Merge branch 'dev' of https://github.com/USGS-Astrogeology/autocnet into mi_matcher

    branches:

      - dev

env:

  isis-root: /usr/share/miniconda/envs/isis/

  isis-data: test-resources/ISISDATA/

  hirise-pds-url: https://hirise-pds.lpl.arizona.edu/PDS/EDR/PSP/ORB_010500_010599/PSP_010502_2090

jobs:

  Build-and-Test:

    runs-on: ${{ matrix.os }}

      run:

        shell: bash -l {0}

    steps:

      - name: ISIS Conda Env

        uses: conda-incubator/setup-miniconda@v2

        with:

          python-version: 3.6

          activate-environment: isis

          channels: usgs-astrogeology, conda-forge

      - name: Install ISIS

        run: |

          conda install -q -y -c usgs-astrogeology isis

      - name: Setup test-resources/

        run: |

          mkdir $GITHUB_WORKSPACE/test-resources/

          mkdir $GITHUB_WORKSPACE/${{ env.isis-data }}

      - name: Download IMG

        run: |

          curl "${{ env.hirise-pds-url }}/PSP_010502_2090_RED5_0.IMG" -o $GITHUB_WORKSPACE/test-resources/PSP_010502_2090_RED5_0.img

          curl "${{ env.hirise-pds-url }}/PSP_010502_2090_RED5_1.IMG" -o $GITHUB_WORKSPACE/test-resources/PSP_010502_2090_RED5_1.img

      - name: Exit isis env

        run: conda deactivate

      - name: Checkout Code

        uses: actions/checkout@v2

      - name: Cache conda

        uses: actions/cache@v2

        env:

          # Increase this value to reset cache if etc/example-environment.yml has not changed

          CACHE_NUMBER: 0

        with:

          path: ~/conda_pkgs_dir

          key:

            ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{

            hashFiles('environment.yml') }}

      - name: Setup ENV

        uses: conda-incubator/setup-miniconda@v2

        with:

          miniconda-version: "latest"

          mamba-version: "*"

          use-mamba: true

          channels: conda-forge, defaults

          channels: conda-forge

          channel-priority: strict

          activate-environment: autocnet

          environment-file: environment.yml

          use-only-tar-bz2: true

          python-version: ${{ matrix.python-version }}

      - name: config ISIS vars

        run: |

          conda env config vars set ISISROOT=${{ env.isis-root }}

          conda env config vars set ISISDATA=$GITHUB_WORKSPACE/${{ env.isis-data }}

      - name: Check build environment

        run: |

          conda list

# .readthedocs.yaml

# Read the Docs configuration file

# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details

# Required

version: 2

# Build documentation in the docs/ directory with Sphinx

sphinx:

  configuration: docs/conf.py

conda:

  environment: docs/environment.yml

Contributors

------------

None yet. Why not be the first?

`Ross Beyer <https://github.com/rbeyer>`_

# Changelog

All changes that impact users of this project will be documented in this file.

The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),

and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

<!---

This document is intended for users of the applications and API. Changes to things

like tests should not be noted in this document.

When updating this file for a PR, add an entry for your change under Unreleased

and one of the following headings:

 - Added - for new features.

 - Changed - for changes in existing functionality.

 - Deprecated - for soon-to-be removed features.

 - Removed - for now removed features.

 - Fixed - for any bug fixes.

 - Security - in case of vulnerabilities.

If the heading does not yet exist under Unreleased, then add it as a 3rd heading,

with three #.

When preparing for a public release candidate add a new 2nd heading, with two #, under

Unreleased with the version number and the release date, in year-month-day

format. Then, add a link for the new version at the bottom of this document and

update the Unreleased link so that it compares against the latest release tag.

When preparing for a bug fix release create a new 2nd heading above the Fixed

heading to indicate that only the bug fixes and security fixes are in the bug fix

release.

