Code

Combine 0.2.x branch with master#124

Code

Merged

sverhoeven merged 178 commits intomastereWaterCycle/grpc4bmi:masterfrom bmi2eWaterCycle/grpc4bmi:bmi2Copy head branch name to clipboardMar 20, 2023

+4,273-3,280

Commits

Commits on Feb 19, 2020

• Merge pull request #58 from eWaterCycle/singularity-from-notebook-56-bmiport-envvar-55

  Show description for 35ebc87
  sverhoeven

  authored
  35ebc87

• Prep for 0.2.4 release

  sverhoeven

  committed
  12d7414

Commits on Mar 13, 2020

• Attempt to create grpc channel on occupied port (#64)

  Show description for 1ef38b6
  sverhoeven

  authored
  1ef38b6

Commits on Mar 24, 2020

• Prep for v0.2.5 release

  sverhoeven

  committed
  2a1cc40

• Prep for 0.2.6 release

  Show description for e73ed9e
  sverhoeven

  committed
  e73ed9e

Commits on Jul 27, 2020

• Added extra_volumes arg to BmiClientDocker

  Show description for f7f422f
  sverhoeven

  committed
  f7f422f

• Added extra_volumes arg to BmiClientSingularity

  Show description for 479a848
  sverhoeven

  committed
  479a848

Commits on Jul 29, 2020

• Merge pull request #71 from eWaterCycle/extra-volumes-0.2.0

  Show description for 82e47a4
  sverhoeven

  authored
  82e47a4

• Prep for 0.2.7 release

  sverhoeven

  authored
  24eccec

Commits on Jul 30, 2020

• Backport 4ca0fe3

  Show description for cb639df
  sverhoeven

  committed
  cb639df

Commits on Aug 11, 2020

• Added test to trigger RESOURCE_EXHAUSTED error

  sverhoeven

  committed
  9ef3a2b

• Implemented chunked get_value

  Show description for b7f1ec2
  sverhoeven

  committed
  b7f1ec2

• Swap travis for GH action

  sverhoeven

  committed
  8c2a915

• Revert "Swap travis for GH action"

  Show description for 51dd5ae
  sverhoeven

  committed
  51dd5ae

• Swap travis for GH action

  sverhoeven

  committed
  3e05977

• Build & install bmi-c

  sverhoeven

  committed
  314fd54

• Added sonar-project.properties

  sverhoeven

  committed
  48d4a32

• Merge branch '0.2-gh-action' into value-too-big-0.2.x

  sverhoeven

  committed
  c285914

• No debug cli arg in 0.2.x branch

  sverhoeven

  committed
  9189b46

• Revert "No debug cli arg in 0.2.x branch"

  Show description for d13ddec
  sverhoeven

  committed
  d13ddec

• No debug cli arg in 0.2.x branch, take 2

  sverhoeven

  committed
  65d985d

• Merge pull request #78 from eWaterCycle/value-too-big-0.2.x

  Show description for 2d00924
  sverhoeven

  authored
  2d00924

• Prep for 0.2.8 release

  sverhoeven

  committed
  15a82db

Commits on Oct 19, 2020

• Added sleep to BmiClientSingularity

  Show description for c1460b7
  sverhoeven

  committed
  c1460b7

• Merge pull request #85 from eWaterCycle/sing-sleep-84

  Show description for f425f68
  sverhoeven

  authored
  f425f68

• Prep for 0.2.9

  sverhoeven

  committed
  1ad1969

• Replace parent env with injected env var

  Show description for 2d49220
  sverhoeven

  committed
  2d49220

• Prep for 0.2.10 release

  sverhoeven

  committed
  fe89680

• Raise required singularity version so --env works.

  sverhoeven

  committed
  7480d73

• Use sing v.3.6.4

  sverhoeven

  committed
  98d7d8a

• Merge pull request #86 from eWaterCycle/sing-env-84

  Show description for 54beca8
  sverhoeven

  authored
  54beca8

Commits on Jan 26, 2021

• Replace bad chars in singularity version

  Show description for a3d1350
  sverhoeven

  committed
  a3d1350

• Use setup-singularity@v5 in CI job

  sverhoeven

  committed
  ad4fa0e

• Use ewatercycle/setup-grpc@v3 in CI

  sverhoeven

  committed
  bfbbc32

• Merge pull request #89 from eWaterCycle/semver-valueerror-88

  Show description for 27b8e22
  sverhoeven

  authored
  27b8e22

• Prep for 0.2.11 release

  sverhoeven

  committed
  dbad2d5

Commits on Mar 5, 2021

• Use ubuntu-20.04 for ci

  sverhoeven

  committed
  4fc30b3

• cpp workflow also compiles grpc instead of using prebuilt binary switching back

