Merge pull request #54 from desihub/pip-installable-package

pip installable package

.coveragerc

@@ -0,0 +1,28 @@
+[run]
+source = py/prospect
+omit =
+   py/prospect/_version.py
+   py/prospect/conftest*
+   py/prospect/cython_version*
+   py/prospect/setup_package*
+   py/prospect/*/setup_package*
+   py/prospect/*/*/setup_package*
+   py/prospect/sphinx/*
+   py/prospect/test/*
+   py/prospect/*/test/*
+   py/prospect/*/*/test/*
+
+[report]
+exclude_lines =
+   # Have to re-enable the standard pragma
+   pragma: no cover
+
+   # Don't complain about packages we have installed
+   except ImportError
+
+   # Don't complain if tests don't hit assertions
+   raise AssertionError
+   raise NotImplementedError
+
+   # Don't complain about script hooks
+   def main\(.*\):

.github/workflows/python-package.yml

@@ -0,0 +1,115 @@
+# Workflow is based on the Astropy GitHub actions workflow, ci_workflows.yml
+name: CI
+
+on:
+    push:
+        branches:
+            - '*'
+        tags:
+            - '*'
+    pull_request:
+
+jobs:
+    tests:
+        name: Unit tests
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: true
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.6, 3.7, 3.8]
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v2
+              with:
+                fetch-depth: 0
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install Python dependencies
+              run: |
+                python -m pip install --upgrade pip wheel
+                python -m pip install pytest
+                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+            - name: Run the test
+              run: pytest
+
+    coverage:
+        name: Test coverage
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: true
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.8]
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v2
+              with:
+                fetch-depth: 0
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install Python dependencies
+              run: |
+                python -m pip install --upgrade pip wheel
+                python -m pip install pytest pytest-cov coveralls
+                if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
+            - name: Run the test with coverage
+              run: pytest --cov
+            - name: Coveralls
+              env:
+                GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+              run: coveralls
+
+    docs:
+        name: Doc test
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.8]
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v2
+              with:
+                fetch-depth: 0
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install Python dependencies
+              run: python -m pip install --upgrade pip wheel Sphinx
+            - name: Test the documentation
+              run: sphinx-build -W --keep-going -b html doc doc/_build/html
+
+    style:
+        name: Style check
+        runs-on: ${{ matrix.os }}
+        strategy:
+            fail-fast: false
+            matrix:
+                os: [ubuntu-latest]
+                python-version: [3.8]
+
+        steps:
+            - name: Checkout code
+              uses: actions/checkout@v2
+              with:
+                fetch-depth: 0
+            - name: Set up Python ${{ matrix.python-version }}
+              uses: actions/setup-python@v2
+              with:
+                python-version: ${{ matrix.python-version }}
+            - name: Install Python dependencies
+              run: python -m pip install --upgrade pip wheel pycodestyle
+            - name: Test the style; failures are allowed
+              # This is equivalent to an allowed falure.
+              continue-on-error: true
+              run: pycodestyle --count py/prospect

.gitignore

@@ -1,17 +1,19 @@
 # Compiled files
+*.py[cod]
 __pycache__
-*.py[co]
 
 # Other generated files
 htmlcov
 .coverage
+py/prospect/.cache
+.pytest_cache
 
 # Sphinx
 doc/api
 doc/_build
 
 # iPython
-docs/nb/.ipynb_checkpoints
+doc/nb/.ipynb_checkpoints
 .ipynb_checkpoints
 
 # Packages/installer info
@@ -20,12 +22,14 @@ docs/nb/.ipynb_checkpoints
 dist
 build
 eggs
+.eggs
 parts
 var
 sdist
 develop-eggs
 .installed.cfg
 distribute-*.tar.gz
+MANIFEST
 
 # Other
 .*.swp

.readthedocs.yml

@@ -0,0 +1,18 @@
+# .readthedocs.yml
+# 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 doc/ directory with Sphinx
+sphinx:
+    configuration: doc/conf.py
+
+# Optionally build your docs in additional formats such as PDF and ePub
+formats: all
+
+# Optionally set the version of Python and requirements required to build your docs
+python:
+    version: 3
+    # system_packages: true

LICENSE.rst

@@ -1,4 +1,4 @@
-Copyright (c) 2014-2017, DESI Collaboration <desi-data@desi.lbl.gov>
+Copyright (c) 2018-2020, DESI Collaboration <desi-data@desi.lbl.gov>
 All rights reserved.
 
