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Devel #2224

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merged 182 commits into from
Dec 23, 2021
Merged

Devel #2224

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d289b7f
requirements: update grpcio requirement from <1.35.0 to <1.41.0 (#2115)
dependabot[bot] Sep 18, 2021
75dbb50
requirements: update grpcio-tools requirement from <1.35.0 to <1.41.0…
dependabot[bot] Sep 21, 2021
25c1f5c
requirements: update rich requirement
dependabot[bot] Sep 21, 2021
b401316
Merge pull request #2123 from PrincetonUniversity/dependabot/pip/deve…
davidt0x Sep 21, 2021
c38c0ff
requirements: update pytest-xdist requirement from <2.4.0 to <2.5.0 (…
dependabot[bot] Sep 22, 2021
de5484e
llvm/udf: Add support for numpy sqrt
jvesely Sep 1, 2021
09857a1
tests/models/Predator-Prey: Use attractor/repeller forces to select t…
jvesely Sep 14, 2021
d3741b2
tests/models/Predator-Prey: Use attractor/repeller forces to select …
jvesely Sep 22, 2021
35cf6ec
github-actions(deps): bump actions/github-script from 4.1 to 5 (#2125)
dependabot[bot] Sep 28, 2021
aea0621
requirements: update toposort requirement from <1.7 to <1.8 (#2129)
dependabot[bot] Sep 29, 2021
b2a1d6a
conftest: Fix typo in func_mode helper
jvesely Sep 20, 2021
232bfae
tests/mechanism/noise_variations: Set seeds of noise function instead…
jvesely Sep 23, 2021
bb67c4b
tests/transfer_mechanism/uniform_to_normal_noise: Set seeds of noise …
jvesely Sep 23, 2021
e70f785
tests/modulation_of_random_seed: Check final model results
jvesely Sep 20, 2021
9240b53
function: parameters.seed should match the seed that was used to init…
jvesely Sep 24, 2021
9e6b1be
functions/parameters: Reset PRNG state on seed assignment or change
jvesely Sep 23, 2021
f32638b
tests/random_state: Update test to check semantics across multiple tr…
jvesely Sep 29, 2021
e33321b
treewide: Use '==' to compare strings
jvesely Sep 29, 2021
b530a4e
treewide: Drop unused imports
jvesely Sep 29, 2021
be60d3d
codestyle: Fix and check E712: Comparison to True/False should use is…
jvesely Sep 29, 2021
ab86c16
codestyle: Fix and check E305: Expected 2 blank lines after class or …
jvesely Sep 29, 2021
42c1e7e
codestyle: Fix and check E117: Overindented
jvesely Sep 29, 2021
e72a4b5
treewide: codestyle fixes (#2131)
jvesely Oct 1, 2021
371b2be
requirements: update rich requirement
dependabot[bot] Oct 1, 2021
2c3a429
Merge pull request #2126 from PrincetonUniversity/dependabot/pip/deve…
davidt0x Oct 1, 2021
429ffea
Merge remote-tracking branch 'origin/devel' into devel
jvesely Oct 1, 2021
5405ac9
Reset random state on seed change (#2130)
jvesely Oct 1, 2021
c5b859b
functions/TransferWithCosts: Convert CostFunctions to IntFlag instead…
jvesely Oct 1, 2021
9545538
tests/control: Add simple test for all possible cost options
jvesely Oct 1, 2021
e20a163
Use IntFlag for cost functions (#2133)
jvesely Oct 1, 2021
e938d45
Parameters: exclude more types from copying (#2134)
kmantel Oct 2, 2021
84d0aa3
requirements: update pytest-cov requirement from <2.12.2 to <3.0.1 (#…
dependabot[bot] Oct 5, 2021
27b910d
UDF: support directly passing parameter values
kmantel Aug 6, 2021
273b1e3
UDF: support string expressions
kmantel Aug 7, 2021
773e11d
UDF: allow integration for one parameter
kmantel Aug 7, 2021
8ed633f
Merge pull request #2132 from kmantel/udf
kmantel Oct 5, 2021
bc8fd74
