dbdreader 0.5.7__tar.gz → 0.6.0.dev1__tar.gz

{dbdreader-0.5.7 → dbdreader-0.6.0.dev1}/MANIFEST.in

@@ -1,4 +1,4 @@
-include README.rst COPYING COPYRIGHT MANIFEST.in INSTALL.rst LICENSE
+include README.md COPYING COPYRIGHT MANIFEST.in INSTALL.rst LICENSE
 include requirements.txt
 include extension/*.c
 include extension/include/*.h

{dbdreader-0.5.7/dbdreader.egg-info → dbdreader-0.6.0.dev1}/PKG-INFO

@@ -1,66 +1,91 @@
-Metadata-Version: 2.1
+Metadata-Version: 2.4
 Name: dbdreader
-Version: 0.5.7
+Version: 0.6.0.dev1
 Summary: A python module to access binary data files generated by Teledyne WebbResearch gliders
-Home-page: https://dbdreader.readthedocs.io/en/latest/
-Author: Lucas Merckelbach
-Author-email: lucas.merckelbach@hereon.de
+Author-email: Lucas Merckelbach <lucas.merckelbach@hereon.de>
+License: GPL-3.0
+Project-URL: Homepage, https://dbdreader.readthedocs.io/en/latest/
 Classifier: Programming Language :: Python :: 3
 Classifier: Intended Audience :: Science/Research
 Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
 Classifier: Operating System :: POSIX
-Description-Content-Type: text/x-rst
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
 License-File: LICENSE
 License-File: COPYING
+Requires-Dist: lz4>=4.4.5
+Requires-Dist: numpy>=2.2.6
+Requires-Dist: scipy>=1.15.3
+Dynamic: license-file
 
-|PyPI version| |Docs badge| |License|
+[![PyPI version](https://badgen.net/pypi/v/dbdreader)](https://pypi.org/project/dbdreader)
+[![Docs badge](https://readthedocs.org/projects/dbdreader/badge/?version=latest)](https://dbdreader.readthedocs.io/en/latest/)
+[![License](https://img.shields.io/badge/License-GPLv3-blue.svg)](https://www.gnu.org/licenses/gpl-3.0)
 
-DBDREADER
-=========
+# DBDREADER
+
+## Synopsis
 
-Synopsis
---------
 Slocum ocean gliders are autonomous underwater vehicles, used for
 making oceanographic measurements. The data that these devices and
 their sensors collect, are stored in binary data files. The python
 module *dbdreader* provides the utilities to extract the data from the
 binary files, so that they can be further analysed.
 
-Change log
-----------
+## Change log
+
+### version 0.5.9
+
+* Handles reading errors that can occur when a compressed file turns
+  out to be corrupted.
+
+### version 0.5.8
+
+* Changes default location for cache files on linux from
+  `$HOME/.dbdreader` to `$HOME/.local/share/dbdreader`
 
-Version 0.5.7
+* Introduces new class DBDCache to manage the location where cache
+  files are looked up. Constructing an object with an arguments (re-)sets a
+  default path, avoiding the need to use the keyword cacheDir when
+  creating objects of DBD and MultiDBD classes.
+
+* Fixes an issue with MultiDBD when a parameter is requested that is
+  not present in all files, but in at least one. The get() method
+  returns just those data that are present. In case of get_sync and
+  friends, data are interpolated if possible, or padded with nans.
+
+### Version 0.5.7
 
 * Drops dependency on python 3.10+, introduced in 0.5.6, and should
   work still with python 3.9.
 
-Version 0.5.6
+### Version 0.5.6
 
 * Moves data directory under dbdreader, making these files accessible
   after an pip install
 
-Version 0.5.5
+### Version 0.5.5
 
 * Makes MultiDBD's get_CTD_sync method compatible with RBR CTD data.
 
-Version 0.5.4
+### Version 0.5.4
 
 * Adds support for reading compressed data files for windows platform.
 * Improved building environment
 
-Version 0.5.1
+### Version 0.5.1
 
 * Adds support for reading compressed data files
-* dbdrename.py now accepts -x and -X options to rename compressed data files as uncompressed data files
+* dbdrename now accepts -x and -X options to rename compressed data files as uncompressed data files
 
-Version 0.4.15
+### Version 0.4.15
 
-* Modifies sorting key algorithm to the DBDList class. This fixes a 
-  bug when glider data filenames are composed of a glider name that 
+* Modifies sorting key algorithm to the DBDList class. This fixes a
+  bug when glider data filenames are composed of a glider name that
   contains a dash. For example, filenames such as hereon-amadeus-2019-3-1.sbd
   would fail, but are valid now.
 
