 distribution 📦 to TestPyPI
+#     needs:
+#     - build
+#     runs-on: ubuntu-latest
+
+#     environment:
+#       name: testpypi
+#       url: https://test.pypi.org/p/snowblind
+
+#     permissions:
+#       id-token: write  # IMPORTANT: mandatory for trusted publishing
+
+#     steps:
+#     - name: Download all the dists
+#       uses: actions/download-artifact@v3
+#       with:
+#         name: python-package-distributions
+#         path: dist/
+#     - name: Publish distribution 📦 to TestPyPI
+#       uses: pypa/gh-action-pypi-publish@release/v1
+#       with:
+#         repository-url: https://test.pypi.org/legacy/

snowblind-0.1.0/.gitignore

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+.DS_Store
+# 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/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+*_version.py
+
+# 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/
+
+# 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/
+docs/api/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.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
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow
+__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/

snowblind-0.1.0/CITATION.cff

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+cff-version: 1.2.0
+title: my_package
+message: If you use this software, please cite as below.
+date-released: 2022-03-29
+url: 'https://github.com/mpi-astronomy/mpia-python-template'
+version: 0.0.1
+type: software
+authors:
+  - family-names: Name
+    given-names: Author
+    email: author.name@email.com
+    affiliation: MPIA
+    orcid: 'https://orcid.org/0000-0003-1665-2073'
+
+# For citing software, see:
+
+# http://journals.aas.org/authors/references.html
+
+# GitHub has Zenodo DOI integration:
+# https://guides.github.com/activities/citable-code/
+
+# What is a CITATION.cff file: 
+# https://citation-file-format.github.io/
+
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!

snowblind-0.1.0/CODE_OF_CONDUCT.md

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+We are committed to providing a strong and
+enforced code of conduct and expect everyone in our community to follow these
+guidelines when interacting with others in all forums. Our goal is to keep ours
+a positive, inclusive, successful, and growing community. 
+
+[ All Max Planck Institute for Astronomy (MPIA) researchers are bound to adhere to the 
+[Max Plack Society Code of Conduct](https://www.mpg.de/14172230/code-of-conduct.pdf) and the [MPIA Work Agreement](https://intranet.mpia.de/4404342/03-Works-agreement-code-of-conduct.pdf) (intranet link). All MPIA employees should attach importance to creating a respectful and healthy atmosphere 
+and a level playing field for research and work. Their goal is to ensure good working conditions 
+for everyone and to provide the basis for individual job satisfaction, personal development, 
+motivation, collegiality and positive interpersonal relations. ]
+
+[ Interactions on GitHub are not limited to those between MPIA employees.] The community of
+participants in open source astronomy projects is made up of members from
+around the globe with a diverse set of skills, personalities, and experiences.
+It is through these differences that our community experiences success and
+continued growth. As members of this global community:
+
+1. We pledge to treat all people with respect and provide a harassment- and bullying-free environment, regardless of sex, sexual orientation and/or gender identity, disability, physical appearance, body size, race, nationality, ethnicity, and religion. In particular, sexual language and imagery, sexist, racist, or otherwise exclusionary jokes are not appropriate.
+2. We pledge to respect the work of others by recognizing acknowledgment/citation requests of original authors. As authors, we pledge to be explicit about how we want our own work to be cited or acknowledged.
+3. We pledge to welcome those interested in joining the community, and realize that including people with a variety of opinions and backgrounds will only serve to enrich our community. In particular, discussions relating to pros/cons of various technologies, programming languages, and so on are welcome, but these should be done with respect, taking proactive measure to ensure that all participants are heard and feel confident that they can freely express their opinions.
+4. We pledge to welcome questions and answer them respectfully, paying particular attention to those new to the community. We pledge to provide respectful criticisms and feedback in forums, especially in discussion threads resulting from code contributions.
+5. We pledge to be conscientious of the perceptions of the wider community and to respond to criticism respectfully. We will strive to model behaviors that encourage productive debate and disagreement, both within our community and where we are criticized. We will treat those outside our community with the same respect as people within our community.
+6. We pledge to help the entire community follow the code of conduct, and to not remain silent when we see violations of the code of conduct. 
+ 
+**This code of conduct applies to all community situations online and offline, including mailing lists, forums, social media, conferences, meetings, associated social events, and one-to-one interactions.**
+
+**Reporting**: Please report any violations of the Code of Conduct to the owners of the [`mpi-astronomy` [GitHub organization](https://github.com/orgs/mpi-astronomy/people)]. As community leaders we are responsible for clarifying and enforcing our standards of acceptable behavior and will take appropriate and fair corrective action in response to any behavior that they deem inappropriate, threatening, offensive, or harmful. All community leaders are obligated to respect the privacy and security of the reporter of any incident.
+
+**Enforcement**: We follow the enforcement guidelines of the [Contributor Covenant](https://www.contributor-covenant.org/version/2/1/code_of_conduct/). [For MPIA employees, the matter will be referred to the contacts listed in Section 7 of the [MPIA Work Agreement](https://intranet.mpia.de/4404342/03-Works-agreement-code-of-conduct.pdf) (intranet link). 
+For external people, the owners of the GitHub organization will decide in consultation with the MPIA directorate.]
+
+Parts of this code of conduct have been adapted from the Astropy and NumFOCUS codes of conduct:
+
+https://www.astropy.org/code_of_conduct.html
+
+https://www.numfocus.org/about/code-of-conduct/
+

