Merge pull request #177 from lbl-anp/release-0.2.2

Release 0.2.2

CONTRIBUTING.md

@@ -4,13 +4,51 @@ Contributions to `becquerel` are welcome and encouraged, whether it is
 reporting bugs, requesting features, or contributing code.
 Please follow these guidelines when contributing to this project.
 
-### Reporting issues
+### Developer Instructions
 
-When reporting issues with `becquerel`, please provide a minimum working example to help identify the problem and tag the issue as a `bug`.
+```
+pip install -r requirements.txt
+pip install -r requirements-dev.txt
+python setup.py develop
+```
 
-### Feature requests
+(It is more convenient to use `develop` so that the code is soft-linked
+from the installation directory, and the installed package will always use
+the current version of code.)
 
-For a feature request, please create an issue and label it as a `new feature`.
+### Running the tests
+
+(Requires `requirements-dev.txt` to be installed)
+To run the tests using `pytest`, from the root directory of the repo:
+
+```
+pytest
+```
+
+(`python setup.py test` is still supported also.)
+By default, a code coverage report is printed to the terminal.
+Tests marked `webtest` or `plottest` are by default skipped for the sake of
+speed. To run all tests, clear the pre-configured markers option:
+
+```
+pytest -m ""
+```
+
+To produce an HTML code coverage report in directory `htmlcov`
+with line-by-line highlighting:
+
+```
+pytest --cov-report html:htmlcov
+```
+
+### Code Style Guide
+
+Use [google standards](https://google.github.io/styleguide/pyguide.html)
+
+### Linter
+
+* Use `flake8` in your IDE
+* Use `pylint` from command line (as in style guide)
 
 ### Checklist for code contributions:
   - [ ] Branch off of `develop` and name the branch `feature-XX` or `issue-XX`

LICENSE.txt

@@ -2,7 +2,7 @@
 
 *** Copyright Notice ***
 
-Becquerel v. 0.2.1, Copyright (c) 2017, The Regents of the University of California (UC), through Lawrence Berkeley National Laboratory, and the UC Berkeley campus (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
+Becquerel v. 0.2.2, Copyright (c) 2017, The Regents of the University of California (UC), through Lawrence Berkeley National Laboratory, and the UC Berkeley campus (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved.
 If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Innovation & Partnerships Office at  IPO@lbl.gov.
 
 NOTICE.  This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights.  As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit other to do so.

README.md

@@ -11,95 +11,52 @@ and pandas. It is intended to be general-purpose enough that it can be useful
 to anyone from an undergraduate taking a laboratory course to the advanced
 researcher.
 
-## Installation instructions
-
-### As a user
-
-```
-pip install -r requirements.txt
-python setup.py install --user
-```
-
-Before reinstalling, be sure to either remove the ```build``` directory
-or run:
-
-```
-python setup.py clean --all
-```
-
-### As a developer
+## Installation
 
 ```
-pip install -r requirements-dev.txt
-python setup.py develop
+pip install becquerel
 ```
 
-(It is more convenient to use `develop` so that the code is soft-linked
-from the installation directory, and the installed package will always use
-the current version of code.)
-
-## Running the tests
+## Features in development (contributions welcome!)
 
-(Requires `requirements-dev.txt` to be installed)
-To run the tests using `pytest`, from the root directory of the repo:
+* Reading additional `Spectrum` file types (N42, CHN, CSV)
+* Writing `Spectrum` objects to various standard formats
+* Fitting spectral features (e.g., gaussian lines with different background models)
 
-```
-pytest
-```
+If you are interested in contributing or are want to install the package from
+source, please see the instructions in [`CONTRIBUTING.md`](./CONTRIBUTING.md).
 
-(`python setup.py test` is still supported also.)
-By default, a code coverage report is printed to the terminal.
-Tests marked `webtest` or `plottest` are by default skipped for the sake of
-speed. To run all tests, clear the pre-configured markers option:
+## Reporting issues
 
-```
-pytest -m ""
-```
+When reporting issues with `becquerel`, please provide a minimum working example to help identify the problem and tag the issue as a `bug`.
 
-To produce an HTML code coverage report in directory `htmlcov`
-with line-by-line highlighting:
+## Feature requests
 
-```
-pytest --cov-report html:htmlcov
-```
+For a feature request, please create an issue and label it as a `new feature`.
 
 ## Dependencies
 
-External dependencies are listed in `requirements.txt` and can be installed
-with `pip` (see [Installation instructions][0]) or manually. The dependencies
-`beautifulsoup4`, `lxml` and `html5lib` are necessary for [`pandas`][1].
-Developers additionally need [`pytest`][2] and are encouraged to use
-[`pylint`][3], [`pycodestyle`][4], [`pydocstyle`][5] and [`yapf`][6] for
-proper code formatting.
+External dependencies are listed in `requirements.txt` and will be installed
+automatically with the standard `pip` installation. They can also be installed
+manually with the package manager of your choice (`pip`, `conda`, etc).
+The dependencies `beautifulsoup4`, `lxml` and `html5lib` are necessary for
+[`pandas`][1].
+
+Developers require additional requirements which are listed in
+`requirements-dev.txt`. We use [`pytest`][2] for unit testing and encourage
+contributors to use [`pylint`][3], [`pycodestyle`][4], [`pydocstyle`][5] and
+[`yapf`][6] for proper code formatting.
 
