Merge 2ea9ce9 into 87c6d0a

.travis.yml

@@ -38,30 +38,15 @@ install:
   - conda info -a
 
   # create environment and install dependencies
-  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION numpy>=1.15.0 scipy nose pip matplotlib coverage
+  - conda create -q -n test-environment python=$TRAVIS_PYTHON_VERSION coveralls
   - source activate test-environment
-  - conda install -c conda-forge healpy aipy
-  - pip install coveralls
-  - pip install h5py
-  - if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then
-      pip install scikit-learn==0.20.3;
-    else
-      pip install scikit-learn;
-    fi
-  - pip install git+https://github.com/HERA-Team/pyuvdata.git$PYUVDATA_VERSION
-  - pip install git+https://github.com/HERA-Team/omnical.git
-  - pip install git+https://github.com/HERA-Team/linsolve.git
-  - pip install git+https://github.com/HERA-Team/hera_qm.git
-  - pip install git+https://github.com/HERA-Team/uvtools.git
-  - pip install git+https://github.com/HERA-Team/hera_cal.git
-  - pip install pyyaml
-  - pip install multiprocess
-  - python setup.py install
+  - conda env update -n test-environment -f environment.yml
+  - pip install .
 
 before_script:
   - "export MPLBACKEND=agg"
 
-script: nosetests hera_pspec --with-coverage --cover-package=hera_pspec --verbose
+script: nosetests -P hera_pspec --with-coverage --cover-package=hera_pspec --verbose
 
 after_success:
   - coveralls

README.md

@@ -9,27 +9,41 @@ The ``hera_pspec`` library provides all of the tools and data structures needed
 For usage examples and documentation, see http://hera-pspec.readthedocs.io/en/latest/.
 
 ## Installation
+Preferred method of installation for users is simply `pip install .`
+(or `pip install git+https://github.com/HERA-Team/hera_pspec`). This will install 
+required dependencies. See below for manual dependency management.
+
+### Dependencies
+If you are using `conda`, you may wish to install the following dependencies manually
+to avoid them being installed automatically by `pip`::
+
+    $ conda install -c conda-forge "numpy>=1.15" "astropy>=2.0" "aipy>=3.0rc2" h5py pyuvdata scipy matplotlib pyyaml h5py scikit-learn
+
+### Developing
+If you are developing `hera_pspec`, it is preferred that you do so in a fresh `conda`
+environment. The following commands will install all relevant development packages::
+
+    $ git clone https://github.com/HERA-Team/hera_pspec.git
+    $ cd hera_pspec
+    $ conda create -n hera_pspec python=3
+    $ conda activate hera_pspec
+    $ conda env update -n hera_pspec -f environment.yml
+    $ pip install -e . 
+
+This will install extra dependencies required for testing/development as well as the 
+standard ones.
+
+### Running Tests
+Uses the `nose` package to execute test suite.
+From the source `hera_pspec` directory run: `nosetests`.
 
-### Code Dependencies
-
-* numpy >= 1.15
-* pyuvdata (`pip install pyuvdata` or use https://github.com/HERA-Team/pyuvdata.git)
-* aipy (```conda install -c conda-forge aipy```)
-* scipy >= 0.19
-* matplotlib >= 2.2
-* astropy >= 2.0
-* hera_cal (https://github.com/HERA-Team/hera_cal.git)
-* pyyaml
-* hdf5
-
-For anaconda users, we suggest using conda to install astropy, numpy and scipy.
-
-### Installing hera_pspec
-Clone the repo using
-`git clone https://github.com/HERA-Team/hera_pspec.git`
-
-Navigate into the directory and run `python setup.py install`.
 
 ## Running `hera_pspec`
 
-See the documentation for an [overview and examples](http://hera-pspec.readthedocs.io/en/latest/pspec.html) of how to run `hera_pspec`. There are also some example Jupyter notebooks, including [`examples/PS_estimation_examples.ipynb`](examples/PS_estimation_example.ipynb) (a brief tutorial on how to create delay spectra), and [`examples/PSpecBeam_tutorial.ipynb`](examples/PSpecBeam_tutorial.ipynb) (a brief tutorial on handling beam objects).
+See the documentation for an 
+[overview and examples](http://hera-pspec.readthedocs.io/en/latest/pspec.html) 
+of how to run `hera_pspec`. There are also some example Jupyter notebooks, 
+including [`examples/PS_estimation_examples.ipynb`](examples/PS_estimation_example.ipynb) 
+(a brief tutorial on how to create delay spectra), and 
+[`examples/PSpecBeam_tutorial.ipynb`](examples/PSpecBeam_tutorial.ipynb) (a brief 
+tutorial on handling beam objects).