 Redistribution and use in source and binary forms, with or without modification,

MANIFEST.in

@@ -0,0 +1,12 @@
+include LICENSE.rst
+include README.rst
+include requirements.txt
+
+graft bin
+graft doc
+graft etc
+
+prune build
+prune dist
+prune htmlcov
+prune doc/_build

README.rst

@@ -0,0 +1,75 @@
+========
+prospect
+========
+Digging into DESI spectra, looking for stuff.
+---------------------------------------------
+
+|Actions Status| |Coveralls Status| |Documentation Status|
+
+This repository is a rewrite of inspector_, which itself is very much a work
+in progress.  This repository is intended to provide similar functionality
+as inspector, but do so without using ipywidgets so that it can be used as
+standalone code outside of Jupyter notebooks, while still also working within
+Jupyter notebooks.
+
+.. image:: screenshot.png
+    :alt: Prospect Screenshot
+
+.. _inspector: https://github.com/desihub/inspector
+
+.. |Actions Status| image:: https://github.com/desihub/prospect/workflows/CI/badge.svg
+    :target: https://github.com/desihub/prospect/actions
+    :alt: GitHub Actions CI Status
+
+.. |Coveralls Status| image:: https://coveralls.io/repos/desihub/prospect/badge.svg?branch=pip-installable-package
+    :target: https://coveralls.io/github/desihub/prospect?branch=pip-installable-package
+    :alt: Test Coverage Status
+
+.. |Documentation Status| image:: https://readthedocs.org/projects/desi-prospect/badge/?version=latest
+    :target: http://desi-prospect.readthedocs.org/en/latest/
+    :alt: Documentation Status
+
+What it does
+~~~~~~~~~~~~
+
+* Provides an interactive spectral viewer for DESI data at NERSC without
+  needing to download or install anything locally.
+* Interative zoom and pan
+* Shows noise estimated for each spectrum.
+* Shows redrock results including the redshift, ZWARN flags, and the
+  best fit model.
+* Mouse over a region of the spectrum to get a real-time zoom in a sub-window;
+  this is handy for inspecting narrow emission lines without zooming in and out
+  on each one.
+* Shows TARGETID and targeting bits from DESI_TARGET, MWS_TARGET,
+  and BGS_TARGET.
+* Highlight common emission / absorption lines.
+* Display imaging of target.
+* Buttons for saving visual inspection results before moving to next target.
+
+Added here but not in the original inspector
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+* Restframe wavelengths
+* User-defined smoothing
+* User-defined redshift
+* Viewing spectra that don't yet have redshift fits
+
+What it doesn't do (yet)
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Any of these could be added later but don't yet exist.
+If you really want a feature, please consider contributing it.
+
+* Show individual exposures (multiple exposures are coadded prior to display)
+* Show masks
+* Show the Nth best fit instead of just the best fit
+* More target info like mags and shapes
+* Displaying model of 2D sky-subtracted raw data
+* Filtering to individual exposures or tiles
+
+-----
+
+:Eric Armengaud: Saclay - CEA
+:Stephen Bailey: Lawrence Berkeley National Lab
+:Benjamin Weaver: NSF's National Optical-Infrared Astronomy Research Laboratory

bin/run_cmx_htmlfiles

@@ -1,15 +1,6 @@
 #!/usr/bin/env python
-#
-# See top-level LICENSE.rst file for Copyright information
-#
-
-"""
-Write html index pages from existing static pages/images produced by other scripts
-"""
-
-import prospect.scripts.prepare_cmx_htmlfiles as prepare_cmx_htmlfiles 
-
-if __name__ == '__main__':
-    args = prepare_cmx_htmlfiles.parse()
-    prepare_cmx_htmlfiles.main(args)
-
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from prospect.scripts.prepare_cmx_htmlfiles import main
+exit(main())

bin/run_htmlfiles

@@ -1,15 +1,6 @@
 #!/usr/bin/env python
-#
-# See top-level LICENSE.rst file for Copyright information
-#
-
-"""
-Write html index pages from existing static pages/images produced by other scripts
-"""
-
-import prospect.scripts.prepare_htmlfiles as prepare_htmlfiles 
-
-if __name__ == '__main__':
-    args = prepare_htmlfiles.parse()
-    prepare_htmlfiles.main(args)
-
+# -*- coding: utf-8 -*-
+# Licensed under a 3-clause BSD style license - see LICENSE.rst
+from sys import exit
+from prospect.scripts.prepare_htmlfiles import main
+exit(main())