Update packaging and add tox

.gitignore

@@ -10,3 +10,7 @@ docs/_build/*
 goodman_pipeline/data/dcr-source/dcr
 goodman_pipeline/data/dcr-source/*.o
 /dev-tools/
+.tox/*
+.tmp/*
+.eggs/*
+.cache/*

README.md

@@ -1,13 +1,12 @@
 # Goodman High Throughput Spectrograph Data Reduction Pipeline
 
-[![Build Status](https://travis-ci.org/soar-telescope/goodman_pipeline.svg?branch=master)](https://travis-ci.org/soar-telescope/goodman_pipeline)
+![Goodman Pipeline](https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline/badge.svg?branch=master)
 [![Coverage Status](https://coveralls.io/repos/github/soar-telescope/goodman_pipeline/badge.svg?branch=master)](https://coveralls.io/github/soar-telescope/goodman_pipeline?branch=master)
 [![Documentation Status](https://readthedocs.org/projects/goodman/badge/?version=latest)](http://goodman.readthedocs.io/en/latest/?badge=latest)
 [![pypi](https://img.shields.io/pypi/v/goodman_pipeline.svg?style=flat)](https://pypi.org/project/goodman-pipeline/)
 [![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/)
 
-![Goodman Pipeline](https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline/badge.svg?branch=master)
-![Goodman Pipeline with Conda](https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline%20with%20Conda/badge.svg)
+
 ![Upload to PYPI](https://github.com/soar-telescope/goodman_pipeline/workflows/Upload%20to%20PYPI/badge.svg)
 
 ## Overview
@@ -51,8 +50,8 @@ open a [new Issue](https://github.com/soar-telescope/goodman_pipeline/issues/new
 
 We acknowledge the important contribution of [David Sanmartim](https://github.com/dsanmartim), who developed
 the initial incarnation of the redccd module. We thank [Tina Armond](https://github.com/tarmond) for her
-invaluable help in adding calibrated comparison lamps to the library of
-reference comparison lamps for wavelngth solution.
+invaluable help in adding calibrated comparison lamps to the [library](https://goodman.readthedocs.io/projects/lamps/en/latest/) of
+reference comparison lamps for wavelength solution.
 
 Our work would not be possible without the friendly work atmosphere at CTIO
 headquarters in La Serena, were we can interact with our SOAR and CTIO

docs/index.rst

@@ -12,8 +12,8 @@
 Welcome to the Goodman HTS Pipeline Documentation
 =================================================
 
-.. image:: https://travis-ci.org/soar-telescope/goodman_pipeline.svg?branch=master
- :target: https://travis-ci.org/soar-telescope/goodman_pipeline
+.. image:: https://github.com/soar-telescope/goodman_pipeline/workflows/Goodman%20Pipeline/badge.svg?branch=master
+ :alt: Goodman Pipeline
 .. image:: https://coveralls.io/repos/github/soar-telescope/goodman_pipeline/badge.svg?branch=master
  :target: https://coveralls.io/github/soar-telescope/goodman_pipeline?branch=master
 .. image:: https://readthedocs.org/projects/goodman/badge/?version=latest

goodman_pipeline/core/tests/test_core.py → goodman_pipeline/tests/test_core.py

@@ -21,62 +21,62 @@
 logging.disable(logging.CRITICAL)
 
 # import all classes in core.py
-from ..core import (GenerateDcrParFile,
- NightDataContainer,
- NoMatchFound,
- NotEnoughLinesDetected,
- NoTargetException,
- ReferenceData,
- SaturationValues,
- SpectroscopicMode)
+from goodman_pipeline.core.core import (GenerateDcrParFile,
+  NightDataContainer,
+  NoMatchFound,
+  NotEnoughLinesDetected,
+  NoTargetException,
+  ReferenceData,
+  SaturationValues,
+  SpectroscopicMode)
 
