Psyclone

1) 602 for 597. Modify Node.ancestor() to optionally include
self.

2) 607 for 457. Add fixtures documentation to the developer
guide and split guide into smaller files.

3) 610 towards 567. Extends the Profile transformation so that
a user can supply name and location strings rather than rely
on the automatic generation of suitable names.

4) 600 for 468. Adds a datatype to literals in the PSyIR.

5) 601 for 599. Add create methods to assist bottom up PSyIR node
creation.

6) 608 for 594. Add 'DEFERRED' and 'ATTRIBUTE' as PSyIR array extents.

7) 606 towards 474. Moves Profile and Extract transformations into
new directory structure (psyir/transformations/). Begin putting
domain-specific transformations into domain/ directory.

8) 618 for 567. Corrects the automatic generation of names for
profiled regions.

9) 624 for 566. Removes the 'force profile' option from the psyclone
script as it is no longer required.

10) 614 for 612. Use the datatype of the Literal node in the SIR
backend rather than assuming all literals are real.

11) 555 for 190. Adds a GlobalsToArguments transformation that
converts kernel accesses to global data into arguments.

12) 627 for 625. Adds SymbolTable.new_symbol_name() method to generate
names that don't clash with existing symbols.

13) 623 for 622. Bug fix for adding loop directives inside
region directives for the nemo api.

14) 631 for 628. Add support for compiling additional
non-library code in compilation tests.

15) 643 for 617. Corrects table widths in the html version of the
documentation and also fixes broken links to developer guide.

16) 632 for 585. Add support for the use of expressions when
assigning values to constant Symbols.

17) 635 for 634. Update PSyclone to use new parent functionality
in fparser and to remove spurious white space in some of the
generated (end do/if) code.

18) 657 towards 474. Moves various node classes out of psyGen
and into the psyclone.psyir.nodes module.

19) 669 towards 474. Move those error/exception classes that
were in psyGen into a new 'errors' module.

20) 656 towards 412. Add PSyIR Range node to support array slice
accesses. This could also be used for loop indices.

21) 672 for 651. Add PSyIR lbound and ubound BinaryOperations.

22) 670 for 666. Make the various GOcean grid properties
configurable (previously the mapping from meta-data name to
corresponding Fortran code was a dict in the code).

23) 671 for 653 and 652. Fixes two issues with OpenCL
generation for the GOcean API (handling of the SAVE attribute
and support for real and integer scalar arguments).

24) 541 for 536. Adds transformations to convert MIN, ABS and
SIGN intrinsics into equivalent PSyIR code and uses these in
NEMO/eg4.

25) 662 for 661. Adds PSyIR support for the MATMUL intrinsic
and renames the dynamo examples to lfric.

26) 665 for 603 and 673. Alters the Reference and Array nodes
so that they refer to a Symbol instead of just a name.

27) 683 for 682. Modifies PSyclone fparser2 front-end reader to
work with the latest version of fparser2 which now correctly deals
with intent attributes.

28) 681 for 680. Small fix to failing profiling test (DM assumed
to be on but not explicitly set).

29) 691 for 690. Fix PSyIR fparser frontend handling of allocatable
array declarations.

30) PR 605 for 150. Implements code generation for reference
element properties in the Dynamo0.3 (LFRic) API.

31) PR 615 for 586 and 323. Improves support for use statements
including unqualified use statements.

32) PR 650 for 583. Implementation of the PSyData API and
refactoring of Extraction and Profiling support. Note that the LFRic
(Dynamo0.3) API is not yet fully supported.

33) PR 702 for 660. Read the default KIND parameters for the LFRic
domain from the configuration file.
NOTE: this change requires that any local config file be updated as
the new KIND mapping is mandatory.

34) PR 704 for 699 and 697. Fixes gocean/eg2 and adds a
--compile option to the check_examples script.

35) PR 684 for 655. Re-factor psy-data-based transformations.

36) PR 700 for 687. Adds support for Fortran array syntax
to the PSyIR Fortran front-/back-ends.

37) PR 707 for 694. Extends gocean/eg5 to produce executables
for the simple_timing, dl_timer and drhook profiling wrappers.