-Version 0.4.14
+### Version 0.4.14
 
 * Adds a new option to the get() method of the MultiDBD class, where
   if the keyword include_sources=True, for each parameter an
@@ -70,7 +95,7 @@ Version 0.4.14
 
   This merges the (modified) pull request #14 by MCazaly.
 
-Version 0.4.13
+### Version 0.4.13
 
 * Modifies behaviour when the user requests a parameter that has no
   data. If the requested parameter is not a valid glider sensor name,
@@ -80,13 +105,13 @@ Version 0.4.13
   This behaviour fixes a bug for MultiDBD:
   each file opened with MultiDBD would fail to produce any data if one or
   more parameters that are asked for, are not present in the file.
-   
+
   New behaviour returns data for the exisiting parameters (only); empty
   array for the missing parameters (or nans if return_nans=True)
 
   Concludes pull request #16 by jklymak.
 
-Version 0.4.12
+### Version 0.4.12
 
 * PatternSelect now accepts the option of a non-standard cache
   directory.
@@ -94,9 +119,9 @@ Version 0.4.12
 
 * MultiDBD's get_sync() now returns nan's for those parameters for
   which no data exist, provided that at least one of the requested
-  parameters contains data. 
-  
-Version 0.4.11
+  parameters contains data.
+
+### Version 0.4.11
 
 * Version 0.4.9 introduced a bug that in some rare circumstances caused
   segmentation faults. This has been fixed.
@@ -106,8 +131,7 @@ Version 0.4.11
   cache file, detailed information can be obtained from the .data
   property of the exception instance.
 
-
-Version 0.4.10
+### Version 0.4.10
 
 * Includes pull request by jklymak, which allows dbdreader to deal
   with empty files, and files capitalised file extensions, as well as
@@ -121,65 +145,61 @@ Version 0.4.10
   pattern. An error is raised if pattern is specified explicitly when
   filenames is given as a string.
 
-Version 0.4.9
+### Version 0.4.9
 
 * Bug fix for handling inf values correctly (issue #8). Thanks to jr3cermak for spotting this bug.
 * Bug fix for incorrect behaviour when reading the time parameter explicitly for example xxx.get("m_present_time").
 
-Version 0.4.8
+### Version 0.4.8
 
 * Support for reading {demnst}bd files from G3S gliders (issue #6). (Thanks to Owain Jones)
 
 * Bug fix for correctly throwing an exception when cache file is missing(issue #5)
 
-Version 0.4.7
+### Version 0.4.7
 
 * Bug fix for reading dbd files on Windows.
 
-* a wheel provided for CPython 3.9 on Windows 64 bit.  
+* a wheel provided for CPython 3.9 on Windows 64 bit.
 
-Version 0.4.6
+### Version 0.4.6
 
 * Added  get_CTD_sync, a convenience method to retrieve CTD data, and other parameters mapped on the CTD time stamps. Also ensures time stamps are monotonically increasing.
 
 * Adds bounds to what values of latitude and longitude are considered valid.
 
-Version 0.4.5
+### Version 0.4.5
 
 * dbdreader now ignores the first line of data in each binary file
-  
-* dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.
-
 
+* dbdreader checks whether the value of the parameters read are finite, ignoring them if they are not.
 
-Installation (linux)
---------------------
+## Installation (linux)
 
 The python module *dbdreader* can be installed from source, using the
 standard method to install python code. Note that this method requires
 an C-extension to be build. (The actual reading from files is done in
 C for speed.) In order to build the extension successfully, you would
 need a C-compiler. On Linux, this can be gcc, with supporting
-development/header files for python. On Fedora you would do ``sudo dnf
-install python3-devel``, or ``sudo apt-get install python3-dev`` on
+development/header files for python. On Fedora you would do `sudo dnf
+install python3-devel`, or `sudo apt-get install python3-dev` on
 Ubuntu.
 