snowblind-0.1.0/LICENSE

@@ -0,0 +1,29 @@
+BSD 3-Clause License
+
+Copyright (c) 2022,  Max Planck Institute for Astronomy
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

snowblind-0.1.0/PKG-INFO

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+Metadata-Version: 2.1
+Name: snowblind
+Version: 0.1.0
+Summary: Mask cosmic ray showers (snowballs) in JWST data
+Author-email: James Davies <jdavies@mpia.de>
+License: BSD 3-Clause License
+        
+        Copyright (c) 2022,  Max Planck Institute for Astronomy
+        All rights reserved.
+        
+        Redistribution and use in source and binary forms, with or without
+        modification, are permitted provided that the following conditions are met:
+        
+        1. Redistributions of source code must retain the above copyright notice, this
+           list of conditions and the following disclaimer.
+        
+        2. Redistributions in binary form must reproduce the above copyright notice,
+           this list of conditions and the following disclaimer in the documentation
+           and/or other materials provided with the distribution.
+        
+        3. Neither the name of the copyright holder nor the names of its
+           contributors may be used to endorse or promote products derived from
+           this software without specific prior written permission.
+        
+        THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+        AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+        IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+        DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+        FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+        DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+        SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+        CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+        OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+        OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+        
+Project-URL: Bug Tracker, https://github.com/mpi-astronomy/snowblind/issues
+Project-URL: Source Code, https://github.com/mpi-astronomy/snowblind
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: BSD License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.9
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: jwst
+Requires-Dist: numpy
+Requires-Dist: scikit-image
+Requires-Dist: stpipe
+Provides-Extra: docs
+Requires-Dist: sphinx; extra == "docs"
+Requires-Dist: sphinx-automodapi; extra == "docs"
+Requires-Dist: numpydoc; extra == "docs"
+Provides-Extra: test
+Requires-Dist: pytest; extra == "test"
+Requires-Dist: flake8; extra == "test"
+Requires-Dist: flake8-pyproject; extra == "test"
+Requires-Dist: codecov; extra == "test"
+Requires-Dist: pytest-cov; extra == "test"
+
+Algorithms for cleaning JWST data.
+
+ - `SnowBlindStep`: mask cosmic ray showers and snowballs
+ - `JumpPlusStep`: flag jumps and saturated pixels caused by cosmic rays properly
+                 when there are frame-averaged groups
+ - `PersistenceFlagStep`: flag pixels due to persistence between exposures
+ - `RcSelfCalStep`: flag new hot pixels
+
+
+## Installation
+
+
+    pip install snowblind
+
+
+## Usage
+
+The steps in snowblind run like any other pipeline steps.  From the command line:
+
+    strun snowblind jw001234_010203_00001_nrcalong_jump.fits --suffix=snowblind
+
+In Python:
+
+    from snowblind import SnowblindStep
+    from jwst.pipeline import Detector1Pipeline
+    from jwst.ramp_fitting import RampFitStep
+
+
+    steps = {
+        "jump": {
+            "save_results": True,
+        }
+        "ramp_fit": {
+            "skip": True
+        }
+    }
+
+    Detector1Pipeline.call("jw001234_010203_00001_nrcalong_uncal.fits", steps=steps)
+    SnowblindStep.call("jw001234_010203_00001_nrcalong_jump.fits", save_results=True, suffix="snowblind")
+    rate, rateints = RampFitStep.call("jw001234_010203_00001_nrcalong_snowblind.fits")
+    rate.save(cal.meta.filename.replace("snowblind", "rate"))
+
+More to come on the other steps available.

