WIP: PrimaryBeam correction

.github/workflows/docs_build.yml

@@ -0,0 +1,57 @@
+name: docs test
+
+# Run this workflow when a review is requested on a PR that targets the main
+# branch, or the PR is closed
+on:
+  pull_request:
+    types: [review_requested, closed]
+  pull_request_target:
+    types: [review_requested, closed]
+
+# Prevent multiple PRs from building/deploying the docs at the same time
+concurrency:
+  group: ${{ github.workflow }}
+
+# test that the docs build
+# (but don't deploy to gh-pages)
+jobs:
+  build_docs:
+    runs-on: ubuntu-20.04
+    strategy:
+      max-parallel: 4
+      matrix:
+        python-version: ["3.8"]
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python
+        uses: actions/setup-python@v4
+        with:
+          python-version: ${{ matrix.python-version }}
+      # cache the Python environment, including installed dependencies
+      # (speeds up tests more than caching pip cache)
+      - name: Cache/Restore the Python env
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-python${{ matrix.python-version }}-env
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+      - name: Install doc dependencies
+        run: |
+          pip install .[docs]
+      - name: Install Pandoc dependency
+        run: |
+          sudo apt-get install pandoc
+      - name: Cache/Restore the .mpol folder cache
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-mpol-dls
+        with:
+          # files are stored in .mpol
+          path: ~/.mpol
+          # the "key" is the hash of the download script
+          key: ${{ hashFiles('docs/download_external_files.py') }}
+      - name: Build the docs
+        run: |
+          make -C docs clean
+          make -C docs html

.github/workflows/gh_docs.yml

@@ -7,16 +7,16 @@ on:
 
 jobs:
   build:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.8
+          python-version: '3.8'
       - name: Install doc deps
         run: |
-          pip install .[docs]
+          pip install .'[docs]'
       - name: Install Pandoc dependency
         run: |
           sudo apt-get install pandoc
@@ -26,7 +26,7 @@ jobs:
         run: |
           npm install @mermaid-js/mermaid-cli
       - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: cache-mpol-dls
         with:

.github/workflows/package.yml

@@ -7,12 +7,12 @@ on:
 
 jobs:
   deploy:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install dependencies
@@ -27,7 +27,7 @@ jobs:
         run: |
           python -m pep517.build --source --binary --out-dir dist/ .
       - name: Publish distribution to PyPI
-        uses: pypa/gh-action-pypi-publish@master
+        uses: pypa/gh-action-pypi-publish@release/v1
         with:
           user: __token__
           password: ${{ secrets.pypi_password }}

.github/workflows/pre-release.yml

@@ -7,18 +7,18 @@ on:
 
 jobs:
   dl_files:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
       - name: Install package deps
         run: |
           pip install .[dev]
       - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: cache-mpol-dls
         with:
@@ -37,32 +37,32 @@ jobs:
       fail-fast: false
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
-        os: [ubuntu-latest, macOS-latest, windows-latest]
+        python-version: ["3.6", "3.7", "3.8", "3.9", "3.10"]
+        os: [ubuntu-20.04, macOS-latest, windows-latest]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
       - name: Install dependencies
         run: |
           pip install --upgrade pip
+      - name: Install vanilla package
+        run: |
+          pip install .
+      - name: Install test deps
+        run: |
+          pip install .[test]
       - name: Lint with flake8
         run: |
           pip install flake8
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --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: Install vanilla package
-        run: |
-          pip install .
-      - name: Install test deps
-        run: |
-          pip install .[test]
       - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: cache-mpol-dls
         with:

.github/workflows/tests.yml

@@ -1,21 +1,24 @@
-name: package test and docs test
+name: package test
 
-on: [push, pull_request]
+on:
+  pull_request_target:
+    types: [opened, synchronize, reopened]
+  push:
 
 jobs:
   dl_files:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: 3.8
-      - name: Install package deps
+      - name: Install dependencies needed to download files
         run: |
-          pip install .[dev]
+          pip install astropy
       - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: cache-mpol-dls
         with:
@@ -29,35 +32,47 @@ jobs:
 
