pyimcom 1.2.1__tar.gz

pyimcom-1.2.1/.copier-answers.yml

@@ -0,0 +1,24 @@
+# Changes here will be overwritten by Copier
+_commit: v2.0.7
+_src_path: gh:lincc-frameworks/python-project-template
+author_email: cao.1191@osu.edu
+author_name: Kaili Cao
+create_example_module: false
+custom_install: true
+enforce_style:
+- ruff_lint
+- ruff_format
+failure_notification: []
+include_benchmarks: false
+include_docs: true
+include_notebooks: false
+mypy_type_checking: none
+package_name: pyimcom
+project_license: none
+project_name: pyimcom
+project_organization: Roman-HLIS-Cosmology-PIT
+python_versions:
+- '3.11'
+- '3.12'
+- '3.13'
+test_lowest_version: none

pyimcom-1.2.1/.git_archival.txt

@@ -0,0 +1,4 @@
+node: $Format:%H$
+node-date: $Format:%cI$
+describe-name: $Format:%(describe:tags=true,match=*[0-9]*)$
+ref-names: $Format:%D$

pyimcom-1.2.1/.gitattributes

@@ -0,0 +1,24 @@
+# For explanation of this file and uses see
+# https://git-scm.com/docs/gitattributes
+# https://developer.lsst.io/git/git-lfs.html#using-git-lfs-enabled-repositories
+# https://lincc-ppt.readthedocs.io/en/latest/practices/git-lfs.html
+#
+# Used by https://github.com/lsst/afwdata.git
+# *.boost filter=lfs diff=lfs merge=lfs -text
+# *.dat filter=lfs diff=lfs merge=lfs -text
+# *.fits filter=lfs diff=lfs merge=lfs -text
+# *.gz filter=lfs diff=lfs merge=lfs -text
+#
+# apache parquet files
+# *.parq	filter=lfs diff=lfs merge=lfs -text
+#
+# sqlite files
+# *.sqlite3	filter=lfs diff=lfs merge=lfs -text
+#
+# gzip files
+# *.gz	filter=lfs diff=lfs merge=lfs -text
+#
+# png image files
+# *.png	filter=lfs diff=lfs merge=lfs -text
+
+.git_archival.txt export-subst

pyimcom-1.2.1/.github/ISSUE_TEMPLATE/0-general_issue.md

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+---
+name: General issue
+about: Quickly create a general issue
+title: ''
+labels: ''
+assignees: ''
+
+---

pyimcom-1.2.1/.github/ISSUE_TEMPLATE/1-bug_report.md

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+---
+name: Bug report
+about: Tell us about a problem to fix
+title: 'Short description'
+labels: 'bug'
+assignees: ''
+
+---
+**Bug report**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the situation in which the bug arose, including what code was executed, information about my environment, and any applicable data others will need to reproduce the problem.
+- [ ] I have included available evidence of the unexpected behavior (including error messages, screenshots, and/or plots) as well as a description of what I expected instead.
+- [ ] If I have a solution in mind, I have provided an explanation and/or pseudocode and/or task list.

pyimcom-1.2.1/.github/ISSUE_TEMPLATE/2-feature_request.md

@@ -0,0 +1,18 @@
+---
+name: Feature request
+about: Suggest an idea for this project
+title: 'Short description'
+labels: 'enhancement'
+assignees: ''
+
+---
+
+**Feature request**
+
+
+**Before submitting**
+Please check the following:
+
+- [ ] I have described the purpose of the suggested change, specifying what I need the enhancement to accomplish, i.e. what problem it solves.
+- [ ] I have included any relevant links, screenshots, environment information, and data relevant to implementing the requested feature, as well as pseudocode for how I want to access the new functionality.
+- [ ] If I have ideas for how the new feature could be implemented, I have provided explanations and/or pseudocode and/or task lists for the steps.