llvm, component: Add 'control_signal' and 'control_signal_params' to …
jvesely Oct 4, 2021
caa194e
llvm, functions: Add compilation support for UniformDist function
jvesely Sep 30, 2021
d005245
llvm, functions/GridSearch: Convert ctypes to numpy before returning …
jvesely Mar 9, 2021
07fc020
llvm, functions/GridSearch: Optionally save used calculated values an…
jvesely Oct 5, 2021
895aabb
llvm: Add missing functionality to OCM (#2137)
jvesely Oct 5, 2021
9b2ab4f
llvm: Add helper function to retrieve and optionally reseed random state
jvesely Sep 30, 2021
591aad8
github-actions: Restrict main CI run to macos-10.15
jvesely Oct 5, 2021
9f83049
functions: _is_identity: add option for defaults (#2136)
kmantel Oct 7, 2021
53f1cd2
llvm, mechanism: Use Parameter class to build a list of needed parame…
jvesely Oct 6, 2021
176813c
requirements: update rich requirement (#2141)
dependabot[bot] Oct 7, 2021
b328551
SharedParameter: improve source detection (#2142)
kmantel Oct 8, 2021
9a59cec
requirements: update grpcio requirement from <1.41.0 to <1.42.0 (#2127)
dependabot[bot] Oct 8, 2021
826379a
requirements: update grpcio-tools requirement from <1.41.0 to <1.42.0…
dependabot[bot] Oct 9, 2021
e99c010
SharedParameter: direct get_previous, get_delta to source Parameter (…
kmantel Oct 13, 2021
800ee1e
llvm, ports: Move cost generation methods to ControlSignal
jvesely Oct 8, 2021
b181aec
llvm, ports/ControlSignal: Always call 'combine_costs' when calculati…
jvesely Oct 13, 2021
6c5cc54
llvm, ports/ControlSignal: Always call 'combine_costs' when calculati…
jvesely Oct 13, 2021
e719c8e
LCAMechanism: allow user-input integrator_function (#2148)
kmantel Oct 14, 2021
a34a32b
requirements: update sphinx requirement from <4.1.3 to <4.2.1 (#2120)
dependabot[bot] Oct 15, 2021
287ce27
github-actions(deps): bump actions/checkout from 2.3.4 to 2.3.5 (#2149)
dependabot[bot] Oct 17, 2021
957ca3d
requirements: update pillow requirement from <8.4.0 to <8.5.0 (#2150)
dependabot[bot] Oct 17, 2021
ad97548
requirements: update elfi requirement from <0.8.1 to <0.8.3
dependabot[bot] Oct 17, 2021
694a240
Merge pull request #2147 from PrincetonUniversity/dependabot/pip/deve…
davidt0x Oct 17, 2021
40d92fd
github-actions: Bump python-3.{8,9} to macos-latest.
jvesely Oct 15, 2021
302dd2f
requirements: update graph-scheduler requirement from <=1.0.0rc2 to <…
kmantel Oct 23, 2021
1373206
requirements: update numpy requirement from <1.21.3 to <1.21.4 (#2152)
dependabot[bot] Oct 23, 2021
3d7c3e7
functions/TransferWithCosts: Change default cost options to CostFunct…
jvesely Oct 27, 2021
7479ef9
github-actions: Drop maxprocesses settings
jvesely Oct 27, 2021
1d98cde
github-actions: Add code coverage job (#2159)
jvesely Oct 29, 2021
34d67c1
github-actions: Do not check for GITHUB_TOKEN env var when uploading …
jvesely Oct 29, 2021
c3024f1
github-actions: Allow RW permissions for jobs updating the online doc…
jvesely Oct 30, 2021
3039b35
Component: add all_dependent_parameters (#2162)
kmantel Nov 2, 2021
d77519a
github-actions(deps): bump actions/checkout from 2.3.5 to 2.4.0 (#2165)
dependabot[bot] Nov 3, 2021
6ae1221
Refactor/pec (#2166)
jdcpni Nov 4, 2021
1826138
github-actions/install-pnl: Support persistent runners (#2167)
jvesely Nov 4, 2021
8ddacc7
maint: remove freeze.txt (#2182)
kmantel Nov 5, 2021
9b97e40
github-actions/release: Add deployment environments
jvesely Nov 4, 2021