snowblind-0.1.0/README.md

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+Algorithms for cleaning JWST data.
+
+ - `SnowBlindStep`: mask cosmic ray showers and snowballs
+ - `JumpPlusStep`: flag jumps and saturated pixels caused by cosmic rays properly
+                 when there are frame-averaged groups
+ - `PersistenceFlagStep`: flag pixels due to persistence between exposures
+ - `RcSelfCalStep`: flag new hot pixels
+
+
+## Installation
+
+
+    pip install snowblind
+
+
+## Usage
+
+The steps in snowblind run like any other pipeline steps.  From the command line:
+
+    strun snowblind jw001234_010203_00001_nrcalong_jump.fits --suffix=snowblind
+
+In Python:
+
+    from snowblind import SnowblindStep
+    from jwst.pipeline import Detector1Pipeline
+    from jwst.ramp_fitting import RampFitStep
+
+
+    steps = {
+        "jump": {
+            "save_results": True,
+        }
+        "ramp_fit": {
+            "skip": True
+        }
+    }
+
+    Detector1Pipeline.call("jw001234_010203_00001_nrcalong_uncal.fits", steps=steps)
+    SnowblindStep.call("jw001234_010203_00001_nrcalong_jump.fits", save_results=True, suffix="snowblind")
+    rate, rateints = RampFitStep.call("jw001234_010203_00001_nrcalong_snowblind.fits")
+    rate.save(cal.meta.filename.replace("snowblind", "rate"))
+
+More to come on the other steps available.

snowblind-0.1.0/docs/Makefile

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+# 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)

snowblind-0.1.0/docs/conf.py

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+# Configuration file for the Sphinx documentation builder.
+#
+# This file only contains a selection of the most common options. For a full
+# list see the documentation:
+# https://www.sphinx-doc.org/en/master/usage/configuration.html
+
+# -- Path setup --------------------------------------------------------------
+
+# If extensions (or modules to document with autodoc) are in another directory,
+# add these directories to sys.path here. If the directory is relative to the
+# documentation root, use os.path.abspath to make it absolute, like shown here.
+#
+# import os
+# import sys
+# sys.path.insert(0, os.path.abspath('.'))
+
+
+# -- Project information -----------------------------------------------------
+
+project = 'my_package'
+copyright = '2022, Author Name'
+author = 'Author Name'
+
+
+# -- General configuration ---------------------------------------------------
+
+# Add any Sphinx extension module names here, as strings. They can be
+# extensions coming with Sphinx (named 'sphinx.ext.*') or your custom
+# ones.
+extensions = ['sphinx_automodapi.automodapi'
+]
+numpydoc_show_class_members = False
+
+# Add any paths that contain templates here, relative to this directory.
+templates_path = ['_templates']
+
+# List of patterns, relative to source directory, that match files and
+# directories to ignore when looking for source files.
+# This pattern also affects html_static_path and html_extra_path.
+exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+
+
+# -- Options for HTML output -------------------------------------------------
+
+# The theme to use for HTML and HTML Help pages.  See the documentation for
+# a list of builtin themes.
+#
+html_theme = 'alabaster'
+
+# Add any paths that contain custom static files (such as style sheets) here,
+# relative to this directory. They are copied after the builtin static files,
+# so a file named "default.css" will overwrite the builtin "default.css".
+html_static_path = ['_static']

snowblind-0.1.0/docs/index.rst

@@ -0,0 +1,67 @@
+.. my_package documentation master file, created by
+   sphinx-quickstart on Tue Mar 22 13:13:41 2022.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to my_package's documentation!
+======================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+
+Here is where you can write the documentation for your package. 
+
+
+Usage
+=====
+
+.. _installation:
+
+Installation
+------------
+
+To use `my_package` you need to install X, Y and Z. 
+
+
+.. _code:
+
+Code
+----
+
+Here is an example of describing the use of your function.
+
+To add one to a number you can use the ``my_package.add_one()`` function:
+
+.. py:function:: my_package.add_one(number)
+
+
+    :param number: Should be integer, floating point number or a string. 
+
+    If ``number`` is not one of these types, an exception will be raised:
+
+    .. py:exception:: TypeError
+
+   Raised if the input is invalid.
+
+More about how to describe code can be hound 
+`here <https://www.sphinx-doc.org/en/master/tutorial/describing-code.html>`_
+
+
+..
+  The following section creates an index, a list of modules and a 
+  search page. 
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+..
+ The following will add the signature of the individual functions and pull
+ their docstrings.
+
+.. automodapi:: my_package.example