38) PR 689 for 312. Removes the Namespace manager and replaces
it with a SymbolTable. This is work towards all code being
generated by the PSyIR backends.

39) PR 722 for 716. Adds support for reference-element normals
and extends the kernel-stub generator to support reference-element
properties.

40) PR 708 for 638. Adds limited support for GOcean grid properties
to the ExtractNode functionality.

41) PR 701 for 193 and 195. Adds support for face and edge
quadrature as well as multiple quadratures in a kernel in the
Dynamo0.3 (LFRic) API. Also extends kernel-stub generator support.

42) PR 709 for 698. Adds the 'target' attribute to declarations
of the PSyData object.

43) PR 729 for 12. Change the Fortran intent of all derived-type
objects passed into the PSy layer in the LFRic API to be 'in'.

44) PR 739 for part of 18. Documents mesh properties that a
kernel can request in LFRic (Dynamo0.3) API.

45) PR 743 for 740. Remove old unused quadrature_mod.f90 from
LFRic (Dynamo0.3 API).

46) PR 734 for 539. Added the Wchi function space to LFRic
(Dynamo0.3 API).

47) PR 728 for 721. Adds DataType hierarchy decoupled from DataSymbol.

48) PR 596 for 500. Makes the NEMO API use the symbol table.

49) PR 686 for 684. Adds the MatMul2CodeTrans which transforms
a MATMUL PSyIR operation into the equivalent PSyIR expression.

50) PR 747 for 18. Implements code generation (PSy-layer and
kernel stub) for mesh properties that a kernel can request in
LFRic (Dynamo0.3) API.

51) PR 731 for 668. Adds support for ProfileInit and ProfileEnd
functions in the PSyData API. Re-structuring of the associated
documentation.

52) PR 756 for 749. Adds the option to generate run-time checks
for the LFRic API that fields are on function spaces consistent
with those specified in kernel metadata.

53) PR 726 for issue 723. Adds the concepts of DataNode and
Statement to the PSyIR and adds checks that ensure that when a
child Node is added to a parent Node, the type of the child Node
is compatible with the type of Node expected by the parent.

54) PR 758 for 733. Shortens the variable names that are
constructed for LFRic PSy-layer variables related to any-space
function spaces.

55) PR 760 for 751. Adds support for W2htrace and W2vtrace
function spaces.

56) PR 762 for 725. Renames the various builtin-operation-to-
code transformations now that they are not NEMO specific.

57) PR 773 for 772 and 715. Adds support for reading Fortran
parameter statements containing symbols into the PSyIR.

58) PR 776 for 775. Small bug fix for upper loop bound in
Matmul2CodeTrans transformation.

59) PR 735 for 732. Add a Visibility attribute to symbols and
fparser2 front-end captures public and private visibilities.

60) PR 770 for 766. Fix operation precedence issues in the Fortran
back-end by inserting parenthesis when needed.

61) PR 769 for 588. Adds frontend support for *N and double
precision type declarations.

1) 579 for 509. Improves the structuring of the html version
of the User Guide.

2) PR 581 for 578. Extends the PSyIR Fortran backend so
that variable declarations include kind information. This
currently only works if kind-parameters are declared or
explicitly imported in the local scope - see 587 and 586.

3) PR 562 for 473. Fixes the DAG generation to allow for
Loops having Schedules and children (e.g. loop limits) that
we want to ignore.

4) PR 535 for part of 150. Implements support for parsing
of reference element metadata in the Dynamo0.3 (LFRic) API.

5) PR 516 for 497. Adds support for translating the Fortran
where construct into the PSyIR.

6) PR 545 for 544 and 543. Moves the Symbol support into
a separate sub-module and adds support for parameter declarations
and the functionality to resolve deferred datatypes.

7) PR 559 for 483. Introduces new InlinedKernel class and
uses this as the base class for all NEMO kernels.

8) PR 580 for 542. Adds a Schedule as a child of ExtractNode and
ProfileNode.

9) PR 573 for 438. Fixes all tests to use the value property of
exceptions rather than str(err).

10) PR 416 for 408. Adds support for non-ascii chars in Fortran
strings.

11) PR 591 for 584. Adds the concept of a deferred interface to
PSyIR symbols. This allows declarations to appear in any order and
helps to deal with kind symbols scoped via module use statements.