  sverhoeven

  committed
  180b3b6

• Use patched version of setup-singularity

  sverhoeven

  committed
  4b90f29

• Use v6 of sing action

  sverhoeven

  committed
  d8bc8b2

Commits on Mar 8, 2021

• Use setup-grpc@v4 action

  sverhoeven

  committed
  d5f8cab

Commits on Mar 18, 2021

• Add unit test for work_dir

  Show description for ded4038
  sverhoeven

  committed
  ded4038

Commits on Mar 19, 2021

• Refactored BmiClientSingularity arguments

  Show description for 0eafaa8
  sverhoeven

  committed
  0eafaa8

• English

  sverhoeven

  committed
  e09fd3b

• Refactored BmiClientDocker to behave similar to BmiClientSingularity

  sverhoeven

  committed
  56f0b67

• Added example for parallel model runs

  sverhoeven

  committed
  c4dc591

• Correct existing tests

  sverhoeven

  committed
  87ca8ab

• For api docs have 1 module per file

  sverhoeven

  committed
  300c695

• Updated docs to use refactored classes

  sverhoeven

  committed
  9a21710

• More checks and tests

  sverhoeven

  committed
  b6d632c

• More docs

  sverhoeven

  committed
  aff4255

• Docs layout

  sverhoeven

  committed
  d55b250

• Explain delay, timeout better

  sverhoeven

  committed
  4ae8070

• Rename utils to contstants as that is all it contains now

  sverhoeven

  committed
  ac02211

• More tests based on examples in doc string

  sverhoeven

  committed
  f23f919

Commits on Mar 22, 2021

• Correct path to data file inside image

  sverhoeven

  committed
  854b809

• Use same version of singularity as installed on Cartesius

  sverhoeven

  committed
  47916f7

• Made work_dir required

  Show description for 37c80eb
  sverhoeven

  committed
  37c80eb

• Remove default work_dir from docstrings

  sverhoeven

  committed
  609fe59

Commits on Mar 24, 2021

• Apply suggestions from code review

  Show description for 4127706
  

  sverhoeven

  and

  SarahAlidoost

  authored
  4127706

• Use *.sif in example

  Show description for c148520
  sverhoeven

  committed
  c148520

• Use the sif

  sverhoeven

  committed
  9523367

• Use typeguard to assert argument types for better errors + explain wflow usecase better.

  sverhoeven

  committed
  0177061

• Add extra check for input_dirs as str == Iterable[str]

