mosdef-hub / mbuild / 1587
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File open fix (#471)

* Fix too many files being left open in packing.py

`tempfile.mkstemp` provides a low level interface for interacting
with temporary files. However, garbage collection (closing files,
deleting files after use) must be manually taken care of.

Packing.py uses temp files when packing or solvating a system,
these files are never closed. This can cause the program to
reach the limit of open files for a process set by the OS level
`ulimit`.

These changes migrate from using `mkstemp` to a higher level interface
`tempfile.NamedTemporaryFile`, providing the same type of temporary
file, but with saner garbage collection and scope.

The sections where temp files are made are now contained in `try
finally` sections, to ensure proper file closure and deletion when the
program finishes, or is interrupted.

* Syntax changes

NamedTemporaryFile provides a file-like object to interact with
compared to mkstemp.

To get the full path, the `name` attribute of the NamedTemporaryFile
is needed.

* remove nested try-finally blocks

* Forgot to pass in path for the solvate method.

* Move file creation to method, move topology generation to file.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Update gitignore file for VSCode
Using Microsoft's VSCode generates an addtional directory
and files to assist the various plugins, save states, etc.

This is not needed for other users.

This has been added to the .gitignore file to prevent these files from
being committed erroneously.

* Fixes issues with packmol input files (#474)

* Fixes issues with packmol input file

Also reports error based on process code instead of output,
which prevented report of error about input issues.

* Bump to version 0.8.1

* Update changelog to 0.8.1

* Small formatting nits

* Run `activate base` before `conda build` in Appveyor (#477)

* Run `activate base` before `conda build`

See https://github.com/C... (continued)

2840 of 3160 relevant lines covered (89.87%)

3.59 hits per line

Jobs
ID Job ID Ran Files Coverage
1 1587.1 (PYTHON_VERSION=2.7) 0
89.87
 Travis Job 1587.1
2 1587.2 (PYTHON_VERSION=3.5) 0
89.87
 Travis Job 1587.2
3 1587.3 (PYTHON_VERSION=2.7) 0
89.46
 Travis Job 1587.3
4 1587.4 (PYTHON_VERSION=3.5) 0
89.46
 Travis Job 1587.4
Source Files on build 1587
Detailed source file information is not available for this build.