1) 245 and PR 247. Extend PSyIR to support common kernel
constructs (e.g. asignments) and generalise ASTProcessor and
CodeBlocks.

2) 275 and PR 276. Update fparser submodule (to point to latest
version) as this was not done at the last release.

3) 269 and PR 273. Remove generation of unnecessary
infrastructure calls when an Invoke only contains calls to
built-ins.

4) 196 and PR 242. Add support for kernels with evaluators on
multiple target function spaces.

5) 270 and PR 271. Add ability to specify include directories in
PSyclone script to allow Fortran include files to be found when
transforming kernels.

6) 201 and PR 224. Add ability to write transformed kernels to
file. Also ensures that kernel and psy-layer names match, allows
an output directory to be specified and supports different output
options when the same kernel is transformed in more than one
location.

7) 126 and PR 283. Update xfailing tests in alggen_test.py which
require multiple quadrature objects in a single invoke to pass.

8) 227 and PR 233. Add a gocean1.0 API OpenACC example.

9) 207 and PR 280. Remove support for gunghoproto API.

10) 174 and PR 216. Adds the ability to generate an OpenCL PSy
layer in the gocean1.0 API (including an OpenCL transformation).

11) 272 and PR 277. Adds an implicit-to-explicit-loop
transformation for the nemo API.

12) PR 255. Construct a KernelSchedule for kernel code with a
SymbolTable to hold information on variables used.

13) PR 302. Fix API's -> APIs typo in documentation.

14) 292 and PR 293. Add allowed list of nodes to RegionTrans.

15) 254 and PR 299. Adds methods to generate C and OpenCL
code for the Symbol Table and for certain PSyIR nodes.

16) PR 301. Adds an extras_require section to setup.py to simplify
installation of dependencies required for docs and tests.

17) 281 and PR 313. Adds support for compiling the code
generated as part of the GOcean 1.0 tests (including OpenCL
code that uses FortCL).

18) 139 and PR 218. Beginning of implementation of kernel-
extraction functionality (PSyKE). Currently only inserts
comments into generated Fortran code.

19) 327 and PR 328. Fix for erroneous xpassing test.

20) 238 and PR 285. Use fparser2 for parsing the
Algorithm layer (instead of fparser1).

21) 321 and PR 325. Document kernel coding restrictions required
for kernel transformations.

22) 326 PR 335. Alters the use of pytest fixtures to remove the now
deprecated use of the global pytest.config.

23) PR 318. Updates the Schedule hierarchy within the PSyIR.
Introduces a new Schedule base class which KernelSchedule and
InvokeSchedule then sub-class.

24) 332 and PR 333. Bug fix for parsing of simple arithmetic
expressions in kernel argument lists in the Algorithm layer.

25) 337 and PR 341. Bug fix to make matching of kernel names
in module use statements (in the Algorithm) case insensitive.

26) 268 and PR 306. Restructure of PSy and stub code generation.

27) 248 and PR 287. Extends OpenACC transformation support to
the nemo api, adds transformations for OpenACC data and kernel
directives and adds a sequential option to the OpenACC loop
directive transformation.

28) 319 and PR 331. Bug fix to make matching of kernel names
in module use statements (in the Kernel) case insensitive.

29) 349 Bug fix for unicode characters in comment strings for
Python 3 to 3.6.

30) 320 and PR 334. Remove obsolete GUI-related code.

31) 322 and PR 343. Add gocean1.0 api example which contains
kernels with use statements.

32) 345 and PR 352. Makes the search for kernels within the parse
tree case insensitive.

33) 350 and PR 351. Bug fix in the stencil lookup for field
vectors in the Dynamo0.3 API.

34) 336 and PR 338. PSyIR Fortran array parsing support (logical
type, a(xx) dimension specifications and array size can be an
integer variable).

35) 346 and PR 357. In the nemo api put do-while loops into a
code block rather than recognising them as do-loops and make
default(present) optional for ACCKernels transformations.

36) 362 and PR 367. Adds the basics of a transformation for identifying
certain LFRic kernel arguments that can be converted to constants.
Currently only identifies candidate arguments and prints them to
stdout.