pyimcom-1.2.1/.github/ISSUE_TEMPLATE/README.md

@@ -0,0 +1,9 @@
+# Configurations
+
+Templates for various different issue types are defined in this directory
+and a pull request template is defined as ``../pull_request_template.md``. Adding,
+removing, and modifying these templates to suit the needs of your project is encouraged.
+
+For more information about these templates, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/issue_pr_templating.html
+
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

pyimcom-1.2.1/.github/dependabot.yml

@@ -0,0 +1,10 @@
+version: 2
+updates:
+  - package-ecosystem: "github-actions"
+    directory: "/"
+    schedule:
+      interval: "monthly"
+  - package-ecosystem: "pip"
+    directory: "/"
+    schedule:
+      interval: "monthly"

pyimcom-1.2.1/.github/pull_request_template.md

@@ -0,0 +1,63 @@
+<!-- 
+Thank you for your contribution to the repo :)
+
+Pull Request (PR) Instructions:
+Provide a general summary of your changes in the Title above. Fill out each section of the template, and replace the space with an `x` in all the boxes that apply. If you're unsure about any of these, don't hesitate to ask. We're here to help! Once you are satisfied with the pull request, click the "Create pull request" button to submit it for review.
+
+Before submitting this PR, please ensure that your input and responses are entered in the designated space provided below each section to keep all project-related information organized and easily accessible.
+ 
+How to link to a PR:
+https://docs.github.com/en/issues/tracking-your-work-with-issues/linking-a-pull-request-to-an-issue 
+-->
+
+## Change Description
+<!--- 
+Describe your changes in detail. In your description, you should answer questions like "Why is this change required? What problem does it solve?".
+
+If it fixes an open issue, please link to the issue here. If this PR closes an issue, put the word 'closes' before the issue link to auto-close the issue when the PR is merged.
+-->
+- [ ] My PR includes a link to the issue that I am addressing
+
+
+
+## Solution Description
+<!-- Please explain the technical solution that I have provided and how it addresses the issue or feature being implemented -->
+
+
+
+## Code Quality
+- [ ] I have read the Contribution Guide
+- [ ] My code follows the code style of this project
+- [ ] My code builds (or compiles) cleanly without any errors or warnings
+- [ ] My code contains relevant comments and necessary documentation
+
+## Project-Specific Pull Request Checklists
+<!--- Please only use the checklist that apply to your change type(s) -->
+
+### Bug Fix Checklist
+- [ ] My fix includes a new test that breaks as a result of the bug (if possible)
+- [ ] My change includes a breaking change
+  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
+
+### New Feature Checklist
+- [ ] I have added or updated the docstrings associated with my feature using the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
+- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
+- [ ] I have added unit/End-to-End (E2E) test cases to cover my new feature
+- [ ] My change includes a breaking change
+  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)
+
+### Documentation Change Checklist
+- [ ] Any updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html)
+
+### Build/CI Change Checklist
+- [ ] If required or optional dependencies have changed (including version numbers), I have updated the README to reflect this
+- [ ] If this is a new CI setup, I have added the associated badge to the README
+
+<!-- ### Version Change Checklist [For Future Use] -->
+
+### Other Change Checklist
+- [ ] Any new or updated docstrings use the [NumPy docstring format](https://numpydoc.readthedocs.io/en/latest/format.html).
+- [ ] I have updated the tutorial to highlight my new feature (if appropriate)
+- [ ] I have added unit/End-to-End (E2E) test cases to cover any changes
+- [ ] My change includes a breaking change
+  - [ ] My change includes backwards compatibility and deprecation warnings (if possible)

pyimcom-1.2.1/.github/workflows/README.md

@@ -0,0 +1,9 @@
+# Workflows
+
+The .yml files in this directory are used to define the various continuous
+integration scripts that will be run on your behalf e.g. nightly as a smoke check,
+or when you create a new PR.
+
+For more information about CI and workflows, look here: https://lincc-ppt.readthedocs.io/en/latest/practices/ci.html
+
+Or if you still have questions contact us: https://lincc-ppt.readthedocs.io/en/latest/source/contact.html