  sverhoeven

  committed
  934ca91

Commits on Mar 26, 2021

• Merge pull request #94 from eWaterCycle/93-workdir-identity-mount

  Show description for 92a60ac
  sverhoeven

  authored
  92a60ac

• Prep for 0.2.12 release

  sverhoeven

  committed
  15213c4

Commits on Mar 30, 2021

• Added MemoizedBmi

  Show description for 5219ea1
  sverhoeven

  committed
  5219ea1

Commits on Jul 16, 2021

• Added stdout, stderr argument to BmiClientSingularity constructor

  sverhoeven

  committed
  c7e3434

• Use correct name

  sverhoeven

  committed
  20f23fc

• Unused import

  sverhoeven

  committed
  d6e6326

Commits on Jul 19, 2021

• Silence semver deprecation warning

  sverhoeven

  committed
  bca8189

• Add logs() to BmiClientSingularity and BmiClientDocker

  Show description for e55e7dc
  sverhoeven

  committed
  e55e7dc

Commits on Jul 20, 2021

• Prep for 0.2.13 release

  sverhoeven

  committed
  659721a

• Use own method

  sverhoeven

  committed
  e9a38b5

• Dedup container exception

  sverhoeven

  committed
  6001693

• Merge pull request #102 from eWaterCycle/sing-capture-output

  Show description for 1882d5f
  sverhoeven

  authored
  1882d5f

Commits on Oct 13, 2021

• Use sing 3.8.3

  sverhoeven

  authored
  bedee90

Commits on Oct 20, 2021

• Merge pull request #107 from eWaterCycle/sing-383-in-ci

  Show description for ec82a5e
  sverhoeven

  authored
  ec82a5e

Commits on Nov 8, 2021

• Use Bmi class from basic_modeling_interface

  Show description for cc355ab
  sverhoeven

  committed
  cc355ab

Commits on Nov 11, 2021

• Merge pull request #97 from eWaterCycle/memoized_bmi_client

  Show description for ada138d
  sverhoeven

  authored
  ada138d

• Prep for 0.2.14 release

  sverhoeven

  committed
  798950a

• Use older docutils to fix build on readthedocs

  sverhoeven

  committed
  d4e644a

Commits on Sep 20, 2022

• Drop futures as it failed to install

  Show description for 0d0f3dd
  sverhoeven

  committed
  0d0f3dd

• Allow apptainer to be used by BmiClientSingularity

  sverhoeven

  committed
  54f3485

• Make sonar cloud happy

  sverhoeven

  committed
  531fcc9

• Dont run double CI on push to PR

  sverhoeven

  committed
  251ed72

• Add test for BmiR

  sverhoeven

  committed
  df506fd

• Use Python 3.10 in CI + use absolute path to fake.r

  sverhoeven

  committed
  d2ee26a

• YAML strips 0, use string instead

  sverhoeven

  committed
  2b407b1

• Pin scipy

  sverhoeven

  committed
  2a30308

• Add R code

  sverhoeven

  committed
  2e84d30

• Make sure pytest has R_LIBS_USER env var set

  sverhoeven

  committed
  00fb1b3

• Use export for env vars

  sverhoeven

  committed
  8d432bc

• For some reason get_value_ref fails on CI, skipping

  sverhoeven

  committed
  d275a4f

Commits on Oct 18, 2022

• Set R_LIBS_USER once

  sverhoeven

  committed
  4646f1e

• Use PEP440 and packaging package to check if apptainer/singularity version is supported

  sverhoeven

  committed
  e1e9608

• Fixed heat model, so no longer need to pin scipy

  Show description for a8cd7ca
  sverhoeven

  committed
  a8cd7ca

• Use setup-r GH action to set R_LIBS_USER env

  sverhoeven

  committed
  89a3b48

• Pin protobuf to v3

  Show description for fc538c3
  sverhoeven

  committed
  fc538c3

• Dont install protobuf v4 and then downgrade

  sverhoeven

  committed
  1e9272a

• Try to figure out which test is hanging

  sverhoeven

  committed
  c1d6f1b

• CI: Use apptainer + use system R

  sverhoeven

  committed
  6d510ea

• Merge pull request #112 from eWaterCycle/allow-apptainer-version

  Show description for ed18d05
  sverhoeven

  authored
  ed18d05

• Prep for 0.2.15 release

  sverhoeven

  committed
  c5ed76f

Commits on Nov 8, 2022

• Add apptainer client

  Show description for a16813e
  sverhoeven

  committed
  a16813e

Commits on Nov 15, 2022

• Add apptainer to some more places.

  sverhoeven

  committed
  17c4abb

• Add required work_dir to examples

  sverhoeven

  committed
  768c10e

• Point doc badge to 0.2.x version on readthedocs.

  sverhoeven

  committed
  00d00fa

• Merge pull request #119 from eWaterCycle/116-apptainer-client

  Show description for ad7fed1
  sverhoeven

  authored
  ad7fed1

• Prep for 0.2.16 release

  sverhoeven

  committed
  1953b8c

Commits on Jan 5, 2023

• Merge remote-tracking branch 'origin/0.2.x' into bmi2

  sverhoeven

  committed
  01826b2

• Replace setup.py + requirements.txt with pyproject.toml

  Show description for 5a138ae
  sverhoeven

  committed
  5a138ae

• Fixing test suite

  Show description for f8f3284
  sverhoeven

  committed
  f8f3284

• Fix protobuf-cpp and protobuf-python have potential Denial of Service issue

  sverhoeven

  committed
  b17a180

Commits on Jan 6, 2023

• Fix tests for MemoizedBmi

  sverhoeven

  committed
  e6cc822

• Enable branch coverage + only look for tests in test/

  sverhoeven

  committed
  50b00d6

• Fix BmiClientDocker tests

  Show description for acc5b64
  sverhoeven

  committed
  acc5b64

• Use latest GH actions

  sverhoeven

  committed
  06faa70

• Fix R tests

  sverhoeven

  committed
  f23154b

• Fix sing tests

  sverhoeven

  committed
  f001150

• Fix legacy server tests

  sverhoeven

  committed
  3461796

• More legacy server tests

  sverhoeven

  committed
  c00852c

• Use newer grpc on CI job for C++

  sverhoeven

  committed
  ebf97bc

• Legacy docs

  sverhoeven

  committed
  86e2608

Commits on Jan 11, 2023

• Fix sphinx warning

  Show description for 68cf69e
  sverhoeven

  committed
  68cf69e

• Heat model now is 1d

  sverhoeven

  committed
  98d5e7e

• Added OptionalDestBmi class

  sverhoeven

  committed
  d450d54

• Force readthedocs build to use Python 3.10

  sverhoeven

  committed
  4f7ff5e

• Force installation of sphinx extensions on readthedocs

  sverhoeven

  committed
  df21720

• Use docs extra + added copy button extension

  sverhoeven

  committed
  1d7f8ac

• Format docstring

  sverhoeven

  committed
  dd0e4e1

Commits on Jan 20, 2023

• Generate bindings with protobuf v4

  sverhoeven

  committed
  49a38ef

• Add Dockerfiles for heat model using different versions

  sverhoeven

  committed
  d36c2d8

• Revert "Add Dockerfiles for heat model using different versions"