37) PR 347 (working towards 256). Adds support for If and CASE
constructs to the PSyIR (superseding and removing the existing, NEMO-
specific support for If constructs).

38) 377 and PR 378. Update fparser submodule to point to latest
fparser master (contains bug fix for Python 2 installation).

39) 329 and PR 371. Removes the global psyGen.MAPPINGS_ACCESSES by
moving the functionality into the api-specific config section of
the configuration file.

40) 361 and PR 365. Identify NemoKernel nodes via the PSyIR
rather than the fparser2 parse tree.

41) 340 and PR 380. Split the documentation into a user-guide
and a developer-guide. These will be available separately on
read-the-docs.

42) 369 and PR 347. Adds support for constant values (fixed compile-time
known values) in the PSyIR Symbol representation.

43) PR 383. Fixes to various pylint errors.

44) PR 384 (working towards 354) Adds support for CASE constructs with
a DEFAULT clause when translating Fortran fparser2 to PSyIR.

45) PR 366 (working towards 323) Improves the Symbol interface
infrastructure with Arguments and FortranGlobals. The Fortran-to-PSyIR
front-end parses the 'use module only' statements.

46) PR 370 for 339. Makes the support for operators in the PSyIR
more robust by using an enumerator. Adds support for some intrinsics.

47) PR 389 for 386. Variable names and associated loop-types
for the NEMO API are now stored in the configuration file.

48) PR 394 for 392. Fixes a bug in the way the test suite checks
for whether the graphviz package is available.

49) PR 387 for 249. Extends OCLTrans() so that all kernels within a
transformed Invoke are converted to OpenCL. Also includes a
work-around for array accesses incorrectly identified as Statement
Functions by fparser2.

50) PR 403 for 390. Use AutoAPI to generate the PSyclone Reference Guide
and build all local documentation using the 'sphinx_rtd_theme'.

51) PR 404 for 364. Re-structure class hierarchy for Kernels, with
CodedKernels and BuiltIns as specialisations.

52) PR 297. Adds support for the Dr Hook profiling library.

53) PR 413 for 411. Adds support for semantic navigation of the
PSyIR tree.

54) PR 376 for 368. Introduces PSyIR back-end infrastructure using the
Visitor Pattern and creates a PSyIR-to-Fortran back-end.

55) PR 428 for 427. Fix to test suite so that empty, transformed
kernel files are not created in the CWD.

56) PR 439 and Issue 438. Instruct pip to install the version of
pytest prior to 5.0 (as changes to the structure of the exception
object break a lot of our tests).

57) PR 420 for 418. Moves the C/OpenCL generation functionality out
of the Node class and implements it as PSyIR backends using the
Visitor Pattern.

58) PR 434 for 354. Add support for translating ranges in
Fortran case statements into PSyIR.

59) PR 421. Alters the generated code for the dynamo 0.3 API so that
the mesh object is obtained from proxy. (Consistent with other accesses
and works around a bug in the PGI compiler.)

60) PR 452 for 397. Removes unnecessary walk_ast() call from the
NemoInvokes constructor.

61) PR 424 for 399. Adds dependence-analysis functionality to
the PSyIR (for reasoning about existing code such as in kernels or
the NEMO API).

62) PR 464 for 443. Adds a coding-style guide to the Developers'
Guide.

63) PR 453 for 449. Adds support for NVIDIA's nvtx profiling
API to the PSyclone profiling interface.

64) PR 454 for 410. Simplifies the Node.walk() method.

65) PR 400 towards 385. Adds support for Fortran Do loops in
the PSyIR - loop bounds are now captured.

66) PR 469 for 465. Removes duplicate lma tests.

67) PR 479 from kinow:fix-gungho-link. Fixes broken GungHo link
in documentation.

68) PR 441 for 373. Adds support for writing transformed LFRic
kernels to file.

69) PR 445 for 442. First step towards supporting OpenACC for
the LFRic (Dynamo0.3 API) PSy layer.

70) PR 466. Adds basic SIR backend to the PSyIR.

71) PR 407 for 315. Use the PSyIR SymbolTable to check for
global symbols (module variables) in kernels. Use this support to
raise an exception in transformations where global symbols are not
supported (e.g. the OpenCL transformation).

