resolved merge conflicts.

.coveragerc

@@ -1,7 +1,6 @@
 [run]
 omit =
     venv/*
-    src/mpol/spheroidal_gridding.py
 relative_files = True
 
 

.github/ISSUE_TEMPLATE/bug_report.md

@@ -10,7 +10,7 @@ assignees: ''
 **Describe the bug**
 A clear and concise description of what the bug is.
 
-**To Reproduce**
+**To reproduce**
 Steps to reproduce the behavior:
 
 **Expected behavior**
@@ -21,8 +21,11 @@ If applicable, add screenshots to help explain your problem.
 
 **Desktop (please complete the following information):**
  - OS: [e.g. Linux + distro, MacOS, Windows]
- - Python Version
- - MPoL Version (`$python -c "import mpol; print(mpol.__version__)"`
+ - Python version
+ - MPoL version (`$python -c "import mpol; print(mpol.__version__)"`
+
+**Suggested fix**
+If you have a suggestion for how to fix the bug, please explain.
 
 **Additional context**
 Add any other context about the problem here.

.github/workflows/docs_build.yml

@@ -5,6 +5,8 @@ name: docs test
 on:
   pull_request:
     types: [review_requested, closed]
+  pull_request_review:
+      types: [submitted, dismissed]
 
 # Prevent multiple PRs from building/deploying the docs at the same time
 concurrency:
@@ -18,7 +20,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.8"]
+        python-version: ["3.10"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python
@@ -36,7 +38,7 @@ jobs:
           key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
       - name: Install doc dependencies
         run: |
-          pip install .[docs]
+          pip install .[dev]
       - name: Install Pandoc dependency
         run: |
           sudo apt-get install pandoc

.github/workflows/gh_docs.yml

@@ -13,10 +13,10 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: '3.8'
+          python-version: '3.10'
       - name: Install doc deps
         run: |
-          pip install .'[docs]'
+          pip install .'[dev]'
       - name: Install Pandoc dependency
         run: |
           sudo apt-get install pandoc

.github/workflows/package.yml

@@ -14,7 +14,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: 3.10
       - name: Install dependencies
         run: |
           pip install --upgrade pip

.github/workflows/pre-release.yml

@@ -13,7 +13,7 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Install package deps
         run: |
           pip install .[dev]
@@ -37,7 +37,7 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11", "3.12"]
         os: [ubuntu-20.04, macOS-latest, windows-latest]
     steps:
       - uses: actions/checkout@v3

.github/workflows/tests.yml

@@ -1,6 +1,8 @@
 name: package test
 
 on:
+  push:
+    branches: [main]
   pull_request:
 
 jobs:
@@ -11,10 +13,14 @@ jobs:
       - name: Set up Python
         uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: "3.10"
       - name: Install dependencies needed to download files
+        # we're just installing mpol here to reference the zenodo record number 
+        # in __init__. below we'll reinstall for the tests.
         run: |
           pip install astropy
+          pip install frank
+          pip install .
       - name: Cache/Restore the .mpol folder cache
         uses: actions/cache@v3
         env:
@@ -34,7 +40,7 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-        python-version: ["3.8", "3.9", "3.10"]
+        python-version: ["3.10", "3.11"]
     steps:
       - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}

.gitignore

@@ -139,5 +139,9 @@ dirty_image_model.pt
 # setup file
 project_setup.sh
 
+# likely folders from testing
 plotsdir
 runs
+
+# hatch-generated version file
+src/mpol/mpol_version.py

.pre-commit-config.yaml

@@ -2,13 +2,14 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.4.0
+    rev: v4.5.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
       - id: check-yaml
+      - id: check-toml
       - id: check-added-large-files
-        args: ["--maxkb=5000"]
+        args: ["--maxkb=2000"]
       - id: detect-private-key
       - id: name-tests-test
   - repo: https://github.com/psf/black