 
 # import of functions in core.py
-from ..core import (astroscrappy_lacosmic,
- add_linear_wavelength_solution,
- add_wcs_keys,
- bias_subtract,
- bin_reference_data,
- call_cosmic_rejection,
- classify_spectroscopic_data,
- combine_data,
- convert_time,
- create_master_bias,
- create_master_flats,
- cross_correlation,
- dcr_cosmicray_rejection,
- define_trim_section,
- extraction,
- extract_fractional_pixel,
- extract_optimal,
- evaluate_wavelength_solution,
- fix_keywords,
- fractional_sum,
- get_best_flat,
- get_central_wavelength,
- get_lines_in_lamp,
- get_overscan_region,
- get_spectral_characteristics,
- get_slit_trim_section,
- get_twilight_time,
- identify_targets,
- image_overscan,
- image_trim,
- interpolate,
- is_file_saturated,
- linearize_spectrum,
- name_master_flats,
- normalize_master_flat,
- ra_dec_to_deg,
- read_fits,
- record_trace_information,
- save_extracted,
- search_comp_group,
- setup_logging,
- trace,
- trace_targets,
- validate_ccd_region,
- write_fits)
+from goodman_pipeline.core.core import (astroscrappy_lacosmic,
+  add_linear_wavelength_solution,
+  add_wcs_keys,
+  bias_subtract,
+  bin_reference_data,
+  call_cosmic_rejection,
+  classify_spectroscopic_data,
+  combine_data,
+  convert_time,
+  create_master_bias,
+  create_master_flats,
+  cross_correlation,
+  dcr_cosmicray_rejection,
+  define_trim_section,
+  extraction,
+  extract_fractional_pixel,
+  extract_optimal,
+  evaluate_wavelength_solution,
+  fix_keywords,
+  fractional_sum,
+  get_best_flat,
+  get_central_wavelength,
+  get_lines_in_lamp,
+  get_overscan_region,
+  get_spectral_characteristics,
+  get_slit_trim_section,
+  get_twilight_time,
+  identify_targets,
+  image_overscan,
+  image_trim,
+  interpolate,
+  is_file_saturated,
+  linearize_spectrum,
+  name_master_flats,
+  normalize_master_flat,
+  ra_dec_to_deg,
+  read_fits,
+  record_trace_information,
+  save_extracted,
+  search_comp_group,
+  setup_logging,
+  trace,
+  trace_targets,
+  validate_ccd_region,
+  write_fits)
 
 
 def fake_subprocess_popen(*args, stdout, stderr):
@@ -233,9 +233,9 @@ class ClassifySpectroscopicData(TestCase):
  def setUp(self):
  self.path = os.path.join(
  os.getcwd(),
- 'goodman_pipeline/data/test_data/test_classify_spectroscopic');
+ 'test_classify_spectroscopic')
  if not os.path.isdir(self.path):
- os.mkdir(self.path)
+ os.makedirs(self.path)
 
  def tearDown(self):
  if os.path.isdir(self.path):
@@ -1386,11 +1386,13 @@ def tearDown(self):
  self.assertFalse(os.path.isfile(norm_flat))
 
  def test_get_best_flat(self):
- # print(self.flat_name_base)
+ print(self.flat_name_base)
+ print(os.path.dirname(__file__))
 
  master_flat, master_flat_name = get_best_flat(
  flat_name=self.flat_name_base,
  path=self.flat_path)
+ print(master_flat_name)
  self.assertIsInstance(master_flat, CCDData)
  self.assertEqual(os.path.basename(master_flat_name),
  self.reference_flat_name)

goodman_pipeline/images/tests/test_data_classifier.py → goodman_pipeline/tests/test_data_classifier.py

@@ -9,7 +9,7 @@
 from ccdproc import CCDData
 from unittest import TestCase, skip
 
-from ..data_classifier import DataClassifier
+from goodman_pipeline.images.data_classifier import DataClassifier
 
 
 class DataClassifierTests(TestCase):

goodman_pipeline/images/tests/test_goodman_ccd.py → goodman_pipeline/tests/test_goodman_ccd.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 from unittest import TestCase, skip
 
-from ..goodman_ccd import get_args, MainApp
+from goodman_pipeline.images.goodman_ccd import get_args, MainApp
 
 
 class MainAppTest(TestCase):

goodman_pipeline/images/tests/test_image_processor.py → goodman_pipeline/tests/test_image_processor.py

@@ -4,9 +4,9 @@
 from unittest import TestCase, skip
 
 from ccdproc import CCDData
-from ...core import NightDataContainer
-from ..image_processor import ImageProcessor
-from ..goodman_ccd import get_args
+from goodman_pipeline.core import NightDataContainer
+from goodman_pipeline.images.image_processor import ImageProcessor
+from goodman_pipeline.images.goodman_ccd import get_args
 
 import numpy as np
 

goodman_pipeline/images/tests/test_night_organizer.py → goodman_pipeline/tests/test_night_organizer.py

@@ -9,7 +9,7 @@
 from ccdproc import CCDData
 from unittest import TestCase, skip
 