72) PR 498 for 388. Documents the PSyIR CodeBlock node and extends
the CodeBlocks with a property to differentiate between statement/s
and expression/s.

73) PR 476 for 429, 432, 433. Fix multi-line codeblocks,
add support for nemo implicit loops and nemo invokes.

74) PR 458 for 425. Add support for profiling in the NEMO API.

75) PR 510 for 419. Code re-structuring - moves what was the
FParser2ASTProcessor into psyir.frontend.fparser2.

76) PR 503 for 502. Adds size intrinsic to PSyIR and makes use
of it in the gocean api's for setting loop bounds.

77) PR 511 for 508. Includes the test directories in the Python
module so that the test utilities are available throught the test
directory hierarchy.

78) PR 496 for 494, 495 and 499. Fixes for OpenCL generation
including the ability to specify kernel local size and command
queue parameters.

79) PR 517 for 513. Adds support for if statements to the SIR
backend.

80) PR 522 for 519. Fix for adding profiling around a select
case construct.

81) PR 460 for 133. Add support for ANY_DISCONTINUOUS_SPACE in
the dynamo0.3 API (LFRic).

82) PR 531 for 455. Add ANY_SPACE_10 to the dynamo0.3 API
(LFRic) to be consistent with LFRic infrastructure.

83) PR 360 for part of 150. Document the rules for reference
element properties in the dynamo0.3 API (LFRic).

84) PR 518 for 393. Add the Container PSyIR node.

85) PR 525 for 459. Bug fix for passing scalar grid properties
to GOcean kernels when using OpenCL.

86) PR 485. Adds a psyclone.psyir.tools.dependency_analysis
module and associated DependencyTools class to help with
dependence analysis in the PSyIR.

87) PR 532 for 204. Adds support for W2broken and W2trace
function spaces in the dynamo0.3 (LFRic) API.

89) PR 515 for 512. Adds PSyIR backend support (Fortran and C)
for Directives.

90) PR 534 for 520. Adds PSyIR Fortran backend support for the
Container Node.

91) 547 and PR 551. Update all READMEs to use MarkDown and correct
paths in documentation on creating built-ins.

92) 546 for PR 553. Rename psyir.psyir.backend.base to visitor.

93) 526 for PR 527. Update fparser submodule and fix parsing of
intrinsics with a single argument.

94) PR 556 for 478. Changes the apply() and validate() methods of
all Transformations to take a dict of options. Also renames any
_validate() methods to validate().

95) PR 558 for 557. Move code-creation out of visitor and into
the appropriate back-ends.

96) PR 565 for 564. Alter implementation of auto-addition of
profiling so that it happens *after* the application of any
transformation script.

97) PR 505 for 303. Restructure view method to move the replicated
logic into the abstract class and add index numbers to the printed
Schedule statements. Also adds a Schedule to encapsulate Directive
children.

98) 570. PSyclone now set to require fparser 0.0.9 on
installation.

99) PR 572 for 571. Bug fixes now that fparser uses unicode.

100) PR 524 for 472. Adds support for scalar variables to the
SIR backend.

101) PR 574 towards 567. Fixes bug in profiling that causes
crash if first kernel in an invoke is a built-in.

102) PR 576 for 530. Includes the repository examples in the
distribution and updates the documentation accordingly.

1) 172 and PR 173 Add support for logical declaration, the save
attribute and initialisation in f2pygen (required for the OpenACC
transformation)

2) 137 Add support for Python 3. Travis now runs the test suite
for both Python 2 and Python 3.

3) 159 and PR 165. Adds a configuration option for the Dynamo
0.3 API to turn on (redundant) computation over annexed dofs in
order to reduce the number of halo exchanges required.

4) 119 and PR 171. Adds support for inserting profiling/
monitoring into a Schedule.

5) 179 and PR 183. Bug fix in CompileError constructor to run
tests under Python 3.

6) 121 and PR 166. Adds a user editable configuration file.

7) 181 and PR 182. Adds support for generating declarations of
character variables and for the target attribute.