   tests:
     needs: dl_files # don't bother running if we didn't succeed getting the files
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-20.04
     strategy:
       max-parallel: 4
       matrix:
-        python-version: [3.6, 3.7, 3.8, 3.9]
+        python-version: ["3.8", "3.9", "3.10"]
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
       - name: Set up Python ${{ matrix.python-version }}
-        uses: actions/setup-python@v2
+        uses: actions/setup-python@v4
         with:
           python-version: ${{ matrix.python-version }}
-      - name: Install dependencies
+      # cache the Python environment, including installed dependencies
+      # (unique to each python-version; speeds up tests more than caching pip cache)
+      - name: Cache/Restore the Python env
+        uses: actions/cache@v3
+        env:
+          cache-name: cache-python${{ matrix.python-version }}-env
+        with:
+          path: ${{ env.pythonLocation }}
+          key: ${{ env.pythonLocation }}-${{ hashFiles('setup.py') }}
+      - name: Install pip
         run: |
           pip install --upgrade pip
+      - name: Install vanilla package
+        run: |
+          pip install .
+      - name: Install test dependencies
+        run: |
+          pip install .[test]
       - name: Lint with flake8
         run: |
           pip install flake8
           # stop the build if there are Python syntax errors or undefined names
           flake8 . --count --select=E9,F63,F7,F82 --show-source --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: Install vanilla package
-        run: |
-          pip install .
-      - name: Install test deps
+      - name: Check types with MyPy
         run: |
-          pip install .[test]
+          mypy src/mpol --pretty
       - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
+        uses: actions/cache@v3
         env:
           cache-name: cache-mpol-dls
         with:
@@ -68,40 +83,3 @@ jobs:
       - name: Run tests with coverage
         run: |
           pytest --cov=mpol
-
-  # if all tests succeed, then
-  # make sure the docs build OK
-  # (but don't deploy to gh-pages)
-  docs:
-    needs: tests # don't bother running if a test failed
-    runs-on: ubuntu-latest
-    steps:
-      - uses: actions/checkout@v2
-      - name: Set up Python
-        uses: actions/setup-python@v2
-        with:
-          python-version: 3.8
-      - name: Install doc deps
-        run: |
-          pip install .[docs]
-      - name: Install Pandoc dependency
-        run: |
-          sudo apt-get install pandoc
-      - name: Set up node
-        uses: actions/setup-node@v2
-      - name: Install mermaid.js dependency
-        run: |
-          npm install @mermaid-js/mermaid-cli
-      - name: Cache/Restore the .mpol folder cache
-        uses: actions/cache@v2
-        env:
-          cache-name: cache-mpol-dls
-        with:
-          # files are stored in .mpol
-          path: ~/.mpol
-          # the "key" is the hash of the download script
-          key: ${{ hashFiles('docs/download_external_files.py') }}
-      - name: Build the docs
-        run: |
-          make -C docs clean
-          make -C docs html MERMAID_PATH="../node_modules/.bin/"

.gitignore

@@ -120,6 +120,10 @@ venv/
 # notebooks produced from jupytext
 docs/ci-tutorials/*.ipynb
 
+docs/ci-tutorials/alma.jpg
+docs/ci-tutorials/mock_data.npz
+
+
 # tensorboard outputs
 docs/ci-tutorials/runs
 docs/large-tutorials/runs
@@ -134,3 +138,6 @@ dirty_image_model.pt
 
 # setup file
 project_setup.sh
+
+plotsdir
+runs

.pre-commit-config.yaml

@@ -2,7 +2,7 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v3.4.0
+    rev: v4.4.0
     hooks:
       - id: trailing-whitespace
       - id: end-of-file-fixer
@@ -12,11 +12,11 @@ repos:
       - id: detect-private-key
       - id: name-tests-test
   - repo: https://github.com/psf/black
-    rev: 22.3.0
+    rev: 23.1.0
     hooks:
       - id: black
   - repo: https://github.com/PyCQA/isort
-    rev: 5.8.0
+    rev: 5.12.0
     hooks:
       - id: isort
         args: []

docs/Makefile

@@ -1,5 +1,4 @@
 # makefile for Sphinx documentation
-#
 
 # You can set these variables from the command line, and also
 # from the environment for the first two.
@@ -15,18 +14,14 @@ help:
 .PHONY: help Makefile html clean
 
 CI-NOTEBOOKS := ci-tutorials/PyTorch.ipynb ci-tutorials/gridder.ipynb ci-tutorials/optimization.ipynb ci-tutorials/crossvalidation.ipynb ci-tutorials/initializedirtyimage.ipynb
-CHARTS := _static/mmd/build/SimpleNet.svg _static/mmd/build/ImageCube.svg _static/mmd/build/BaseCube.svg _static/mmd/build/SkyModel.svg
 clean:
 	rm -rf _build
-	rm -rf ${CI-NOTEBOOKS}
 	rm -rf ci-tutorials/.ipynb_checkpoints
 	rm -rf ci-tutorials/runs
-	rm -rf ${CHARTS}
+	rm -rf ci-tutorials/alma.jpg
+	rm -rf ci-tutorials/mock_data.npz
 	rm -rf _static/baselines/build/baselines.csv
 
-ci-tutorials/%.ipynb: ci-tutorials/%.py ${CHARTS}
-	jupytext --to ipynb --execute $<
-
 # baseline table
 _static/baselines/build/baselines.csv: _static/baselines/src/print_conversions.py
 	mkdir -p _static/baselines/build
@@ -37,10 +32,5 @@ _static/fftshift/build/plot.png: _static/fftshift/src/plot.py
 	mkdir -p _static/fftshift/build
 	python _static/fftshift/src/plot.py $@
 
-# mermaid.js files
-_static/mmd/build/%.svg: _static/mmd/src/%.mmd
-	mkdir -p _static/mmd/build
-	${MERMAID_PATH}mmdc -i $^ -o $@
-
-html: ${CI-NOTEBOOKS} ${CHARTS} _static/baselines/build/baselines.csv _static/fftshift/build/plot.png
+html: _static/baselines/build/baselines.csv _static/fftshift/build/plot.png
 	python -m sphinx -T -E -b html -d _build/doctrees -D language=en . _build/html

docs/_static/mmd/src/Parametric.mmd

@@ -0,0 +1,5 @@
+graph TD
+pm(DiskModel) --> ImageCube
+ImageCube --> FourierLayer
+FourierLayer --> il([Loss])
+ad[[Dataset]] --> il([Loss])