* add tests for correctness of step and time written in XTC and DCD
* improve tests
* improve xtc tests
* fix XTC/DCD time/step writing
* different approach by changing the reporters to not pass currentStep as firstStep but instead interval
* undo change
* Preliminary work on XTC reporter
1. Move and adapt xtc writer/reader from moleculekit (explicit permission
granted by the authors to do so)
2. Create XTCTrajectoryFile
3. Create XTCReporter
* Add licence and attribution to c++ xtc library
Apply clang-format to it
Remove some unused functions and document the rest
* Add attribution and licence to cython wrappers for the xtc library
Remove some unused functions
* Change XTCTrajectoryFile to XTCFile
Simplify the interface and document the class
* Add test for the xtc file parser
* Update XTC reporter with new parser name
* Fix incorrect function name in XTCReporter
* XTCFile:
* Add function to get number of frames
* Add function to read a group of frames from a file
* Add tests for the above
* Ensure data is passed as float32 in XTC file
* Add XTCReporter and tests
* Add more tests to XTCReporter
* Remove unnecessary pdb reporter in XTC tests
* Copy test xtc file in python/tests/systems to build directory for testing
* Remove XTC file reading from the interface
Make XTCFile mimic DCDFile more closely
* Use xtc_read to test the correctness of the XTC reporter
* Add a test for reporting triclinic boxes
* Make XTC library compatible with triclinic boxes.
Adapt XTCFile to triclinic boxes
* Change XTCFile to take a file as argument instead of a filename
* Match DCDFile handling of the box
* Fix comment
* Revert "Change XTCFile to take a file as argument instead of a filename"
This reverts commit 9815d4790b.
* Fix dangling file name issue
* Remove index file functionality from XTC parser.
Remove unused define switch PLATFORM_Linux
* Fix formatting
* Remove inconsistent variable naming in xtcfile.py
* Change file argument name to match other reporters
* Do not turn off error checking in cython wrappers
* Fix leftover fileName in reporter
* Rewrite wrapper to xtclib in C++
* Small changes to wrapper code
* Small changes to wrapper code
* Small changes to wrapper code
* XTCFile: Get number of atoms directly from topology
* DCDFile: Get number of atoms directly from topology
* Change constexpr to const
* Check precision in XTC file matches the written one
* Add a write function to XTCFrame.
Make write check for errors C++ side.
* Rewrite large trajectory files without loading the whole file to memory
* Remove unused code in XTC test
* Avoid spurious copy of the positions array when calling xtc_write_frame
* Pass box as reference
* Remove unnecessary imports and definitions
* Fix formatting
* Use std::string instead of char*
* Use .c_str() instead of .data()
* Fix crash in Mac by correctly checking precision
* Use TemporaryDirectory for tests instead of NamedTemporaryFile (Fixes windows ci)
* Remove unnecessary file creation
* Propagate exceptions via cython
* Switch to TemporaryDirectory in xtcfile.py
* Remove unnecessary include
* Update some comments and document functions
* Add XTC reporter to the docs
