Occult 2 (#31)

* added helpers

* Added skeleton of the occult

* added return part

* Added tests for helpers

* Moved to  test folder

* Fixed the test

* Added changelog

* fixed pep8

* Changed Return typr

* Major modifications, closer to IDL

* Fixed zeroing out

* Fixed reference

* removed some bugs

* Fixed the mean calculations

* fixed background

* negated smaller loops

* added some docs

* Tidy up of the code and other items.

* added exact idl replica

* sub functions

* fixed occult

* docs completed

* few tests and examples

* more tests

* main test

* fixed extra loop points

* Apply suggestions from code review

Co-Authored-By: Nabil Freij <nabil.freij@gmail.com>

* tests complete

* some fixes

* vectorize attempt

* Apply suggestions from code review

Co-Authored-By: Nabil Freij <nabil.freij@gmail.com>

* fixed unintended changes

* Further fixes

* vectorized

* fixed hash

* docs

* test file reduced

* ran linters

* changed to online

* fixing setup.cfg

* updated tox.ini

* fixed pyproject.toml

* changed setup.py

* fix things

*  circleci update

*  circleci update v2

*  circleci update v3

* moved to utils

* fixed pep8

* ran linters

* fixed docs

Author: vatch123

.circleci/config.yml

@@ -11,28 +11,24 @@ merge-check: &merge-check
       git checkout -qf pr/$CIRCLE_PR_NUMBER/merge
     fi
 
-apt-run: &apt-install
-  name: Install apt packages
-  command: |
-    sudo apt update
-    sudo apt install -y graphviz
-
 permission-run: &permission-run
   name: Fix permssions for installing
   command: |
     sudo chown -R circleci:circleci /usr/local/bin
     sudo chown -R circleci:circleci /usr/local/lib/python3.7/site-packages
     sudo chown -R circleci:circleci /usr/local/share/
 
-tox-install: &tox-install
-  name: Install Tox
+apt-run: &apt-install
+  name: Install apt packages
   command: |
-    pip install tox
+    apt update
+    apt install -y graphviz build-essential libopenjp2-7 git
 
-tox-conda-install: &tox-conda-install
-  name: Install Tox-Conda
+sudo-apt-run: &sudo-apt-install
+  name: Install apt packages
   command: |
-    pip install tox-conda
+    sudo apt update
+    sudo apt install -y graphviz build-essential libopenjp2-7 git
 
 version: 2
 jobs:
@@ -54,24 +50,31 @@ jobs:
       - run: *merge-check
       - run: python setup.py egg_info
 
+  twine-check:
+    docker:
+      - image: circleci/python:3.7
+    steps:
+      - checkout
+      - run: *skip-check
+      - run: *merge-check
+      - run: *permission-run
+      - run: python setup.py sdist
+      - run: python -m pip install -U --force-reinstall twine
+      - run: python -m twine check dist/*
+
   pip-install:
     docker:
       - image: circleci/python:3.7
     steps:
       - checkout
       - run: *skip-check
       - run: *merge-check
-      - run: *apt-install
+      - run: *sudo-apt-install
       - run: *permission-run
-      - run:
-          name: Update pip
-          command: pip install -U pip
-      - run:
-          name: Install sunkit_image
-          command: |
-            pip install --progress-bar off .[all,dev]
-            pip install --no-use-pep517 -e .[all,dev]
-            python setup.py develop
+      - run: pip install -U pip
+      - run: pip install --progress-bar off .[all,dev]
+      - run: pip install -e .[all,dev]
+      - run: python setup.py develop
 
   figure-tests-37:
     docker:
@@ -80,10 +83,9 @@ jobs:
       - checkout
       - run: *skip-check
       - run: *merge-check
-      - run: *tox-install
-      - run: *tox-conda-install
+      - run: *apt-install
+      - run: pip install -U tox tox-conda codecov
       - run: tox -e figure
-      - run: pip install codecov
       - run: codecov
       - store_artifacts:
           path: figure_test_images
@@ -98,9 +100,9 @@ jobs:
       - checkout
       - run: *skip-check
       - run: *merge-check
-      - run: *apt-install
       - run: *permission-run
-      - run: *tox-install
+      - run: *sudo-apt-install
+      - run: pip install -U tox
       - run: tox -e build_docs
       - store_artifacts:
           path: docs/_build/html
@@ -117,14 +119,18 @@ workflows:
       - egg-info-36
       - egg-info-37
 
-  figure-tests:
+  twine-check:
     jobs:
-      - figure-tests-37
+      - twine-check
 
   pip-install:
     jobs:
       - pip-install
 
+  figure-tests:
+    jobs:
+      - figure-tests-37
+
   test-documentation:
     jobs:
       - html-docs

.gitignore

@@ -220,3 +220,4 @@ tags
 
 # Release script
 .github_cache
+examples/loops.txt

astropy_helpers

@@ -13,15 +13,15 @@ jobs:
 
 - template: azure-templates.yml
   parameters:
-    name: macOS_37_offline
+    name: macOS_37_online
     os: macos
-    tox: py37-offline --
+    tox: py37-online --
 
 - template: azure-templates.yml
   parameters:
-    name: Windows_36_offline
+    name: Windows_36_online
     os: windows
-    tox: py36-offline --
+    tox: py36-online --
 
 - template: azure-templates.yml
   parameters:

azure-pipelines.yml

@@ -0,0 +1 @@
+Added a new function (`sunkit_image.trace.occult2`) to automatically trace out loops/curved structures in an image.

changelog/31.feature.rst

@@ -8,6 +8,7 @@ Code Reference
    :maxdepth: 2
 
    sunkit_image
+   enhance
    radial
+   trace
    utils
-   enhance

docs/code_ref/index.rst

@@ -0,0 +1,7 @@
+*****
+trace
+*****
+
+This package implements tracing routines for solar physics data.
+
+.. automodapi:: sunkit_image.trace

docs/code_ref/trace.rst

@@ -1,6 +1,7 @@
 import os
 import sys
 import datetime
+
 # Get configuration information from setup.cfg
 from configparser import ConfigParser
 
@@ -95,13 +96,17 @@
         "plot_gallery": True,
     }
 
-# Write the latest changelog into the documentation.
+"""
+Write the latest changelog into the documentation.
+"""
 target_file = os.path.abspath("./whatsnew/latest_changelog.txt")
 try:
     from sunpy.util.towncrier import generate_changelog_for_docs
 
     if is_development:
         generate_changelog_for_docs("../", target_file)
+    else:
+        open(target_file, "a").close()
 except Exception:
     # If we can't generate it, we need to make sure it exists or else sphinx
     # will complain.

docs/conf.py

@@ -10,8 +10,8 @@
 
 import matplotlib.pyplot as plt
 
-import sunpy.map
 import sunpy.data.sample
+import sunpy.map
 
 import sunkit_image.enhance as enhance
 

examples/multiscale_gaussian_normalization.py

@@ -11,9 +11,8 @@
 import matplotlib.pyplot as plt
 
 import astropy.units as u
-
-import sunpy.map
 import sunpy.data.sample
+import sunpy.map
 
 import sunkit_image.radial as radial
 from sunkit_image.utils import equally_spaced_bins