CONTRIBUTORS.md

@@ -1,7 +1,12 @@
 Contributors
 * Ian Czekala, `@iancze`
-* Brianna Zawadski, `@briannazawadzki`
+* Jeff Jennings, `@jeffjennings`
+* Brianna Zawadzki, `@briannazawadzki`
 * Ryan Loomis, `@ryanaloomis`
-* Tyler Quinn, `@trq5014`
-* Hannah Grzybowski, `@hgrzy`
+* Kadri Nizam, `@kadri-nizam`
+* Megan Delamer
+* Kaylee de Soto, `@kdesoto-astro`
 * Robert Frazier, `@RCF42`
+* Hannah Grzybowski, `@hgrzy`
+* Mary Ogborn
+* Tyler Quinn, `@trq5014`

LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2019 Ian Czekala
+Copyright (c) 2019 - 2023 Ian Czekala and contributors
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

README.md

@@ -1,34 +1,68 @@
 # MPoL
 
-[![Tests](https://github.com/MPoL-dev/MPoL/actions/workflows/tests.yml/badge.svg)](https://github.com/MPoL-dev/MPoL/actions/workflows/tests.yml)
+[![Tests](https://github.com/MPoL-dev/MPoL/actions/workflows/tests.yml/badge.svg?branch=main)](https://github.com/MPoL-dev/MPoL/actions/workflows/tests.yml)
 [![gh-pages docs](https://github.com/MPoL-dev/MPoL/actions/workflows/gh_docs.yml/badge.svg)](https://mpol-dev.github.io/MPoL/)
 [![DOI](https://zenodo.org/badge/224543208.svg)](https://zenodo.org/badge/latestdoi/224543208)
 
-A Million Points of Light are needed to synthesize image cubes from interferometers.
 
-MPoL is a flexible Python package designed for Regularized Maximum Likelihood imaging. We focus on supporting spectral line and continuum observations from interferometers like the Atacama Large Millimeter/Submillimeter Array (ALMA) and the Karl G. Jansky Very Large Array (VLA). There is potential to extend the package to work on other Fourier reconstruction problems like sparse aperture masking and kernel phase interferometry.
 
-Documentation and installation instructions: [https://mpol-dev.github.io/MPoL/](https://mpol-dev.github.io/MPoL/)
+MPoL is a [PyTorch](https://pytorch.org/) *library* built for Regularized Maximum Likelihood (RML) imaging and Bayesian Inference with datasets from interferometers like the Atacama Large Millimeter/Submillimeter Array ([ALMA](https://www.almaobservatory.org/en/home/)) and the Karl G. Jansky Very Large Array ([VLA](https://public.nrao.edu/telescopes/vla/)). 
+
+As a PyTorch *library*, MPoL is designed expecting that the user will write Python code that uses MPoL primitives as building blocks to solve their interferometric imaging workflow, much the same way the artificial intelligence community writes Python code that uses PyTorch layers to implement new neural network architectures (for [example](https://github.com/pytorch/examples)). You will find MPoL easiest to use if you adhere to PyTorch customs and idioms, e.g., feed-forward neural networks, data storage, GPU acceleration, and train/test optimization loops. Therefore, a basic familiarity with PyTorch is considered a prerequisite for MPoL.
+
+MPoL is *not* an imaging application nor a pipeline, though such programs could be built for specialized workflows using MPoL components. We are focused on providing a numerically correct and expressive set of core primitives so the user can leverage the full power of the PyTorch (and Python) ecosystem to solve their research-grade imaging tasks. This is already a significant development and maintenance burden for our small research team, so our immediate scope must necessarily be limited.
+
+Installation instructions, documentation, and examples at: [https://mpol-dev.github.io/MPoL/](https://mpol-dev.github.io/MPoL/)
+
+
 
 ## Citation
 
-If you use this package or derivatives of it, please cite
+If you use this package or derivatives of it, please cite the following two references:
 