-[0]: #installation-instructions
 [1]: https://pandas.pydata.org/pandas-docs/stable/install.html#dependencies
 [2]: https://docs.pytest.org
 [3]: https://pylint.readthedocs.io
 [4]: http://pycodestyle.pycqa.org
 [5]: http://www.pydocstyle.org
 [6]: https://github.com/google/yapf
 
-## Code Style Guide
-
-Use [google standards](https://google.github.io/styleguide/pyguide.html)
-
-## Linter
-
-* Use `flake8` in your IDE
-* Use `pylint` from command line (as in style guide)
-
-## Features in development (contributions welcome!)
-
-* Reading additional `Spectrum` file types (N42, CHN, CSV)
-* Writing `Spectrum` objects to various standard formats
-* Fitting spectral features (e.g., gaussian lines with different background models)
-
-If you are interested in contributing, please see the guidelines in [`CONTRIBUTING.md`](./CONTRIBUTING.md).
-
 ## Copyright Notice
 
-Becquerel v. 0.2.1, Copyright (c) 2017, The Regents of the University of
+Becquerel v. 0.2.2, Copyright (c) 2017, The Regents of the University of
 California (UC), through Lawrence Berkeley National Laboratory, and the UC
 Berkeley campus (subject to receipt of any required approvals from the U.S.
 Dept. of Energy). All rights reserved. If you have questions about your rights

becquerel/core/spectrum.py

@@ -449,10 +449,8 @@ def from_file(cls, infilename):
         spect_file_obj = _get_file_object(infilename)
 
         kwargs = {'counts': spect_file_obj.data,
-                  'input_file_object': spect_file_obj}
-
-        if spect_file_obj.cal_coeff:
-            kwargs['bin_edges_kev'] = spect_file_obj.energy_bin_edges
+                  'input_file_object': spect_file_obj,
+                  'bin_edges_kev': spect_file_obj.bin_edges_kev}
 
         # TODO Get more attributes from self.infileobj
 

becquerel/parsers/README.markdown

@@ -17,8 +17,9 @@ Other data available include:
 
 * `spec.livetime`
 * `spec.realtime`
+* `spec.bin_edges_kev`
 * `spec.energy_bin_widths`
-
+* `spec.energy_bin_edges` (deprecated)
 
 Some parsers extract more information than others either because of their
 stage of development or because the file format may not carry certain

becquerel/parsers/cnf_file.py

@@ -93,7 +93,9 @@ class CnfFile(SpectrumFile):
         spec.data [counts]
         spec.channels
         spec.energies
+        spec.bin_edges_kev
         spec.energy_bin_widths
+        spec.energy_bin_edges (deprecated)
 
     """
 

becquerel/parsers/spc_file.py

@@ -24,7 +24,9 @@ class SpcFile(SpectrumFile):
         spec.data [counts]
         spec.channels
         spec.energies
+        spec.bin_edges_kev
         spec.energy_bin_widths
+        spec.energy_bin_edges (deprecated)
 
     ORTEC's SPC file format is divided into records of 128 bytes each. The
     specifications for what each record should contain can be found on pages

becquerel/parsers/spe_file.py

@@ -32,7 +32,9 @@ class SpeFile(SpectrumFile):
         spec.data [counts]
         spec.channels
         spec.energies
+        spec.bin_edges_kev
         spec.energy_bin_widths
+        spec.energy_bin_edges (deprecated)
 
     ORTEC's SPE file format is given on page 73 of this document:
         http://www.ortec-online.com/download/ortec-software-file-structure-manual.pdf

becquerel/parsers/spectrum_file.py

@@ -29,7 +29,9 @@ class SpectrumFile(object):
         spec.data [counts]
         spec.channels
         spec.energies
+        spec.bin_edges_kev
         spec.energy_bin_widths
+        spec.energy_bin_edges (deprecated)
 
     """
 
@@ -56,8 +58,7 @@ def __init__(self, filename):
         self.cal_coeff = []
         # arrays to be calculated using calibration
         self.energies = np.array([], dtype=np.float)
-        self.energy_bin_widths = np.array([], dtype=np.float)
-        self.energy_bin_edges = np.array([], dtype=np.float)
+        self.bin_edges_kev = None
 
     def __str__(self):
         """String form of the spectrum."""
@@ -100,6 +101,17 @@ def __str__(self):
             s += '    [length {}]\n'.format(len(self.data))
         return s
 
