Backports to the 0.10 release branch #456

Luthaf · 2022-07-20T18:29:16Z

This backports #443, #444, #445, #447, #450, #451, #452, and #455 to the 0.10 release branch.

ARM & x64 can disagree on the final few decimal places, and we don't really care

The variable errno seems to be only set when an error occured and not for reads beyond EOF.

This is detected by Valgrind.

Also, add reading and writing with pre-allocated vectors to BinaryFile.

Overload read/write functions to take pre-allocated vectors of a given type. These functions are implemented for all types used by the binary file.

… point differences

Luthaf and others added 30 commits July 19, 2022 21:22

Upate compiler versions in CI

5aa0a07

Add helper function to read text/binary files in tests

393e765

Abstract over reading/writing binary files

982f730

Manual implementation of netcdf reader using BinaryFile abstraction

776d306

Implement writting NetCDF 3 files

6916b8b

Unify variables and record variables under a single API

572103e

Re-implement Amber NetCDF format using the new NetCDF3 file

cafd717

Optimize reading and writing to binary files with mmap

9665889

Only write fill values to netcdf files when required

77d676a

Update internal documentation

d769b37

Handle non-standard units in netcdf files

5b859c1

Remove all traces of netcdf-c from cmake & documentation

278c990

Update to the latest Catch version

9f5fda4

Update precision in lammps trajectory tests to 1e-12 instead of 1e-16

33c9e48

ARM & x64 can disagree on the final few decimal places, and we don't really care

refactor(span): use nullptr instead of NULL

bacb0d6

refactor(CML): read whole file content with dedicated function

1a199b9

feat(BinaryFile): get the file size and skip bytes

a298909

refactor(BinaryFile): remove buffer for swapping

c49a339

refactor(BinaryFile): use buffer for endianness swapping

16c8407

refactor(NetCDF): skip padding instead of reading bytes

3ee57c1

refactor(BinaryFile): indicate reads beyond EOF in error msg

0df8af7

The variable errno seems to be only set when an error occured and not for reads beyond EOF.

Fix writing of unit cells with negative values in extended XYZ

f716a3e

refactor: rewrite XDRFile

140a0b5

fix(XTC): read out of bounds in array for last atom

a01d778

This is detected by Valgrind.

fix(XTC): large coord index overflow

2baba6c

refactor(tests): fix conversion warning for AmberNetCDF

168dcd2

refactor(XDRFile): used fixed size types for compression

667ddae

feat(tests): read double precision TRR

5f6ae05

feat(tests): check reading all cell shapes from TRR/XTC

31cbe1d

refactor(TRR/XTC): use fixed-size integers in header

58d163f

ezavod and others added 5 commits July 20, 2022 13:24

refactor(XDRFile): remove redundant BinaryFile functions

5a4e8c4

Also, add reading and writing with pre-allocated vectors to BinaryFile.

refactor(BinaryFile): overload read/write functions for vector

5e13217

Overload read/write functions to take pre-allocated vectors of a given type. These functions are implemented for all types used by the binary file.

More tweaks to LAMMPSData cell output format to remove small floating…

9e81368

… point differences

Fix small warnings in XDR tests

59b38d8

Re-enable automatic deployment of nightly documentation

a94ab28

Luthaf merged commit 2b53c9c into chemfiles:release-0.10 Jul 21, 2022

Luthaf deleted the backports branch July 21, 2022 01:57

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Backports to the 0.10 release branch #456

Backports to the 0.10 release branch #456

Luthaf commented Jul 20, 2022

Backports to the 0.10 release branch #456

Backports to the 0.10 release branch #456

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Luthaf commented Jul 20, 2022