9a78bbc
github-actions/release: Use TWINE_REPOSITORY_URL instead of TWINE_REP…
jvesely Nov 4, 2021
01f7106
github-actions/release: rest API methods were moved to github.rest.*
jvesely Nov 5, 2021
a18fa67
github-actions/release: Create full release instead of prerelease on tag
jvesely Nov 6, 2021
7648c14
github-actions/release: Drop limitation to max 2 test processes
jvesely Nov 6, 2021
6bd7e07
github-actions/release: Consolidate into one workflow
jvesely Nov 6, 2021
ef014f5
github-actions/release: Consolidate test and release CI (#2185)
jvesely Nov 6, 2021
a18e5e5
requirements: Require minimum numpy version to include Philox PRNG
jvesely Nov 7, 2021
193aab6
tests/llvm: Rename random tests to include a reference to MT PRNG
jvesely Oct 31, 2021
6ab62a3
llvm: Implement integer and uniform FP Philox PRNG
jvesely Nov 1, 2021
601e886
llvm/helpers: Add helpers for log and log1p
jvesely Nov 7, 2021
60ecaec
llvm/builtins: Implement the ziggurat method for generating Normal di…
jvesely Nov 7, 2021
c1927fb
Refactor/controlmech and ocm (#2186)
jdcpni Nov 7, 2021
2eb1f4f
llvm: Destroy global LLVMBuilderContext instance on cleanup
jvesely Nov 7, 2021
1c13080
llvm: Move builtin generation to LLVMBuilderContext contruction
jvesely Nov 7, 2021
fe92b72
llvm/BuilderContext: Allow specifying custom (fp32/fp64) floating poi…
jvesely Nov 7, 2021
3813c13
Docs/comp ctlmech ocm pec (#2187)
jdcpni Nov 8, 2021
b030ddb
llvm: Create JIT engines on demand
jvesely Nov 7, 2021
22fa345
tests/llvm: Add rudimentary fp32 testing
jvesely Nov 8, 2021
39bb028
Merge remote-tracking branch 'origin/devel' into flexible-types
jvesely Nov 8, 2021
21033d2
llvm: Initialize builder context and jit engines on demand (#2188)
jvesely Nov 8, 2021
8f9a6fe
Merge branch 'flexible-types' into devel
jvesely Nov 8, 2021
b4425ef
llvm/random: Drop type suffix from philox normal function
jvesely Nov 8, 2021
32d04a4
llvm/builtins: Implement philox fp32 normal distribution
jvesely Nov 8, 2021
cb84c0e
llvm, function: Move SeededRandomState to utilities
jvesely Nov 9, 2021
c873195
Function_Base: Reuse the PRNG type when crating a copy using new seed
jvesely Nov 8, 2021
f2d0603
tests/functions/memory: Move test ids with the rest of the params
jvesely Nov 9, 2021
09c86a8
llvm: Enable and test compiled Philox PRNG
jvesely Nov 8, 2021
736fccf
github-actions/pnl-ci-docs: Force creation of temporary version tag (…
jvesely Nov 9, 2021
2e66553
Merge remote-tracking branch 'origin/devel' into devel
jvesely Nov 9, 2021
99da97a
llvm: Add support for Philox PRNG (#2194)
jvesely Nov 9, 2021
90ba999
tests/ddm: Disable Bogacz test with Philox prng (#2195)
jvesely Nov 10, 2021
5f79271
github-actions/comment: Add PR write permission and use github.rest.*…
jvesely Nov 10, 2021
62cbe3d
llvm, mechanisms/DDM: Pass correct parameter structure for seed reset…
jvesely Nov 10, 2021
2e2bc63
llvm/codegen: Use correct helper to get state member offset
jvesely Nov 10, 2021
1966701
llvm/helpers: Add basic sanity checks to get_{param,state}_ptr helpers
jvesely Nov 10, 2021
695dc51
llvm, autodiffcomposition: Add id for the optimizer state
jvesely Nov 10, 2021
91f710a
llvm: Check for correct use of get_{param,state}_ptr helpers (#2198)
jvesely Nov 10, 2021
bf9d5da
tests/models/predator-prey: Restore checks of results (#2202)
jvesely Nov 11, 2021
c0a683a
llvm, mechanism/ocm: Add extra checks for simulation input construction.