     @software{mpol,
     author       = {Ian Czekala and
+                    Jeff Jennings and   
                     Brianna Zawadzki and
                     Ryan Loomis and
-                    Hannah Grzybowski and
+                    Kadri Nizam and 
+                    Megan Delamer and 
+                    Kaylee de Soto and
                     Robert Frazier and
+                    Hannah Grzybowski and
+                    Mary Ogborn and                    
                     Tyler Quinn},
-    title        = {MPoL-dev/MPoL: v0.1.1 Release},
-    month        = jun,
-    year         = 2021,
+    title        = {MPoL-dev/MPoL: v0.2.0 Release},
+    month        = nov,
+    year         = 2023,
     publisher    = {Zenodo},
-    version      = {v0.1.1},
-    doi          = {10.5281/zenodo.4939048},
-    url          = {https://doi.org/10.5281/zenodo.4939048}
+    version      = {v0.2.0},
+    doi          = {10.5281/zenodo.3594081},
+    url          = {https://doi.org/10.5281/zenodo.3594081}
+    }
+
+and 
+
+    @ARTICLE{2023PASP..135f4503Z,
+        author = {{Zawadzki}, Brianna and {Czekala}, Ian and {Loomis}, Ryan A. and {Quinn}, Tyler and {Grzybowski}, Hannah and {Frazier}, Robert C. and {Jennings}, Jeff and {Nizam}, Kadri M. and {Jian}, Yina},
+            title = "{Regularized Maximum Likelihood Image Synthesis and Validation for ALMA Continuum Observations of Protoplanetary Disks}",
+        journal = {\pasp},
+        keywords = {Protoplanetary disks, Submillimeter astronomy, Radio interferometry, Deconvolution, Open source software, 1300, 1647, 1346, 1910, 1866, Astrophysics - Earth and Planetary Astrophysics, Astrophysics - Instrumentation and Methods for Astrophysics},
+            year = 2023,
+            month = jun,
+        volume = {135},
+        number = {1048},
+            eid = {064503},
+            pages = {064503},
+            doi = {10.1088/1538-3873/acdf84},
+    archivePrefix = {arXiv},
+        eprint = {2209.11813},
+    primaryClass = {astro-ph.EP},
+        adsurl = {https://ui.adsabs.harvard.edu/abs/2023PASP..135f4503Z},
+        adsnote = {Provided by the SAO/NASA Astrophysics Data System}
     }
 
 ---
-Copyright Ian Czekala and contributors 2019-21
+Copyright Ian Czekala and contributors 2019-24
+
+A Million Points of Light are needed to synthesize image cubes from interferometers.

docs/_static/mmd/src/SimpleNet.mmd → docs/_static/mmd/src/GriddedNet.mmd

@@ -1,5 +1,5 @@
 graph TD
-    subgraph SimpleNet
+    subgraph GriddedNet
     bc(BaseCube) --> HannConvCube
     HannConvCube --> ImageCube
     ImageCube --> FourierLayer

docs/api/analysis.md

@@ -0,0 +1,6 @@
+# Analysis
+
+```{eval-rst}
+.. automodule:: mpol.onedim
+    :members:
+```

docs/api/coordinates.md

@@ -0,0 +1,6 @@
+# Coordinates
+
+```{eval-rst}
+.. automodule:: mpol.coordinates
+    :members:
+```

docs/api/crossval.md

@@ -0,0 +1,6 @@
+# Cross-validation
+
+```{eval-rst}
+.. automodule:: mpol.crossval
+    :members:
+```

docs/api/datasets.md

@@ -0,0 +1,6 @@
+# Datasets
+
+```{eval-rst}
+.. automodule:: mpol.datasets
+    :members:
+```

docs/api/fourier.md

@@ -0,0 +1,6 @@
+# Fourier
+
+```{eval-rst}
+.. automodule:: mpol.fourier
+    :members:
+```

docs/api/geometry.md

@@ -0,0 +1,6 @@
+# Geometry
+
+```{eval-rst}
+.. automodule:: mpol.geometry
+    :members:
+```