  Show description for 2017ecb
  sverhoeven

  committed
  2017ecb

• Add Dockerfiles for heat model using different versions

  sverhoeven

  committed
  56a1fc3

• Use latest @actions/cache

  sverhoeven

  committed
  939dff0

• Working on wrapping heatcxx in a grpc4bmi server container image

  sverhoeven

  committed
  75856ca

Commits on Jan 23, 2023

• Move bmi-c submodule to v2.1 tag

  sverhoeven

  committed
  99e0a47

• Stuck on linker

  sverhoeven

  committed
  8a4024b

• Get grpc4bmi from gh instead of local mount

  sverhoeven

  committed
  f0e0e14

Commits on Jan 26, 2023

• Fix compile

  sverhoeven

  committed
  ede0a47

• const

  sverhoeven

  committed
  117dc24

• Dont install

  sverhoeven

  committed
  3bb6070

• More debug

  sverhoeven

  committed
  a573637

• More prints

  sverhoeven

  committed
  19247c4

• Add reflection

  sverhoeven

  committed
  8c5849d

Commits on Jan 30, 2023

• Ignore sif files for git and docker

  sverhoeven

  committed
  3adfe23

• Prefer install of bmi-c + bmi-cxx over git submodule

  sverhoeven

  committed
  84fb60d

• Got working server from bmi-example-cxx

  Show description for 727f3bc
  sverhoeven

  committed
  727f3bc

• More cleanup

  sverhoeven

  committed
  0926af9

• Remove deps of deps

  sverhoeven

  committed
  80dd5b9

• Make sure bmi.hxx is imported

  sverhoeven

  committed
  f0fce18

• Wrap bmiheatc with grpc

  sverhoeven

  committed
  2241fe8

• Install bmi-c and bmi-cxx in CI

  sverhoeven

  committed
  2e937b3

Commits on Jan 31, 2023

• Allocate strings

  Show description for 4fb5946
  

  sverhoeven

  and

  jhidding

  committed
  4fb5946

• Drop cache buster

  sverhoeven

  authored
  f4d5155

Commits on Feb 8, 2023

• Old python heat model is missing get_var_itemsize, added workaround

  sverhoeven

  committed
  c606b5a

• Add image with run-bmi-server --bmi-version 0.2 ...

  sverhoeven

  committed
  f3323b9

Commits on Feb 21, 2023

• Add build command + simplify non-python dirs

  sverhoeven

  committed
  e023b4a

• Correct GetGridRank wrapper c function was calling get_grid_size

  sverhoeven

  committed
  732f5fd

• Structure readme

  sverhoeven

  committed
  3798bbc

Commits on Mar 16, 2023

• Make typeguard==3 compatible

  sverhoeven

  committed
  5a129ad

• Add check back as str is iterable which passes typechecked

  sverhoeven

  committed
  6ab8927

• Fix thing I broke with prev commit

  sverhoeven

  committed
  b12e5f3

• One more test to fix

  sverhoeven

  committed
  11c7965

• Pin protobuf to v4

  sverhoeven

  committed
  4850b2c

• Merge pull request #129 from eWaterCycle/typeguard3-compat

  Show description for c209b22
  sverhoeven

  authored
  c209b22

• Apply suggestions from code review

  Show description for 570a1b6
  

  sverhoeven

  and

  Peter9192

  authored
  570a1b6

• Made py image names consistent

  sverhoeven

  committed
  cf9928f

Commits on Mar 20, 2023

• Merge pull request #126 from eWaterCycle/latest-protobuf

  Show description for eb91cfc
  sverhoeven

  authored
  eb91cfc

• Document how legacy containers can be used

  sverhoeven

  committed
  5cbfd99

• Sync version in docs/conf.py with pyproject.toml

  sverhoeven

  committed
  b091821

• Prep for 0.4.0 release

  sverhoeven

  committed
  c55ceb0

• Make sif create command multiline

  sverhoeven

  committed
  487899a

• Clearify dest2 is same as dest

  sverhoeven

  committed
  13cde02

• Mention get_value_at_indices signature change in class docstring

  sverhoeven

  committed
  c5cc9b9

• Dont use branches that are removed after PR is merged.

  sverhoeven

  committed
  f6a7679

• Use builtin int instead of numpy.int_ alias

  sverhoeven

  committed
  48d8e31