jvesely Nov 12, 2021
7f410f1
tests/control: Set state features explicitly in modulation tests
jvesely Nov 12, 2021
110dc84
llvm, ports/ControlSignal: Add shape workarounds and allow Costfuncti…
jvesely Oct 13, 2021
e08473d
llvm, ports/ControlSignal: Add support for CostFunctions.NONE (#2203)
jvesely Nov 12, 2021
96dbec9
tests/predator-prey: Mark the 101 level test instance as 'stress' tes…
jvesely Nov 12, 2021
819faca
tests/llvm: Add Philox PRNG tests with different seeds (#2205)
jvesely Nov 14, 2021
a4be2e6
pnl-ci: build docs-only branches (#2206)
kmantel Nov 16, 2021
5f5708d
requirements: update psyneulink-sphinx-theme requirement (#2201)
dependabot[bot] Nov 17, 2021
ec5d2d9
GatingMechanism: properly set gating_allocation as value alias (#2191)
kmantel Nov 18, 2021
b354849
ControlProjection: correct control_signal to SharedParameter (#2212)
kmantel Nov 18, 2021
5d32243
github-actions(deps): bump actions/setup-python from 2.2.2 to 2.3.0 (…
dependabot[bot] Nov 19, 2021
fc9dc9b
llvm/execution: Do not require declaring cached compiled structures
jvesely Nov 21, 2021
42faac9
llvm/execution: Reuse helper functions to generate structures for 'ev…
jvesely Nov 21, 2021
37b917a
llvm/execution: Report timing information for creating binary structures
jvesely Nov 21, 2021
bb97db1
llvm/debug: Remove unused debug setting 'no_ref_pass'
jvesely Nov 21, 2021
a2a4829
llvm/execution: Drop ctype types for input/output in FuncExecution
jvesely Nov 21, 2021
0185842
llvm/execution: Improve comments and variable naming
jvesely Nov 21, 2021
9239e36
llvm: Cleanup execution of compiled functions (#2214)
jvesely Nov 25, 2021
af04641
github-actions(deps): bump actions/cache from 2.1.6 to 2.1.7 (#2213)
dependabot[bot] Nov 26, 2021
08eadd9
setup/coverage: Correct option name multiprocess -> multiprocessing (…
jvesely Nov 30, 2021
f6bd046
github-actions(deps): bump actions/setup-python from 2.3.0 to 2.3.1 (…
dependabot[bot] Dec 1, 2021
4b88849
tests/show_graph: Strip whitespace before comparing expected dot outp…
jvesely Dec 2, 2021
99dd9e8
requirements: update graphviz requirement from <0.18.0 to <0.20.0 (#2…
dependabot[bot] Dec 2, 2021
a1d4f2a
Refactor/ocm/state input ports (#2221)
jdcpni Dec 3, 2021
002ff21
Misc/ocm/docs and tests (#2223)
jdcpni Dec 5, 2021
aa29fa2
requirements: update grpcio-tools requirement from <1.42.0 to <1.43.0…
dependabot[bot] Dec 7, 2021
406f8e2
Docs/ocm/revs (#2225)
jdcpni Dec 7, 2021
1fe3407
Docs/ocm/revs (#2227)
jdcpni Dec 7, 2021
004a8e6
tests/report: Drop redundant calls to clear_registry
jvesely Dec 3, 2021
d34bff3
tests/report: Use capsys fixture to redirect stdout/stderr
jvesely Dec 3, 2021
2937a92
Feat/ocm/random params (#2231)
jdcpni Dec 9, 2021
78fe80a
github-actions(deps): bump actions/upload-artifact from 2.2.4 to 2.3.…
dependabot[bot] Dec 9, 2021
b28e615
ControlMechanism: fix default allocation for new control signal
kmantel Dec 7, 2021
cef8bc4
tests: add minimal OCM control variations
kmantel Dec 2, 2021
82f6379
Merge pull request #2226 from kmantel/control
kmantel Dec 10, 2021
52c626d
requirements: update grpcio requirement from <1.42.0 to <1.43.0 (#2211)
dependabot[bot] Dec 10, 2021
ee1f894
Feat/ocm/node role probe (#2232)
jdcpni Dec 10, 2021
3b6389a
Feat/composition/probes (#2235)
jdcpni Dec 12, 2021
da204cb
requirements: update pytest-xdist requirement from <2.5.0 to <2.6.0 (…
dependabot[bot] Dec 13, 2021
3b06d8e
Feat/composition/probes (#2236)
jdcpni Dec 13, 2021