environment.yml

@@ -0,0 +1,24 @@
+name: hera_pspec
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - aipy>=3.0.0rc2
+  - astropy>=2.0
+  - h5py
+  - matplotlib>=2.0
+  - nose
+  - numpy>=1.15
+  - pip
+  - pyyaml
+  - scikit-learn
+  - scipy
+  - six
+  - pyuvdata>=1.4.1
+  - pip:
+    - git+https://github.com/HERA-Team/linsolve
+    - git+https://github.com/HERA-Team/uvtools
+    - git+https://github.com/HERA-Team/hera_cal
+    - pyephem
+    - multiprocess
+

hera_pspec/tests/test_version.py

@@ -1,39 +1,74 @@
 """Tests for version.py."""
-import nose.tools as nt
-import sys
 import os
+import sys
+
+import nose.tools as nt
+
 try:
     # Python 2
     from cStringIO import StringIO
 except:
     # Python 3
     from io import StringIO
-import subprocess
 import hera_pspec
+from hera_pspec import version
+import json
 
 
 def test_main():
-    version_info = hera_pspec.version.construct_version_info()
-    
+    version_info = version.construct_version_info()
+
     saved_stdout = sys.stdout
     try:
         out = StringIO()
         sys.stdout = out
         hera_pspec.version.main()
         output = out.getvalue()
         nt.assert_equal(output, 'Version = {v}\ngit origin = {o}\n'
-                        'git branch = {b}\ngit description = {d}\n'
+                                'git branch = {b}\ngit description = {d}\n'
                         .format(v=version_info['version'],
                                 o=version_info['git_origin'],
                                 b=version_info['git_branch'],
                                 d=version_info['git_description']))
-
-        git_info = hera_pspec.version._get_gitinfo_file()
-
+
+
     finally:
         sys.stdout = saved_stdout
-    
+
     # Test history string function
     history = hera_pspec.version.history_string()
 
 
+def test_get_gitinfo_file():
+    dir = version.hera_pspec_dir
+
+    git_file = os.path.join(dir, 'GIT_INFO')
+    if not os.path.exists(git_file):
+        # write a file to read in
+        temp_git_file = os.path.join(dir, 'GIT_INFO')
+        version_info = version.construct_version_info()
+        data = [version_info['git_origin'], version_info['git_origin'],
+                version_info['git_origin'], version_info['git_origin']]
+        with open(temp_git_file, 'w') as outfile:
+            json.dump(data, outfile)
+        git_file = temp_git_file
+
+    with open(git_file) as data_file:
+        data = [version._unicode_to_str(x) for x in json.loads(data_file.read().strip())]
+        git_origin = data[0]
+        git_hash = data[1]
+        git_description = data[2]
+        git_branch = data[3]
+
+    test_file_info = {
+        'git_origin': git_origin, 'git_hash': git_hash,
+        'git_description': git_description, 'git_branch': git_branch
+    }
+
+    if 'temp_git_file' in locals():
+        file_info = version._get_gitinfo_file(git_file=temp_git_file)
+        os.remove(temp_git_file)
+    else:
+        file_info = version._get_gitinfo_file()
+
+    assert file_info == test_file_info

hera_pspec/utils.py

@@ -5,7 +5,6 @@
 import aipy, uvtools
 from hera_cal import redcal
 from collections import OrderedDict as odict
-from pyuvdata import utils as uvutils
 from pyuvdata import UVData
 from datetime import datetime
 

hera_pspec/uvpspec.py

@@ -3,7 +3,6 @@
 import os, copy, shutil, operator, ast, fnmatch
 from pyuvdata import uvutils as uvutils
 import h5py
-import operator
 import warnings
 import json
 

hera_pspec/version.py

@@ -4,14 +4,16 @@
 
 from __future__ import print_function, division, absolute_import
 
+import inspect
+import json
 import os
-import six
 import subprocess
-import json
-import inspect
+import sys
 
 hera_pspec_dir = os.path.dirname(os.path.realpath(__file__))
 
+PY2 = sys.version_info < (3, 0)
+
 
 def _get_git_output(args, capture_stderr=False):
     """
@@ -27,7 +29,7 @@ def _get_git_output(args, capture_stderr=False):
 
     data = data.strip()
 
-    if six.PY2:
+    if PY2:
         return data
     return data.decode('utf8')
 
@@ -51,7 +53,7 @@ def _get_gitinfo_file(git_file=None):
 
 
 def _unicode_to_str(u):
-    if six.PY2:
+    if PY2:
         return u.encode('utf8')
     return u
 