-from ..night_organizer import NightOrganizer
+from goodman_pipeline.images.night_organizer import NightOrganizer
 
 
 def create_fake_data(technique, instrument, path):

goodman_pipeline/spectroscopy/tests/test_redspec.py → goodman_pipeline/tests/test_redspec.py

@@ -5,7 +5,7 @@
 import shutil
 from unittest import TestCase
 
-from ...spectroscopy.redspec import (get_args, MainApp)
+from goodman_pipeline.spectroscopy.redspec import (get_args, MainApp)
 
 
 class TestArguments(TestCase):
@@ -103,8 +103,8 @@ def test_destination_path_sysexit(self):
 
 
 def test_get_args():
- from ...spectroscopy.redspec import get_args
- import argparse
+ # from ...spectroscopy.redspec import get_args
+ # import argparse
  arguments = ['--data-path', './',
  '--proc-path', './',
  '--search-pattern', 'test-pattern',

goodman_pipeline/spectroscopy/tests/test_wavelength.py → goodman_pipeline/tests/test_wavelength.py

@@ -10,11 +10,11 @@
 from astropy.modeling import models, Model
 from ccdproc import CCDData
 from unittest import TestCase, skip
-from ..wavelength import (WavelengthCalibration)
+from goodman_pipeline.spectroscopy.wavelength import (WavelengthCalibration)
 
-from ..redspec import get_args
-from ...core import add_wcs_keys, write_fits
-from ...core import ReferenceData, NoMatchFound
+from goodman_pipeline.spectroscopy.redspec import get_args
+from goodman_pipeline.core import add_wcs_keys, write_fits
+from goodman_pipeline.core import ReferenceData, NoMatchFound
 
 
 class WavelengthCalibrationTests(TestCase):

goodman_pipeline/wcs/tests/test_functional.py → goodman_pipeline/tests/test_wcs_functional.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 
 from unittest import TestCase, skip
-from ..wcs import WCS
+from goodman_pipeline.wcs.wcs import WCS
 import numpy as np
 import os
 import re

goodman_pipeline/wcs/tests/test_unittest.py → goodman_pipeline/tests/test_wcs_unittest.py

@@ -1,7 +1,7 @@
 from __future__ import absolute_import
 
 from unittest import TestCase, skip
-from ..wcs import WCS
+from goodman_pipeline.wcs.wcs import WCS
 import numpy as np
 import os
 import re

goodman_pipeline/version.py

@@ -1,2 +1,2 @@
 # This is an automatic generated file please do not edit
-__version__ = '1.3.2.dev1'
+__version__ = '1.3.2'

pyproject.toml

@@ -0,0 +1,7 @@
+[build-system]
+
+requires = ["setuptools",
+ "setuptools_scm",
+ "wheel"]
+
+build-backend = 'setuptools.build_meta'

setup.cfg

@@ -22,6 +22,16 @@ license = BSD-3-Clause
 # url =
 edit_on_github = False
 github_project = soar-telescope/goodman_pipeline
+
+# version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
+version = 1.3.2
+
+[options]
+zip_safe = False
+include_package_data = True
+packages = find:
+python_requires = >=3.6
+setup_requires = setuptools_scm
 install_requires =
  numpy
  pandas
@@ -31,5 +41,13 @@ install_requires =
  astropy
  ccdproc
  astroplan
-# version should be PEP440 compatible (http://www.python.org/dev/peps/pep-0440)
-version = 1.3.2
+
+# [options.entry_points]
+# console_scripts =
+# astropy-package-template-example = packagename.example_mod:main
+
+[options.extras_require]
+test =
+ requests
+docs =
+ sphinx-astropy

setup.py

@@ -48,6 +48,7 @@ def create_version_py(packagename, version, source_dir='.'):
 # conf.read([os.path.join(os.path.dirname(__file__), '..', 'setup.cfg')])
 conf.read([os.path.join(os.path.dirname(__file__), 'setup.cfg')])
 metadata = dict(conf.items('metadata'))
+options = dict(conf.items('options'))
 
 PACKAGENAME = metadata['package_name']
 
@@ -65,7 +66,7 @@ def create_version_py(packagename, version, source_dir='.'):
 
 AUTHOR_EMAIL = metadata['author_email']
 
-INSTALL_REQUIRES = metadata['install_requires'].split()
+INSTALL_REQUIRES = options['install_requires'].split()
 
 # freezes version information in version.py
 create_version_py(PACKAGENAME, VERSION)