pyimcom-1.2.1/.github/workflows/build-documentation.yml

@@ -0,0 +1,36 @@
+
+# This workflow will install Python dependencies, build the package and then build the documentation.
+
+name: Build documentation
+
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python 3.12
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        if [ -f docs/requirements.txt ]; then pip install -r docs/requirements.txt; fi
+        pip install .
+    - name: Build docs
+      run: |
+        sphinx-build -T -E -b html -d docs/build/doctrees ./docs docs/build/html

pyimcom-1.2.1/.github/workflows/pre-commit-ci.yml

@@ -0,0 +1,36 @@
+
+# This workflow runs pre-commit hooks on pushes and pull requests to main
+# to enforce coding style. To ensure correct configuration, please refer to:
+#  https://lincc-ppt.readthedocs.io/en/latest/practices/ci_precommit.html
+name: Run pre-commit hooks
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  pre-commit-ci:
+    runs-on: ubuntu-latest
+    steps:
+    - uses: actions/checkout@v6
+      with:
+        fetch-depth: 0 
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+    - uses: pre-commit/action@v3.0.1
+      with:
+        extra_args: --all-files --verbose
+      env:
+        SKIP: "check-lincc-frameworks-template-version,no-commit-to-branch,check-added-large-files,validate-pyproject,sphinx-build,pytest-check"
+    - uses: pre-commit-ci/lite-action@v1.1.0
+      if: failure() && github.event_name == 'pull_request' && github.event.pull_request.draft == false

pyimcom-1.2.1/.github/workflows/publish-to-pypi.yml

@@ -0,0 +1,39 @@
+
+# This workflow will upload a Python Package using Twine when a release is created
+# For more information see: https://github.com/pypa/gh-action-pypi-publish#trusted-publishing
+
+# This workflow uses actions that are not certified by GitHub.
+# They are provided by a third-party and are governed by
+# separate terms of service, privacy policy, and support
+# documentation.
+
+name: Upload Python Package
+
+on:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+permissions:
+  contents: read
+
+jobs:
+  deploy:
+
+    runs-on: ubuntu-latest
+    permissions:
+      id-token: write
+    steps:
+    - uses: actions/checkout@v6
+    - name: Set up Python
+      uses: actions/setup-python@v6
+      with:
+        python-version: '3.12'
+    - name: Install dependencies
+      run: |
+        python -m pip install --upgrade pip
+        pip install build
+    - name: Build package
+      run: python -m build
+    - name: Publish package
+      uses: pypa/gh-action-pypi-publish@release/v1

pyimcom-1.2.1/.github/workflows/smoke-test.yml

@@ -0,0 +1,58 @@
+# This workflow will run 3 days per week at 06:00.
+# It will install Python dependencies and run tests with a variety of Python versions.
+# See documentation for help debugging smoke test issues:
+#    https://lincc-ppt.readthedocs.io/en/latest/practices/ci_testing.html#version-culprit
+
+name: Unit test smoke test
+
+on:
+
+  # Runs this workflow automatically
+  schedule:
+    - cron: 0 6 * * 1,3,5
+    
+  # Allows you to run this workflow manually from the Actions tab
+  workflow_dispatch:
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12', '3.13', '3.14']
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Install TeX Live packages
+      run: |
+        sudo apt-get update -y
+        sudo apt-get install -y \
+          dvipng \
+          texlive-base \
+          texlive-latex-base \
+          texlive-latex-recommended \
+          texlive-latex-extra \
+          texlive-fonts-recommended \
+          latexmk \
+          lmodern \
+          cm-super
+        # use apt-get for ubuntu
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install git+https://github.com/rmjarvis/Piff@main
+        # test with main branch of Piff
+    - name: List dependencies
+      run: |
+        pip list
+    - name: Run unit tests with pytest
+      run: |
+        python -m pytest

