Initial implementation

Author: 5tefan

.gitignore

@@ -0,0 +1,125 @@
+# Created by .ignore support plugin (hsz.mobi)
+### JetBrains template
+# Covers JetBrains IDEs: IntelliJ, RubyMine, PhpStorm, AppCode, PyCharm, CLion, Android Studio and Webstorm
+# Reference: https://intellij-support.jetbrains.com/hc/en-us/articles/206544839
+.idea
+
+## Plugin-specific files:
+
+# IntelliJ
+/out/
+
+# mpeltonen/sbt-idea plugin
+.idea_modules/
+
+# JIRA plugin
+atlassian-ide-plugin.xml
+
+# Crashlytics plugin (for Android Studio and IntelliJ)
+com_crashlytics_export_strings.xml
+crashlytics.properties
+crashlytics-build.properties
+fabric.properties
+### Vim template
+# swap
+[._]*.s[a-w][a-z]
+[._]s[a-w][a-z]
+# session
+Session.vim
+# temporary
+.netrwhist
+*~
+# auto-generated tag files
+tags
+### Python template
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*,cover
+.hypothesis/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# dotenv
+.env
+
+# virtualenv
+.venv/
+venv/
+ENV/
+
+# Spyder project settings
+.spyderproject
+
+# Rope project settings
+.ropeproject
+

CHANGELOG.md

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2017 Stefan Codrescu
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

LICENSE

@@ -0,0 +1,85 @@
+# NetCDF Flag Wrapper (ncflag)
+
+So... you want to inspect CF compliant NetCDF flag Variables?
+
+
+## TL;DR
+
+Install the utility with with pip:
+```
+pip install ncflag
+```
+
+On the command line, use `ncflag`:
+
+```
+Usage: ncflag [OPTIONS] NCFILE FLAG
+
+Options:
+  -v, --version                   Show the version and exit.
+  --show_flags PATH               Print the flags this tool can inspect.
+  --use_time_var TEXT
+  -l [DEBUG|INFO|WARNING|ERROR|CRITICAL]
+                                  log level
+  --help                          Show this message and exit.
+
+```
+
+Notes:
+
+Use --show_flags to discover what flags can be inspected.
+
+Limitation: can only inspect flags of at most one dimension. See details below for dealing with multidimensional flags.
+
+
+The nominal output with --use_time_var specified is shown below. Without use_time_var, the index along the
+dimension will be printed instead of a iso 8601 timestamp.
+```text
+2017-11-27T21:07:41.543778: [u'data_quality_error']
+2017-11-27T21:07:42.543812: [u'good_data']
+2017-11-27T21:07:43.543807: [u'good_data']
+2017-11-27T21:07:44.543802: [u'good_data']
+```
+
+## Multidimensional Flags
+
+Occasionally, by some poor misfortune, you may encounter multidimensional flag variables. These are currently not
+supported by the Command Line Interface (CLI), however, the FlagWrap class can still be used in code, or through an
+interactive (IPython) session. The `FlagWrap.get_flags_set_at_index` can be passed a tuple to get the flags set in
+a multidimensional flag variable. Below is an example. 
+
+```python
+from ncflag import FlagWrap
+import netCDF4 as nc
+
+with nc.Dataset("somenetcdf.nc") as nc_in:
+    v = nc_in.variables["mutidim_variable"]
+    print(v.shape)  # --> (2, 10)
+    w = FlagWrap(v)
+    print(w.get_flags_set_at_index((0, 0)))  # --> ["good_quality_qf"]
+```
+
+## Testing
+
+TODO!
+
+## Development
+
+Setting up a virtualenv is recommended for development.
+
+```
+virtualenv venv
+. venv/bin/activate
+pip install --editable .
+```
+
+---------------------
+
+Deploy to pip, after testing with python2 and python3:
+
+```bash
+rm -r dist/
+python setup.py bdist_wheel --universal
+twine upload dist/*
+```
+

README.md

@@ -0,0 +1 @@
+from flag_wrapper import FlagWrap

ncflag/__init__.py

@@ -0,0 +1,59 @@
+import click
+import logging
+import pkg_resources
+import netCDF4 as nc
+from flag_wrapper import FlagWrap
+
+try:
+    version = pkg_resources.require("ncflag")[0].version
+except pkg_resources.DistributionNotFound:
+    version = "unknown"
+
+def show_flags(ctx, param, ncfile):
+    if not ncfile or ctx.resilient_parsing:
+        return
+    valid_flags = []
+    with nc.Dataset(ncfile) as nc_in:  # type: nc.Dataset
+        for k, v in nc_in.variables.items():
+            if hasattr(v, "flag_values") and hasattr(v, "flag_meanings") and len(v.dimensions) == 1:
+                valid_flags.append(k)
+    click.echo("Inspectable flags: %s" % map(str, valid_flags))
+    ctx.exit()
+
+
+@click.command()
+@click.version_option(version, "-v", "--version")
+@click.option("--show_flags", callback=show_flags, expose_value=False, is_eager=True,
+              type=click.Path(exists=True, dir_okay=False), help="Print the flags this tool can inspect.")
+@click.argument("ncfile", type=click.Path(exists=True, dir_okay=False))
+@click.argument("flag", type=click.STRING)
+@click.option("--use_time_var", type=click.STRING, default=None)
+@click.option("-l", help="log level", type=click.Choice(['DEBUG', 'INFO', 'WARNING', 'ERROR', 'CRITICAL']),
+              default="WARNING")
+def cli(ncfile, flag, use_time_var, l):
+    logging.getLogger().setLevel(l)
+    with nc.Dataset(ncfile) as nc_in:  # type: nc.Dataset
+        # initial checks
+        v = nc_in.variables[flag]  # type: nc.Variable
+        assert hasattr(v, "flag_values"), "%s is not CF compliant flag, missing flag_values" % flag
+        assert hasattr(v, "flag_meanings"), "%s is not CF compliant flag, missing flag_meanings" % flag
+        assert len(v.dimensions) == 1, "multidimensional flags are not supported, see docs and use ipython instead"
+        w = FlagWrap(v)
+        if use_time_var is not None:
+            t = nc_in.variables[use_time_var]  # type: nc.Variable
+            assert t.dimensions == v.dimensions, "To print flags by time, time flag must share dimensions"
+            assert hasattr(t, "units"), "did not find units on time flag %s" % use_time_var
+            for i, dt in enumerate(nc.num2date(t[:], t.units)):
+                out_time = dt.isoformat() if dt is not None else "__________________________"
+                click.echo("%s: %s" % (out_time, w.get_flags_set_at_index(i)))
+        else:
+            for i in range(v.size):
+                click.echo("%s: %s" % (i, w.get_flags_set_at_index(i)))
+
+
+if __name__ == "__main__":
+
+    console = logging.StreamHandler()
+    logging.getLogger().addHandler(console)
+
+    cli()