+    @property
+    def energy_bin_edges(self):
+        warnings.warn('The use of energy_bin_edges is deprecated, ' +
+                      'use bin_edges_kev instead', DeprecationWarning)
+        return self.bin_edges_kev
+
+    @property
+    def energy_bin_widths(self):
+        """Retrieve the calibrated width of all the bins."""
+        return self.bin_width(self.channels)
+
     def read(self, verbose=False):
         """Read in the file."""
         raise NotImplementedError('read method not implemented')
@@ -111,16 +123,17 @@ def write(self, filename):
     def apply_calibration(self):
         """Calculate energies corresponding to channels."""
         self.energies = self.channel_to_energy(self.channels)
-        self.energy_bin_widths = self.bin_width(self.channels)
         n_edges = len(self.energies) + 1
         channel_edges = np.linspace(-0.5, self.channels[-1] + 0.5, num=n_edges)
-        self.energy_bin_edges = self.channel_to_energy(channel_edges)
+        self.bin_edges_kev = self.channel_to_energy(channel_edges)
 
         # check that calibration makes sense, remove calibration if not
         if np.any(np.diff(self.energies) <= 0):
             warnings.warn(
-                'Ignoring calibration; energies not monotonically increasing')
-            self.cal_coeff = []
+                'Spectrum will be initated without an energy calibration;' +
+                'invalid calibration, energies not monotonically increasing.',
+                SpectrumFileParsingWarning)
+            self.bin_edges_kev = None
 
     def channel_to_energy(self, channel):
         """Apply energy calibration to the given channel(s)."""

becquerel/tools/materials.py

@@ -71,10 +71,20 @@ def fetch_element_data():
 
     """
     req = _get_request(_URL_TABLE1)
-    # remove extra columns in Hydrogen row and extra empty rows
     text = req.text
-    text = text.replace('<TD ROWSPAN="92">&nbsp;</TD>', '')
+    # rename first two header columns
+    text = text.replace(
+        '<TH scope="col" COLSPAN="2"><I>Z</I></TH>',
+        '<TH scope="col">Z</TH><TH scope="col">Symbol</TH>')
+    # remove row that makes the table too wide
+    text = text.replace('<TD COLSPAN="10"><HR SIZE="1" NOSHADE></TD>', '')
+    # remove extra header columns
+    text = text.replace('<TD COLSPAN="2">', '<TD>')
+    text = text.replace('<TD COLSPAN="4">', '<TD>')
     text = text.replace('TD>&nbsp;</TD>', '')
+    # remove extra columns in Hydrogen row
+    text = text.replace('<TD ROWSPAN="92">&nbsp;</TD>', '')
+    # remove open <TR> at the end of the table
     text = text.replace('</TD></TR><TR>', '</TD></TR>')
     # read HTML table into pandas DataFrame
     tables = pd.read_html(text, header=0, skiprows=[1, 2])
@@ -85,7 +95,11 @@ def fetch_element_data():
     if len(df) != MAX_Z:
         raise NISTMaterialsRequestError(
             '{} elements expected, but found {}'.format(MAX_Z, len(df)))
-    # set column names
+    if len(df.columns) != 6:
+        raise NISTMaterialsRequestError(
+            '10 columns expected, but found {} ({})'.format(
+                len(df.columns), df.columns))
+    # rename columns
     df.columns = ['Z', 'Symbol', 'Element', 'Z_over_A', 'I_eV', 'Density']
     return df
 
@@ -145,10 +159,16 @@ def fetch_compound_data():
 
     """
     req = _get_request(_URL_TABLE2)
-    # remove extra columns and replace <BR> symbols in composition lists
     text = req.text
+    # remove extra header columns
     text = text.replace('<TD ROWSPAN="2">&nbsp;</TD>', '')
+    # remove extra rows in header row
+    text = text.replace(' ROWSPAN="2"', '')
+    # remove extra columns in third header row
+    text = text.replace('<TD COLSPAN="9"><HR SIZE="1" NOSHADE></TD>', '')
+    # remove extra columns in the first material row
     text = text.replace('<TD ROWSPAN="50"> &nbsp; </TD>', '')
+    # replace <BR> symbols in composition lists with semicolons
     text = text.replace('<BR>', ';')
     # read HTML table into pandas DataFrame
     tables = pd.read_html(text, header=0, skiprows=[1, 2])
@@ -159,7 +179,11 @@ def fetch_compound_data():
     if len(df) != N_COMPOUNDS:
         raise NISTMaterialsRequestError(
             '{} compounds expected, but found {}'.format(N_COMPOUNDS, len(df)))
-    # set column names
+    if len(df.columns) != 5:
+        raise NISTMaterialsRequestError(
+            '5 columns expected, but found {} ({})'.format(
+                len(df.columns), df.columns))
+    # rename columns
     df.columns = ['Material', 'Z_over_A', 'I_eV', 'Density', 'Composition_Z']
     # clean up Z composition
     df['Composition_Z'] = [

setup.py

@@ -8,7 +8,7 @@
 
 MAJOR = 0
 MINOR = 2
-MICRO = 1
+MICRO = 2
 VERSION = '{}.{}.{}'.format(MAJOR, MINOR, MICRO)
 
 DESCRIPTION = __doc__.split('\n')[0].split(': ')[-1]