@@ -71,16 +73,16 @@ def construct_version_info():
 
     try:
         version_info['git_origin'] = _get_git_output(
-                                      ['config', '--get', 'remote.origin.url'], 
-                                      capture_stderr=True)
+            ['config', '--get', 'remote.origin.url'],
+            capture_stderr=True)
         version_info['git_hash'] = _get_git_output(
-                                      ['rev-parse', 'HEAD'], 
-                                      capture_stderr=True)
+            ['rev-parse', 'HEAD'],
+            capture_stderr=True)
         version_info['git_description'] = _get_git_output(
-                                   ['describe', '--dirty', '--tag', '--always'])
+            ['describe', '--dirty', '--tag', '--always'])
         version_info['git_branch'] = _get_git_output(
-                                      ['rev-parse', '--abbrev-ref', 'HEAD'], 
-                                      capture_stderr=True)
+            ['rev-parse', '--abbrev-ref', 'HEAD'],
+            capture_stderr=True)
     except subprocess.CalledProcessError:  # pragma: no cover
         try:
             # Check if a GIT_INFO file was created when installing package
@@ -97,22 +99,23 @@ def history_string(notes=''):
     disk can use. Optionally add notes.
     """
     history = '\n------------\nThis file was produced by the function ' \
-            + str(inspect.stack()[1][3]) + '()'
+              + str(inspect.stack()[1][3]) + '()'
     # inspect.stack()[1][3] is the name of the function that called this fn
-    
+
     history += ' in ' + os.path.basename(inspect.stack()[1][1]) + ' using: '
     # inspect.stack()[1][1] is path to the file that contains the function 
     # that called this function
     version_info = construct_version_info()
-    
+
     for v in sorted(version_info.keys()):
         history += '\n    ' + v + ': ' + version_info[v]
-    
+
     if (notes is not None) and (notes != ''):
         history += '\n\nNotes:\n'
         history += notes
     return history + '\n------------\n'
 
+
 def print_version_info():
     """
     Print git/version info.
@@ -122,6 +125,7 @@ def print_version_info():
     print('git branch = {0}'.format(git_branch))
     print('git description = {0}'.format(git_description))
 
+
 version_info = construct_version_info()
 version = version_info['version']
 git_origin = version_info['git_origin']
@@ -133,5 +137,6 @@ def print_version_info():
 def main():
     print_version_info()
 
+
 if __name__ == '__main__':
     main()

setup.py

@@ -1,13 +1,17 @@
-from setuptools import setup
-import sys
-import os
-from hera_pspec import version
 import json
+import os
+import sys
+
+from setuptools import setup
+
+sys.path.append("hera_pspec")
+import version
 
 data = [version.git_origin, version.git_hash, version.git_description, version.git_branch]
 with open(os.path.join('hera_pspec', 'GIT_INFO'), 'w') as outfile:
     json.dump(data, outfile, default=str)
 
+
 def package_files(package_dir, subdirectory):
     # walk the input package_dir/subdirectory
     # return a package_data list
@@ -18,23 +22,36 @@ def package_files(package_dir, subdirectory):
             path = path.replace(package_dir + '/', '')
             paths.append(os.path.join(path, filename))
     return paths
+
+
 data_files = package_files('hera_pspec', 'data') + package_files('hera_pspec', '../pipelines')
 
 setup_args = {
-    'name':         'hera_pspec',
-    'author':       'HERA Team',
-    'url':          'https://github.com/HERA-Team/hera_pspec',
-    'license':      'BSD',
-    'version':      version.version,
-    'description':  'HERA Power Spectrum Estimator Code.',
-    'packages':     ['hera_pspec'],
-    'package_dir':  {'hera_pspec': 'hera_pspec'},
+    'name': 'hera_pspec',
+    'author': 'HERA Team',
+    'url': 'https://github.com/HERA-Team/hera_pspec',
+    'license': 'BSD',
+    'version': version.version,
+    'description': 'HERA Power Spectrum Estimator Code.',
+    'packages': ['hera_pspec'],
+    'package_dir': {'hera_pspec': 'hera_pspec'},
     'package_data': {'hera_pspec': data_files},
-    'install_requires': ['numpy>=1.15', 'scipy','matplotlib>=2.2'],
+    'install_requires': [
+        'numpy>=1.15',
+        'scipy',
+        'matplotlib>=2.2'
+        'pyuvdata',
+        'astropy>=2.0',
+        'aipy>=3.0rc2',
+        'pyyaml',
+        'h5py',
+        'uvtools @ git+git://github.com/HERA-Team/uvtools',
+        'hera_cal @ git+git://github.com/HERA-Team/hera_cal'
+    ],
     'include_package_data': True,
     'scripts': ['scripts/pspec_run.py', 'scripts/pspec_red.py',
                 'scripts/bootstrap_run.py'],
-    'zip_safe':     False,
+    'zip_safe': False,
 }
 
 if __name__ == '__main__':