adds docs, reformat with ruff, set up package

.github/workflows/CI.yml

@@ -0,0 +1,46 @@
+# This workflow will install Python dependencies, run tests and lint with a variety of Python versions
+# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
+
+name: CI
+
+on:
+  push:
+  pull_request:
+  schedule:
+    - cron: '0 8 * * *'
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+    strategy:
+      fail-fast: false
+      matrix:
+        python-version: ["3.9", "3.10", "3.11", "3.12"]
+
+    steps:
+    - uses: actions/checkout@v3
+    - name: Set up Python ${{ matrix.python-version }}
+      uses: actions/setup-python@v3
+      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 --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: Test with pytest
+      run: |
+        pip install .
+        python setup.py pytest --addopts "--cov ."
+#    - name: Upload coverage to Codecov
+#      uses: codecov/codecov-action@v4
+#      env:
+#        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
+#      with:
+#        fail_ci_if_error: true
+#        verbose: true

.gitignore

@@ -162,4 +162,4 @@ cython_debug/
 
 # overlappogram data
 data/
-output/
+output/

.pre-commit-config.yaml

@@ -0,0 +1,39 @@
+repos:
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: "v0.1.5"
+    hooks:
+      - id: ruff
+        args: ["--fix"]
+
+  - repo: https://github.com/PyCQA/isort
+    rev: 5.12.0
+    hooks:
+    - id: isort
+      name: isort
+      entry: isort
+      require_serial: true
+      language: python
+      types:
+      - python
+
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v4.4.0
+    hooks:
+      - id: check-ast
+      - id: check-case-conflict
+      - id: trailing-whitespace
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf)"
+      - id: check-yaml
+      - id: debug-statements
+      - id: check-added-large-files
+      - id: end-of-file-fixer
+        exclude: ".*(.fits|.fts|.fit|.txt|.pro|.asdf|.bib|tca.*)"
+      - id: mixed-line-ending
+        exclude: ".*(.fits|.fts|.fit|.txt|.bib|.asdf|tca.*)"
+
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.6
+    hooks:
+      - id: codespell
+        additional_dependencies:
+        - tomli

ECCCO_multiion_inversion.py

@@ -1,31 +1,21 @@
 #!/usr/bin/env python3
-# -*- coding: utf-8 -*-
 """
 Created on Wed Jun  9 08:52:51 2021
 
 @author: dbeabout
 """
-from magixs_data_products import MaGIXSDataProducts
-from overlappogram.create_gnt_image import create_gnt_image
-from overlappogram.create_color_color_plot import create_color_color_plot
+import os
+# from overlappogram.lassolars_model import LassoLarsModel as llars_model
+import time
+
 import numpy as np
 from astropy.io import fits
-import os
-import re
-import matplotlib.pyplot as plt
-from overlappogram.inversion_field_angles import Inversion
 #from overlappogram.inversion_field_angles_logts_ions import Inversion
-from sklearn.linear_model import ElasticNet as enet, SGDRegressor, Ridge
+from sklearn.linear_model import ElasticNet as enet
+
+from magixs_data_products import MaGIXSDataProducts
 from overlappogram.elasticnet_model import ElasticNetModel as model
-from overlappogram.sgd_model import SGDModel
-from overlappogram.ridge_model import RidgeModel
-from sklearn.linear_model import LassoLars as llars
-# from overlappogram.lassolars_model import LassoLarsModel as llars_model
-import time
-import pandas as pd
-from joblib import Parallel, delayed, parallel_backend
-import warnings
-from sklearn.exceptions import ConvergenceWarning
+from overlappogram.inversion_field_angles import Inversion
 
 '''def calculate_weights(data, weights, sig_read, exp_time):
     # Read image
@@ -117,7 +107,13 @@
         rhos = [.1]
         for rho in rhos:
             for alpha in alphas:
-                enet_model = enet(alpha=alpha, l1_ratio=rho, max_iter=100000,precompute=True, positive=True, fit_intercept=False, selection='cyclic')
+                enet_model = enet(alpha=alpha,
+                                  l1_ratio=rho,
+                                  max_iter=100000,
+                                  precompute=True,
+                                  positive=True,
+                                  fit_intercept=False,
+                                  selection='cyclic')
                 inv_model = model(enet_model)
 
                 # regressor = SGDRegressor(penalty='elasticnet', alpha=alpha, l1_ratio=rho, fit_intercept=False)
@@ -131,19 +127,8 @@
                 start = time.time()
                 inversion.multiprocessing_invert(inv_model, inversion_dir, output_file_prefix=basename,
                 #inversion.invert(inv_model, inversion_dir, output_file_prefix=basename,
-                            output_file_postfix='x'+str(solution_fov_width)+'_'+str(rho*10)+'_'+str(alpha)+'_wpsf' ,detector_row_range=detector_row_range, score=False)
+                            output_file_postfix='x'+str(solution_fov_width)+'_'+str(rho*10)+'_'+str(alpha)+'_wpsf' ,
+                                                 detector_row_range=detector_row_range,
+                                                 score=False)
                 end = time.time()
                 print("Inversion Time =", end - start)
-
-            ##create spectrally pure
-     ####           mdp = MaGIXSDataProducts()
-    ####            dir_path=inversion_dir
-     #           image_list = [dir_path + 'eccco_lw_forwardmodel_thermal_response_psf'+str(psf)+'pix_el_decon_em_data_cube_x'+str(solution_fov_width)+'_'+str(rho*10)+'_'+str(alpha)+'.fits]'
-    ####            image_list = [dir_path + 'eccco_is_lw_psf'+str(psf)+'pix_el_em_data_cube_x'+str(solution_fov_width)+'_'+str(rho*10)+'_'+str(alpha)+'_wpsf.fits']
-    ####            gnt_dir=response_dir
-     ####           gnt_file = gnt_dir + 'master_gnt_eccco_inelectrons_cm3perspersr_with_tables.fits'
-
-    ####            rsp_dep_list = np.round((np.arange(56, 68, 1) / 10.0), decimals=1)
-    ####            mdp.create_level2_0_spectrally_pure_images(image_list, gnt_file, rsp_dep_list, dir_path)
-
-