-->

## [0.6.0]

### Added

- Abstract DEM interface that supports ellipsoids #576

- Fourier-Mellon subpixel registration #558

### Changed

- Updates center of gravity style subpixel matcher to use scipy.ndimage.center_of_mass of determining subpixel shifts

- Use `kalisiris` instead of `pysis` #573

- Moved `acn_submit` cluster submission script into the library and added tests for cluster submission #567

- Point identifier no longer needs to be a unique string

### Fixed

- Image to ground to support multiple input types with proper output type handling #580

- Support for ISIS special pixels in image data #577

- Fix for no correlation map returned from `geom_match_simple` #556

.PHONY: clean clean-test clean-pyc clean-build docs help

.DEFAULT_GOAL := help

define BROWSER_PYSCRIPT

import os, webbrowser, sys

from urllib.request import pathname2url

webbrowser.open("file://" + pathname2url(os.path.abspath(sys.argv[1])))

endef

export BROWSER_PYSCRIPT

define PRINT_HELP_PYSCRIPT

import re, sys

for line in sys.stdin:

	match = re.match(r'^([a-zA-Z_-]+):.*?## (.*)$$', line)

	if match:

		target, help = match.groups()

		print("%-20s %s" % (target, help))

endef

export PRINT_HELP_PYSCRIPT

define DOWNLOAD_PYSCRIPT

import urllib.request, sys

urllib.request.urlretrieve(sys.argv[1],sys.argv[2])

endef

export DOWNLOAD_PYSCRIPT

BROWSER := python -c "$$BROWSER_PYSCRIPT"

DOWNLOAD := python -c "$$DOWNLOAD_PYSCRIPT"

help:

	@python -c "$$PRINT_HELP_PYSCRIPT" < $(MAKEFILE_LIST)

clean: clean-build clean-pyc clean-test ## remove all build, test, coverage and Python artifacts

clean-build: ## remove build artifacts

	rm -fr build/

	rm -fr dist/

	rm -fr .eggs/

	find . -name '*.egg-info' -exec rm -fr {} +

	find . -name '*.egg' -exec rm -f {} +

clean-pyc: ## remove Python file artifacts

	find . -name '*.pyc' -exec rm -f {} +

	find . -name '*.pyo' -exec rm -f {} +

	find . -name '*~' -exec rm -f {} +

	find . -name '__pycache__' -exec rm -fr {} +

clean-test: ## remove test and coverage artifacts

	rm -fr .tox/

	rm -f .coverage

	rm -fr htmlcov/

	rm -fr .pytest_cache

	rm -fr test-resources

lint: ## check style with flake8

	flake8 --max-complexity 10 --ignore E203,E501,W503 autocnet tests

test: ## run tests quickly with the default Python

	pytest autocnet

test-resources: ## Download what we need for testing

	mkdir test-resources

	$(DOWNLOAD) https://hirise-pds.lpl.arizona.edu/PDS/EDR/PSP/ORB_010500_010599/PSP_010502_2090/PSP_010502_2090_RED5_0.IMG test-resources/PSP_010502_2090_RED5_0.img

	$(DOWNLOAD) https://hirise-pds.lpl.arizona.edu/PDS/EDR/PSP/ORB_010500_010599/PSP_010502_2090/PSP_010502_2090_RED5_1.IMG test-resources/PSP_010502_2090_RED5_1.img

test-all: ## run tests on every Python version with tox

	tox

coverage: test  ## check code coverage quickly with the default Python

	coverage report -m

	coverage html

	$(BROWSER) htmlcov/index.html

docs: ## generate Sphinx HTML documentation, including API docs

	rm -f docs/autocnet.rst

	rm -f docs/modules.rst

	sphinx-apidoc -o docs/ autocnet

	$(MAKE) -C docs clean

	$(MAKE) -C docs html

	$(BROWSER) docs/_build/html/index.html

servedocs: docs ## compile the docs watching for changes

	watchmedo shell-command -p '*.rst' -c '$(MAKE) -C docs html' -R -D .

release: dist ## package and upload a release

	twine upload dist/*

dist: clean ## builds source and wheel package

	python setup.py sdist

	python setup.py bdist_wheel

	ls -l dist

install: clean ## install the package to the active Python's site-packages

	python setup.py install