pyimcom-1.2.1/.github/workflows/testing-and-coverage.yml

@@ -0,0 +1,58 @@
+
+# This workflow will install Python dependencies, run tests and report code coverage with a variety of Python versions
+# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
+
+name: Unit test and code coverage
+
+on:
+  push:
+    branches: [ main ]
+  pull_request:
+    branches: [ main ]
+
+jobs:
+  build:
+
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        python-version: ['3.12', '3.13', '3.14']
+
+    steps:
+    - uses: actions/checkout@v6
+    - name: Install TeX Live packages
+      run: |
+        sudo apt-get update -y
+        sudo apt-get install -y \
+          dvipng \
+          texlive-base \
+          texlive-latex-base \
+          texlive-latex-recommended \
+          texlive-latex-extra \
+          texlive-fonts-recommended \
+          latexmk \
+          lmodern \
+          cm-super
+        # use apt-get for ubuntu
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v6
+      with:
+        python-version: ${{ matrix.python-version }}
+    - name: Install dependencies
+      run: |
+        sudo apt-get update
+        sudo apt-get install -y libfftw3-dev
+        python -m pip install --upgrade pip
+        pip install -e .[dev]
+        if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+        pip install git+https://github.com/rmjarvis/Piff@main
+        # test with main branch of Piff
+    - name: Run unit tests with pytest
+      run: |
+        NUMBA_DISABLE_JIT=1 python -m pytest --cov=pyimcom --cov-report=xml
+        # njit is disabled so the lines coverage in those functions is tracked 
+    - name: Upload coverage report to codecov
+      uses: codecov/codecov-action@v6
+      with:
+        token: ${{ secrets.CODECOV_TOKEN }}
+        slug: Roman-HLIS-Cosmology-PIT/pyimcom

pyimcom-1.2.1/.gitignore

@@ -0,0 +1,165 @@
+# 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/
+_readthedocs/
+
+# 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
+
+# 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
+__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/
+
+# vscode
+.vscode/
+
+# dask
+dask-worker-space/
+
+# tmp directory
+tmp/
+
+# Mac OS
+.DS_Store
+
+# Airspeed Velocity performance results
+_results/
+_html/
+
+# Project initialization script
+.initialize_new_project.sh

pyimcom-1.2.1/.idea/.gitignore

@@ -0,0 +1,3 @@
+# Default ignored files
+/shelf/
+/workspace.xml

pyimcom-1.2.1/.idea/inspectionProfiles/profiles_settings.xml

@@ -0,0 +1,6 @@
+<component name="InspectionProjectProfileManager">
+  <settings>
+    <option name="USE_PROJECT_PROFILE" value="false" />
+    <version value="1.0" />
+  </settings>
+</component>

pyimcom-1.2.1/.idea/misc.xml

@@ -0,0 +1,7 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="Black">
+    <option name="sdkName" value="Python 3.8" />
+  </component>
+  <component name="ProjectRootManager" version="2" project-jdk-name="Python 3.8" project-jdk-type="Python SDK" />
+</project>

pyimcom-1.2.1/.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/pyimcom.iml" filepath="$PROJECT_DIR$/.idea/pyimcom.iml" />
+    </modules>
+  </component>
+</project>

pyimcom-1.2.1/.idea/pyimcom.iml

@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<module type="PYTHON_MODULE" version="4">
+  <component name="NewModuleRootManager">
+    <content url="file://$MODULE_DIR$" />
+    <orderEntry type="jdk" jdkName="Python 3.8" jdkType="Python SDK" />
+    <orderEntry type="sourceFolder" forTests="false" />
+  </component>
+  <component name="PyDocumentationSettings">
+    <option name="format" value="NUMPY" />
+    <option name="myDocStringFormat" value="NumPy" />
+  </component>
+</module>

pyimcom-1.2.1/.idea/vcs.xml

@@ -0,0 +1,6 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<project version="4">
+  <component name="VcsDirectoryMappings">
+    <mapping directory="$PROJECT_DIR$" vcs="Git" />
+  </component>
+</project>