8) 170 and PR 177. Adds OpenACC transformations for use with the
GOcean1.0 API. Appropriate Kernel transformations need to be added
for full automated OpenACC code parallelisation.

9) 164 and PR 184. Updates documentation to refer to psyclone
script instead of generator.py.

10) PR 187. Add example transformation scripts for the Dynamo
0.3 API.

11) PR 180. Makes the specification of loop limits in the GOcean
API more flexible. This will enable us to support single-iteration
loops.

12) 188 and PR 189. Bug fix to ensure that the name of profiling
regions remains the same when gen() is called multiple times.

13) 176 and PR 200. Introduce new RegionTrans base class and
add _validate method to ensure that the list of nodes to
be transformed (with OpenMP or OpenACC) is correct.

14) 197. Tidying of the test suite to use the new, get_invoke()
utility everywhere.

15) 212 and PR 213. Adds fparser as a submodule of psyclone to
allow concurrent development of PSyclone and fparser (by allowing
development versions of PSyclone to point to development versions
of fparser).

16) 185 and PR 202. Adds ability to modify a kernel in PSyclone
using fparser2 and includes an OpenACC transformation to specify a
kernel is an OpenACC kernel by adding an appropriate
directive. Currently it is not possible to write the modified
kernel to file.

17) 134 and PR 217. Add support for colouring intergrid kernels.

18) 196 and PR 210. Adds metadata support for evaluators on
multiple function spaces in the Dynamo 0.3 API.

19) 191 and PR 215. Add ability to specify iteration space
definitions to the configuration file.

20) 228 and PR 232. Fix for examples and travis now checks
examples at the same time as coverage and code style.

21) 219 and PR 225. Refactor dependence analysis and fix bug
that meant that unnecessary halo exchanges of vector components
were not being removed (following a redundant computation
transformation).

22) 27 and PR 209. Created initial NEMO api. Needs lots of work
but it provides a starting point.

23) 214 and PR 221. Adds a transformation to convert a
synchronous halo exchange into an asynchronous halo exchange.

24) 235 and PR 243. Removes dependency on Habakkuk in NEMO API.

25) 134 and PR 236. Adds support for adding OpenMP to intergrid
kernels.

26) 198 and PR 223. Updates PSyclone to use the latest
version of dl_esm_inf which has "GO_" prefixed to all public
quantities. Adds dl_esm_inf as a git submodule.

27) 158 and PR 253. Fix to remove unnecessary halo exchanges
related to GH_INC updates to kernel arguments.

28) 317 and PR 330. Fix to allow module use statements to be
added to functions.

29) 330 and PR 422. Adds PSyIR node to represent Nary operators and
increases the number of supported operators.

1) 250. Change setup.py (used for pip installation) to only use
version 0.0.7 of fparser.

1) 91 and PR 111 Remove unnecessary __init__.py files.

2) PR 107 Fix errors in Fortran test files revealed by update
to fparser 0.0.6. Update to catch new AnalyzeError raised by
fparser.

3) 90 and PR 102 Add support for integer, read-only, scalar
arguments to built-in kernels. Add new inc_X_powint_n Built-in
that raises a field to an integer power.

4) 67 Bug fix - printing Invoke object caused crash.

5) 112 and PR 113 - add travis support for codecov coverage tool

6) 118 and PR 122 - add .pylintrc file in tests directory
to disable some warnings that we don't care about (for testing
code).

7) 117 and PR 125 - bug fix for passing kernel arguments by value
in the GOcean API.

8) 105 and PR 115 - add support for coloured loops when
performing redundant computation.

9) 84 and PR 128 - make w2v and wtheta discontinuous function
spaces

10) PR 93 - add support for a swap-loop transform for the GOcean
API.

11) PR 152 - add pylintrc so that pylint's line-length limit
matches that of pep8.

12) PR 143 - bug fix for DAG generation in the GOcean API.

13) PR 153 - added -v option to the psyclone script to show the
version

14) PR 136 - add support for intergrid kernels (required for
multigrid)

15) PR 149 - add support for GH_READWRITE access for
discontinuous fields

16) PR 163 - updating PSyclone to work with the latest version of
the parser (0.0.7) as the API has changed

17) PR 169 - add support for specifying stencils in the GOcean
kernel meta-data.