e8ec02a
llvm, mechanisms/optimizationcontrolmechanism: Allow setting compiled…
jvesely Nov 17, 2021
634ed9d
llvm/jit_engine: Allow selecting optimization level via env var
jvesely Nov 17, 2021
b81afa8
llvm/jit_engine: Allow setting CUDA_MAX_REGS via PNL_LLVM_DEBUG env var
jvesely Nov 17, 2021
25ab0de
llvm: Export compiler control options via PNL_LLVM_DEBUG env var (#2239)
jvesely Dec 13, 2021
144ccf1
Docs/cim (#2240)
jdcpni Dec 13, 2021
083966e
PEC: fix constructor context execution_id (#2234)
kmantel Dec 14, 2021
fe87a57
tests: ocm control variations auto search_space
kmantel Dec 10, 2021
18b67cd
OCM: update default value based on control signals not counter
kmantel Dec 10, 2021
e41f205
OCM: handle mechanism-control spec for randomization_control_signal
kmantel Dec 10, 2021
b768759
Merge pull request #2241 from kmantel/control
kmantel Dec 14, 2021
18a4196
dependabot: Do not autorebase pending PRs (#2242)
jvesely Dec 14, 2021
818478e
github-actions(deps): bump actions/upload-artifact from 2.3.0 to 2.3.…
dependabot[bot] Dec 16, 2021
2e8fd68
llvm/debug: Document cuda_max_regs option (#2244)
jvesely Dec 16, 2021
19540e6
logging: don't throw exception when called from Function parameter (#…
kmantel Dec 17, 2021
a9459ce
SharedParameter: set _source_exists only when necessary
kmantel Dec 16, 2021
6ca8cd3
Parameter: make inherited cache/restore methods
kmantel Dec 16, 2021
cb08f78
SharedParameter: do not cache and restore shared attributes
kmantel Dec 16, 2021
3997caa
SharedParameter: set shared attribute value on source
kmantel Dec 16, 2021
2acc88e
Merge pull request #2246 from kmantel/sharedparameter
kmantel Dec 18, 2021
7c2d3cf
Component: _initialize_parameters: always ensure None context set (#2…
kmantel Dec 18, 2021
57f9f28
Feat/comp/mult proj between nodes (#2251)
jdcpni Dec 18, 2021
4bcf8e8
Docs/cim figure (#2252)
jdcpni Dec 19, 2021
629a4b6
Function_Base: when copying, reset seed for all contexts
kmantel Nov 18, 2021
ee997be
functions: set fallback_default=True for seed parameter
kmantel Nov 9, 2021
a2afe77
Merge pull request #2250 from kmantel/seed
kmantel Dec 21, 2021
cc6242b
Feat/comp/inputs (#2256)
jdcpni Dec 21, 2021
5f89ce5
Parameter: rename _port -> port and document
kmantel Dec 17, 2021
b45400a
Component: use ParameterValue objects only when ParameterPort exists
kmantel Nov 12, 2021
2e86c0b
ParameterPort: create ports including all subfunctions recursively
kmantel Nov 4, 2021
47abfd9
Merge pull request #2255 from kmantel/ports
kmantel Dec 21, 2021
9979c07
Feat/comp/inputs (#2257)
jdcpni Dec 23, 2021
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github-actions: Drop maxprocesses settings 
all cloud hosted runners should be able to run one test worker per core.
(see
https://docs.github.com/en/actions/using-github-hosted-runners/about-github-hosted-runners#supported-runners-and-hardware-resources )
Signed-off-by: Jan Vesely <[email protected]>
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@jvesely
jvesely committed Oct 27, 2021
commit 7479ef9255c2c2961b04526153940e75d7c24c83
2 changes: 1 addition & 1 deletion .github/workflows/pnl-ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -80,7 +80,7 @@ jobs:

- name: Test with pytest
timeout-minutes: 80
run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto --maxprocesses=2
run: pytest --junit-xml=tests_out.xml --verbosity=0 -n auto

- name: Upload test results
uses: actions/[email protected]
Expand Down