 Furthermore, as of version 0.5, which adds support for reading
 compressed files, a dependency on the lz4 library is introduced. If
 available, the system-wide library will be used (recommended
 approach). Alternatively, the lz4.[ch] files from the original source
-(https://github.com/lz4/lz4), and included in this package, will be
+(<https://github.com/lz4/lz4>), and included in this package, will be
 compiled into the C-extension. To install the system-wide lz4 library
-on Fedora you would do ``sudo dnf install lz4-devel lz4-libs``. On
-Ubuntu this can be achieved by ``sudo apt-get install liblz4-dev
-liblz4-1``.
+on Fedora you would do `sudo dnf install lz4-devel lz4-libs`. On
+Ubuntu this can be achieved by `sudo apt-get install liblz4-dev
+liblz4-1`.
 
-Alternatively, dbdreader can also be installed from PyPi, using ``pip3
-install dbdreader``.
+Alternatively, dbdreader can also be installed from PyPi, using `pip3
+install dbdreader`.
 
+## Installation on Windows
 
-Installation on Windows
------------------------
 If you want to install dbdreader from source, you will need a C
 compiler as well to compile the C-extension. Besides the Python
 environment you will need to install the Microsoft Visual Studio
@@ -188,29 +208,29 @@ you tick the box *python development* during the setup. Once installed
 dbdreader can be installed, and the C-extension should be compiled
 automatically.
 
-
-Installiation using pip, for example as in ``py -m pip install
-dbdreader`` also requires the C compiler. For Python version 3.9,
+Installiation using pip, for example as in `py -m pip install
+dbdreader` also requires the C compiler. For Python version 3.9,
 however, a wheel is provided, which can be installed adding the option
-``--only-binary :all:`` to the pip command: ::
+`--only-binary :all:` to the pip command:
+
+```
+$ pip install --only-binary :all: dbdreader
+```
 
-  $ pip install --only-binary :all: dbdreader
+## Documentation
 
+Comprehensive documentation is provided at <https://dbdreader.readthedocs.io/en/latest/>
 
-Documentation
--------------
-Comprehensive documentation is provided at https://dbdreader.readthedocs.io/en/latest/
+## Quick-start
 
-Quick-start
------------
 For the impatient...
 
 The dbdreader module implements a class DBD() which provides the
 machinery to read a single dbd file. The most commonly used methods
 are:
 
-* get(parametername)
-* get_sync(parametername, \*other_parameternames)
+* `get(parametername)`
+* `get_sync(parametername, *other_parameternames)`
 
 The first method returs a tuple with time and values for requested
 parameter. The second method, returns a tuple with time and values of
@@ -222,40 +242,31 @@ number of them. This interface is implemented by the MultiDBD
 class. Files can either be specified as a list of filenames, or as a
 pattern using wildcards.
 
-Examples
-^^^^^^^^
+### Examples
 
-To read a single file::
+To read a single file:
 
-  >>> dbd = DBD("00010010.dbd")
-  >>> t, pitch = dbd.get("m_pitch")
-  >>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll)
+```python
+>>> dbd = DBD("00010010.dbd")
+>>> t, pitch = dbd.get("m_pitch")
+>>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll")
+```
 
-Or, doing the same, but using both dbd and ebd files::
-  
-  >>> dbd = DBD(pattern="00010010.[de]bd")
-  >>> t, pitch = dbd.get("m_pitch")
-  >>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll")
-  >>> t, p_ctd, p_nav = dbd.get_sync("sci_water_pressure", "m_water_pressure")
+Or, doing the same, but using both dbd and ebd files:
 
-  
+```python
+>>> dbd = DBD(pattern="00010010.[de]bd")
+>>> t, pitch = dbd.get("m_pitch")
+>>> t, hdg, ptch, roll = dbd.get_sync("m_heading", "m_pitch", "m_roll")
+>>> t, p_ctd, p_nav = dbd.get_sync("sci_water_pressure", "m_water_pressure")
+```
+
+## Python 2
 
-Python 2
---------
 Python 2.7 is not supported anymore. However, you should be able to
 make the code able to run on python2.7 using the *future* package.
 
 * pip install future
 * pasteurize dbdreader.
 
-For details see http://python-future.org/pasteurize.html.
-
-
-.. |PyPI version| image:: https://badgen.net/pypi/v/dbdreader
-   :target: https://pypi.org/project/dbdreader
-.. |Docs badge| image:: https://readthedocs.org/projects/dbdreader/badge/?version=latest
-   :target: https://dbdreader.readthedocs.io/en/latest/
-.. |License| image:: https://img.shields.io/badge/License-GPLv3-blue.svg
-   :target: https://www.gnu.org/licenses/gpl-3.0
-
-	 
+For details see <http://python-future.org/pasteurize.html>.