Add function for fitting EM slope in multiple pixels and do a lot of …

…retemplating (#93)

* first iteration of EM slope calculation in analysis subpackage

* change units from ct to DN

* improvements to slope fitting

* more fixes

* update integration routine

* do the retemplate dance

* no unpacking while indexing below 3.11

.github/workflows/run-tests.yml

@@ -1,54 +1,74 @@
-name: Run tests
+name: CI
 
 on:
   push:
-    branches: [ main ]
+    branches:
+      - 'main'
+      - '*.*'
+      - '!*backport*'
+    tags:
+      - 'v*'
+      - '!*dev*'
+      - '!*pre*'
+      - '!*post*'
   pull_request:
-    branches: [ main ]
+  # Allow manual runs through the web UI
+  workflow_dispatch:
 
 jobs:
-  build:
+  core:
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: tox-pypi-filter
+      envs: |
+        - linux: py312
+      coverage: 'codecov'
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-    runs-on: ${{ matrix.os }}
-    strategy:
-      fail-fast: false
-      matrix:
-        include:
-        # Test the oldest and newest configuration on Mac and Windows
-        - os: macos-latest
-          python-version: 3.9
-          toxenv: py39
-        - os: macos-latest
-          python-version: "3.11"
-          toxenv: py311
-        # Test all configurations on Linux
-        - os: ubuntu-latest
-          python-version: 3.9
-          toxenv: py39
-        - os: ubuntu-latest
-          python-version: "3.10"
-          toxenv: py310
-        - os: ubuntu-latest
-          python-version: "3.11"
-          toxenv: py311
-        # Docs
-        - os: ubuntu-latest
-          python-version: "3.11"
-          toxenv: build_docs
-        # Code style checks
-        - os: ubuntu-latest
-          python-version: "3.11"
-          toxenv: codestyle
+  tests:
+    needs: [core]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: tox-pypi-filter
+      envs: |
+        - macos: py311
+        - windows: py310
+      coverage: 'codecov'
+    secrets:
+      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
-    steps:
-    - uses: actions/checkout@v2
-    - 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 tox codecov
-    - name: Run tox
-      run: python -m tox -e  ${{ matrix.toxenv }}
-    - name: Report coverage
-      run: codecov
+  docs:
+    needs: [tests]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/tox.yml@v1
+    with:
+      toxdeps: tox-pypi-filter
+      envs: |
+        - linux: build_docs-gallery
+          python-version: '3.12'
+      libraries: |
+        apt:
+          - graphviz
+
+  publish:
+    # Build wheels when pushing to any branch except main
+    # publish.yml will only publish if tagged ^v.*
+    if: |
+      (
+        github.event_name != 'pull_request' && (
+          github.ref_name != 'main' ||
+          github.event_name == 'workflow_dispatch'
+        )
+      ) || (
+        github.event_name == 'pull_request' &&
+        contains(github.event.pull_request.labels.*.name, 'Run publish')
+      )
+    needs: [tests]
+    uses: OpenAstronomy/github-actions-workflows/.github/workflows/publish_pure_python.yml@main
+    with:
+      test_extras: 'dev'
+      test_command: 'pytest -p no:warnings --doctest-rst --pyargs synthesizAR'
+      submodules: false
+      python-version: '3.12'
+    secrets:
+      pypi_token: ${{ secrets.PYPI_TOKEN }}

.pre-commit-config.yaml

@@ -1,41 +1,39 @@
 repos:
-  # The warnings/errors we check for here are:
-  # E101 - mix of tabs and spaces
-  # W191 - use of tabs
-  # W291 - trailing whitespace
-  # W292 - no newline at end of file
-  # W293 - trailing whitespace
-  # W391 - blank line at end of file
-  # E111 - 4 spaces per indentation level
-  # E112 - 4 spaces per indentation level
-  # E113 - 4 spaces per indentation level
-  # E303 - too many blank lines (3)
-  # E304 - blank lines found after function decorator
-  # E305 - expected 2 blank lines after class or function definition
-  # E306 - expected 1 blank line before a nested definition
-  # E502 - the backslash is redundant between brackets
-  # E722 - do not use bare except
-  # E901 - SyntaxError or IndentationError
-  # E902 - IOError
-  # F822: undefined name in __all__
-  # F823: local variable name referenced before assignment
-  - repo: https://github.com/pycqa/flake8
-    rev: 3.7.9
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.4.4"
     hooks:
-      - id: flake8
-        args: ['--count', '--select', 'E101,W191,W291,W292,W293,W391,E111,E112,E113,E303,E304,E306,E502,E722,E901,E902,F822,F823']
+      - id: ruff
+        args: ["--fix"]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.13.2
+    hooks:
+    - id: isort
+      name: isort
+      entry: isort
+      require_serial: true
+      language: python
+      types:
+      - python
 
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.4.0
+    rev: v4.6.0
     hooks:
       - id: check-ast
       - id: check-case-conflict
       - id: trailing-whitespace
-        exclude: ".*(.fits|.fts|.fit|.txt|.asdf|.json)$"
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json)$"
       - id: check-yaml
       - id: debug-statements
       - id: check-added-large-files
       - id: end-of-file-fixer
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|.asdf|.json)$"
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.json|.bib|tca.*)$"
       - id: mixed-line-ending
-        exclude: ".*(.fits|.fts|.fit|.txt|tca.*|.asdf|.json)$"
+        exclude: ".*(.fits|.fts|.fit|.txt|.bib|.pro|.asdf|.json|tca.*)$"
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+        - tomli

.readthedocs.yml

@@ -1,24 +1,30 @@
 version: 2
 
 build:
-  os: ubuntu-22.04
+  os: ubuntu-lts-latest
   tools:
-    python: "3.11"
+    python: "mambaforge-latest"
   jobs:
     post_checkout:
       - git fetch --unshallow || true
     pre_install:
-      - git update-index --assume-unchanged docs/conf.py
+      - git update-index --assume-unchanged .rtd-environment.yml docs/conf.py
+
+conda:
+  environment: .rtd-environment.yml
 
 sphinx:
   builder: html
   configuration: docs/conf.py
   fail_on_warning: false
 
+formats:
+  - htmlzip
+
 python:
-   install:
-     - method: pip
-       extra_requirements:
+  install:
+    - method: pip
+      extra_requirements:
         - all
         - docs
-       path: .
+      path: .

.rtd-environment.yml

@@ -0,0 +1,7 @@
+name: rtd_synthesizAR
+channels:
+- conda-forge
+dependencies:
+  - python=3.12
+  - pip
+  - graphviz!=2.42.*,!=2.43.*

docs/code_ref/index.rst

@@ -1,6 +1,6 @@
-=============
-API Reference
-=============
+===
+API
+===
 
 .. toctree::
    :maxdepth: 1

docs/code_ref/synthesizar.rst

@@ -4,4 +4,3 @@ synthesizAR
 .. automodapi:: synthesizAR
    :no-heading:
    :no-inheritance-diagram:
-   :skip: test